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.TestGSDI;
91 import org.forester.sequence.BasicSequence;
92 import org.forester.sequence.Sequence;
93 import org.forester.surfacing.TestSurfacing;
94 import org.forester.tools.ConfidenceAssessor;
95 import org.forester.tools.SupportCount;
96 import org.forester.tools.TreeSplitMatrix;
97 import org.forester.util.AsciiHistogram;
98 import org.forester.util.BasicDescriptiveStatistics;
99 import org.forester.util.BasicTable;
100 import org.forester.util.BasicTableParser;
101 import org.forester.util.DescriptiveStatistics;
102 import org.forester.util.ForesterConstants;
103 import org.forester.util.ForesterUtil;
104 import org.forester.util.GeneralTable;
105 import org.forester.util.SequenceIdParser;
106 import org.forester.ws.seqdb.SequenceDatabaseEntry;
107 import org.forester.ws.seqdb.SequenceDbWsTools;
108 import org.forester.ws.seqdb.UniProtTaxonomy;
109 import org.forester.ws.wabi.TxSearch;
110 import org.forester.ws.wabi.TxSearch.RANKS;
111 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
112 import org.forester.ws.wabi.TxSearch.TAX_RANK;
114 @SuppressWarnings( "unused")
115 public final class Test {
117 private final static double ZERO_DIFF = 1.0E-9;
118 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
119 + ForesterUtil.getFileSeparator() + "test_data"
120 + ForesterUtil.getFileSeparator();
121 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
122 + ForesterUtil.getFileSeparator() + "resources"
123 + ForesterUtil.getFileSeparator();
124 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
125 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
126 + ForesterConstants.PHYLO_XML_VERSION + "/"
127 + ForesterConstants.PHYLO_XML_XSD;
128 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
129 + ForesterConstants.PHYLO_XML_VERSION + "/"
130 + ForesterConstants.PHYLO_XML_XSD;
132 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
133 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
137 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
138 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
139 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
142 public static boolean isEqual( final double a, final double b ) {
143 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
146 public static void main( final String[] args ) {
147 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
148 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
150 Locale.setDefault( Locale.US );
151 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
154 System.out.print( "[Test if directory with files for testing exists/is readable: " );
155 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
156 System.out.println( "OK.]" );
159 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
160 System.out.println( "Testing aborted." );
163 System.out.print( "[Test if resources directory exists/is readable: " );
164 if ( testDir( PATH_TO_RESOURCES ) ) {
165 System.out.println( "OK.]" );
168 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
169 System.out.println( "Testing aborted." );
172 final long start_time = new Date().getTime();
173 System.out.print( "Sequence id parsing: " );
174 if ( testSequenceIdParsing() ) {
175 System.out.println( "OK." );
179 System.out.println( "failed." );
180 System.exit( -1 ); //TODO FIXME remove me!! ~
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Basic node construction and parsing of NHX (node level): " );
202 if ( Test.testNHXNodeParsing() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "NH parsing: " );
211 if ( Test.testNHParsing() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Conversion to NHX (node level): " );
220 if ( Test.testNHXconversion() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing: " );
229 if ( Test.testNHXParsing() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NHX parsing with quotes: " );
238 if ( Test.testNHXParsingQuotes() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "NHX parsing (MrBayes): " );
247 if ( Test.testNHXParsingMB() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "Nexus characters parsing: " );
256 if ( Test.testNexusCharactersParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "Nexus tree parsing: " );
265 if ( Test.testNexusTreeParsing() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "Nexus tree parsing (translating): " );
274 if ( Test.testNexusTreeParsingTranslating() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus matrix parsing: " );
283 if ( Test.testNexusMatrixParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Basic phyloXML parsing: " );
292 if ( Test.testBasicPhyloXMLparsing() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Basic phyloXML parsing (validating against schema): " );
301 if ( testBasicPhyloXMLparsingValidating() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
310 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "phyloXML Distribution Element: " );
319 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Tol XML parsing: " );
328 if ( Test.testBasicTolXMLparsing() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Copying of node data: " );
337 if ( Test.testCopyOfNodeData() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Basic tree methods: " );
346 if ( Test.testBasicTreeMethods() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "Postorder Iterator: " );
355 if ( Test.testPostOrderIterator() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Preorder Iterator: " );
364 if ( Test.testPreOrderIterator() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Levelorder Iterator: " );
373 if ( Test.testLevelOrderIterator() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Re-id methods: " );
382 if ( Test.testReIdMethods() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Methods on last external nodes: " );
391 if ( Test.testLastExternalNodeMethods() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Methods on external nodes: " );
400 if ( Test.testExternalNodeRelatedMethods() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Deletion of external nodes: " );
409 if ( Test.testDeletionOfExternalNodes() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Subtree deletion: " );
418 if ( Test.testSubtreeDeletion() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Phylogeny branch: " );
427 if ( Test.testPhylogenyBranch() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Rerooting: " );
436 if ( Test.testRerooting() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Mipoint rooting: " );
445 if ( Test.testMidpointrooting() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Support count: " );
454 if ( Test.testSupportCount() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Support transfer: " );
463 if ( Test.testSupportTransfer() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Finding of LCA: " );
472 if ( Test.testGetLCA() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Calculation of distance between nodes: " );
481 if ( Test.testGetDistance() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "SDIse: " );
490 if ( Test.testSDIse() ) {
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 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 ];
1918 if ( t4.getNumberOfExternalNodes() != 9 ) {
1921 if ( t4.getHeight() != 11 ) {
1924 if ( t4.isCompletelyBinary() ) {
1927 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)" );
1928 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1929 if ( t5.getNumberOfExternalNodes() != 8 ) {
1932 if ( t5.getHeight() != 15 ) {
1935 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)" );
1936 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1937 if ( t6.getHeight() != 15 ) {
1940 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)" );
1941 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1942 if ( t7.getHeight() != 15 ) {
1945 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)" );
1946 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1947 if ( t8.getNumberOfExternalNodes() != 10 ) {
1950 if ( t8.getHeight() != 15 ) {
1953 final char[] a9 = new char[] {};
1954 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1955 if ( t9.getHeight() != 0 ) {
1958 final char[] a10 = new char[] { 'a', ':', '6' };
1959 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1960 if ( t10.getHeight() != 6 ) {
1964 catch ( final Exception e ) {
1965 e.printStackTrace( System.out );
1971 private static boolean testConfidenceAssessor() {
1973 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1974 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1975 final Phylogeny[] ev0 = factory
1976 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1978 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1979 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1982 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1985 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1986 final Phylogeny[] ev1 = factory
1987 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1989 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1990 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1993 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1996 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1997 final Phylogeny[] ev_b = factory
