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.BasicMsa;
58 import org.forester.msa.Mafft;
59 import org.forester.msa.Msa;
60 import org.forester.msa.MsaInferrer;
61 import org.forester.msa.MsaMethods;
62 import org.forester.pccx.TestPccx;
63 import org.forester.phylogeny.Phylogeny;
64 import org.forester.phylogeny.PhylogenyBranch;
65 import org.forester.phylogeny.PhylogenyMethods;
66 import org.forester.phylogeny.PhylogenyNode;
67 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
68 import org.forester.phylogeny.data.BinaryCharacters;
69 import org.forester.phylogeny.data.BranchWidth;
70 import org.forester.phylogeny.data.Confidence;
71 import org.forester.phylogeny.data.Distribution;
72 import org.forester.phylogeny.data.DomainArchitecture;
73 import org.forester.phylogeny.data.Event;
74 import org.forester.phylogeny.data.Identifier;
75 import org.forester.phylogeny.data.PhylogenyData;
76 import org.forester.phylogeny.data.PhylogenyDataUtil;
77 import org.forester.phylogeny.data.Polygon;
78 import org.forester.phylogeny.data.PropertiesMap;
79 import org.forester.phylogeny.data.Property;
80 import org.forester.phylogeny.data.Property.AppliesTo;
81 import org.forester.phylogeny.data.ProteinDomain;
82 import org.forester.phylogeny.data.Taxonomy;
83 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
84 import org.forester.phylogeny.factories.PhylogenyFactory;
85 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
86 import org.forester.protein.Protein;
87 import org.forester.sdi.SDI;
88 import org.forester.sdi.SDIR;
89 import org.forester.sdi.SDIse;
90 import org.forester.sdi.TaxonomyAssigner;
91 import org.forester.sdi.TestGSDI;
92 import org.forester.sequence.BasicSequence;
93 import org.forester.sequence.Sequence;
94 import org.forester.surfacing.TestSurfacing;
95 import org.forester.tools.ConfidenceAssessor;
96 import org.forester.tools.SupportCount;
97 import org.forester.tools.TreeSplitMatrix;
98 import org.forester.util.AsciiHistogram;
99 import org.forester.util.BasicDescriptiveStatistics;
100 import org.forester.util.BasicTable;
101 import org.forester.util.BasicTableParser;
102 import org.forester.util.DescriptiveStatistics;
103 import org.forester.util.ForesterConstants;
104 import org.forester.util.ForesterUtil;
105 import org.forester.util.GeneralTable;
106 import org.forester.ws.uniprot.DatabaseTools;
107 import org.forester.ws.uniprot.SequenceDatabaseEntry;
108 import org.forester.ws.uniprot.UniProtTaxonomy;
109 import org.forester.ws.uniprot.UniProtWsTools;
110 import org.forester.ws.wabi.TxSearch;
111 import org.forester.ws.wabi.TxSearch.RANKS;
112 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
113 import org.forester.ws.wabi.TxSearch.TAX_RANK;
115 @SuppressWarnings( "unused")
116 public final class Test {
118 private final static double ZERO_DIFF = 1.0E-9;
119 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
120 + ForesterUtil.getFileSeparator() + "test_data"
121 + ForesterUtil.getFileSeparator();
122 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
123 + ForesterUtil.getFileSeparator() + "resources"
124 + ForesterUtil.getFileSeparator();
125 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
126 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
127 + ForesterConstants.PHYLO_XML_VERSION + "/"
128 + ForesterConstants.PHYLO_XML_XSD;
129 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
130 + ForesterConstants.PHYLO_XML_VERSION + "/"
131 + ForesterConstants.PHYLO_XML_XSD;
133 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
134 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
138 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
139 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
140 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Hmmscan output parser: " );
175 if ( testHmmscanOutputParser() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
183 System.out.print( "Basic node methods: " );
184 if ( Test.testBasicNodeMethods() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node construction and parsing of NHX (node level): " );
193 if ( Test.testNHXNodeParsing() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "NH parsing: " );
202 if ( Test.testNHParsing() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "Conversion to NHX (node level): " );
211 if ( Test.testNHXconversion() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "NHX parsing: " );
220 if ( Test.testNHXParsing() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing with quotes: " );
229 if ( Test.testNHXParsingQuotes() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NHX parsing (MrBayes): " );
238 if ( Test.testNHXParsingMB() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "Nexus characters parsing: " );
247 if ( Test.testNexusCharactersParsing() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "Nexus tree parsing: " );
256 if ( Test.testNexusTreeParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "Nexus tree parsing (translating): " );
265 if ( Test.testNexusTreeParsingTranslating() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "Nexus matrix parsing: " );
274 if ( Test.testNexusMatrixParsing() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Basic phyloXML parsing: " );
283 if ( Test.testBasicPhyloXMLparsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Basic phyloXML parsing (validating against schema): " );
292 if ( testBasicPhyloXMLparsingValidating() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
301 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "phyloXML Distribution Element: " );
310 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "Tol XML parsing: " );
319 if ( Test.testBasicTolXMLparsing() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Copying of node data: " );
328 if ( Test.testCopyOfNodeData() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Basic tree methods: " );
337 if ( Test.testBasicTreeMethods() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Postorder Iterator: " );
346 if ( Test.testPostOrderIterator() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "Preorder Iterator: " );
355 if ( Test.testPreOrderIterator() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Levelorder Iterator: " );
364 if ( Test.testLevelOrderIterator() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Re-id methods: " );
373 if ( Test.testReIdMethods() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Methods on last external nodes: " );
382 if ( Test.testLastExternalNodeMethods() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Methods on external nodes: " );
391 if ( Test.testExternalNodeRelatedMethods() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Deletion of external nodes: " );
400 if ( Test.testDeletionOfExternalNodes() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Subtree deletion: " );
409 if ( Test.testSubtreeDeletion() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Phylogeny branch: " );
418 if ( Test.testPhylogenyBranch() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Rerooting: " );
427 if ( Test.testRerooting() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Mipoint rooting: " );
436 if ( Test.testMidpointrooting() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Support count: " );
445 if ( Test.testSupportCount() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Support transfer: " );
454 if ( Test.testSupportTransfer() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Finding of LCA: " );
463 if ( Test.testGetLCA() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Calculation of distance between nodes: " );
472 if ( Test.testGetDistance() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "SDIse: " );
481 if ( Test.testSDIse() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "Taxonomy assigner: " );
490 if ( Test.testTaxonomyAssigner() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "SDIunrooted: " );
499 if ( Test.testSDIunrooted() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "GSDI: " );
508 if ( TestGSDI.test() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Descriptive statistics: " );
517 if ( Test.testDescriptiveStatistics() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Data objects and methods: " );
526 if ( Test.testDataObjects() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Properties map: " );
535 if ( Test.testPropertiesMap() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Phylogeny reconstruction:" );
544 System.out.println();
545 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Analysis of domain architectures: " );
554 System.out.println();
555 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "GO: " );
564 System.out.println();
565 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
566 System.out.println( "OK." );
570 System.out.println( "failed." );
573 System.out.print( "Modeling tools: " );
574 if ( TestPccx.test() ) {
575 System.out.println( "OK." );
579 System.out.println( "failed." );
582 System.out.print( "Split Matrix strict: " );
583 if ( Test.testSplitStrict() ) {
584 System.out.println( "OK." );
588 System.out.println( "failed." );
591 System.out.print( "Split Matrix: " );
592 if ( Test.testSplit() ) {
593 System.out.println( "OK." );
597 System.out.println( "failed." );
600 System.out.print( "Confidence Assessor: " );
601 if ( Test.testConfidenceAssessor() ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "Basic table: " );
610 if ( Test.testBasicTable() ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "General table: " );
619 if ( Test.testGeneralTable() ) {
620 System.out.println( "OK." );
624 System.out.println( "failed." );
627 System.out.print( "Amino acid sequence: " );
628 if ( Test.testAminoAcidSequence() ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "General MSA parser: " );
637 if ( Test.testGeneralMsaParser() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Fasta parser for msa: " );
646 if ( Test.testFastaParser() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Creation of balanced phylogeny: " );
655 if ( Test.testCreateBalancedPhylogeny() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "EMBL Entry Retrieval: " );
664 if ( Test.testEmblEntryRetrieval() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Uniprot Entry Retrieval: " );
673 if ( Test.testUniprotEntryRetrieval() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "Uniprot Taxonomy Search: " );
682 if ( Test.testUniprotTaxonomySearch() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 if ( Mafft.isInstalled() ) {
691 System.out.print( "MAFFT (external program): " );
692 if ( Test.testMafft() ) {
693 System.out.println( "OK." );
697 System.out.println( "failed [will not count towards failed tests]" );
700 System.out.print( "Next nodes with collapsed: " );
701 if ( Test.testNextNodeWithCollapsing() ) {
702 System.out.println( "OK." );
706 System.out.println( "failed." );
709 System.out.print( "Simple MSA quality: " );
710 if ( Test.testMsaQualityMethod() ) {
711 System.out.println( "OK." );
715 System.out.println( "failed." );
718 // System.out.print( "WABI TxSearch: " );
719 // if ( Test.testWabiTxSearch() ) {
720 // System.out.println( "OK." );
725 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
727 System.out.println();
728 final Runtime rt = java.lang.Runtime.getRuntime();
729 final long free_memory = rt.freeMemory() / 1000000;
730 final long total_memory = rt.totalMemory() / 1000000;
731 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
732 + free_memory + "MB, total memory: " + total_memory + "MB)" );
733 System.out.println();
734 System.out.println( "Successful tests: " + succeeded );
735 System.out.println( "Failed tests: " + failed );
736 System.out.println();
738 System.out.println( "OK." );
741 System.out.println( "Not OK." );
743 // System.out.println();
744 // Development.setTime( true );
746 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
747 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
748 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
749 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
750 // "multifurcations_ex_1.nhx";
751 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
752 // final Phylogeny t1 = factory.create( new File( domains ), new
753 // NHXParser() )[ 0 ];
754 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
756 // catch ( final Exception e ) {
757 // e.printStackTrace();
759 // t1.getRoot().preorderPrint();
760 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
764 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
765 // + "\\AtNBSpos.nhx" ) );
767 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
768 // new NHXParser() );
769 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
770 // + "\\AtNBSpos.nhx" ) );
772 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
773 // new NHXParser() );
776 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
777 // + "\\big_tree.nhx" ) );
778 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
779 // + "\\big_tree.nhx" ) );
781 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
782 // new NHXParser() );
784 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
785 // new NHXParser() );
787 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
788 // + "\\big_tree.nhx" ) );
789 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
790 // + "\\big_tree.nhx" ) );
793 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
794 // new NHXParser() );
796 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
797 // new NHXParser() );
799 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
800 // + "\\AtNBSpos.nhx" ) );
802 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
803 // new NHXParser() );
806 // catch ( IOException e ) {
807 // // TODO Auto-generated catch block
808 // e.printStackTrace();
812 private static boolean testBasicNodeMethods() {
814 if ( PhylogenyNode.getNodeCount() != 0 ) {
817 final PhylogenyNode n1 = new PhylogenyNode();
818 final PhylogenyNode n2 = PhylogenyNode
819 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
820 final PhylogenyNode n3 = PhylogenyNode
821 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
822 final PhylogenyNode n4 = PhylogenyNode
823 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
824 if ( n1.isHasAssignedEvent() ) {
827 if ( PhylogenyNode.getNodeCount() != 4 ) {
830 if ( n3.getIndicator() != 0 ) {
833 if ( n3.getNumberOfExternalNodes() != 1 ) {
836 if ( !n3.isExternal() ) {
839 if ( !n3.isRoot() ) {
842 if ( !n4.getName().equals( "n4" ) ) {
846 catch ( final Exception e ) {
847 e.printStackTrace( System.out );
853 private static boolean testBasicPhyloXMLparsing() {
855 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
856 final PhyloXmlParser xml_parser = new PhyloXmlParser();
857 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
859 if ( xml_parser.getErrorCount() > 0 ) {
860 System.out.println( xml_parser.getErrorMessages().toString() );
863 if ( phylogenies_0.length != 4 ) {
866 final Phylogeny t1 = phylogenies_0[ 0 ];
867 final Phylogeny t2 = phylogenies_0[ 1 ];
868 final Phylogeny t3 = phylogenies_0[ 2 ];
869 final Phylogeny t4 = phylogenies_0[ 3 ];
870 if ( t1.getNumberOfExternalNodes() != 1 ) {
873 if ( !t1.isRooted() ) {
876 if ( t1.isRerootable() ) {
879 if ( !t1.getType().equals( "gene_tree" ) ) {
882 if ( t2.getNumberOfExternalNodes() != 2 ) {
885 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
888 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
891 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
894 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
897 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
900 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
903 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
904 .startsWith( "actgtgggggt" ) ) {
907 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
908 .startsWith( "ctgtgatgcat" ) ) {
911 if ( t3.getNumberOfExternalNodes() != 4 ) {
914 if ( !t1.getName().equals( "t1" ) ) {
917 if ( !t2.getName().equals( "t2" ) ) {
920 if ( !t3.getName().equals( "t3" ) ) {
923 if ( !t4.getName().equals( "t4" ) ) {
926 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
929 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
932 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
935 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
936 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
939 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
942 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
945 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
948 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
949 .equals( "apoptosis" ) ) {
952 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
953 .equals( "GO:0006915" ) ) {
956 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
957 .equals( "UniProtKB" ) ) {
960 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
961 .equals( "experimental" ) ) {
964 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
965 .equals( "function" ) ) {
968 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
972 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
973 .getType().equals( "ml" ) ) {
976 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
977 .equals( "apoptosis" ) ) {
980 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
981 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
984 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
985 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
988 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
989 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
992 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
993 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
996 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
997 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1000 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1001 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1004 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1005 .equals( "GO:0005829" ) ) {
1008 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1009 .equals( "intracellular organelle" ) ) {
1012 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1015 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1016 .equals( "UniProt link" ) ) ) {
1019 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1022 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1025 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1028 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1031 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1034 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1037 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1040 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1043 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1046 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1049 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1050 // .equals( "B" ) ) {
1053 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1056 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1059 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1062 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1063 // .getConfidence() != 2144 ) {
1066 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1067 // .equals( "pfam" ) ) {
1070 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1073 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1076 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1079 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1082 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1083 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1087 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1090 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1093 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1096 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1099 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1102 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1105 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1108 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1110 // if ( xml_parser.getErrorCount() > 0 ) {
1111 // System.out.println( xml_parser.getErrorMessages().toString() );
1114 // if ( phylogenies_1.length != 2 ) {
1117 // final Phylogeny a = phylogenies_1[ 0 ];
1118 // if ( !a.getName().equals( "tree 4" ) ) {
1121 // if ( a.getNumberOfExternalNodes() != 3 ) {
1124 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1127 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1131 catch ( final Exception e ) {
1132 e.printStackTrace( System.out );
1138 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1140 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1141 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1142 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1143 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1146 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1148 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1150 if ( xml_parser.getErrorCount() > 0 ) {
1151 System.out.println( xml_parser.getErrorMessages().toString() );
1154 if ( phylogenies_0.length != 4 ) {
1157 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1158 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1159 if ( phylogenies_t1.length != 1 ) {
1162 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1163 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1166 if ( !t1_rt.isRooted() ) {
1169 if ( t1_rt.isRerootable() ) {
1172 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1175 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1176 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1177 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1178 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1181 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1184 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1187 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1190 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1191 .startsWith( "actgtgggggt" ) ) {
1194 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1195 .startsWith( "ctgtgatgcat" ) ) {
1198 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1199 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1200 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1201 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1202 if ( phylogenies_1.length != 1 ) {
1205 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1206 if ( !t3_rt.getName().equals( "t3" ) ) {
1209 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1212 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1215 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1218 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1221 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1222 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1225 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1228 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1231 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1232 .equals( "UniProtKB" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1236 .equals( "apoptosis" ) ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1240 .equals( "GO:0006915" ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1244 .equals( "UniProtKB" ) ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1248 .equals( "experimental" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1252 .equals( "function" ) ) {
1255 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1256 .getValue() != 1 ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1260 .getType().equals( "ml" ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1264 .equals( "apoptosis" ) ) {
1267 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1268 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1271 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1272 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1275 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1276 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1279 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1280 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1283 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1284 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1287 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1288 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1291 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1292 .equals( "GO:0005829" ) ) {
1295 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1296 .equals( "intracellular organelle" ) ) {
1299 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1302 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1303 .equals( "UniProt link" ) ) ) {
1306 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1309 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1312 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1313 .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." ) ) ) {
1316 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1319 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1322 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1325 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1328 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1329 .equals( "ncbi" ) ) {
1332 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1335 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1336 .getName().equals( "B" ) ) {
1339 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1340 .getFrom() != 21 ) {
1343 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1346 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1347 .getLength() != 24 ) {
1350 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1351 .getConfidence() != 2144 ) {
1354 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1355 .equals( "pfam" ) ) {
1358 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1361 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1364 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1367 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1370 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1371 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1374 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1377 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1380 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1383 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1386 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1389 if ( taxbb.getSynonyms().size() != 2 ) {
1392 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1395 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1398 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1401 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1404 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1407 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1408 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1412 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1415 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1418 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1421 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1424 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1427 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1430 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1434 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1437 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1438 .equalsIgnoreCase( "435" ) ) {
1441 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1444 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1445 .equalsIgnoreCase( "443.7" ) ) {
1448 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1451 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1454 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1455 .equalsIgnoreCase( "433" ) ) {
1459 catch ( final Exception e ) {
1460 e.printStackTrace( System.out );
1466 private static boolean testBasicPhyloXMLparsingValidating() {
1468 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1469 PhyloXmlParser xml_parser = null;
1471 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1473 catch ( final Exception e ) {
1474 // Do nothing -- means were not running from jar.