1998 .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",
2000 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2001 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2002 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2005 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2009 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2010 final Phylogeny[] ev1x = factory
2011 .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)));",
2013 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2014 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2017 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2020 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2021 final Phylogeny[] ev_bx = factory
2022 .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",
2024 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2025 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2028 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2032 final Phylogeny[] t2 = factory
2033 .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);",
2035 final Phylogeny[] ev2 = factory
2036 .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);",
2038 for( final Phylogeny target : t2 ) {
2039 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2042 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2043 new NHXParser() )[ 0 ];
2044 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2045 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2046 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2049 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2052 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2056 catch ( final Exception e ) {
2057 e.printStackTrace();
2063 private static boolean testCopyOfNodeData() {
2065 final PhylogenyNode n1 = PhylogenyNode
2066 .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]" );
2067 final PhylogenyNode n2 = n1.copyNodeData();
2068 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2072 catch ( final Exception e ) {
2073 e.printStackTrace();
2079 private static boolean testDataObjects() {
2081 final Confidence s0 = new Confidence();
2082 final Confidence s1 = new Confidence();
2083 if ( !s0.isEqual( s1 ) ) {
2086 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2087 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2088 if ( s2.isEqual( s1 ) ) {
2091 if ( !s2.isEqual( s3 ) ) {
2094 final Confidence s4 = ( Confidence ) s3.copy();
2095 if ( !s4.isEqual( s3 ) ) {
2102 final Taxonomy t1 = new Taxonomy();
2103 final Taxonomy t2 = new Taxonomy();
2104 final Taxonomy t3 = new Taxonomy();
2105 final Taxonomy t4 = new Taxonomy();
2106 final Taxonomy t5 = new Taxonomy();
2107 t1.setIdentifier( new Identifier( "ecoli" ) );
2108 t1.setTaxonomyCode( "ECOLI" );
2109 t1.setScientificName( "E. coli" );
2110 t1.setCommonName( "coli" );
2111 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2112 if ( !t1.isEqual( t0 ) ) {
2115 t2.setIdentifier( new Identifier( "ecoli" ) );
2116 t2.setTaxonomyCode( "OTHER" );
2117 t2.setScientificName( "what" );
2118 t2.setCommonName( "something" );
2119 if ( !t1.isEqual( t2 ) ) {
2122 t2.setIdentifier( new Identifier( "nemve" ) );
2123 if ( t1.isEqual( t2 ) ) {
2126 t1.setIdentifier( null );
2127 t3.setTaxonomyCode( "ECOLI" );
2128 t3.setScientificName( "what" );
2129 t3.setCommonName( "something" );
2130 if ( !t1.isEqual( t3 ) ) {
2133 t1.setIdentifier( null );
2134 t1.setTaxonomyCode( "" );
2135 t4.setScientificName( "E. ColI" );
2136 t4.setCommonName( "something" );
2137 if ( !t1.isEqual( t4 ) ) {
2140 t4.setScientificName( "B. subtilis" );
2141 t4.setCommonName( "something" );
2142 if ( t1.isEqual( t4 ) ) {
2145 t1.setIdentifier( null );
2146 t1.setTaxonomyCode( "" );
2147 t1.setScientificName( "" );
2148 t5.setCommonName( "COLI" );
2149 if ( !t1.isEqual( t5 ) ) {
2152 t5.setCommonName( "vibrio" );
2153 if ( t1.isEqual( t5 ) ) {
2158 final Identifier id0 = new Identifier( "123", "pfam" );
2159 final Identifier id1 = ( Identifier ) id0.copy();
2160 if ( !id1.isEqual( id1 ) ) {
2163 if ( !id1.isEqual( id0 ) ) {
2166 if ( !id0.isEqual( id1 ) ) {
2173 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2174 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2175 if ( !pd1.isEqual( pd1 ) ) {
2178 if ( !pd1.isEqual( pd0 ) ) {
2183 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2184 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2185 if ( !pd3.isEqual( pd3 ) ) {
2188 if ( !pd2.isEqual( pd3 ) ) {
2191 if ( !pd0.isEqual( pd3 ) ) {
2196 // DomainArchitecture
2197 // ------------------
2198 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2199 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2200 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2201 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2202 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2203 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2208 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2209 if ( ds0.getNumberOfDomains() != 4 ) {
2212 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2213 if ( !ds0.isEqual( ds0 ) ) {
2216 if ( !ds0.isEqual( ds1 ) ) {
2219 if ( ds1.getNumberOfDomains() != 4 ) {
2222 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2227 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2228 if ( ds0.isEqual( ds2 ) ) {
2234 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2235 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2236 System.out.println( ds3.toNHX() );
2239 if ( ds3.getNumberOfDomains() != 3 ) {
2244 final Event e1 = new Event( Event.EventType.fusion );
2245 if ( e1.isDuplication() ) {
2248 if ( !e1.isFusion() ) {
2251 if ( !e1.asText().toString().equals( "fusion" ) ) {
2254 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2257 final Event e11 = new Event( Event.EventType.fusion );
2258 if ( !e11.isEqual( e1 ) ) {
2261 if ( !e11.toNHX().toString().equals( "" ) ) {
2264 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2265 if ( e2.isDuplication() ) {
2268 if ( !e2.isSpeciationOrDuplication() ) {
2271 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2274 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2277 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2280 if ( e11.isEqual( e2 ) ) {
2283 final Event e2c = ( Event ) e2.copy();
2284 if ( !e2c.isEqual( e2 ) ) {
2287 Event e3 = new Event( 1, 2, 3 );
2288 if ( e3.isDuplication() ) {
2291 if ( e3.isSpeciation() ) {
2294 if ( e3.isGeneLoss() ) {
2297 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2300 final Event e3c = ( Event ) e3.copy();
2301 final Event e3cc = ( Event ) e3c.copy();
2302 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2306 if ( !e3c.isEqual( e3cc ) ) {
2309 Event e4 = new Event( 1, 2, 3 );
2310 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2313 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2316 final Event e4c = ( Event ) e4.copy();
2318 final Event e4cc = ( Event ) e4c.copy();
2319 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2322 if ( !e4c.isEqual( e4cc ) ) {
2325 final Event e5 = new Event();
2326 if ( !e5.isUnassigned() ) {
2329 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2332 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2335 final Event e6 = new Event( 1, 0, 0 );
2336 if ( !e6.asText().toString().equals( "duplication" ) ) {
2339 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2342 final Event e7 = new Event( 0, 1, 0 );
2343 if ( !e7.asText().toString().equals( "speciation" ) ) {
2346 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2349 final Event e8 = new Event( 0, 0, 1 );
2350 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2353 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2357 catch ( final Exception e ) {
2358 e.printStackTrace( System.out );
2364 private static boolean testDeletionOfExternalNodes() {
2366 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2367 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2368 final PhylogenyWriter w = new PhylogenyWriter();
2369 if ( t0.isEmpty() ) {
2372 if ( t0.getNumberOfExternalNodes() != 1 ) {
2375 t0.deleteSubtree( t0.getNode( "A" ), false );
2376 if ( t0.getNumberOfExternalNodes() != 0 ) {
2379 if ( !t0.isEmpty() ) {
2382 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2383 if ( t1.getNumberOfExternalNodes() != 2 ) {
2386 t1.deleteSubtree( t1.getNode( "A" ), false );
2387 if ( t1.getNumberOfExternalNodes() != 1 ) {
2390 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2393 t1.deleteSubtree( t1.getNode( "B" ), false );
2394 if ( t1.getNumberOfExternalNodes() != 1 ) {
2397 t1.deleteSubtree( t1.getNode( "r" ), false );
2398 if ( !t1.isEmpty() ) {
2401 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2402 if ( t2.getNumberOfExternalNodes() != 3 ) {
2405 t2.deleteSubtree( t2.getNode( "B" ), false );
2406 if ( t2.getNumberOfExternalNodes() != 2 ) {
2409 t2.toNewHampshireX();
2410 PhylogenyNode n = t2.getNode( "A" );
2411 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2414 t2.deleteSubtree( t2.getNode( "A" ), false );
2415 if ( t2.getNumberOfExternalNodes() != 2 ) {
2418 t2.deleteSubtree( t2.getNode( "C" ), true );