1476 if ( xml_parser == null ) {
1477 xml_parser = new PhyloXmlParser();
1478 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1479 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1482 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1485 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1487 if ( xml_parser.getErrorCount() > 0 ) {
1488 System.out.println( xml_parser.getErrorMessages().toString() );
1491 if ( phylogenies_0.length != 4 ) {
1494 final Phylogeny t1 = phylogenies_0[ 0 ];
1495 final Phylogeny t2 = phylogenies_0[ 1 ];
1496 final Phylogeny t3 = phylogenies_0[ 2 ];
1497 final Phylogeny t4 = phylogenies_0[ 3 ];
1498 if ( !t1.getName().equals( "t1" ) ) {
1501 if ( !t2.getName().equals( "t2" ) ) {
1504 if ( !t3.getName().equals( "t3" ) ) {
1507 if ( !t4.getName().equals( "t4" ) ) {
1510 if ( t1.getNumberOfExternalNodes() != 1 ) {
1513 if ( t2.getNumberOfExternalNodes() != 2 ) {
1516 if ( t3.getNumberOfExternalNodes() != 4 ) {
1519 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1520 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1521 if ( xml_parser.getErrorCount() > 0 ) {
1522 System.out.println( "errors:" );
1523 System.out.println( xml_parser.getErrorMessages().toString() );
1526 if ( phylogenies_1.length != 4 ) {
1529 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1531 if ( xml_parser.getErrorCount() > 0 ) {
1532 System.out.println( "errors:" );
1533 System.out.println( xml_parser.getErrorMessages().toString() );
1536 if ( phylogenies_2.length != 1 ) {
1539 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1542 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1544 if ( xml_parser.getErrorCount() > 0 ) {
1545 System.out.println( xml_parser.getErrorMessages().toString() );
1548 if ( phylogenies_3.length != 2 ) {
1551 final Phylogeny a = phylogenies_3[ 0 ];
1552 if ( !a.getName().equals( "tree 4" ) ) {
1555 if ( a.getNumberOfExternalNodes() != 3 ) {
1558 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1561 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1564 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1566 if ( xml_parser.getErrorCount() > 0 ) {
1567 System.out.println( xml_parser.getErrorMessages().toString() );
1570 if ( phylogenies_4.length != 1 ) {
1573 final Phylogeny s = phylogenies_4[ 0 ];
1574 if ( s.getNumberOfExternalNodes() != 6 ) {
1577 s.getNode( "first" );
1579 s.getNode( "\"<a'b&c'd\">\"" );
1580 s.getNode( "'''\"" );
1581 s.getNode( "\"\"\"" );
1582 s.getNode( "dick & doof" );
1584 catch ( final Exception e ) {
1585 e.printStackTrace( System.out );
1591 private static boolean testBasicTable() {
1593 final BasicTable<String> t0 = new BasicTable<String>();
1594 if ( t0.getNumberOfColumns() != 0 ) {
1597 if ( t0.getNumberOfRows() != 0 ) {
1600 t0.setValue( 3, 2, "23" );
1601 t0.setValue( 10, 1, "error" );
1602 t0.setValue( 10, 1, "110" );
1603 t0.setValue( 9, 1, "19" );
1604 t0.setValue( 1, 10, "101" );
1605 t0.setValue( 10, 10, "1010" );
1606 t0.setValue( 100, 10, "10100" );
1607 t0.setValue( 0, 0, "00" );
1608 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1611 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1614 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1617 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1620 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1623 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1626 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1629 if ( t0.getNumberOfColumns() != 101 ) {
1632 if ( t0.getNumberOfRows() != 11 ) {
1635 if ( t0.getValueAsString( 49, 4 ) != null ) {
1638 final String l = ForesterUtil.getLineSeparator();
1639 final StringBuffer source = new StringBuffer();
1640 source.append( "" + l );
1641 source.append( "# 1 1 1 1 1 1 1 1" + l );
1642 source.append( " 00 01 02 03" + l );
1643 source.append( " 10 11 12 13 " + l );
1644 source.append( "20 21 22 23 " + l );
1645 source.append( " 30 31 32 33" + l );
1646 source.append( "40 41 42 43" + l );
1647 source.append( " # 1 1 1 1 1 " + l );
1648 source.append( "50 51 52 53 54" + l );
1649 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1650 if ( t1.getNumberOfColumns() != 5 ) {
1653 if ( t1.getNumberOfRows() != 6 ) {
1656 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1659 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1662 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1665 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1668 final StringBuffer source1 = new StringBuffer();
1669 source1.append( "" + l );
1670 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1671 source1.append( " 00; 01 ;02;03" + l );
1672 source1.append( " 10; 11; 12; 13 " + l );
1673 source1.append( "20; 21; 22; 23 " + l );
1674 source1.append( " 30; 31; 32; 33" + l );
1675 source1.append( "40;41;42;43" + l );
1676 source1.append( " # 1 1 1 1 1 " + l );
1677 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1678 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1679 if ( t2.getNumberOfColumns() != 5 ) {
1682 if ( t2.getNumberOfRows() != 6 ) {
1685 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1688 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1691 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1694 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1697 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1700 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1703 final StringBuffer source2 = new StringBuffer();
1704 source2.append( "" + l );
1705 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1706 source2.append( " 00; 01 ;02;03" + l );
1707 source2.append( " 10; 11; 12; 13 " + l );
1708 source2.append( "20; 21; 22; 23 " + l );
1709 source2.append( " " + l );
1710 source2.append( " 30; 31; 32; 33" + l );
1711 source2.append( "40;41;42;43" + l );
1712 source2.append( " comment: 1 1 1 1 1 " + l );
1713 source2.append( ";;;50 ; 52; 53;;54 " + l );
1714 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1719 if ( tl.size() != 2 ) {
1722 final BasicTable<String> t3 = tl.get( 0 );
1723 final BasicTable<String> t4 = tl.get( 1 );
1724 if ( t3.getNumberOfColumns() != 4 ) {
1727 if ( t3.getNumberOfRows() != 3 ) {
1730 if ( t4.getNumberOfColumns() != 4 ) {
1733 if ( t4.getNumberOfRows() != 3 ) {
1736 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1739 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1743 catch ( final Exception e ) {
1744 e.printStackTrace( System.out );
1750 private static boolean testBasicTolXMLparsing() {
1752 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1753 final TolParser parser = new TolParser();
1754 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1755 if ( parser.getErrorCount() > 0 ) {
1756 System.out.println( parser.getErrorMessages().toString() );
1759 if ( phylogenies_0.length != 1 ) {
1762 final Phylogeny t1 = phylogenies_0[ 0 ];
1763 if ( t1.getNumberOfExternalNodes() != 5 ) {
1766 if ( !t1.isRooted() ) {
1769 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1772 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1775 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1778 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1781 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1782 if ( parser.getErrorCount() > 0 ) {
1783 System.out.println( parser.getErrorMessages().toString() );
1786 if ( phylogenies_1.length != 1 ) {
1789 final Phylogeny t2 = phylogenies_1[ 0 ];
1790 if ( t2.getNumberOfExternalNodes() != 664 ) {
1793 if ( !t2.isRooted() ) {
1796 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1799 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1802 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1805 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1808 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1811 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1812 .equals( "Aquifex" ) ) {
1815 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1816 if ( parser.getErrorCount() > 0 ) {
1817 System.out.println( parser.getErrorMessages().toString() );
1820 if ( phylogenies_2.length != 1 ) {
1823 final Phylogeny t3 = phylogenies_2[ 0 ];
1824 if ( t3.getNumberOfExternalNodes() != 184 ) {
1827 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1830 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1833 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1836 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1837 if ( parser.getErrorCount() > 0 ) {
1838 System.out.println( parser.getErrorMessages().toString() );
1841 if ( phylogenies_3.length != 1 ) {
1844 final Phylogeny t4 = phylogenies_3[ 0 ];
1845 if ( t4.getNumberOfExternalNodes() != 1 ) {
1848 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1851 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1854 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1857 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1858 if ( parser.getErrorCount() > 0 ) {
1859 System.out.println( parser.getErrorMessages().toString() );
1862 if ( phylogenies_4.length != 1 ) {
1865 final Phylogeny t5 = phylogenies_4[ 0 ];
1866 if ( t5.getNumberOfExternalNodes() != 13 ) {
1869 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1872 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1875 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1879 catch ( final Exception e ) {
1880 e.printStackTrace( System.out );
1886 private static boolean testBasicTreeMethods() {
1888 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1889 final Phylogeny t1 = factory.create();
1890 if ( !t1.isEmpty() ) {
1893 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1894 if ( t2.getNumberOfExternalNodes() != 4 ) {
1897 if ( t2.getHeight() != 8.5 ) {
1900 if ( !t2.isCompletelyBinary() ) {
1903 if ( t2.isEmpty() ) {
1906 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1907 if ( t3.getNumberOfExternalNodes() != 5 ) {
1910 if ( t3.getHeight() != 11 ) {
1913 if ( t3.isCompletelyBinary() ) {
1916 final PhylogenyNode n = t3.getNode( "ABC" );
1917 PhylogenyNodeIterator it;
1918 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1921 for( it.reset(); it.hasNext(); ) {
1924 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1925 if ( !it2.next().getName().equals( "A" ) ) {
1928 if ( !it2.next().getName().equals( "B" ) ) {
1931 if ( !it2.next().getName().equals( "C" ) ) {
1934 if ( it2.hasNext() ) {
1937 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 ];
1938 if ( t4.getNumberOfExternalNodes() != 9 ) {
1941 if ( t4.getHeight() != 11 ) {
1944 if ( t4.isCompletelyBinary() ) {
1947 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)" );
1948 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1949 if ( t5.getNumberOfExternalNodes() != 8 ) {
1952 if ( t5.getHeight() != 15 ) {
1955 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)" );
1956 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1957 if ( t6.getHeight() != 15 ) {
1960 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)" );
1961 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1962 if ( t7.getHeight() != 15 ) {
1965 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)" );
1966 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1967 if ( t8.getNumberOfExternalNodes() != 10 ) {
1970 if ( t8.getHeight() != 15 ) {
1973 final char[] a9 = new char[] {};
1974 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1975 if ( t9.getHeight() != 0 ) {
1978 final char[] a10 = new char[] { 'a', ':', '6' };
1979 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1980 if ( t10.getHeight() != 6 ) {
1984 catch ( final Exception e ) {
1985 e.printStackTrace( System.out );
1991 private static boolean testConfidenceAssessor() {
1993 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1994 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1995 final Phylogeny[] ev0 = factory
1996 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1998 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1999 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2002 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2005 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2006 final Phylogeny[] ev1 = factory
2007 .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)));",
2009 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2010 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2013 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2016 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2017 final Phylogeny[] ev_b = factory
2018 .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",
2020 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2021 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2022 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2025 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2029 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2030 final Phylogeny[] ev1x = factory
2031 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
2033 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2034 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2037 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2040 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2041 final Phylogeny[] ev_bx = factory
2042 .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",
2044 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2045 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2048 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2052 final Phylogeny[] t2 = factory
2053 .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);",
2055 final Phylogeny[] ev2 = factory
2056 .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);",
2058 for( final Phylogeny target : t2 ) {
2059 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2062 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2063 new NHXParser() )[ 0 ];
2064 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2065 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2066 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2069 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2072 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2076 catch ( final Exception e ) {
2077 e.printStackTrace();
2083 private static boolean testCopyOfNodeData() {
2085 final PhylogenyNode n1 = PhylogenyNode
2086 .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]" );
2087 final PhylogenyNode n2 = n1.copyNodeData();
2088 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2092 catch ( final Exception e ) {
2093 e.printStackTrace();
2099 private static boolean testDataObjects() {
2101 final Confidence s0 = new Confidence();
2102 final Confidence s1 = new Confidence();
2103 if ( !s0.isEqual( s1 ) ) {
2106 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2107 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2108 if ( s2.isEqual( s1 ) ) {
2111 if ( !s2.isEqual( s3 ) ) {
2114 final Confidence s4 = ( Confidence ) s3.copy();
2115 if ( !s4.isEqual( s3 ) ) {
2122 final Taxonomy t1 = new Taxonomy();
2123 final Taxonomy t2 = new Taxonomy();
2124 final Taxonomy t3 = new Taxonomy();
2125 final Taxonomy t4 = new Taxonomy();
2126 final Taxonomy t5 = new Taxonomy();
2127 t1.setIdentifier( new Identifier( "ecoli" ) );
2128 t1.setTaxonomyCode( "ECOLI" );
2129 t1.setScientificName( "E. coli" );
2130 t1.setCommonName( "coli" );
2131 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2132 if ( !t1.isEqual( t0 ) ) {
2135 t2.setIdentifier( new Identifier( "ecoli" ) );
2136 t2.setTaxonomyCode( "other" );
2137 t2.setScientificName( "what" );
2138 t2.setCommonName( "something" );
2139 if ( !t1.isEqual( t2 ) ) {
2142 t2.setIdentifier( new Identifier( "nemve" ) );
2143 if ( t1.isEqual( t2 ) ) {
2146 t1.setIdentifier( null );
2147 t3.setTaxonomyCode( "ECOLI" );
2148 t3.setScientificName( "what" );
2149 t3.setCommonName( "something" );
2150 if ( !t1.isEqual( t3 ) ) {
2153 t1.setIdentifier( null );
2154 t1.setTaxonomyCode( "" );
2155 t4.setScientificName( "E. ColI" );
2156 t4.setCommonName( "something" );
2157 if ( !t1.isEqual( t4 ) ) {
2160 t4.setScientificName( "B. subtilis" );
2161 t4.setCommonName( "something" );
2162 if ( t1.isEqual( t4 ) ) {
2165 t1.setIdentifier( null );
2166 t1.setTaxonomyCode( "" );
2167 t1.setScientificName( "" );
2168 t5.setCommonName( "COLI" );
2169 if ( !t1.isEqual( t5 ) ) {
2172 t5.setCommonName( "vibrio" );
2173 if ( t1.isEqual( t5 ) ) {
2178 final Identifier id0 = new Identifier( "123", "pfam" );
2179 final Identifier id1 = ( Identifier ) id0.copy();
2180 if ( !id1.isEqual( id1 ) ) {
2183 if ( !id1.isEqual( id0 ) ) {
2186 if ( !id0.isEqual( id1 ) ) {
2193 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2194 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2195 if ( !pd1.isEqual( pd1 ) ) {
2198 if ( !pd1.isEqual( pd0 ) ) {
2203 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2204 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2205 if ( !pd3.isEqual( pd3 ) ) {
2208 if ( !pd2.isEqual( pd3 ) ) {
2211 if ( !pd0.isEqual( pd3 ) ) {
2216 // DomainArchitecture
2217 // ------------------
2218 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2219 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2220 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2221 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2222 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2223 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2228 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2229 if ( ds0.getNumberOfDomains() != 4 ) {
2232 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2233 if ( !ds0.isEqual( ds0 ) ) {
2236 if ( !ds0.isEqual( ds1 ) ) {
2239 if ( ds1.getNumberOfDomains() != 4 ) {
2242 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2247 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2248 if ( ds0.isEqual( ds2 ) ) {
2254 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2255 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2256 System.out.println( ds3.toNHX() );
2259 if ( ds3.getNumberOfDomains() != 3 ) {
2264 final Event e1 = new Event( Event.EventType.fusion );
2265 if ( e1.isDuplication() ) {
2268 if ( !e1.isFusion() ) {
2271 if ( !e1.asText().toString().equals( "fusion" ) ) {
2274 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2277 final Event e11 = new Event( Event.EventType.fusion );
2278 if ( !e11.isEqual( e1 ) ) {
2281 if ( !e11.toNHX().toString().equals( "" ) ) {
2284 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2285 if ( e2.isDuplication() ) {
2288 if ( !e2.isSpeciationOrDuplication() ) {
2291 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2294 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2297 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2300 if ( e11.isEqual( e2 ) ) {
2303 final Event e2c = ( Event ) e2.copy();
2304 if ( !e2c.isEqual( e2 ) ) {
2307 Event e3 = new Event( 1, 2, 3 );
2308 if ( e3.isDuplication() ) {
2311 if ( e3.isSpeciation() ) {
2314 if ( e3.isGeneLoss() ) {
2317 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2320 final Event e3c = ( Event ) e3.copy();
2321 final Event e3cc = ( Event ) e3c.copy();
2322 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2326 if ( !e3c.isEqual( e3cc ) ) {
2329 Event e4 = new Event( 1, 2, 3 );
2330 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2333 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2336 final Event e4c = ( Event ) e4.copy();
2338 final Event e4cc = ( Event ) e4c.copy();
2339 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2342 if ( !e4c.isEqual( e4cc ) ) {
2345 final Event e5 = new Event();
2346 if ( !e5.isUnassigned() ) {
2349 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2352 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2355 final Event e6 = new Event( 1, 0, 0 );
2356 if ( !e6.asText().toString().equals( "duplication" ) ) {
2359 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2362 final Event e7 = new Event( 0, 1, 0 );
2363 if ( !e7.asText().toString().equals( "speciation" ) ) {
2366 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2369 final Event e8 = new Event( 0, 0, 1 );
2370 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2373 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2377 catch ( final Exception e ) {
2378 e.printStackTrace( System.out );
2384 private static boolean testDeletionOfExternalNodes() {
2386 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2387 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2388 final PhylogenyWriter w = new PhylogenyWriter();
2389 if ( t0.isEmpty() ) {
2392 if ( t0.getNumberOfExternalNodes() != 1 ) {
2395 t0.deleteSubtree( t0.getNode( "A" ), false );
2396 if ( t0.getNumberOfExternalNodes() != 0 ) {
2399 if ( !t0.isEmpty() ) {
2402 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2403 if ( t1.getNumberOfExternalNodes() != 2 ) {
2406 t1.deleteSubtree( t1.getNode( "A" ), false );
2407 if ( t1.getNumberOfExternalNodes() != 1 ) {
2410 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2413 t1.deleteSubtree( t1.getNode( "B" ), false );
2414 if ( t1.getNumberOfExternalNodes() != 1 ) {
2417 t1.deleteSubtree( t1.getNode( "r" ), false );
2418 if ( !t1.isEmpty() ) {
2421 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2422 if ( t2.getNumberOfExternalNodes() != 3 ) {
2425 t2.deleteSubtree( t2.getNode( "B" ), false );
2426 if ( t2.getNumberOfExternalNodes() != 2 ) {
2429 t2.toNewHampshireX();
2430 PhylogenyNode n = t2.getNode( "A" );
2431 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2434 t2.deleteSubtree( t2.getNode( "A" ), false );
2435 if ( t2.getNumberOfExternalNodes() != 2 ) {
2438 t2.deleteSubtree( t2.getNode( "C" ), true );
2439 if ( t2.getNumberOfExternalNodes() != 1 ) {
2442 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2443 if ( t3.getNumberOfExternalNodes() != 4 ) {
2446 t3.deleteSubtree( t3.getNode( "B" ), true );
2447 if ( t3.getNumberOfExternalNodes() != 3 ) {
2450 n = t3.getNode( "A" );
2451 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2454 n = n.getNextExternalNode();
2455 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2458 t3.deleteSubtree( t3.getNode( "A" ), true );
2459 if ( t3.getNumberOfExternalNodes() != 2 ) {
2462 n = t3.getNode( "C" );
2463 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2466 t3.deleteSubtree( t3.getNode( "C" ), true );
2467 if ( t3.getNumberOfExternalNodes() != 1 ) {
2470 t3.deleteSubtree( t3.getNode( "D" ), true );
2471 if ( t3.getNumberOfExternalNodes() != 0 ) {
2474 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2475 if ( t4.getNumberOfExternalNodes() != 6 ) {
2478 t4.deleteSubtree( t4.getNode( "B2" ), true );
2479 if ( t4.getNumberOfExternalNodes() != 5 ) {
2482 String s = w.toNewHampshire( t4, false, true ).toString();
2483 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2486 t4.deleteSubtree( t4.getNode( "B11" ), true );
2487 if ( t4.getNumberOfExternalNodes() != 4 ) {
2490 t4.deleteSubtree( t4.getNode( "C" ), true );
2491 if ( t4.getNumberOfExternalNodes() != 3 ) {
2494 n = t4.getNode( "A" );
2495 n = n.getNextExternalNode();
2496 if ( !n.getName().equals( "B12" ) ) {
2499 n = n.getNextExternalNode();
2500 if ( !n.getName().equals( "D" ) ) {
2503 s = w.toNewHampshire( t4, false, true ).toString();
2504 if ( !s.equals( "((A,B12),D);" ) ) {
2507 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2508 t5.deleteSubtree( t5.getNode( "A" ), true );
2509 if ( t5.getNumberOfExternalNodes() != 5 ) {
2512 s = w.toNewHampshire( t5, false, true ).toString();
2513 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2516 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2517 t6.deleteSubtree( t6.getNode( "B11" ), true );
2518 if ( t6.getNumberOfExternalNodes() != 5 ) {
2521 s = w.toNewHampshire( t6, false, false ).toString();
2522 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2525 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2526 t7.deleteSubtree( t7.getNode( "B12" ), true );
2527 if ( t7.getNumberOfExternalNodes() != 5 ) {
2530 s = w.toNewHampshire( t7, false, true ).toString();
2531 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2534 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2535 t8.deleteSubtree( t8.getNode( "B2" ), true );
2536 if ( t8.getNumberOfExternalNodes() != 5 ) {
2539 s = w.toNewHampshire( t8, false, false ).toString();
2540 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2543 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2544 t9.deleteSubtree( t9.getNode( "C" ), true );
2545 if ( t9.getNumberOfExternalNodes() != 5 ) {
2548 s = w.toNewHampshire( t9, false, true ).toString();
2549 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2552 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2553 t10.deleteSubtree( t10.getNode( "D" ), true );
2554 if ( t10.getNumberOfExternalNodes() != 5 ) {
2557 s = w.toNewHampshire( t10, false, true ).toString();
2558 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2561 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2562 t11.deleteSubtree( t11.getNode( "A" ), true );
2563 if ( t11.getNumberOfExternalNodes() != 2 ) {
2566 s = w.toNewHampshire( t11, false, true ).toString();
2567 if ( !s.equals( "(B,C);" ) ) {
2570 t11.deleteSubtree( t11.getNode( "C" ), true );
2571 if ( t11.getNumberOfExternalNodes() != 1 ) {
2574 s = w.toNewHampshire( t11, false, false ).toString();
2575 if ( !s.equals( "B;" ) ) {
2578 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2579 t12.deleteSubtree( t12.getNode( "B2" ), true );
2580 if ( t12.getNumberOfExternalNodes() != 8 ) {
2583 s = w.toNewHampshire( t12, false, true ).toString();
2584 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2587 t12.deleteSubtree( t12.getNode( "B3" ), true );
2588 if ( t12.getNumberOfExternalNodes() != 7 ) {
2591 s = w.toNewHampshire( t12, false, true ).toString();
2592 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2595 t12.deleteSubtree( t12.getNode( "C3" ), true );
2596 if ( t12.getNumberOfExternalNodes() != 6 ) {
2599 s = w.toNewHampshire( t12, false, true ).toString();
2600 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2603 t12.deleteSubtree( t12.getNode( "A1" ), true );
2604 if ( t12.getNumberOfExternalNodes() != 5 ) {
2607 s = w.toNewHampshire( t12, false, true ).toString();
2608 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2611 t12.deleteSubtree( t12.getNode( "B1" ), true );
2612 if ( t12.getNumberOfExternalNodes() != 4 ) {
2615 s = w.toNewHampshire( t12, false, true ).toString();
2616 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2619 t12.deleteSubtree( t12.getNode( "A3" ), true );
2620 if ( t12.getNumberOfExternalNodes() != 3 ) {
2623 s = w.toNewHampshire( t12, false, true ).toString();
2624 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2627 t12.deleteSubtree( t12.getNode( "A2" ), true );
2628 if ( t12.getNumberOfExternalNodes() != 2 ) {
2631 s = w.toNewHampshire( t12, false, true ).toString();
2632 if ( !s.equals( "(C1,C2);" ) ) {
2635 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2636 t13.deleteSubtree( t13.getNode( "D" ), true );
2637 if ( t13.getNumberOfExternalNodes() != 4 ) {
2640 s = w.toNewHampshire( t13, false, true ).toString();
2641 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2644 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2645 t14.deleteSubtree( t14.getNode( "E" ), true );
2646 if ( t14.getNumberOfExternalNodes() != 5 ) {
2649 s = w.toNewHampshire( t14, false, true ).toString();
2650 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2653 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2654 t15.deleteSubtree( t15.getNode( "B2" ), true );
2655 if ( t15.getNumberOfExternalNodes() != 11 ) {
2658 t15.deleteSubtree( t15.getNode( "B1" ), true );
2659 if ( t15.getNumberOfExternalNodes() != 10 ) {
2662 t15.deleteSubtree( t15.getNode( "B3" ), true );
2663 if ( t15.getNumberOfExternalNodes() != 9 ) {
2666 t15.deleteSubtree( t15.getNode( "B4" ), true );
2667 if ( t15.getNumberOfExternalNodes() != 8 ) {
2670 t15.deleteSubtree( t15.getNode( "A1" ), true );
2671 if ( t15.getNumberOfExternalNodes() != 7 ) {
2674 t15.deleteSubtree( t15.getNode( "C4" ), true );
2675 if ( t15.getNumberOfExternalNodes() != 6 ) {
2679 catch ( final Exception e ) {
2680 e.printStackTrace( System.out );
2686 private static boolean testDescriptiveStatistics() {
2688 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2689 dss1.addValue( 82 );
2690 dss1.addValue( 78 );
2691 dss1.addValue( 70 );
2692 dss1.addValue( 58 );
2693 dss1.addValue( 42 );
2694 if ( dss1.getN() != 5 ) {
2697 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2700 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2703 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2706 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2709 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2712 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2715 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2718 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2721 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2724 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2727 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2730 dss1.addValue( 123 );
2731 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2734 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2737 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2740 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2741 dss2.addValue( -1.85 );
2742 dss2.addValue( 57.5 );
2743 dss2.addValue( 92.78 );
2744 dss2.addValue( 57.78 );
2745 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2748 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2751 final double[] a = dss2.getDataAsDoubleArray();
2752 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2755 dss2.addValue( -100 );
2756 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2759 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2762 final double[] ds = new double[ 14 ];
2777 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2778 if ( bins.length != 4 ) {
2781 if ( bins[ 0 ] != 2 ) {
2784 if ( bins[ 1 ] != 3 ) {
2787 if ( bins[ 2 ] != 4 ) {
2790 if ( bins[ 3 ] != 5 ) {
2793 final double[] ds1 = new double[ 9 ];
2803 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2804 if ( bins1.length != 4 ) {
2807 if ( bins1[ 0 ] != 2 ) {
2810 if ( bins1[ 1 ] != 3 ) {
2813 if ( bins1[ 2 ] != 0 ) {
2816 if ( bins1[ 3 ] != 4 ) {
2819 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2820 if ( bins1_1.length != 3 ) {
2823 if ( bins1_1[ 0 ] != 3 ) {
2826 if ( bins1_1[ 1 ] != 2 ) {
2829 if ( bins1_1[ 2 ] != 4 ) {
2832 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2833 if ( bins1_2.length != 3 ) {
2836 if ( bins1_2[ 0 ] != 2 ) {
2839 if ( bins1_2[ 1 ] != 2 ) {
2842 if ( bins1_2[ 2 ] != 2 ) {
2845 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2859 dss3.addValue( 10 );
2860 dss3.addValue( 10 );
2861 dss3.addValue( 10 );
2862 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2863 histo.toStringBuffer( 10, '=', 40, 5 );
2864 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2866 catch ( final Exception e ) {
2867 e.printStackTrace( System.out );
2873 private static boolean testDir( final String file ) {
2875 final File f = new File( file );
2876 if ( !f.exists() ) {
2879 if ( !f.isDirectory() ) {
2882 if ( !f.canRead() ) {
2886 catch ( final Exception e ) {
2892 private static boolean testExternalNodeRelatedMethods() {
2894 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2895 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2896 PhylogenyNode n = t1.getNode( "A" );
2897 n = n.getNextExternalNode();
2898 if ( !n.getName().equals( "B" ) ) {
2901 n = n.getNextExternalNode();
2902 if ( !n.getName().equals( "C" ) ) {
2905 n = n.getNextExternalNode();
2906 if ( !n.getName().equals( "D" ) ) {
2909 n = t1.getNode( "B" );
2910 while ( !n.isLastExternalNode() ) {
2911 n = n.getNextExternalNode();
2913 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2914 n = t2.getNode( "A" );
2915 n = n.getNextExternalNode();
2916 if ( !n.getName().equals( "B" ) ) {
2919 n = n.getNextExternalNode();
2920 if ( !n.getName().equals( "C" ) ) {
2923 n = n.getNextExternalNode();
2924 if ( !n.getName().equals( "D" ) ) {
2927 n = t2.getNode( "B" );
2928 while ( !n.isLastExternalNode() ) {
2929 n = n.getNextExternalNode();
2931 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2932 n = t3.getNode( "A" );
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "B" ) ) {
2937 n = n.getNextExternalNode();
2938 if ( !n.getName().equals( "C" ) ) {
2941 n = n.getNextExternalNode();
2942 if ( !n.getName().equals( "D" ) ) {
2945 n = n.getNextExternalNode();
2946 if ( !n.getName().equals( "E" ) ) {
2949 n = n.getNextExternalNode();
2950 if ( !n.getName().equals( "F" ) ) {
2953 n = n.getNextExternalNode();
2954 if ( !n.getName().equals( "G" ) ) {
2957 n = n.getNextExternalNode();
2958 if ( !n.getName().equals( "H" ) ) {
2961 n = t3.getNode( "B" );
2962 while ( !n.isLastExternalNode() ) {
2963 n = n.getNextExternalNode();
2965 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2966 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2967 final PhylogenyNode node = iter.next();
2969 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2970 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2971 final PhylogenyNode node = iter.next();
2974 catch ( final Exception e ) {
2975 e.printStackTrace( System.out );
2981 private static boolean testGeneralTable() {
2983 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2984 t0.setValue( 3, 2, "23" );
2985 t0.setValue( 10, 1, "error" );
2986 t0.setValue( 10, 1, "110" );
2987 t0.setValue( 9, 1, "19" );
2988 t0.setValue( 1, 10, "101" );
2989 t0.setValue( 10, 10, "1010" );
2990 t0.setValue( 100, 10, "10100" );
2991 t0.setValue( 0, 0, "00" );
2992 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2995 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2998 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
3001 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
3004 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
3007 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
3010 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3013 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3016 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3019 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3020 t1.setValue( "3", "2", "23" );
3021 t1.setValue( "10", "1", "error" );
3022 t1.setValue( "10", "1", "110" );
3023 t1.setValue( "9", "1", "19" );
3024 t1.setValue( "1", "10", "101" );
3025 t1.setValue( "10", "10", "1010" );
3026 t1.setValue( "100", "10", "10100" );
3027 t1.setValue( "0", "0", "00" );
3028 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3029 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3032 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3035 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3038 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3041 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3044 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3047 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3050 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3053 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3056 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3060 catch ( final Exception e ) {
3061 e.printStackTrace( System.out );
3067 private static boolean testGetDistance() {
3069 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3070 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",
3071 new NHXParser() )[ 0 ];
3072 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3073 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3076 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3079 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3082 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3085 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3088 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3091 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3094 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3097 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3100 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3103 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3106 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3109 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3112 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3115 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3118 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3121 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3124 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3127 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3130 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3133 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3136 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3139 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3142 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3145 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3148 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3151 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3154 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3157 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3160 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3163 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3166 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",
3167 new NHXParser() )[ 0 ];
3168 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3171 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3174 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3177 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3180 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3183 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3186 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3189 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3192 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3195 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3198 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3202 catch ( final Exception e ) {
3203 e.printStackTrace( System.out );
3209 private static boolean testGetLCA() {
3211 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3212 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3213 new NHXParser() )[ 0 ];
3214 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3215 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3216 if ( !A.getName().equals( "A" ) ) {
3219 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3220 if ( !gh.getName().equals( "gh" ) ) {
3223 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3224 if ( !ab.getName().equals( "ab" ) ) {
3227 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3228 if ( !ab2.getName().equals( "ab" ) ) {
3231 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3232 if ( !gh2.getName().equals( "gh" ) ) {
3235 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3236 if ( !gh3.getName().equals( "gh" ) ) {
3239 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3240 if ( !abc.getName().equals( "abc" ) ) {
3243 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3244 if ( !abc2.getName().equals( "abc" ) ) {
3247 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3248 if ( !abcd.getName().equals( "abcd" ) ) {
3251 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3252 if ( !abcd2.getName().equals( "abcd" ) ) {
3255 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3256 if ( !abcdef.getName().equals( "abcdef" ) ) {
3259 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3260 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3263 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3264 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3267 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3268 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3271 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3272 if ( !abcde.getName().equals( "abcde" ) ) {
3275 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3276 if ( !abcde2.getName().equals( "abcde" ) ) {
3279 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3280 if ( !r.getName().equals( "abcdefgh" ) ) {
3283 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3284 if ( !r2.getName().equals( "abcdefgh" ) ) {
3287 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3288 if ( !r3.getName().equals( "abcdefgh" ) ) {
3291 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3292 if ( !abcde3.getName().equals( "abcde" ) ) {
3295 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3296 if ( !abcde4.getName().equals( "abcde" ) ) {
3299 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3300 if ( !ab3.getName().equals( "ab" ) ) {
3303 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3304 if ( !ab4.getName().equals( "ab" ) ) {
3307 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3308 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3309 if ( !cd.getName().equals( "cd" ) ) {
3312 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3313 if ( !cd2.getName().equals( "cd" ) ) {
3316 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3317 if ( !cde.getName().equals( "cde" ) ) {
3320 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3321 if ( !cde2.getName().equals( "cde" ) ) {
3324 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3325 if ( !cdef.getName().equals( "cdef" ) ) {
3328 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3329 if ( !cdef2.getName().equals( "cdef" ) ) {
3332 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3333 if ( !cdef3.getName().equals( "cdef" ) ) {
3336 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3337 if ( !rt.getName().equals( "r" ) ) {
3340 final Phylogeny p3 = factory
3341 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3342 new NHXParser() )[ 0 ];
3343 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3344 if ( !bc_3.getName().equals( "bc" ) ) {
3347 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3348 if ( !ac_3.getName().equals( "abc" ) ) {
3351 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3352 if ( !ad_3.getName().equals( "abcde" ) ) {
3355 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3356 if ( !af_3.getName().equals( "abcdef" ) ) {
3359 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3360 if ( !ag_3.getName().equals( "" ) ) {
3363 if ( !ag_3.isRoot() ) {
3366 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3367 if ( !al_3.getName().equals( "" ) ) {
3370 if ( !al_3.isRoot() ) {
3373 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3374 if ( !kl_3.getName().equals( "" ) ) {
3377 if ( !kl_3.isRoot() ) {
3380 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3381 if ( !fl_3.getName().equals( "" ) ) {
3384 if ( !fl_3.isRoot() ) {
3387 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3388 if ( !gk_3.getName().equals( "ghijk" ) ) {
3391 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3392 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3393 if ( !r_4.getName().equals( "r" ) ) {
3396 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3397 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3398 if ( !r_5.getName().equals( "root" ) ) {
3401 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3402 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3403 if ( !r_6.getName().equals( "rot" ) ) {
3406 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3407 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3408 if ( !r_7.getName().equals( "rott" ) ) {
3412 catch ( final Exception e ) {
3413 e.printStackTrace( System.out );