2419 if ( t2.getNumberOfExternalNodes() != 1 ) {
2422 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2423 if ( t3.getNumberOfExternalNodes() != 4 ) {
2426 t3.deleteSubtree( t3.getNode( "B" ), true );
2427 if ( t3.getNumberOfExternalNodes() != 3 ) {
2430 n = t3.getNode( "A" );
2431 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2434 n = n.getNextExternalNode();
2435 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2438 t3.deleteSubtree( t3.getNode( "A" ), true );
2439 if ( t3.getNumberOfExternalNodes() != 2 ) {
2442 n = t3.getNode( "C" );
2443 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2446 t3.deleteSubtree( t3.getNode( "C" ), true );
2447 if ( t3.getNumberOfExternalNodes() != 1 ) {
2450 t3.deleteSubtree( t3.getNode( "D" ), true );
2451 if ( t3.getNumberOfExternalNodes() != 0 ) {
2454 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2455 if ( t4.getNumberOfExternalNodes() != 6 ) {
2458 t4.deleteSubtree( t4.getNode( "B2" ), true );
2459 if ( t4.getNumberOfExternalNodes() != 5 ) {
2462 String s = w.toNewHampshire( t4, false, true ).toString();
2463 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2466 t4.deleteSubtree( t4.getNode( "B11" ), true );
2467 if ( t4.getNumberOfExternalNodes() != 4 ) {
2470 t4.deleteSubtree( t4.getNode( "C" ), true );
2471 if ( t4.getNumberOfExternalNodes() != 3 ) {
2474 n = t4.getNode( "A" );
2475 n = n.getNextExternalNode();
2476 if ( !n.getName().equals( "B12" ) ) {
2479 n = n.getNextExternalNode();
2480 if ( !n.getName().equals( "D" ) ) {
2483 s = w.toNewHampshire( t4, false, true ).toString();
2484 if ( !s.equals( "((A,B12),D);" ) ) {
2487 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2488 t5.deleteSubtree( t5.getNode( "A" ), true );
2489 if ( t5.getNumberOfExternalNodes() != 5 ) {
2492 s = w.toNewHampshire( t5, false, true ).toString();
2493 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2496 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2497 t6.deleteSubtree( t6.getNode( "B11" ), true );
2498 if ( t6.getNumberOfExternalNodes() != 5 ) {
2501 s = w.toNewHampshire( t6, false, false ).toString();
2502 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2505 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2506 t7.deleteSubtree( t7.getNode( "B12" ), true );
2507 if ( t7.getNumberOfExternalNodes() != 5 ) {
2510 s = w.toNewHampshire( t7, false, true ).toString();
2511 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2514 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2515 t8.deleteSubtree( t8.getNode( "B2" ), true );
2516 if ( t8.getNumberOfExternalNodes() != 5 ) {
2519 s = w.toNewHampshire( t8, false, false ).toString();
2520 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2523 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2524 t9.deleteSubtree( t9.getNode( "C" ), true );
2525 if ( t9.getNumberOfExternalNodes() != 5 ) {
2528 s = w.toNewHampshire( t9, false, true ).toString();
2529 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2532 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2533 t10.deleteSubtree( t10.getNode( "D" ), true );
2534 if ( t10.getNumberOfExternalNodes() != 5 ) {
2537 s = w.toNewHampshire( t10, false, true ).toString();
2538 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2541 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2542 t11.deleteSubtree( t11.getNode( "A" ), true );
2543 if ( t11.getNumberOfExternalNodes() != 2 ) {
2546 s = w.toNewHampshire( t11, false, true ).toString();
2547 if ( !s.equals( "(B,C);" ) ) {
2550 t11.deleteSubtree( t11.getNode( "C" ), true );
2551 if ( t11.getNumberOfExternalNodes() != 1 ) {
2554 s = w.toNewHampshire( t11, false, false ).toString();
2555 if ( !s.equals( "B;" ) ) {
2558 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2559 t12.deleteSubtree( t12.getNode( "B2" ), true );
2560 if ( t12.getNumberOfExternalNodes() != 8 ) {
2563 s = w.toNewHampshire( t12, false, true ).toString();
2564 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2567 t12.deleteSubtree( t12.getNode( "B3" ), true );
2568 if ( t12.getNumberOfExternalNodes() != 7 ) {
2571 s = w.toNewHampshire( t12, false, true ).toString();
2572 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2575 t12.deleteSubtree( t12.getNode( "C3" ), true );
2576 if ( t12.getNumberOfExternalNodes() != 6 ) {
2579 s = w.toNewHampshire( t12, false, true ).toString();
2580 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2583 t12.deleteSubtree( t12.getNode( "A1" ), true );
2584 if ( t12.getNumberOfExternalNodes() != 5 ) {
2587 s = w.toNewHampshire( t12, false, true ).toString();
2588 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2591 t12.deleteSubtree( t12.getNode( "B1" ), true );
2592 if ( t12.getNumberOfExternalNodes() != 4 ) {
2595 s = w.toNewHampshire( t12, false, true ).toString();
2596 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2599 t12.deleteSubtree( t12.getNode( "A3" ), true );
2600 if ( t12.getNumberOfExternalNodes() != 3 ) {
2603 s = w.toNewHampshire( t12, false, true ).toString();
2604 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2607 t12.deleteSubtree( t12.getNode( "A2" ), true );
2608 if ( t12.getNumberOfExternalNodes() != 2 ) {
2611 s = w.toNewHampshire( t12, false, true ).toString();
2612 if ( !s.equals( "(C1,C2);" ) ) {
2615 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2616 t13.deleteSubtree( t13.getNode( "D" ), true );
2617 if ( t13.getNumberOfExternalNodes() != 4 ) {
2620 s = w.toNewHampshire( t13, false, true ).toString();
2621 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2624 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2625 t14.deleteSubtree( t14.getNode( "E" ), true );
2626 if ( t14.getNumberOfExternalNodes() != 5 ) {
2629 s = w.toNewHampshire( t14, false, true ).toString();
2630 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2633 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2634 t15.deleteSubtree( t15.getNode( "B2" ), true );
2635 if ( t15.getNumberOfExternalNodes() != 11 ) {
2638 t15.deleteSubtree( t15.getNode( "B1" ), true );
2639 if ( t15.getNumberOfExternalNodes() != 10 ) {
2642 t15.deleteSubtree( t15.getNode( "B3" ), true );
2643 if ( t15.getNumberOfExternalNodes() != 9 ) {
2646 t15.deleteSubtree( t15.getNode( "B4" ), true );
2647 if ( t15.getNumberOfExternalNodes() != 8 ) {
2650 t15.deleteSubtree( t15.getNode( "A1" ), true );
2651 if ( t15.getNumberOfExternalNodes() != 7 ) {
2654 t15.deleteSubtree( t15.getNode( "C4" ), true );
2655 if ( t15.getNumberOfExternalNodes() != 6 ) {
2659 catch ( final Exception e ) {
2660 e.printStackTrace( System.out );
2666 private static boolean testDescriptiveStatistics() {
2668 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2669 dss1.addValue( 82 );
2670 dss1.addValue( 78 );
2671 dss1.addValue( 70 );
2672 dss1.addValue( 58 );
2673 dss1.addValue( 42 );
2674 if ( dss1.getN() != 5 ) {
2677 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2680 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2683 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2686 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2689 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2692 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2695 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2698 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2701 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2704 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2707 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2710 dss1.addValue( 123 );
2711 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2714 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2717 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2720 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2721 dss2.addValue( -1.85 );
2722 dss2.addValue( 57.5 );
2723 dss2.addValue( 92.78 );
2724 dss2.addValue( 57.78 );
2725 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2728 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2731 final double[] a = dss2.getDataAsDoubleArray();
2732 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2735 dss2.addValue( -100 );
2736 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2739 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2742 final double[] ds = new double[ 14 ];
2757 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2758 if ( bins.length != 4 ) {
2761 if ( bins[ 0 ] != 2 ) {
2764 if ( bins[ 1 ] != 3 ) {
2767 if ( bins[ 2 ] != 4 ) {
2770 if ( bins[ 3 ] != 5 ) {
2773 final double[] ds1 = new double[ 9 ];
2783 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2784 if ( bins1.length != 4 ) {
2787 if ( bins1[ 0 ] != 2 ) {
2790 if ( bins1[ 1 ] != 3 ) {
2793 if ( bins1[ 2 ] != 0 ) {
2796 if ( bins1[ 3 ] != 4 ) {
2799 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2800 if ( bins1_1.length != 3 ) {
2803 if ( bins1_1[ 0 ] != 3 ) {
2806 if ( bins1_1[ 1 ] != 2 ) {
2809 if ( bins1_1[ 2 ] != 4 ) {
2812 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2813 if ( bins1_2.length != 3 ) {
2816 if ( bins1_2[ 0 ] != 2 ) {
2819 if ( bins1_2[ 1 ] != 2 ) {
2822 if ( bins1_2[ 2 ] != 2 ) {
2825 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2839 dss3.addValue( 10 );