3419 private static boolean testHmmscanOutputParser() {
3420 final String test_dir = Test.PATH_TO_TEST_DATA;
3422 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3423 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3425 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3426 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3427 final List<Protein> proteins = parser2.parse();
3428 if ( parser2.getProteinsEncountered() != 4 ) {
3431 if ( proteins.size() != 4 ) {
3434 if ( parser2.getDomainsEncountered() != 69 ) {
3437 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3440 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3443 final Protein p1 = proteins.get( 0 );
3444 if ( p1.getNumberOfProteinDomains() != 15 ) {
3447 if ( p1.getLength() != 850 ) {
3450 final Protein p2 = proteins.get( 1 );
3451 if ( p2.getNumberOfProteinDomains() != 51 ) {
3454 if ( p2.getLength() != 1291 ) {
3457 final Protein p3 = proteins.get( 2 );
3458 if ( p3.getNumberOfProteinDomains() != 2 ) {
3461 final Protein p4 = proteins.get( 3 );
3462 if ( p4.getNumberOfProteinDomains() != 1 ) {
3465 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3468 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3471 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3474 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3477 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3480 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3483 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3486 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3489 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3493 catch ( final Exception e ) {
3494 e.printStackTrace( System.out );
3500 private static boolean testLastExternalNodeMethods() {
3502 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3503 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3504 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3505 final PhylogenyNode n1 = t0.getNode( "A" );
3506 if ( n1.isLastExternalNode() ) {
3509 final PhylogenyNode n2 = t0.getNode( "B" );
3510 if ( n2.isLastExternalNode() ) {
3513 final PhylogenyNode n3 = t0.getNode( "C" );
3514 if ( n3.isLastExternalNode() ) {
3517 final PhylogenyNode n4 = t0.getNode( "D" );
3518 if ( !n4.isLastExternalNode() ) {
3522 catch ( final Exception e ) {
3523 e.printStackTrace( System.out );
3529 private static boolean testLevelOrderIterator() {
3531 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3532 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3533 PhylogenyNodeIterator it0;
3534 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3537 for( it0.reset(); it0.hasNext(); ) {
3540 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3541 if ( !it.next().getName().equals( "r" ) ) {
3544 if ( !it.next().getName().equals( "ab" ) ) {
3547 if ( !it.next().getName().equals( "cd" ) ) {
3550 if ( !it.next().getName().equals( "A" ) ) {
3553 if ( !it.next().getName().equals( "B" ) ) {
3556 if ( !it.next().getName().equals( "C" ) ) {
3559 if ( !it.next().getName().equals( "D" ) ) {
3562 if ( it.hasNext() ) {
3565 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",
3566 new NHXParser() )[ 0 ];
3567 PhylogenyNodeIterator it2;
3568 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3571 for( it2.reset(); it2.hasNext(); ) {
3574 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3575 if ( !it3.next().getName().equals( "r" ) ) {
3578 if ( !it3.next().getName().equals( "abc" ) ) {
3581 if ( !it3.next().getName().equals( "defg" ) ) {
3584 if ( !it3.next().getName().equals( "A" ) ) {
3587 if ( !it3.next().getName().equals( "B" ) ) {
3590 if ( !it3.next().getName().equals( "C" ) ) {
3593 if ( !it3.next().getName().equals( "D" ) ) {
3596 if ( !it3.next().getName().equals( "E" ) ) {
3599 if ( !it3.next().getName().equals( "F" ) ) {
3602 if ( !it3.next().getName().equals( "G" ) ) {
3605 if ( !it3.next().getName().equals( "1" ) ) {
3608 if ( !it3.next().getName().equals( "2" ) ) {
3611 if ( !it3.next().getName().equals( "3" ) ) {
3614 if ( !it3.next().getName().equals( "4" ) ) {
3617 if ( !it3.next().getName().equals( "5" ) ) {
3620 if ( !it3.next().getName().equals( "6" ) ) {
3623 if ( !it3.next().getName().equals( "f1" ) ) {
3626 if ( !it3.next().getName().equals( "f2" ) ) {
3629 if ( !it3.next().getName().equals( "f3" ) ) {
3632 if ( !it3.next().getName().equals( "a" ) ) {
3635 if ( !it3.next().getName().equals( "b" ) ) {
3638 if ( !it3.next().getName().equals( "f21" ) ) {
3641 if ( !it3.next().getName().equals( "X" ) ) {
3644 if ( !it3.next().getName().equals( "Y" ) ) {
3647 if ( !it3.next().getName().equals( "Z" ) ) {
3650 if ( it3.hasNext() ) {
3653 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3654 PhylogenyNodeIterator it4;
3655 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3658 for( it4.reset(); it4.hasNext(); ) {
3661 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3662 if ( !it5.next().getName().equals( "r" ) ) {
3665 if ( !it5.next().getName().equals( "A" ) ) {
3668 if ( !it5.next().getName().equals( "B" ) ) {
3671 if ( !it5.next().getName().equals( "C" ) ) {
3674 if ( !it5.next().getName().equals( "D" ) ) {
3677 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3678 PhylogenyNodeIterator it6;
3679 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3682 for( it6.reset(); it6.hasNext(); ) {
3685 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3686 if ( !it7.next().getName().equals( "A" ) ) {
3689 if ( it.hasNext() ) {
3693 catch ( final Exception e ) {
3694 e.printStackTrace( System.out );
3700 private static boolean testMidpointrooting() {
3702 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3703 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",
3704 new NHXParser() )[ 0 ];
3705 if ( !t1.isRooted() ) {
3708 PhylogenyMethods.midpointRoot( t1 );
3709 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3712 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3715 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3718 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3721 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3724 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3727 t1.reRoot( t1.getNode( "A" ) );
3728 PhylogenyMethods.midpointRoot( t1 );
3729 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3732 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3735 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3738 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3741 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3744 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3748 catch ( final Exception e ) {
3749 e.printStackTrace( System.out );
3755 private static boolean testNexusCharactersParsing() {
3757 final NexusCharactersParser parser = new NexusCharactersParser();
3758 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3760 String[] labels = parser.getCharStateLabels();
3761 if ( labels.length != 7 ) {
3764 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3767 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3770 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3773 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3776 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3779 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3782 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3785 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3787 labels = parser.getCharStateLabels();
3788 if ( labels.length != 7 ) {
3791 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3794 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3797 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3800 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3803 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3806 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3809 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3813 catch ( final Exception e ) {
3814 e.printStackTrace( System.out );
3820 private static boolean testNexusMatrixParsing() {
3822 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3823 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3825 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3826 if ( m.getNumberOfCharacters() != 9 ) {
3829 if ( m.getNumberOfIdentifiers() != 5 ) {
3832 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3835 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3838 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3841 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3844 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3847 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3850 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3853 // if ( labels.length != 7 ) {
3856 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3859 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3862 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3865 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3868 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3871 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3874 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3877 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3879 // labels = parser.getCharStateLabels();
3880 // if ( labels.length != 7 ) {
3883 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3886 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3889 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3892 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3895 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3898 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3901 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3905 catch ( final Exception e ) {
3906 e.printStackTrace( System.out );
3912 private static boolean testNexusTreeParsing() {
3914 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3915 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3916 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3917 if ( phylogenies.length != 1 ) {
3920 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3923 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3927 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3928 if ( phylogenies.length != 1 ) {
3931 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3934 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3938 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3939 if ( phylogenies.length != 1 ) {
3942 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3945 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3948 if ( phylogenies[ 0 ].isRooted() ) {
3952 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3953 if ( phylogenies.length != 18 ) {
3956 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3959 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3962 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3965 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3968 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3971 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3974 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3977 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3980 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3983 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3986 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3989 if ( phylogenies[ 8 ].isRooted() ) {
3992 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3995 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3998 if ( !phylogenies[ 9 ].isRooted() ) {
4001 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4004 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4007 if ( !phylogenies[ 10 ].isRooted() ) {
4010 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4013 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4016 if ( phylogenies[ 11 ].isRooted() ) {
4019 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4022 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4025 if ( !phylogenies[ 12 ].isRooted() ) {
4028 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4031 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4034 if ( !phylogenies[ 13 ].isRooted() ) {
4037 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4040 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4043 if ( !phylogenies[ 14 ].isRooted() ) {
4046 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4049 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4052 if ( phylogenies[ 15 ].isRooted() ) {
4055 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4058 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4061 if ( !phylogenies[ 16 ].isRooted() ) {
4064 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4067 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4070 if ( phylogenies[ 17 ].isRooted() ) {
4073 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4077 catch ( final Exception e ) {
4078 e.printStackTrace( System.out );
4084 private static boolean testNexusTreeParsingTranslating() {
4086 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4087 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4088 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4089 if ( phylogenies.length != 1 ) {
4092 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4095 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4098 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4101 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4104 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4105 .equals( "Aranaeus" ) ) {
4109 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4110 if ( phylogenies.length != 3 ) {
4113 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4116 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4119 if ( phylogenies[ 0 ].isRooted() ) {
4122 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4125 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4128 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4129 .equals( "Aranaeus" ) ) {
4132 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4135 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4138 if ( phylogenies[ 1 ].isRooted() ) {
4141 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4144 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4147 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4148 .equals( "Aranaeus" ) ) {
4151 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4154 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4157 if ( !phylogenies[ 2 ].isRooted() ) {
4160 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4163 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4166 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4167 .equals( "Aranaeus" ) ) {
4171 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4172 if ( phylogenies.length != 3 ) {
4175 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4178 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4181 if ( phylogenies[ 0 ].isRooted() ) {
4184 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4187 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4190 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4191 .equals( "Aranaeus" ) ) {
4194 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4197 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4200 if ( phylogenies[ 1 ].isRooted() ) {
4203 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4206 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4209 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4210 .equals( "Aranaeus" ) ) {
4213 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4216 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4219 if ( !phylogenies[ 2 ].isRooted() ) {
4222 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4225 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4228 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4229 .equals( "Aranaeus" ) ) {
4233 catch ( final Exception e ) {
4234 e.printStackTrace( System.out );
4240 private static boolean testNHParsing() {
4242 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4243 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4244 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4247 final NHXParser nhxp = new NHXParser();
4248 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4249 nhxp.setReplaceUnderscores( true );
4250 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4251 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4254 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4257 final Phylogeny p1b = factory
4258 .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 ",
4259 new NHXParser() )[ 0 ];
4260 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4263 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4266 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4267 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4268 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4269 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4270 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4271 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4272 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4273 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4274 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4275 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4276 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4277 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4278 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4280 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4283 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4286 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4289 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4292 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4293 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4294 final String p16_S = "((A,B),C)";
4295 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4296 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4299 final String p17_S = "(C,(A,B))";
4300 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4301 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4304 final String p18_S = "((A,B),(C,D))";
4305 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4306 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4309 final String p19_S = "(((A,B),C),D)";
4310 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4311 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4314 final String p20_S = "(A,(B,(C,D)))";
4315 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4316 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4319 final String p21_S = "(A,(B,(C,(D,E))))";
4320 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4321 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4324 final String p22_S = "((((A,B),C),D),E)";
4325 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4326 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4329 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4330 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4331 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4334 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4335 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4336 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4339 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4340 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4341 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4342 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4345 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4348 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4349 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4350 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4351 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4352 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4353 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4354 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4355 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4356 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4357 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4360 final String p26_S = "(A,B)ab";
4361 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4362 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4365 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4366 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4368 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4371 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4372 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4373 final String p28_S3 = "(A,B)ab";
4374 final String p28_S4 = "((((A,B),C),D),;E;)";
4375 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4377 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4380 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4383 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4386 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4389 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";
4390 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4391 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4394 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";
4395 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4396 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4399 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4400 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4401 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4404 final String p33_S = "A";
4405 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4406 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4409 final String p34_S = "B;";
4410 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4411 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4414 final String p35_S = "B:0.2";
4415 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4416 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4419 final String p36_S = "(A)";
4420 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4421 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4424 final String p37_S = "((A))";
4425 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4426 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4429 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4430 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4431 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4434 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4435 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4436 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4439 final String p40_S = "(A,B,C)";
4440 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4441 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4444 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4445 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4446 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4449 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4450 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4451 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4454 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)";
4455 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4456 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4459 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)))";
4460 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4461 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4464 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4465 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4466 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4469 final String p46_S = "";
4470 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4471 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4474 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4475 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4478 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4479 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4482 final Phylogeny p49 = factory
4483 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4484 new NHXParser() )[ 0 ];
4485 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4488 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4489 if ( p50.getNode( "A" ) == null ) {
4492 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4493 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4496 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4499 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4500 .equals( "((A,B)88:2.0,C);" ) ) {
4503 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4504 if ( p51.getNode( "A(A" ) == null ) {
4507 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4508 if ( p52.getNode( "A(A" ) == null ) {
4511 final Phylogeny p53 = factory
4512 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4513 new NHXParser() )[ 0 ];
4514 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4518 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4519 if ( p54.getNode( "A" ) == null ) {
4522 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4523 .equals( "((A,B)[88],C);" ) ) {
4527 catch ( final Exception e ) {
4528 e.printStackTrace( System.out );
4534 private static boolean testNHXconversion() {
4536 final PhylogenyNode n1 = new PhylogenyNode();
4537 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4538 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4539 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4540 final PhylogenyNode n5 = PhylogenyNode
4541 .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]" );
4542 final PhylogenyNode n6 = PhylogenyNode
4543 .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]" );
4544 if ( !n1.toNewHampshireX().equals( "" ) ) {
4547 if ( !n2.toNewHampshireX().equals( "" ) ) {
4550 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4553 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4556 if ( !n5.toNewHampshireX()
4557 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4560 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4564 catch ( final Exception e ) {
4565 e.printStackTrace( System.out );
4571 private static boolean testNHXNodeParsing() {
4573 final PhylogenyNode n1 = new PhylogenyNode();
4574 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4575 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4576 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4577 final PhylogenyNode n5 = PhylogenyNode
4578 .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]" );
4579 if ( !n3.getName().equals( "n3" ) ) {
4582 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4585 if ( n3.isDuplication() ) {
4588 if ( n3.isHasAssignedEvent() ) {
4591 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4594 if ( !n4.getName().equals( "n4" ) ) {
4597 if ( n4.getDistanceToParent() != 0.01 ) {
4600 if ( !n5.getName().equals( "n5" ) ) {
4603 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4606 if ( n5.getDistanceToParent() != 0.1 ) {
4609 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4612 if ( !n5.isDuplication() ) {
4615 if ( !n5.isHasAssignedEvent() ) {
4618 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4621 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4624 final PhylogenyNode n8 = PhylogenyNode
4625 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4626 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4627 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4630 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4633 final PhylogenyNode n9 = PhylogenyNode
4634 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4635 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4636 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4639 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4642 final PhylogenyNode n10 = PhylogenyNode
4643 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4644 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4647 final PhylogenyNode n20 = PhylogenyNode
4648 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4649 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4652 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4655 final PhylogenyNode n20x = PhylogenyNode
4656 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4657 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4660 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4663 final PhylogenyNode n20xx = PhylogenyNode
4664 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4665 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4668 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4671 final PhylogenyNode n20xxx = PhylogenyNode
4672 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4673 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4676 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4679 final PhylogenyNode n20xxxx = PhylogenyNode
4680 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4681 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4684 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4687 final PhylogenyNode n21 = PhylogenyNode
4688 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4689 if ( !n21.getName().equals( "n21_PIG" ) ) {
4692 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4695 final PhylogenyNode n21x = PhylogenyNode
4696 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4697 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4700 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4703 final PhylogenyNode n22 = PhylogenyNode
4704 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4705 if ( !n22.getName().equals( "n22/PIG" ) ) {
4708 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4711 final PhylogenyNode n23 = PhylogenyNode
4712 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4713 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4716 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4719 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4720 final PhylogenyNode a = PhylogenyNode
4721 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4722 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4723 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4726 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4729 final PhylogenyNode b = PhylogenyNode
4730 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4731 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4732 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4735 if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
4738 final PhylogenyNode c = PhylogenyNode
4739 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4740 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4741 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4744 if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
4747 final PhylogenyNode c1 = PhylogenyNode
4748 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4749 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4750 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4753 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4756 final PhylogenyNode c2 = PhylogenyNode
4757 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4758 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4759 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4762 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4765 final PhylogenyNode d = PhylogenyNode
4766 .createInstanceFromNhxString( "n10_RAT1/1-2",
4767 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4768 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4771 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4774 final PhylogenyNode e = PhylogenyNode
4775 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4776 if ( !e.getName().equals( "n10_RAT1" ) ) {
4779 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4783 final PhylogenyNode n11 = PhylogenyNode
4784 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4785 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4786 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4789 if ( n11.getDistanceToParent() != 0.4 ) {
4792 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4795 final PhylogenyNode n12 = PhylogenyNode
4796 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4797 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4798 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4801 if ( n12.getDistanceToParent() != 0.4 ) {
4804 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4807 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4808 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4809 if ( !tvu1.getRef().equals( "tag1" ) ) {
4812 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4815 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4818 if ( !tvu1.getValue().equals( "value1" ) ) {
4821 if ( !tvu3.getRef().equals( "tag3" ) ) {
4824 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4827 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4830 if ( !tvu3.getValue().equals( "value3" ) ) {
4833 if ( n1.getName().compareTo( "" ) != 0 ) {
4836 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4839 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4842 if ( n2.getName().compareTo( "" ) != 0 ) {
4845 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4848 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4851 final PhylogenyNode n00 = PhylogenyNode
4852 .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]" );
4853 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4856 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4859 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4862 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4865 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4868 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4871 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4874 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4877 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4878 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4881 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4882 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4885 final PhylogenyNode n13 = PhylogenyNode
4886 .createInstanceFromNhxString( "blah_12345/1-2",
4887 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4888 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4891 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4894 final PhylogenyNode n14 = PhylogenyNode
4895 .createInstanceFromNhxString( "blah_12X45/1-2",
4896 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4897 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4900 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4903 final PhylogenyNode n15 = PhylogenyNode
4904 .createInstanceFromNhxString( "something_wicked[123]",
4905 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4906 if ( !n15.getName().equals( "something_wicked" ) ) {
4909 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4912 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4915 final PhylogenyNode n16 = PhylogenyNode
4916 .createInstanceFromNhxString( "something_wicked2[9]",
4917 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4918 if ( !n16.getName().equals( "something_wicked2" ) ) {
4921 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4924 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4927 final PhylogenyNode n17 = PhylogenyNode
4928 .createInstanceFromNhxString( "something_wicked3[a]",
4929 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4930 if ( !n17.getName().equals( "something_wicked3" ) ) {
4933 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4936 final PhylogenyNode n18 = PhylogenyNode
4937 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4938 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4941 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4944 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4948 catch ( final Exception e ) {
4949 e.printStackTrace( System.out );
4955 private static boolean testNHXParsing() {
4957 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4958 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4959 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4962 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]";
4963 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4964 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4967 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]";
4968 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4969 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4972 final Phylogeny[] p3 = factory
4973 .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]",
4975 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4978 final Phylogeny[] p4 = factory
4979 .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(]",
4981 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4984 final Phylogeny[] p5 = factory
4985 .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(((]",
4987 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4990 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)";
4991 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)";
4992 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4993 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4996 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)))";
4997 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)))";
4998 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4999 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5002 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]) ))[,,, ])))))))";
5003 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5004 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5005 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5008 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5009 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5012 final Phylogeny p10 = factory
5013 .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]",
5014 new NHXParser() )[ 0 ];
5015 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5019 catch ( final Exception e ) {
5020 e.printStackTrace( System.out );
5026 private static boolean testNHXParsingQuotes() {
5028 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5029 final NHXParser p = new NHXParser();
5030 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5031 if ( phylogenies_0.length != 5 ) {
5034 final Phylogeny phy = phylogenies_0[ 4 ];
5035 if ( phy.getNumberOfExternalNodes() != 7 ) {
5038 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5041 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5044 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5045 .getScientificName().equals( "hsapiens" ) ) {
5048 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5051 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5054 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5057 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5060 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5063 final NHXParser p1p = new NHXParser();
5064 p1p.setIgnoreQuotes( true );
5065 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5066 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5069 final NHXParser p2p = new NHXParser();
5070 p1p.setIgnoreQuotes( false );
5071 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5072 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5075 final NHXParser p3p = new NHXParser();
5076 p3p.setIgnoreQuotes( false );
5077 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5078 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5081 final NHXParser p4p = new NHXParser();
5082 p4p.setIgnoreQuotes( false );
5083 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5084 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5087 final Phylogeny p10 = factory
5088 .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]",
5089 new NHXParser() )[ 0 ];
5090 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5091 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5094 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5095 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5099 final Phylogeny p12 = factory
5100 .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]",
5101 new NHXParser() )[ 0 ];
5102 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5103 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5106 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5107 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5110 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;";
5111 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5114 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5115 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5119 catch ( final Exception e ) {
5120 e.printStackTrace( System.out );
5126 private static boolean testNHXParsingMB() {
5128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5129 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5130 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5131 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5132 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5133 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5134 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5135 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5136 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5137 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5138 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5141 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5144 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5145 0.1100000000000000e+00 ) ) {
5148 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5151 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5154 final Phylogeny p2 = factory
5155 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5156 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5157 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5158 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5159 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5160 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5161 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5162 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5163 + "7.369400000000000e-02}])",
5164 new NHXParser() )[ 0 ];
5165 if ( p2.getNode( "1" ) == null ) {
5168 if ( p2.getNode( "2" ) == null ) {
5172 catch ( final Exception e ) {
5173 e.printStackTrace( System.out );
5180 private static boolean testPhylogenyBranch() {
5182 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5183 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5184 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5185 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5186 if ( !a1b1.equals( a1b1 ) ) {
5189 if ( !a1b1.equals( b1a1 ) ) {
5192 if ( !b1a1.equals( a1b1 ) ) {
5195 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5196 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5197 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5198 if ( a1_b1.equals( b1_a1 ) ) {
5201 if ( a1_b1.equals( a1_b1_ ) ) {
5204 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5205 if ( !a1_b1.equals( b1_a1_ ) ) {
5208 if ( a1_b1_.equals( b1_a1_ ) ) {
5211 if ( !a1_b1_.equals( b1_a1 ) ) {
5215 catch ( final Exception e ) {
5216 e.printStackTrace( System.out );
5222 private static boolean testPhyloXMLparsingOfDistributionElement() {
5224 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5225 PhyloXmlParser xml_parser = null;
5227 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5229 catch ( final Exception e ) {
5230 // Do nothing -- means were not running from jar.