2840 dss3.addValue( 10 );
2841 dss3.addValue( 10 );
2842 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2843 histo.toStringBuffer( 10, '=', 40, 5 );
2844 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2846 catch ( final Exception e ) {
2847 e.printStackTrace( System.out );
2853 private static boolean testDir( final String file ) {
2855 final File f = new File( file );
2856 if ( !f.exists() ) {
2859 if ( !f.isDirectory() ) {
2862 if ( !f.canRead() ) {
2866 catch ( final Exception e ) {
2872 private static boolean testExternalNodeRelatedMethods() {
2874 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2875 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2876 PhylogenyNode n = t1.getNode( "A" );
2877 n = n.getNextExternalNode();
2878 if ( !n.getName().equals( "B" ) ) {
2881 n = n.getNextExternalNode();
2882 if ( !n.getName().equals( "C" ) ) {
2885 n = n.getNextExternalNode();
2886 if ( !n.getName().equals( "D" ) ) {
2889 n = t1.getNode( "B" );
2890 while ( !n.isLastExternalNode() ) {
2891 n = n.getNextExternalNode();
2893 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2894 n = t2.getNode( "A" );
2895 n = n.getNextExternalNode();
2896 if ( !n.getName().equals( "B" ) ) {
2899 n = n.getNextExternalNode();
2900 if ( !n.getName().equals( "C" ) ) {
2903 n = n.getNextExternalNode();
2904 if ( !n.getName().equals( "D" ) ) {
2907 n = t2.getNode( "B" );
2908 while ( !n.isLastExternalNode() ) {
2909 n = n.getNextExternalNode();
2911 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2912 n = t3.getNode( "A" );
2913 n = n.getNextExternalNode();
2914 if ( !n.getName().equals( "B" ) ) {
2917 n = n.getNextExternalNode();
2918 if ( !n.getName().equals( "C" ) ) {
2921 n = n.getNextExternalNode();
2922 if ( !n.getName().equals( "D" ) ) {
2925 n = n.getNextExternalNode();
2926 if ( !n.getName().equals( "E" ) ) {
2929 n = n.getNextExternalNode();
2930 if ( !n.getName().equals( "F" ) ) {
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "G" ) ) {
2937 n = n.getNextExternalNode();
2938 if ( !n.getName().equals( "H" ) ) {
2941 n = t3.getNode( "B" );
2942 while ( !n.isLastExternalNode() ) {
2943 n = n.getNextExternalNode();
2945 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2946 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2947 final PhylogenyNode node = iter.next();
2949 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2950 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2951 final PhylogenyNode node = iter.next();
2954 catch ( final Exception e ) {
2955 e.printStackTrace( System.out );
2961 private static boolean testGeneralTable() {
2963 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2964 t0.setValue( 3, 2, "23" );
2965 t0.setValue( 10, 1, "error" );
2966 t0.setValue( 10, 1, "110" );
2967 t0.setValue( 9, 1, "19" );
2968 t0.setValue( 1, 10, "101" );
2969 t0.setValue( 10, 10, "1010" );
2970 t0.setValue( 100, 10, "10100" );
2971 t0.setValue( 0, 0, "00" );
2972 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2975 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2978 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2981 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2984 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2987 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2990 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2993 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2996 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2999 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3000 t1.setValue( "3", "2", "23" );
3001 t1.setValue( "10", "1", "error" );
3002 t1.setValue( "10", "1", "110" );
3003 t1.setValue( "9", "1", "19" );
3004 t1.setValue( "1", "10", "101" );
3005 t1.setValue( "10", "10", "1010" );
3006 t1.setValue( "100", "10", "10100" );
3007 t1.setValue( "0", "0", "00" );
3008 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3009 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3012 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3015 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3018 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3021 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3024 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3027 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3030 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3033 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3036 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3040 catch ( final Exception e ) {
3041 e.printStackTrace( System.out );
3047 private static boolean testGetDistance() {
3049 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3050 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",
3051 new NHXParser() )[ 0 ];
3052 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3053 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3056 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3059 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3062 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3065 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3068 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3071 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3074 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3077 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3080 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3083 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3086 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3089 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3092 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3095 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3098 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3101 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3104 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3107 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3110 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3113 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3116 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3119 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3122 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3125 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3128 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3131 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3134 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3137 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3140 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3143 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3146 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",
3147 new NHXParser() )[ 0 ];
3148 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3151 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3154 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3157 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3160 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3163 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3166 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3169 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3172 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3175 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3178 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3182 catch ( final Exception e ) {
3183 e.printStackTrace( System.out );
3189 private static boolean testGetLCA() {
3191 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3192 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3193 new NHXParser() )[ 0 ];
3194 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3195 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3196 if ( !A.getName().equals( "A" ) ) {
3199 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3200 if ( !gh.getName().equals( "gh" ) ) {
3203 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3204 if ( !ab.getName().equals( "ab" ) ) {
3207 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3208 if ( !ab2.getName().equals( "ab" ) ) {
3211 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3212 if ( !gh2.getName().equals( "gh" ) ) {
3215 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3216 if ( !gh3.getName().equals( "gh" ) ) {
3219 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3220 if ( !abc.getName().equals( "abc" ) ) {
3223 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3224 if ( !abc2.getName().equals( "abc" ) ) {
3227 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3228 if ( !abcd.getName().equals( "abcd" ) ) {
3231 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3232 if ( !abcd2.getName().equals( "abcd" ) ) {
3235 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3236 if ( !abcdef.getName().equals( "abcdef" ) ) {
3239 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3240 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3243 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3244 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3247 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3248 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3251 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3252 if ( !abcde.getName().equals( "abcde" ) ) {