5232 if ( xml_parser == null ) {
5233 xml_parser = new PhyloXmlParser();
5234 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5235 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5238 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5241 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5243 if ( xml_parser.getErrorCount() > 0 ) {
5244 System.out.println( xml_parser.getErrorMessages().toString() );
5247 if ( phylogenies_0.length != 1 ) {
5250 final Phylogeny t1 = phylogenies_0[ 0 ];
5251 PhylogenyNode n = null;
5252 Distribution d = null;
5253 n = t1.getNode( "root node" );
5254 if ( !n.getNodeData().isHasDistribution() ) {
5257 if ( n.getNodeData().getDistributions().size() != 1 ) {
5260 d = n.getNodeData().getDistribution();
5261 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5264 if ( d.getPoints().size() != 1 ) {
5267 if ( d.getPolygons() != null ) {
5270 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5273 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5276 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5279 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5282 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5285 n = t1.getNode( "node a" );
5286 if ( !n.getNodeData().isHasDistribution() ) {
5289 if ( n.getNodeData().getDistributions().size() != 2 ) {
5292 d = n.getNodeData().getDistribution( 1 );
5293 if ( !d.getDesc().equals( "San Diego" ) ) {
5296 if ( d.getPoints().size() != 1 ) {
5299 if ( d.getPolygons() != null ) {
5302 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5305 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5308 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5311 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5314 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5317 n = t1.getNode( "node bb" );
5318 if ( !n.getNodeData().isHasDistribution() ) {
5321 if ( n.getNodeData().getDistributions().size() != 1 ) {
5324 d = n.getNodeData().getDistribution( 0 );
5325 if ( d.getPoints().size() != 3 ) {
5328 if ( d.getPolygons().size() != 2 ) {
5331 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5334 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5337 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5340 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5343 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5346 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5349 Polygon p = d.getPolygons().get( 0 );
5350 if ( p.getPoints().size() != 3 ) {
5353 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5356 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5359 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5362 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5365 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5368 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5371 p = d.getPolygons().get( 1 );
5372 if ( p.getPoints().size() != 3 ) {
5375 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5378 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5381 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5385 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5386 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5387 if ( rt.length != 1 ) {
5390 final Phylogeny t1_rt = rt[ 0 ];
5391 n = t1_rt.getNode( "root node" );
5392 if ( !n.getNodeData().isHasDistribution() ) {
5395 if ( n.getNodeData().getDistributions().size() != 1 ) {
5398 d = n.getNodeData().getDistribution();
5399 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5402 if ( d.getPoints().size() != 1 ) {
5405 if ( d.getPolygons() != null ) {
5408 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5411 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5414 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5417 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5420 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5423 n = t1_rt.getNode( "node a" );
5424 if ( !n.getNodeData().isHasDistribution() ) {
5427 if ( n.getNodeData().getDistributions().size() != 2 ) {
5430 d = n.getNodeData().getDistribution( 1 );
5431 if ( !d.getDesc().equals( "San Diego" ) ) {
5434 if ( d.getPoints().size() != 1 ) {
5437 if ( d.getPolygons() != null ) {
5440 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5443 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5446 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5449 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5452 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5455 n = t1_rt.getNode( "node bb" );
5456 if ( !n.getNodeData().isHasDistribution() ) {
5459 if ( n.getNodeData().getDistributions().size() != 1 ) {
5462 d = n.getNodeData().getDistribution( 0 );
5463 if ( d.getPoints().size() != 3 ) {
5466 if ( d.getPolygons().size() != 2 ) {
5469 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5472 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5475 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5478 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5481 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5484 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5487 p = d.getPolygons().get( 0 );
5488 if ( p.getPoints().size() != 3 ) {
5491 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5494 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5497 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5500 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5503 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5506 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5509 p = d.getPolygons().get( 1 );
5510 if ( p.getPoints().size() != 3 ) {
5513 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5516 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5519 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5523 catch ( final Exception e ) {
5524 e.printStackTrace( System.out );
5530 private static boolean testPostOrderIterator() {
5532 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5533 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5534 PhylogenyNodeIterator it0;
5535 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5538 for( it0.reset(); it0.hasNext(); ) {
5541 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5542 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5543 if ( !it.next().getName().equals( "A" ) ) {
5546 if ( !it.next().getName().equals( "B" ) ) {
5549 if ( !it.next().getName().equals( "ab" ) ) {
5552 if ( !it.next().getName().equals( "C" ) ) {
5555 if ( !it.next().getName().equals( "D" ) ) {
5558 if ( !it.next().getName().equals( "cd" ) ) {
5561 if ( !it.next().getName().equals( "abcd" ) ) {
5564 if ( !it.next().getName().equals( "E" ) ) {
5567 if ( !it.next().getName().equals( "F" ) ) {
5570 if ( !it.next().getName().equals( "ef" ) ) {
5573 if ( !it.next().getName().equals( "G" ) ) {
5576 if ( !it.next().getName().equals( "H" ) ) {
5579 if ( !it.next().getName().equals( "gh" ) ) {
5582 if ( !it.next().getName().equals( "efgh" ) ) {
5585 if ( !it.next().getName().equals( "r" ) ) {
5588 if ( it.hasNext() ) {
5592 catch ( final Exception e ) {
5593 e.printStackTrace( System.out );
5599 private static boolean testPreOrderIterator() {
5601 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5602 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5603 PhylogenyNodeIterator it0;
5604 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5607 for( it0.reset(); it0.hasNext(); ) {
5610 PhylogenyNodeIterator it = t0.iteratorPreorder();
5611 if ( !it.next().getName().equals( "r" ) ) {
5614 if ( !it.next().getName().equals( "ab" ) ) {
5617 if ( !it.next().getName().equals( "A" ) ) {
5620 if ( !it.next().getName().equals( "B" ) ) {
5623 if ( !it.next().getName().equals( "cd" ) ) {
5626 if ( !it.next().getName().equals( "C" ) ) {
5629 if ( !it.next().getName().equals( "D" ) ) {
5632 if ( it.hasNext() ) {
5635 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5636 it = t1.iteratorPreorder();
5637 if ( !it.next().getName().equals( "r" ) ) {
5640 if ( !it.next().getName().equals( "abcd" ) ) {
5643 if ( !it.next().getName().equals( "ab" ) ) {
5646 if ( !it.next().getName().equals( "A" ) ) {
5649 if ( !it.next().getName().equals( "B" ) ) {
5652 if ( !it.next().getName().equals( "cd" ) ) {
5655 if ( !it.next().getName().equals( "C" ) ) {
5658 if ( !it.next().getName().equals( "D" ) ) {
5661 if ( !it.next().getName().equals( "efgh" ) ) {
5664 if ( !it.next().getName().equals( "ef" ) ) {
5667 if ( !it.next().getName().equals( "E" ) ) {
5670 if ( !it.next().getName().equals( "F" ) ) {
5673 if ( !it.next().getName().equals( "gh" ) ) {
5676 if ( !it.next().getName().equals( "G" ) ) {
5679 if ( !it.next().getName().equals( "H" ) ) {
5682 if ( it.hasNext() ) {
5686 catch ( final Exception e ) {
5687 e.printStackTrace( System.out );
5693 private static boolean testPropertiesMap() {
5695 final PropertiesMap pm = new PropertiesMap();
5696 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5697 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5698 final Property p2 = new Property( "something:else",
5700 "improbable:research",
5703 pm.addProperty( p0 );
5704 pm.addProperty( p1 );
5705 pm.addProperty( p2 );
5706 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5709 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5712 if ( pm.getProperties().size() != 3 ) {
5715 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5718 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5721 if ( pm.getProperties().size() != 3 ) {
5724 pm.removeProperty( "dimensions:diameter" );
5725 if ( pm.getProperties().size() != 2 ) {
5728 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5731 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5735 catch ( final Exception e ) {
5736 e.printStackTrace( System.out );
5742 private static boolean testReIdMethods() {
5744 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5745 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5746 final int count = PhylogenyNode.getNodeCount();
5748 if ( p.getNode( "r" ).getId() != count ) {
5751 if ( p.getNode( "A" ).getId() != count + 1 ) {
5754 if ( p.getNode( "B" ).getId() != count + 1 ) {
5757 if ( p.getNode( "C" ).getId() != count + 1 ) {
5760 if ( p.getNode( "1" ).getId() != count + 2 ) {
5763 if ( p.getNode( "2" ).getId() != count + 2 ) {
5766 if ( p.getNode( "3" ).getId() != count + 2 ) {
5769 if ( p.getNode( "4" ).getId() != count + 2 ) {
5772 if ( p.getNode( "5" ).getId() != count + 2 ) {
5775 if ( p.getNode( "6" ).getId() != count + 2 ) {
5778 if ( p.getNode( "a" ).getId() != count + 3 ) {
5781 if ( p.getNode( "b" ).getId() != count + 3 ) {
5784 if ( p.getNode( "X" ).getId() != count + 4 ) {
5787 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5790 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5794 catch ( final Exception e ) {
5795 e.printStackTrace( System.out );
5801 private static boolean testRerooting() {
5803 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5804 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",
5805 new NHXParser() )[ 0 ];
5806 if ( !t1.isRooted() ) {
5809 t1.reRoot( t1.getNode( "D" ) );
5810 t1.reRoot( t1.getNode( "CD" ) );
5811 t1.reRoot( t1.getNode( "A" ) );
5812 t1.reRoot( t1.getNode( "B" ) );
5813 t1.reRoot( t1.getNode( "AB" ) );
5814 t1.reRoot( t1.getNode( "D" ) );
5815 t1.reRoot( t1.getNode( "C" ) );
5816 t1.reRoot( t1.getNode( "CD" ) );
5817 t1.reRoot( t1.getNode( "A" ) );
5818 t1.reRoot( t1.getNode( "B" ) );
5819 t1.reRoot( t1.getNode( "AB" ) );
5820 t1.reRoot( t1.getNode( "D" ) );
5821 t1.reRoot( t1.getNode( "D" ) );
5822 t1.reRoot( t1.getNode( "C" ) );
5823 t1.reRoot( t1.getNode( "A" ) );
5824 t1.reRoot( t1.getNode( "B" ) );
5825 t1.reRoot( t1.getNode( "AB" ) );
5826 t1.reRoot( t1.getNode( "C" ) );
5827 t1.reRoot( t1.getNode( "D" ) );
5828 t1.reRoot( t1.getNode( "CD" ) );
5829 t1.reRoot( t1.getNode( "D" ) );
5830 t1.reRoot( t1.getNode( "A" ) );
5831 t1.reRoot( t1.getNode( "B" ) );
5832 t1.reRoot( t1.getNode( "AB" ) );
5833 t1.reRoot( t1.getNode( "C" ) );
5834 t1.reRoot( t1.getNode( "D" ) );
5835 t1.reRoot( t1.getNode( "CD" ) );
5836 t1.reRoot( t1.getNode( "D" ) );
5837 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5840 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5843 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5846 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5849 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5852 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5855 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",
5856 new NHXParser() )[ 0 ];
5857 t2.reRoot( t2.getNode( "A" ) );
5858 t2.reRoot( t2.getNode( "D" ) );
5859 t2.reRoot( t2.getNode( "ABC" ) );
5860 t2.reRoot( t2.getNode( "A" ) );
5861 t2.reRoot( t2.getNode( "B" ) );
5862 t2.reRoot( t2.getNode( "D" ) );
5863 t2.reRoot( t2.getNode( "C" ) );
5864 t2.reRoot( t2.getNode( "ABC" ) );
5865 t2.reRoot( t2.getNode( "A" ) );
5866 t2.reRoot( t2.getNode( "B" ) );
5867 t2.reRoot( t2.getNode( "AB" ) );
5868 t2.reRoot( t2.getNode( "AB" ) );
5869 t2.reRoot( t2.getNode( "D" ) );
5870 t2.reRoot( t2.getNode( "C" ) );
5871 t2.reRoot( t2.getNode( "B" ) );
5872 t2.reRoot( t2.getNode( "AB" ) );
5873 t2.reRoot( t2.getNode( "D" ) );
5874 t2.reRoot( t2.getNode( "D" ) );
5875 t2.reRoot( t2.getNode( "ABC" ) );
5876 t2.reRoot( t2.getNode( "A" ) );
5877 t2.reRoot( t2.getNode( "B" ) );
5878 t2.reRoot( t2.getNode( "AB" ) );
5879 t2.reRoot( t2.getNode( "D" ) );
5880 t2.reRoot( t2.getNode( "C" ) );
5881 t2.reRoot( t2.getNode( "ABC" ) );
5882 t2.reRoot( t2.getNode( "A" ) );
5883 t2.reRoot( t2.getNode( "B" ) );
5884 t2.reRoot( t2.getNode( "AB" ) );
5885 t2.reRoot( t2.getNode( "D" ) );
5886 t2.reRoot( t2.getNode( "D" ) );
5887 t2.reRoot( t2.getNode( "C" ) );
5888 t2.reRoot( t2.getNode( "A" ) );
5889 t2.reRoot( t2.getNode( "B" ) );
5890 t2.reRoot( t2.getNode( "AB" ) );
5891 t2.reRoot( t2.getNode( "C" ) );
5892 t2.reRoot( t2.getNode( "D" ) );
5893 t2.reRoot( t2.getNode( "ABC" ) );
5894 t2.reRoot( t2.getNode( "D" ) );
5895 t2.reRoot( t2.getNode( "A" ) );
5896 t2.reRoot( t2.getNode( "B" ) );
5897 t2.reRoot( t2.getNode( "AB" ) );
5898 t2.reRoot( t2.getNode( "C" ) );
5899 t2.reRoot( t2.getNode( "D" ) );
5900 t2.reRoot( t2.getNode( "ABC" ) );
5901 t2.reRoot( t2.getNode( "D" ) );
5902 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5905 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5908 t2.reRoot( t2.getNode( "ABC" ) );
5909 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5912 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5915 t2.reRoot( t2.getNode( "AB" ) );
5916 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5919 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5922 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5925 t2.reRoot( t2.getNode( "AB" ) );
5926 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5929 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5932 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5935 t2.reRoot( t2.getNode( "D" ) );
5936 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5939 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5942 t2.reRoot( t2.getNode( "ABC" ) );
5943 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5946 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5949 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5950 new NHXParser() )[ 0 ];
5951 t3.reRoot( t3.getNode( "B" ) );
5952 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5955 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5958 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5961 t3.reRoot( t3.getNode( "B" ) );
5962 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5965 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5968 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5971 t3.reRoot( t3.getRoot() );
5972 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5975 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5978 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5982 catch ( final Exception e ) {
5983 e.printStackTrace( System.out );
5989 private static boolean testSDIse() {
5991 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5992 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5993 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5994 gene1.setRooted( true );
5995 species1.setRooted( true );
5996 final SDI sdi = new SDIse( gene1, species1 );
5997 if ( !gene1.getRoot().isDuplication() ) {
6000 final Phylogeny species2 = factory
6001 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6002 new NHXParser() )[ 0 ];
6003 final Phylogeny gene2 = factory
6004 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6005 new NHXParser() )[ 0 ];
6006 species2.setRooted( true );
6007 gene2.setRooted( true );
6008 final SDI sdi2 = new SDIse( gene2, species2 );
6009 if ( sdi2.getDuplicationsSum() != 0 ) {
6012 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6015 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6018 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6021 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6024 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6027 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6030 final Phylogeny species3 = factory
6031 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6032 new NHXParser() )[ 0 ];
6033 final Phylogeny gene3 = factory
6034 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6035 new NHXParser() )[ 0 ];
6036 species3.setRooted( true );
6037 gene3.setRooted( true );
6038 final SDI sdi3 = new SDIse( gene3, species3 );
6039 if ( sdi3.getDuplicationsSum() != 1 ) {
6042 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6045 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6048 final Phylogeny species4 = factory
6049 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6050 new NHXParser() )[ 0 ];
6051 final Phylogeny gene4 = factory
6052 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6053 new NHXParser() )[ 0 ];
6054 species4.setRooted( true );
6055 gene4.setRooted( true );
6056 final SDI sdi4 = new SDIse( gene4, species4 );
6057 if ( sdi4.getDuplicationsSum() != 1 ) {
6060 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6063 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6066 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6069 if ( species4.getNumberOfExternalNodes() != 6 ) {
6072 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6075 final Phylogeny species5 = factory
6076 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6077 new NHXParser() )[ 0 ];
6078 final Phylogeny gene5 = factory
6079 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6080 new NHXParser() )[ 0 ];
6081 species5.setRooted( true );
6082 gene5.setRooted( true );
6083 final SDI sdi5 = new SDIse( gene5, species5 );
6084 if ( sdi5.getDuplicationsSum() != 2 ) {
6087 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6090 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6093 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6096 if ( species5.getNumberOfExternalNodes() != 6 ) {
6099 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6102 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6103 // Conjecture for Comparing Molecular Phylogenies"
6104 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6105 final Phylogeny species6 = factory
6106 .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,"
6107 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6108 new NHXParser() )[ 0 ];
6109 final Phylogeny gene6 = factory
6110 .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,"
6111 + "((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,"
6112 + "(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;",
6113 new NHXParser() )[ 0 ];
6114 species6.setRooted( true );
6115 gene6.setRooted( true );
6116 final SDI sdi6 = new SDIse( gene6, species6 );
6117 if ( sdi6.getDuplicationsSum() != 3 ) {
6120 if ( !gene6.getNode( "r" ).isDuplication() ) {
6123 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6126 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6129 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6132 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6135 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6138 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6141 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6144 sdi6.computeMappingCostL();
6145 if ( sdi6.computeMappingCostL() != 17 ) {
6148 if ( species6.getNumberOfExternalNodes() != 9 ) {
6151 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6154 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6155 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6156 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6157 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6158 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6159 species7.setRooted( true );
6160 final Phylogeny gene7_1 = Test
6161 .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])" );
6162 gene7_1.setRooted( true );
6163 final SDI sdi7 = new SDIse( gene7_1, species7 );
6164 if ( sdi7.getDuplicationsSum() != 0 ) {
6167 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6170 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6173 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6176 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6179 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6182 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6185 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6188 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6191 final Phylogeny gene7_2 = Test
6192 .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])" );
6193 gene7_2.setRooted( true );
6194 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6195 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6198 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6201 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6204 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6207 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6210 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6213 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6216 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6219 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6222 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6226 catch ( final Exception e ) {
6232 private static boolean testSDIunrooted() {
6234 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6235 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6236 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6237 final Iterator<PhylogenyBranch> iter = l.iterator();
6238 PhylogenyBranch br = iter.next();
6239 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6242 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6246 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6249 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6253 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6256 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6260 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6263 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6267 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6270 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6274 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6277 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6281 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6284 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6288 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6291 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6295 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6298 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6302 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6305 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6309 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6312 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6316 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6319 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6323 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6326 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6330 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6333 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6337 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6340 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6343 if ( iter.hasNext() ) {
6346 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6347 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6348 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6350 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6353 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6357 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6360 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6364 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6367 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6370 if ( iter1.hasNext() ) {
6373 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6374 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6375 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6377 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6380 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6384 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6387 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6391 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6394 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6397 if ( iter2.hasNext() ) {
6400 final Phylogeny species0 = factory
6401 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6402 new NHXParser() )[ 0 ];
6403 final Phylogeny gene1 = factory
6404 .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])",
6405 new NHXParser() )[ 0 ];
6406 species0.setRooted( true );
6407 gene1.setRooted( true );
6408 final SDIR sdi_unrooted = new SDIR();
6409 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6410 if ( sdi_unrooted.getCount() != 1 ) {
6413 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6416 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6419 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6422 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6425 final Phylogeny gene2 = factory
6426 .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])",
6427 new NHXParser() )[ 0 ];
6428 gene2.setRooted( true );
6429 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6430 if ( sdi_unrooted.getCount() != 1 ) {
6433 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6436 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6439 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6442 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6445 final Phylogeny species6 = factory
6446 .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,"
6447 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6448 new NHXParser() )[ 0 ];
6449 final Phylogeny gene6 = factory
6450 .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],"
6451 + "(((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],"
6452 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6453 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6454 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6455 new NHXParser() )[ 0 ];
6456 species6.setRooted( true );
6457 gene6.setRooted( true );
6458 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6459 if ( sdi_unrooted.getCount() != 1 ) {
6462 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6465 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6468 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6471 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6474 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6477 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6480 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6483 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6486 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6489 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6492 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6495 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6499 final Phylogeny species7 = factory
6500 .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,"
6501 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6502 new NHXParser() )[ 0 ];
6503 final Phylogeny gene7 = factory
6504 .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],"
6505 + "(((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],"
6506 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6507 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6508 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6509 new NHXParser() )[ 0 ];
6510 species7.setRooted( true );
6511 gene7.setRooted( true );
6512 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6513 if ( sdi_unrooted.getCount() != 1 ) {
6516 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6519 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6522 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6525 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6528 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6531 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6534 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6537 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6540 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6543 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6546 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6549 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6553 final Phylogeny species8 = factory
6554 .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,"
6555 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6556 new NHXParser() )[ 0 ];
6557 final Phylogeny gene8 = factory
6558 .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],"
6559 + "(((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],"
6560 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6561 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6562 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6563 new NHXParser() )[ 0 ];
6564 species8.setRooted( true );
6565 gene8.setRooted( true );
6566 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6567 if ( sdi_unrooted.getCount() != 1 ) {
6570 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6573 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6576 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6579 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6582 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6585 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6588 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6591 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6594 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6597 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6600 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6603 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6608 catch ( final Exception e ) {
6609 e.printStackTrace( System.out );
6615 private static boolean testSplit() {
6617 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6618 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6619 //Archaeopteryx.createApplication( p0 );
6620 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6621 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6622 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6623 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6624 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6625 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6626 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6627 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6628 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6629 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6630 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6631 // System.out.println( s0.toString() );
6633 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6636 if ( s0.match( query_nodes ) ) {
6639 query_nodes = new HashSet<PhylogenyNode>();
6640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6647 if ( !s0.match( query_nodes ) ) {
6651 query_nodes = new HashSet<PhylogenyNode>();
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6655 if ( !s0.match( query_nodes ) ) {
6659 query_nodes = new HashSet<PhylogenyNode>();
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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( "B" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6673 if ( !s0.match( query_nodes ) ) {
6677 query_nodes = new HashSet<PhylogenyNode>();
6678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6681 if ( !s0.match( query_nodes ) ) {
6685 query_nodes = new HashSet<PhylogenyNode>();
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6688 if ( !s0.match( query_nodes ) ) {
6692 query_nodes = new HashSet<PhylogenyNode>();
6693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6698 if ( !s0.match( query_nodes ) ) {
6702 query_nodes = new HashSet<PhylogenyNode>();
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6706 if ( !s0.match( query_nodes ) ) {
6710 query_nodes = new HashSet<PhylogenyNode>();
6711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6714 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6715 if ( !s0.match( query_nodes ) ) {
6719 query_nodes = new HashSet<PhylogenyNode>();
6720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6722 if ( s0.match( query_nodes ) ) {
6726 query_nodes = new HashSet<PhylogenyNode>();
6727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6731 if ( s0.match( query_nodes ) ) {
6735 query_nodes = new HashSet<PhylogenyNode>();
6736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6741 if ( s0.match( query_nodes ) ) {
6745 query_nodes = new HashSet<PhylogenyNode>();
6746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6749 if ( s0.match( query_nodes ) ) {
6753 query_nodes = new HashSet<PhylogenyNode>();
6754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6756 if ( s0.match( query_nodes ) ) {
6760 query_nodes = new HashSet<PhylogenyNode>();
6761 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6763 if ( s0.match( query_nodes ) ) {
6767 query_nodes = new HashSet<PhylogenyNode>();
6768 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6770 if ( s0.match( query_nodes ) ) {
6774 query_nodes = new HashSet<PhylogenyNode>();
6775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6777 if ( s0.match( query_nodes ) ) {
6781 query_nodes = new HashSet<PhylogenyNode>();
6782 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6784 if ( s0.match( query_nodes ) ) {
6788 query_nodes = new HashSet<PhylogenyNode>();
6789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6791 if ( s0.match( query_nodes ) ) {
6795 query_nodes = new HashSet<PhylogenyNode>();
6796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6798 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6799 if ( s0.match( query_nodes ) ) {
6803 query_nodes = new HashSet<PhylogenyNode>();
6804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6807 if ( s0.match( query_nodes ) ) {
6811 query_nodes = new HashSet<PhylogenyNode>();
6812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6815 if ( s0.match( query_nodes ) ) {
6819 query_nodes = new HashSet<PhylogenyNode>();
6820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6821 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6824 if ( s0.match( query_nodes ) ) {
6828 // query_nodes = new HashSet<PhylogenyNode>();
6829 // query_nodes.add( new PhylogenyNode( "X" ) );
6830 // query_nodes.add( new PhylogenyNode( "Y" ) );
6831 // query_nodes.add( new PhylogenyNode( "A" ) );
6832 // query_nodes.add( new PhylogenyNode( "B" ) );
6833 // query_nodes.add( new PhylogenyNode( "C" ) );
6834 // query_nodes.add( new PhylogenyNode( "D" ) );
6835 // query_nodes.add( new PhylogenyNode( "E" ) );
6836 // query_nodes.add( new PhylogenyNode( "F" ) );
6837 // query_nodes.add( new PhylogenyNode( "G" ) );
6838 // if ( !s0.match( query_nodes ) ) {
6841 // query_nodes = new HashSet<PhylogenyNode>();
6842 // query_nodes.add( new PhylogenyNode( "X" ) );
6843 // query_nodes.add( new PhylogenyNode( "Y" ) );
6844 // query_nodes.add( new PhylogenyNode( "A" ) );
6845 // query_nodes.add( new PhylogenyNode( "B" ) );
6846 // query_nodes.add( new PhylogenyNode( "C" ) );
6847 // if ( !s0.match( query_nodes ) ) {
6851 // query_nodes = new HashSet<PhylogenyNode>();
6852 // query_nodes.add( new PhylogenyNode( "X" ) );
6853 // query_nodes.add( new PhylogenyNode( "Y" ) );
6854 // query_nodes.add( new PhylogenyNode( "D" ) );
6855 // query_nodes.add( new PhylogenyNode( "E" ) );
6856 // query_nodes.add( new PhylogenyNode( "F" ) );
6857 // query_nodes.add( new PhylogenyNode( "G" ) );
6858 // if ( !s0.match( query_nodes ) ) {
6862 // query_nodes = new HashSet<PhylogenyNode>();
6863 // query_nodes.add( new PhylogenyNode( "X" ) );
6864 // query_nodes.add( new PhylogenyNode( "Y" ) );
6865 // query_nodes.add( new PhylogenyNode( "A" ) );
6866 // query_nodes.add( new PhylogenyNode( "B" ) );
6867 // query_nodes.add( new PhylogenyNode( "C" ) );
6868 // query_nodes.add( new PhylogenyNode( "D" ) );
6869 // if ( !s0.match( query_nodes ) ) {
6873 // query_nodes = new HashSet<PhylogenyNode>();
6874 // query_nodes.add( new PhylogenyNode( "X" ) );
6875 // query_nodes.add( new PhylogenyNode( "Y" ) );
6876 // query_nodes.add( new PhylogenyNode( "E" ) );
6877 // query_nodes.add( new PhylogenyNode( "F" ) );
6878 // query_nodes.add( new PhylogenyNode( "G" ) );
6879 // if ( !s0.match( query_nodes ) ) {
6883 // query_nodes = new HashSet<PhylogenyNode>();
6884 // query_nodes.add( new PhylogenyNode( "X" ) );
6885 // query_nodes.add( new PhylogenyNode( "Y" ) );
6886 // query_nodes.add( new PhylogenyNode( "F" ) );
6887 // query_nodes.add( new PhylogenyNode( "G" ) );
6888 // if ( !s0.match( query_nodes ) ) {
6892 query_nodes = new HashSet<PhylogenyNode>();
6893 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6897 if ( s0.match( query_nodes ) ) {
6901 query_nodes = new HashSet<PhylogenyNode>();
6902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6906 if ( s0.match( query_nodes ) ) {
6909 ///////////////////////////
6911 query_nodes = new HashSet<PhylogenyNode>();
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6916 if ( s0.match( query_nodes ) ) {
6920 query_nodes = new HashSet<PhylogenyNode>();
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6925 if ( s0.match( query_nodes ) ) {
6929 query_nodes = new HashSet<PhylogenyNode>();
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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( "X" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6943 if ( s0.match( query_nodes ) ) {
6947 query_nodes = new HashSet<PhylogenyNode>();
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6952 if ( s0.match( query_nodes ) ) {
6956 query_nodes = new HashSet<PhylogenyNode>();
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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( "X" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6969 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6970 if ( s0.match( query_nodes ) ) {
6974 query_nodes = new HashSet<PhylogenyNode>();
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6978 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6980 if ( s0.match( query_nodes ) ) {
6984 query_nodes = new HashSet<PhylogenyNode>();
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6990 if ( s0.match( query_nodes ) ) {
6994 query_nodes = new HashSet<PhylogenyNode>();
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7001 if ( s0.match( query_nodes ) ) {
7005 catch ( final Exception e ) {
7006 e.printStackTrace();
7012 private static boolean testSplitStrict() {
7014 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7015 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7016 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7017 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7018 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7019 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7020 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7021 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7022 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7023 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7024 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7025 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7028 if ( s0.match( query_nodes ) ) {
7031 query_nodes = new HashSet<PhylogenyNode>();
7032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7036 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7037 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7039 if ( !s0.match( query_nodes ) ) {
7043 query_nodes = new HashSet<PhylogenyNode>();
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7047 if ( !s0.match( query_nodes ) ) {
7051 query_nodes = new HashSet<PhylogenyNode>();
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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( "B" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7065 if ( !s0.match( query_nodes ) ) {
7069 query_nodes = new HashSet<PhylogenyNode>();
7070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7073 if ( !s0.match( query_nodes ) ) {
7077 query_nodes = new HashSet<PhylogenyNode>();
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7080 if ( !s0.match( query_nodes ) ) {
7084 query_nodes = new HashSet<PhylogenyNode>();
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7090 if ( !s0.match( query_nodes ) ) {
7094 query_nodes = new HashSet<PhylogenyNode>();
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7098 if ( !s0.match( query_nodes ) ) {
7102 query_nodes = new HashSet<PhylogenyNode>();
7103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7107 if ( !s0.match( query_nodes ) ) {
7111 query_nodes = new HashSet<PhylogenyNode>();
7112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7114 if ( s0.match( query_nodes ) ) {
7118 query_nodes = new HashSet<PhylogenyNode>();
7119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7123 if ( s0.match( query_nodes ) ) {
7127 query_nodes = new HashSet<PhylogenyNode>();
7128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7133 if ( s0.match( query_nodes ) ) {
7137 query_nodes = new HashSet<PhylogenyNode>();
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7141 if ( s0.match( query_nodes ) ) {
7145 query_nodes = new HashSet<PhylogenyNode>();
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7148 if ( s0.match( query_nodes ) ) {
7152 query_nodes = new HashSet<PhylogenyNode>();
7153 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7155 if ( s0.match( query_nodes ) ) {
7159 query_nodes = new HashSet<PhylogenyNode>();
7160 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7162 if ( s0.match( query_nodes ) ) {
7166 query_nodes = new HashSet<PhylogenyNode>();
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7169 if ( s0.match( query_nodes ) ) {
7173 query_nodes = new HashSet<PhylogenyNode>();
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7176 if ( s0.match( query_nodes ) ) {
7180 query_nodes = new HashSet<PhylogenyNode>();
7181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7183 if ( s0.match( query_nodes ) ) {
7187 query_nodes = new HashSet<PhylogenyNode>();
7188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7190 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7191 if ( s0.match( query_nodes ) ) {
7195 query_nodes = new HashSet<PhylogenyNode>();
7196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7197 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7199 if ( s0.match( query_nodes ) ) {
7203 query_nodes = new HashSet<PhylogenyNode>();
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7207 if ( s0.match( query_nodes ) ) {
7211 query_nodes = new HashSet<PhylogenyNode>();
7212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7216 if ( s0.match( query_nodes ) ) {
7220 catch ( final Exception e ) {
7221 e.printStackTrace();
7227 private static boolean testSubtreeDeletion() {
7229 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7230 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7231 t1.deleteSubtree( t1.getNode( "A" ), false );
7232 if ( t1.getNumberOfExternalNodes() != 5 ) {
7235 t1.toNewHampshireX();
7236 t1.deleteSubtree( t1.getNode( "E" ), false );
7237 if ( t1.getNumberOfExternalNodes() != 4 ) {
7240 t1.toNewHampshireX();
7241 t1.deleteSubtree( t1.getNode( "F" ), false );
7242 if ( t1.getNumberOfExternalNodes() != 3 ) {
7245 t1.toNewHampshireX();
7246 t1.deleteSubtree( t1.getNode( "D" ), false );
7247 t1.toNewHampshireX();
7248 if ( t1.getNumberOfExternalNodes() != 3 ) {
7251 t1.deleteSubtree( t1.getNode( "def" ), false );
7252 t1.toNewHampshireX();
7253 if ( t1.getNumberOfExternalNodes() != 2 ) {
7256 t1.deleteSubtree( t1.getNode( "B" ), false );
7257 t1.toNewHampshireX();
7258 if ( t1.getNumberOfExternalNodes() != 1 ) {
7261 t1.deleteSubtree( t1.getNode( "C" ), false );
7262 t1.toNewHampshireX();
7263 if ( t1.getNumberOfExternalNodes() != 1 ) {
7266 t1.deleteSubtree( t1.getNode( "abc" ), false );
7267 t1.toNewHampshireX();
7268 if ( t1.getNumberOfExternalNodes() != 1 ) {
7271 t1.deleteSubtree( t1.getNode( "r" ), false );
7272 if ( t1.getNumberOfExternalNodes() != 0 ) {
7275 if ( !t1.isEmpty() ) {
7278 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7279 t2.deleteSubtree( t2.getNode( "A" ), false );
7280 t2.toNewHampshireX();
7281 if ( t2.getNumberOfExternalNodes() != 5 ) {
7284 t2.deleteSubtree( t2.getNode( "abc" ), false );
7285 t2.toNewHampshireX();
7286 if ( t2.getNumberOfExternalNodes() != 3 ) {
7289 t2.deleteSubtree( t2.getNode( "def" ), false );
7290 t2.toNewHampshireX();
7291 if ( t2.getNumberOfExternalNodes() != 1 ) {
7295 catch ( final Exception e ) {
7296 e.printStackTrace( System.out );
7302 private static boolean testSupportCount() {
7304 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7305 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7306 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7307 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7308 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7309 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7310 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7312 SupportCount.count( t0_1, phylogenies_1, true, false );
7313 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7314 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7315 + "(((((A,B),C),D),E),((F,G),X))"
7316 + "(((((A,Y),B),C),D),((F,G),E))"
7317 + "(((((A,B),C),D),E),(F,G))"
7318 + "(((((A,B),C),D),E),(F,G))"
7319 + "(((((A,B),C),D),E),(F,G))"
7320 + "(((((A,B),C),D),E),(F,G),Z)"
7321 + "(((((A,B),C),D),E),(F,G))"
7322 + "((((((A,B),C),D),E),F),G)"
7323 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7325 SupportCount.count( t0_2, phylogenies_2, true, false );
7326 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7327 while ( it.hasNext() ) {
7328 final PhylogenyNode n = it.next();
7329 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7333 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7334 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7335 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7336 SupportCount.count( t0_3, phylogenies_3, true, false );
7337 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7338 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7341 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7344 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7347 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7350 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7353 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7356 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7359 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7362 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7365 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7368 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7369 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7370 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7371 SupportCount.count( t0_4, phylogenies_4, true, false );
7372 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7373 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7376 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7379 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7382 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7385 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7388 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7391 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7394 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7397 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7400 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7403 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7404 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7405 double d = SupportCount.compare( b1, a, true, true, true );
7406 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7409 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7410 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7411 d = SupportCount.compare( b2, a, true, true, true );
7412 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7415 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7416 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7417 d = SupportCount.compare( b3, a, true, true, true );
7418 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7421 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7422 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7423 d = SupportCount.compare( b4, a, true, true, false );
7424 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7428 catch ( final Exception e ) {
7429 e.printStackTrace( System.out );
7435 private static boolean testSupportTransfer() {
7437 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7438 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)",
7439 new NHXParser() )[ 0 ];
7440 final Phylogeny p2 = factory
7441 .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 ];
7442 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7445 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7448 support_transfer.moveBranchLengthsToBootstrap( p1 );
7449 support_transfer.transferSupportValues( p1, p2 );
7450 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7453 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7456 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7459 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7462 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7465 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7468 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7471 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7475 catch ( final Exception e ) {
7476 e.printStackTrace( System.out );
7482 private static boolean testTaxonomyAssigner() {
7484 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]";
7485 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7486 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7487 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7488 s0.setRooted( true );
7489 g0.setRooted( true );
7490 TaxonomyAssigner.execute( g0, s0 );
7491 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7494 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7497 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7500 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7501 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7502 g0.setRooted( true );
7503 TaxonomyAssigner.execute( g0, s0 );
7504 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7507 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7510 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7513 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7514 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7515 g0.setRooted( true );
7516 TaxonomyAssigner.execute( g0, s0 );
7517 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7520 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7523 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7526 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7527 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7528 g0.setRooted( true );
7529 TaxonomyAssigner.execute( g0, s0 );
7530 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7533 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7536 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7539 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7540 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7541 g0.setRooted( true );
7542 TaxonomyAssigner.execute( g0, s0 );
7543 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7546 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7549 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7552 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7553 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7554 g0.setRooted( true );
7555 TaxonomyAssigner.execute( g0, s0 );
7556 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7559 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7562 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7565 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7566 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7567 g0.setRooted( true );
7568 TaxonomyAssigner.execute( g0, s0 );
7569 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7572 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7575 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7578 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7579 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7580 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7581 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7582 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7583 s0.setRooted( true );
7584 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7585 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7586 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7587 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7588 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7589 g0.setRooted( true );
7590 TaxonomyAssigner.execute( g0, s0 );
7591 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7594 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7597 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7600 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7603 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7606 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7607 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7608 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7609 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7610 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7611 g0.setRooted( true );
7612 TaxonomyAssigner.execute( g0, s0 );
7613 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7616 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7619 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7622 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7625 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7628 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7629 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7630 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7631 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7632 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7633 g0.setRooted( true );
7634 TaxonomyAssigner.execute( g0, s0 );
7635 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7638 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7641 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7644 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7647 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7650 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7651 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7652 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7653 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7654 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7655 g0.setRooted( true );
7656 TaxonomyAssigner.execute( g0, s0 );
7657 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7660 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7663 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7666 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7669 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7672 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
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( "A" ) ) {
7679 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7682 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7685 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7686 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7687 g0.setRooted( true );