3255 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3256 if ( !abcde2.getName().equals( "abcde" ) ) {
3259 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3260 if ( !r.getName().equals( "abcdefgh" ) ) {
3263 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3264 if ( !r2.getName().equals( "abcdefgh" ) ) {
3267 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3268 if ( !r3.getName().equals( "abcdefgh" ) ) {
3271 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3272 if ( !abcde3.getName().equals( "abcde" ) ) {
3275 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3276 if ( !abcde4.getName().equals( "abcde" ) ) {
3279 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3280 if ( !ab3.getName().equals( "ab" ) ) {
3283 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3284 if ( !ab4.getName().equals( "ab" ) ) {
3287 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3288 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3289 if ( !cd.getName().equals( "cd" ) ) {
3292 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3293 if ( !cd2.getName().equals( "cd" ) ) {
3296 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3297 if ( !cde.getName().equals( "cde" ) ) {
3300 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3301 if ( !cde2.getName().equals( "cde" ) ) {
3304 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3305 if ( !cdef.getName().equals( "cdef" ) ) {
3308 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3309 if ( !cdef2.getName().equals( "cdef" ) ) {
3312 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3313 if ( !cdef3.getName().equals( "cdef" ) ) {
3316 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3317 if ( !rt.getName().equals( "r" ) ) {
3320 final Phylogeny p3 = factory
3321 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3322 new NHXParser() )[ 0 ];
3323 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3324 if ( !bc_3.getName().equals( "bc" ) ) {
3327 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3328 if ( !ac_3.getName().equals( "abc" ) ) {
3331 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3332 if ( !ad_3.getName().equals( "abcde" ) ) {
3335 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3336 if ( !af_3.getName().equals( "abcdef" ) ) {
3339 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3340 if ( !ag_3.getName().equals( "" ) ) {
3343 if ( !ag_3.isRoot() ) {
3346 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3347 if ( !al_3.getName().equals( "" ) ) {
3350 if ( !al_3.isRoot() ) {
3353 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3354 if ( !kl_3.getName().equals( "" ) ) {
3357 if ( !kl_3.isRoot() ) {
3360 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3361 if ( !fl_3.getName().equals( "" ) ) {
3364 if ( !fl_3.isRoot() ) {
3367 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3368 if ( !gk_3.getName().equals( "ghijk" ) ) {
3371 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3372 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3373 if ( !r_4.getName().equals( "r" ) ) {
3376 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3377 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3378 if ( !r_5.getName().equals( "root" ) ) {
3381 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3382 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3383 if ( !r_6.getName().equals( "rot" ) ) {
3386 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3387 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3388 if ( !r_7.getName().equals( "rott" ) ) {
3392 catch ( final Exception e ) {
3393 e.printStackTrace( System.out );
3399 private static boolean testHmmscanOutputParser() {
3400 final String test_dir = Test.PATH_TO_TEST_DATA;
3402 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3403 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3405 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3406 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3407 final List<Protein> proteins = parser2.parse();
3408 if ( parser2.getProteinsEncountered() != 4 ) {
3411 if ( proteins.size() != 4 ) {
3414 if ( parser2.getDomainsEncountered() != 69 ) {
3417 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3420 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3423 final Protein p1 = proteins.get( 0 );
3424 if ( p1.getNumberOfProteinDomains() != 15 ) {
3427 if ( p1.getLength() != 850 ) {
3430 final Protein p2 = proteins.get( 1 );
3431 if ( p2.getNumberOfProteinDomains() != 51 ) {
3434 if ( p2.getLength() != 1291 ) {
3437 final Protein p3 = proteins.get( 2 );
3438 if ( p3.getNumberOfProteinDomains() != 2 ) {
3441 final Protein p4 = proteins.get( 3 );
3442 if ( p4.getNumberOfProteinDomains() != 1 ) {
3445 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3448 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3451 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3454 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3457 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3460 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3463 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3466 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3469 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3473 catch ( final Exception e ) {
3474 e.printStackTrace( System.out );
3480 private static boolean testLastExternalNodeMethods() {
3482 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3483 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3484 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3485 final PhylogenyNode n1 = t0.getNode( "A" );
3486 if ( n1.isLastExternalNode() ) {
3489 final PhylogenyNode n2 = t0.getNode( "B" );
3490 if ( n2.isLastExternalNode() ) {
3493 final PhylogenyNode n3 = t0.getNode( "C" );
3494 if ( n3.isLastExternalNode() ) {
3497 final PhylogenyNode n4 = t0.getNode( "D" );
3498 if ( !n4.isLastExternalNode() ) {
3502 catch ( final Exception e ) {
3503 e.printStackTrace( System.out );
3509 private static boolean testLevelOrderIterator() {
3511 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3512 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3513 PhylogenyNodeIterator it0;
3514 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3517 for( it0.reset(); it0.hasNext(); ) {
3520 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3521 if ( !it.next().getName().equals( "r" ) ) {
3524 if ( !it.next().getName().equals( "ab" ) ) {
3527 if ( !it.next().getName().equals( "cd" ) ) {
3530 if ( !it.next().getName().equals( "A" ) ) {
3533 if ( !it.next().getName().equals( "B" ) ) {
3536 if ( !it.next().getName().equals( "C" ) ) {
3539 if ( !it.next().getName().equals( "D" ) ) {
3542 if ( it.hasNext() ) {
3545 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",
3546 new NHXParser() )[ 0 ];
3547 PhylogenyNodeIterator it2;
3548 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3551 for( it2.reset(); it2.hasNext(); ) {
3554 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3555 if ( !it3.next().getName().equals( "r" ) ) {
3558 if ( !it3.next().getName().equals( "abc" ) ) {
3561 if ( !it3.next().getName().equals( "defg" ) ) {
3564 if ( !it3.next().getName().equals( "A" ) ) {
3567 if ( !it3.next().getName().equals( "B" ) ) {
3570 if ( !it3.next().getName().equals( "C" ) ) {
3573 if ( !it3.next().getName().equals( "D" ) ) {
3576 if ( !it3.next().getName().equals( "E" ) ) {
3579 if ( !it3.next().getName().equals( "F" ) ) {
3582 if ( !it3.next().getName().equals( "G" ) ) {
3585 if ( !it3.next().getName().equals( "1" ) ) {
3588 if ( !it3.next().getName().equals( "2" ) ) {
3591 if ( !it3.next().getName().equals( "3" ) ) {
3594 if ( !it3.next().getName().equals( "4" ) ) {
3597 if ( !it3.next().getName().equals( "5" ) ) {
3600 if ( !it3.next().getName().equals( "6" ) ) {
3603 if ( !it3.next().getName().equals( "f1" ) ) {
3606 if ( !it3.next().getName().equals( "f2" ) ) {
3609 if ( !it3.next().getName().equals( "f3" ) ) {
3612 if ( !it3.next().getName().equals( "a" ) ) {
3615 if ( !it3.next().getName().equals( "b" ) ) {
3618 if ( !it3.next().getName().equals( "f21" ) ) {
3621 if ( !it3.next().getName().equals( "X" ) ) {
3624 if ( !it3.next().getName().equals( "Y" ) ) {
3627 if ( !it3.next().getName().equals( "Z" ) ) {
3630 if ( it3.hasNext() ) {
3633 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3634 PhylogenyNodeIterator it4;
3635 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3638 for( it4.reset(); it4.hasNext(); ) {
3641 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3642 if ( !it5.next().getName().equals( "r" ) ) {
3645 if ( !it5.next().getName().equals( "A" ) ) {
3648 if ( !it5.next().getName().equals( "B" ) ) {
3651 if ( !it5.next().getName().equals( "C" ) ) {
3654 if ( !it5.next().getName().equals( "D" ) ) {
3657 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3658 PhylogenyNodeIterator it6;
3659 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3662 for( it6.reset(); it6.hasNext(); ) {
3665 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3666 if ( !it7.next().getName().equals( "A" ) ) {
3669 if ( it.hasNext() ) {
3673 catch ( final Exception e ) {
3674 e.printStackTrace( System.out );
3680 private static boolean testMidpointrooting() {