7688 TaxonomyAssigner.execute( g0, s0 );
7689 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7692 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7695 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7698 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7699 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7700 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7701 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7702 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7703 g0.setRooted( true );
7704 TaxonomyAssigner.execute( g0, s0 );
7705 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7708 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7711 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7714 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7717 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7720 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7723 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7726 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7727 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7728 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7729 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7730 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7731 g0.setRooted( true );
7732 TaxonomyAssigner.execute( g0, s0 );
7733 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7736 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7739 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7742 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7745 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7748 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7751 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7754 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7755 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7756 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7757 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7758 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7759 g0.setRooted( true );
7760 TaxonomyAssigner.execute( g0, s0 );
7761 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7764 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7767 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7770 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7773 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7776 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7779 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7782 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7783 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7784 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7785 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7786 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7787 g0.setRooted( true );
7788 TaxonomyAssigner.execute( g0, s0 );
7789 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7792 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7795 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7798 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7801 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7804 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7807 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7810 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7811 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7812 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7813 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7814 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7815 s0.setRooted( true );
7816 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7817 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7818 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7819 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7820 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7821 g0.setRooted( true );
7822 TaxonomyAssigner.execute( g0, s0 );
7823 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7826 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7830 catch ( final Exception e ) {
7831 e.printStackTrace( System.out );
7837 private static boolean testUniprotTaxonomySearch() {
7839 List<UniProtTaxonomy> results = UniProtWsTools
7840 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7841 if ( results.size() != 1 ) {
7844 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7847 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7850 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7853 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7856 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7860 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7861 if ( results.size() != 1 ) {
7864 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7867 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7870 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7873 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7876 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7880 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7881 if ( results.size() != 1 ) {
7884 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7887 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7890 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7893 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7896 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7900 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7901 if ( results.size() != 1 ) {
7904 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7907 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7910 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7913 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7916 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7919 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7922 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7925 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7926 .equals( "Nematostella vectensis" ) ) {
7927 System.out.println( results.get( 0 ).getLineage() );
7931 catch ( final IOException e ) {
7932 System.out.println();
7933 System.out.println( "the following might be due to absence internet connection:" );
7934 e.printStackTrace( System.out );
7937 catch ( final Exception e ) {
7943 private static boolean testEmblEntryRetrieval() {
7944 //The format for GenBank Accession numbers are:
7945 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7946 //Protein: 3 letters + 5 numerals
7947 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7948 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7951 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7954 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7957 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7960 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7963 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7966 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7969 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7972 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7975 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7978 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7981 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7984 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7990 private static boolean testUniprotEntryRetrieval() {
7991 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7994 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7997 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8000 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8003 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8006 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8009 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8012 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8015 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8018 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8021 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8024 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8027 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8031 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
8032 if ( !entry.getAccession().equals( "P12345" ) ) {
8035 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8038 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8041 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8044 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8048 catch ( final IOException e ) {
8049 System.out.println();
8050 System.out.println( "the following might be due to absence internet connection:" );
8051 e.printStackTrace( System.out );
8054 catch ( final Exception e ) {
8060 private static boolean testWabiTxSearch() {
8063 result = TxSearch.searchSimple( "nematostella" );
8064 result = TxSearch.getTxId( "nematostella" );
8065 if ( !result.equals( "45350" ) ) {
8068 result = TxSearch.getTxName( "45350" );
8069 if ( !result.equals( "Nematostella" ) ) {
8072 result = TxSearch.getTxId( "nematostella vectensis" );
8073 if ( !result.equals( "45351" ) ) {
8076 result = TxSearch.getTxName( "45351" );
8077 if ( !result.equals( "Nematostella vectensis" ) ) {
8080 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8081 if ( !result.equals( "536089" ) ) {
8084 result = TxSearch.getTxName( "536089" );
8085 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8088 final List<String> queries = new ArrayList<String>();
8089 queries.add( "Campylobacter coli" );
8090 queries.add( "Escherichia coli" );
8091 queries.add( "Arabidopsis" );
8092 queries.add( "Trichoplax" );
8093 queries.add( "Samanea saman" );
8094 queries.add( "Kluyveromyces marxianus" );
8095 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8096 queries.add( "Bornavirus parrot/PDD/2008" );
8097 final List<RANKS> ranks = new ArrayList<RANKS>();
8098 ranks.add( RANKS.SUPERKINGDOM );
8099 ranks.add( RANKS.KINGDOM );
8100 ranks.add( RANKS.FAMILY );
8101 ranks.add( RANKS.GENUS );
8102 ranks.add( RANKS.TRIBE );
8103 result = TxSearch.searchLineage( queries, ranks );
8104 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8105 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8107 catch ( final Exception e ) {
8108 System.out.println();
8109 System.out.println( "the following might be due to absence internet connection:" );
8110 e.printStackTrace( System.out );
8116 private static boolean testAminoAcidSequence() {
8118 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8119 if ( aa1.getLength() != 13 ) {
8122 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8125 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8128 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8131 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8132 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8135 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8136 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8139 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8140 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8144 catch ( final Exception e ) {
8145 e.printStackTrace();
8151 private static boolean testCreateBalancedPhylogeny() {
8153 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8154 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8157 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8160 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8161 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8164 if ( p1.getNumberOfExternalNodes() != 100 ) {
8168 catch ( final Exception e ) {
8169 e.printStackTrace();
8175 private static boolean testFastaParser() {
8177 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8180 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8183 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8184 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8187 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8190 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8193 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8196 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8199 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8203 catch ( final Exception e ) {
8204 e.printStackTrace();
8210 private static boolean testGeneralMsaParser() {
8212 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8213 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8214 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8215 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8216 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8217 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8218 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8219 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8220 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8223 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8226 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8229 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8232 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8235 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8238 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8241 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8244 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8247 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8250 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8253 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8256 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8257 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8260 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8263 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8266 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8267 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8270 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8273 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8276 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8277 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8280 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8283 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8287 catch ( final Exception e ) {
8288 e.printStackTrace();
8294 private static boolean testMafft() {
8296 final List<String> opts = new ArrayList<String>();
8297 opts.add( "--maxiterate" );
8299 opts.add( "--localpair" );
8300 opts.add( "--quiet" );
8302 final MsaInferrer mafft = Mafft.createInstance();
8303 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8304 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8307 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8311 catch ( final Exception e ) {
8312 e.printStackTrace( System.out );
8318 private static boolean testNextNodeWithCollapsing() {
8320 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8322 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8323 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8324 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8325 t0.getNode( "cd" ).setCollapse( true );
8326 t0.getNode( "cde" ).setCollapse( true );
8327 n = t0.getFirstExternalNode();
8328 while ( n != null ) {
8330 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8332 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8335 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8338 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8341 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8344 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8347 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8351 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8352 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8353 t1.getNode( "ab" ).setCollapse( true );
8354 t1.getNode( "cd" ).setCollapse( true );
8355 t1.getNode( "cde" ).setCollapse( true );
8356 n = t1.getNode( "ab" );
8357 ext = new ArrayList<PhylogenyNode>();
8358 while ( n != null ) {
8360 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8362 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8365 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8368 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8371 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8374 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8380 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8381 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8382 t2.getNode( "ab" ).setCollapse( true );
8383 t2.getNode( "cd" ).setCollapse( true );
8384 t2.getNode( "cde" ).setCollapse( true );
8385 t2.getNode( "c" ).setCollapse( true );
8386 t2.getNode( "d" ).setCollapse( true );
8387 t2.getNode( "e" ).setCollapse( true );
8388 t2.getNode( "gh" ).setCollapse( true );
8389 n = t2.getNode( "ab" );
8390 ext = new ArrayList<PhylogenyNode>();
8391 while ( n != null ) {
8393 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8395 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8398 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8401 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8404 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8410 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8411 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8412 t3.getNode( "ab" ).setCollapse( true );
8413 t3.getNode( "cd" ).setCollapse( true );
8414 t3.getNode( "cde" ).setCollapse( true );
8415 t3.getNode( "c" ).setCollapse( true );
8416 t3.getNode( "d" ).setCollapse( true );
8417 t3.getNode( "e" ).setCollapse( true );
8418 t3.getNode( "gh" ).setCollapse( true );
8419 t3.getNode( "fgh" ).setCollapse( true );
8420 n = t3.getNode( "ab" );
8421 ext = new ArrayList<PhylogenyNode>();
8422 while ( n != null ) {
8424 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8426 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8429 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8432 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8438 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8439 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8440 t4.getNode( "ab" ).setCollapse( true );
8441 t4.getNode( "cd" ).setCollapse( true );
8442 t4.getNode( "cde" ).setCollapse( true );
8443 t4.getNode( "c" ).setCollapse( true );
8444 t4.getNode( "d" ).setCollapse( true );
8445 t4.getNode( "e" ).setCollapse( true );
8446 t4.getNode( "gh" ).setCollapse( true );
8447 t4.getNode( "fgh" ).setCollapse( true );
8448 t4.getNode( "abcdefgh" ).setCollapse( true );
8449 n = t4.getNode( "abcdefgh" );
8450 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8455 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8456 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8458 n = t5.getFirstExternalNode();
8459 while ( n != null ) {
8461 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8463 if ( ext.size() != 8 ) {
8466 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8469 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8472 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8475 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8478 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8481 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8484 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8487 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8492 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8493 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8495 t6.getNode( "ab" ).setCollapse( true );
8496 n = t6.getNode( "ab" );
8497 while ( n != null ) {
8499 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8501 if ( ext.size() != 7 ) {
8504 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8507 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8510 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8513 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8516 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8519 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8522 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8527 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8528 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8530 t7.getNode( "cd" ).setCollapse( true );
8531 n = t7.getNode( "a" );
8532 while ( n != null ) {
8534 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8536 if ( ext.size() != 7 ) {
8539 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8542 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8545 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8548 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8551 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8554 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8557 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8562 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8563 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8565 t8.getNode( "cd" ).setCollapse( true );
8566 t8.getNode( "c" ).setCollapse( true );
8567 t8.getNode( "d" ).setCollapse( true );
8568 n = t8.getNode( "a" );
8569 while ( n != null ) {
8571 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8573 if ( ext.size() != 7 ) {
8576 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8579 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8582 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8583 System.out.println( "2 fail" );
8586 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8589 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8592 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8595 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8600 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8601 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8603 t9.getNode( "gh" ).setCollapse( true );
8604 n = t9.getNode( "a" );
8605 while ( n != null ) {
8607 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8609 if ( ext.size() != 7 ) {
8612 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8615 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8618 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8621 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8624 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8627 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8630 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8635 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8636 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8638 t10.getNode( "gh" ).setCollapse( true );
8639 t10.getNode( "g" ).setCollapse( true );
8640 t10.getNode( "h" ).setCollapse( true );
8641 n = t10.getNode( "a" );
8642 while ( n != null ) {
8644 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8646 if ( ext.size() != 7 ) {
8649 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8652 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8655 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8658 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8661 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8664 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8667 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8672 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8673 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8675 t11.getNode( "gh" ).setCollapse( true );
8676 t11.getNode( "fgh" ).setCollapse( true );
8677 n = t11.getNode( "a" );
8678 while ( n != null ) {
8680 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8682 if ( ext.size() != 6 ) {
8685 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8688 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8691 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8694 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8697 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8700 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8705 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8706 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8708 t12.getNode( "gh" ).setCollapse( true );
8709 t12.getNode( "fgh" ).setCollapse( true );
8710 t12.getNode( "g" ).setCollapse( true );
8711 t12.getNode( "h" ).setCollapse( true );
8712 t12.getNode( "f" ).setCollapse( true );
8713 n = t12.getNode( "a" );
8714 while ( n != null ) {
8716 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8718 if ( ext.size() != 6 ) {
8721 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8724 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8727 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8730 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8733 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8736 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8741 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8742 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8744 t13.getNode( "ab" ).setCollapse( true );
8745 t13.getNode( "b" ).setCollapse( true );
8746 t13.getNode( "fgh" ).setCollapse( true );
8747 t13.getNode( "gh" ).setCollapse( true );
8748 n = t13.getNode( "ab" );
8749 while ( n != null ) {
8751 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8753 if ( ext.size() != 5 ) {
8756 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8759 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8762 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8765 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8768 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8773 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8774 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8776 t14.getNode( "ab" ).setCollapse( true );
8777 t14.getNode( "a" ).setCollapse( true );
8778 t14.getNode( "fgh" ).setCollapse( true );
8779 t14.getNode( "gh" ).setCollapse( true );
8780 n = t14.getNode( "ab" );
8781 while ( n != null ) {
8783 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8785 if ( ext.size() != 5 ) {
8788 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8791 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8794 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8797 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8800 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8805 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" );
8806 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8808 t15.getNode( "ab" ).setCollapse( true );
8809 t15.getNode( "a" ).setCollapse( true );
8810 t15.getNode( "fgh" ).setCollapse( true );
8811 t15.getNode( "gh" ).setCollapse( true );
8812 n = t15.getNode( "ab" );
8813 while ( n != null ) {
8815 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8817 if ( ext.size() != 6 ) {
8820 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8823 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8826 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8829 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8832 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8835 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8840 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" );
8841 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8843 t16.getNode( "ab" ).setCollapse( true );
8844 t16.getNode( "a" ).setCollapse( true );
8845 t16.getNode( "fgh" ).setCollapse( true );
8846 t16.getNode( "gh" ).setCollapse( true );
8847 t16.getNode( "cd" ).setCollapse( true );
8848 t16.getNode( "cde" ).setCollapse( true );
8849 t16.getNode( "d" ).setCollapse( true );
8850 t16.getNode( "x" ).setCollapse( true );
8851 n = t16.getNode( "ab" );
8852 while ( n != null ) {
8854 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8856 if ( ext.size() != 4 ) {
8859 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8862 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8865 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8868 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8872 catch ( final Exception e ) {
8873 e.printStackTrace( System.out );
8879 private static boolean testMsaQualityMethod() {
8881 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8882 final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
8883 final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
8884 final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
8885 final List<Sequence> l = new ArrayList<Sequence>();
8890 final Msa msa = BasicMsa.createInstance( l );
8891 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8894 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8897 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8900 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8904 catch ( final Exception e ) {
8905 e.printStackTrace( System.out );