3682 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3683 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",
3684 new NHXParser() )[ 0 ];
3685 if ( !t1.isRooted() ) {
3688 PhylogenyMethods.midpointRoot( t1 );
3689 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3692 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3695 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3698 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3701 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3704 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3707 t1.reRoot( t1.getNode( "A" ) );
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 ) ) {
3728 catch ( final Exception e ) {
3729 e.printStackTrace( System.out );
3735 private static boolean testNexusCharactersParsing() {
3737 final NexusCharactersParser parser = new NexusCharactersParser();
3738 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3740 String[] labels = parser.getCharStateLabels();
3741 if ( labels.length != 7 ) {
3744 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3747 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3750 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3753 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3756 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3759 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3762 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3765 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3767 labels = parser.getCharStateLabels();
3768 if ( labels.length != 7 ) {
3771 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3774 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3777 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3780 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3783 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3786 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3789 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3793 catch ( final Exception e ) {
3794 e.printStackTrace( System.out );
3800 private static boolean testNexusMatrixParsing() {
3802 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3803 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3805 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3806 if ( m.getNumberOfCharacters() != 9 ) {
3809 if ( m.getNumberOfIdentifiers() != 5 ) {
3812 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3815 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3818 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3821 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3824 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3827 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3830 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3833 // if ( labels.length != 7 ) {
3836 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3839 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3842 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3845 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3848 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3851 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3854 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3857 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3859 // labels = parser.getCharStateLabels();
3860 // if ( labels.length != 7 ) {
3863 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3866 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3869 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3872 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3875 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3878 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3881 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3885 catch ( final Exception e ) {
3886 e.printStackTrace( System.out );
3892 private static boolean testNexusTreeParsing() {
3894 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3895 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3896 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3897 if ( phylogenies.length != 1 ) {
3900 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3903 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3907 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3908 if ( phylogenies.length != 1 ) {
3911 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3914 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3918 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3919 if ( phylogenies.length != 1 ) {
3922 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3925 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3928 if ( phylogenies[ 0 ].isRooted() ) {
3932 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3933 if ( phylogenies.length != 18 ) {
3936 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3939 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3942 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3945 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3948 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3951 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3954 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3957 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3960 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3963 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3966 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3969 if ( phylogenies[ 8 ].isRooted() ) {
3972 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3975 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3978 if ( !phylogenies[ 9 ].isRooted() ) {
3981 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3984 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3987 if ( !phylogenies[ 10 ].isRooted() ) {
3990 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3993 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3996 if ( phylogenies[ 11 ].isRooted() ) {
3999 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4002 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4005 if ( !phylogenies[ 12 ].isRooted() ) {
4008 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4011 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4014 if ( !phylogenies[ 13 ].isRooted() ) {
4017 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4020 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4023 if ( !phylogenies[ 14 ].isRooted() ) {
4026 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4029 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4032 if ( phylogenies[ 15 ].isRooted() ) {
4035 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4038 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4041 if ( !phylogenies[ 16 ].isRooted() ) {
4044 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4047 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4050 if ( phylogenies[ 17 ].isRooted() ) {
4053 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4057 catch ( final Exception e ) {
4058 e.printStackTrace( System.out );
4064 private static boolean testNexusTreeParsingTranslating() {
4066 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4067 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4068 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4069 if ( phylogenies.length != 1 ) {
4072 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4075 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4078 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4081 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4084 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4085 .equals( "Aranaeus" ) ) {
4089 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4090 if ( phylogenies.length != 3 ) {
4093 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4096 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4099 if ( phylogenies[ 0 ].isRooted() ) {
4102 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4105 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4108 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4109 .equals( "Aranaeus" ) ) {
4112 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4115 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4118 if ( phylogenies[ 1 ].isRooted() ) {
4121 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4124 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4127 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4128 .equals( "Aranaeus" ) ) {
4131 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4134 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4137 if ( !phylogenies[ 2 ].isRooted() ) {
4140 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4143 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4146 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4147 .equals( "Aranaeus" ) ) {
4151 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4152 if ( phylogenies.length != 3 ) {
4155 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4158 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4161 if ( phylogenies[ 0 ].isRooted() ) {
4164 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4167 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4170 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4171 .equals( "Aranaeus" ) ) {
4174 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4177 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4180 if ( phylogenies[ 1 ].isRooted() ) {
4183 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4186 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4189 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4190 .equals( "Aranaeus" ) ) {
4193 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4196 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4199 if ( !phylogenies[ 2 ].isRooted() ) {
4202 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4205 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4208 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4209 .equals( "Aranaeus" ) ) {
4213 catch ( final Exception e ) {
4214 e.printStackTrace( System.out );
4220 private static boolean testNHParsing() {
4222 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4223 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4224 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4227 final NHXParser nhxp = new NHXParser();
4228 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4229 nhxp.setReplaceUnderscores( true );
4230 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4231 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4234 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4237 final Phylogeny p1b = factory
4238 .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 ",
4239 new NHXParser() )[ 0 ];
4240 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4243 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4246 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4247 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4248 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4249 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4250 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4251 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4252 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4253 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4254 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4255 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4256 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4257 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4258 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4260 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4263 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4266 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4269 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4272 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4273 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4274 final String p16_S = "((A,B),C)";
4275 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4276 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4279 final String p17_S = "(C,(A,B))";
4280 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4281 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4284 final String p18_S = "((A,B),(C,D))";
4285 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4286 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4289 final String p19_S = "(((A,B),C),D)";
4290 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4291 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4294 final String p20_S = "(A,(B,(C,D)))";
4295 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4296 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4299 final String p21_S = "(A,(B,(C,(D,E))))";
4300 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4301 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4304 final String p22_S = "((((A,B),C),D),E)";
4305 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4306 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4309 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4310 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4311 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4314 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4315 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4316 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4319 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4320 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4321 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4322 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4325 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4328 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4329 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4330 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4331 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4332 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4333 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4334 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4335 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4336 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4337 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4340 final String p26_S = "(A,B)ab";
4341 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4342 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4345 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4346 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4348 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4351 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4352 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4353 final String p28_S3 = "(A,B)ab";
4354 final String p28_S4 = "((((A,B),C),D),;E;)";
4355 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4357 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4360 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4363 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4366 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4369 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";
4370 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4371 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4374 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";
4375 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4376 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4379 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4380 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4381 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4384 final String p33_S = "A";
4385 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4386 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4389 final String p34_S = "B;";
4390 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4391 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4394 final String p35_S = "B:0.2";
4395 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4396 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4399 final String p36_S = "(A)";
4400 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4401 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4404 final String p37_S = "((A))";
4405 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4406 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4409 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4410 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4411 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4414 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4415 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4416 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4419 final String p40_S = "(A,B,C)";
4420 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4421 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4424 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4425 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4426 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4429 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4430 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4431 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4434 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)";
4435 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4436 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4439 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)))";
4440 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4441 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4444 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4445 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4446 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4449 final String p46_S = "";
4450 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4451 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4454 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4455 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4458 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4459 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4462 final Phylogeny p49 = factory
4463 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4464 new NHXParser() )[ 0 ];
4465 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4468 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4469 if ( p50.getNode( "A" ) == null ) {
4472 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4473 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4476 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4479 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4480 .equals( "((A,B)88:2.0,C);" ) ) {
4483 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4484 if ( p51.getNode( "A(A" ) == null ) {
4487 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4488 if ( p52.getNode( "A(A" ) == null ) {
4491 final Phylogeny p53 = factory
4492 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4493 new NHXParser() )[ 0 ];
4494 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4498 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4499 if ( p54.getNode( "A" ) == null ) {
4502 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4503 .equals( "((A,B)[88],C);" ) ) {
4507 catch ( final Exception e ) {
4508 e.printStackTrace( System.out );
4514 private static boolean testNHXconversion() {
4516 final PhylogenyNode n1 = new PhylogenyNode();
4517 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4518 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4519 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4520 final PhylogenyNode n5 = PhylogenyNode
4521 .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]" );
4522 final PhylogenyNode n6 = PhylogenyNode
4523 .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]" );
4524 if ( !n1.toNewHampshireX().equals( "" ) ) {
4527 if ( !n2.toNewHampshireX().equals( "" ) ) {
4530 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4533 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4536 if ( !n5.toNewHampshireX()
4537 .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]" ) ) {
4540 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]" ) ) {
4544 catch ( final Exception e ) {
4545 e.printStackTrace( System.out );
4551 private static boolean testNHXNodeParsing() {
4553 final PhylogenyNode n1 = new PhylogenyNode();
4554 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4555 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4556 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4557 final PhylogenyNode n5 = PhylogenyNode
4558 .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]" );
4559 if ( !n3.getName().equals( "n3" ) ) {
4562 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4565 if ( n3.isDuplication() ) {
4568 if ( n3.isHasAssignedEvent() ) {
4571 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4574 if ( !n4.getName().equals( "n4" ) ) {
4577 if ( n4.getDistanceToParent() != 0.01 ) {
4580 if ( !n5.getName().equals( "n5" ) ) {
4583 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4586 if ( n5.getDistanceToParent() != 0.1 ) {
4589 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4592 if ( !n5.isDuplication() ) {
4595 if ( !n5.isHasAssignedEvent() ) {
4598 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4601 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4604 final PhylogenyNode n8 = PhylogenyNode
4605 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4606 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4607 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4610 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4613 final PhylogenyNode n9 = PhylogenyNode
4614 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4615 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4616 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4619 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4622 final PhylogenyNode n10 = PhylogenyNode
4623 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4624 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4627 final PhylogenyNode n20 = PhylogenyNode
4628 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4629 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4632 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4635 final PhylogenyNode n20x = PhylogenyNode
4636 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4637 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4640 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4643 final PhylogenyNode n20xx = PhylogenyNode
4644 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4645 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4648 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4651 final PhylogenyNode n20xxx = PhylogenyNode
4652 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4653 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4656 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4659 final PhylogenyNode n20xxxx = PhylogenyNode
4660 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4661 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4664 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4667 final PhylogenyNode n21 = PhylogenyNode
4668 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4669 if ( !n21.getName().equals( "n21_PIG" ) ) {
4672 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4675 final PhylogenyNode n21x = PhylogenyNode
4676 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4677 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4680 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4683 final PhylogenyNode n22 = PhylogenyNode
4684 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4685 if ( !n22.getName().equals( "n22/PIG" ) ) {
4688 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4691 final PhylogenyNode n23 = PhylogenyNode
4692 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4693 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4696 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4699 final PhylogenyNode a = PhylogenyNode
4700 .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4701 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4704 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4707 final PhylogenyNode b = PhylogenyNode
4708 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4709 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4710 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4713 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4716 final PhylogenyNode c = PhylogenyNode
4717 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4718 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4719 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4722 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4725 final PhylogenyNode c1 = PhylogenyNode
4726 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4727 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4728 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4731 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4734 final PhylogenyNode c2 = PhylogenyNode
4735 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4736 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4737 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4740 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4743 final PhylogenyNode d = PhylogenyNode
4744 .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4745 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4748 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4751 final PhylogenyNode e = PhylogenyNode
4752 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4753 if ( !e.getName().equals( "n10_RAT1" ) ) {
4756 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4759 final PhylogenyNode e2 = PhylogenyNode
4760 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4761 if ( !e2.getName().equals( "n10_RAT1" ) ) {
4764 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
4767 final PhylogenyNode e3 = PhylogenyNode
4768 .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4769 if ( !e3.getName().equals( "n10_RAT~" ) ) {
4772 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
4775 final PhylogenyNode n11 = PhylogenyNode
4776 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4777 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4778 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4781 if ( n11.getDistanceToParent() != 0.4 ) {
4784 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4787 final PhylogenyNode n12 = PhylogenyNode
4788 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4789 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4790 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4793 if ( n12.getDistanceToParent() != 0.4 ) {
4796 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4799 final PhylogenyNode m = PhylogenyNode
4800 .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4801 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
4804 if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
4807 final PhylogenyNode o = PhylogenyNode
4808 .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4809 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
4812 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
4815 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4816 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4817 if ( !tvu1.getRef().equals( "tag1" ) ) {
4820 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4823 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4826 if ( !tvu1.getValue().equals( "value1" ) ) {
4829 if ( !tvu3.getRef().equals( "tag3" ) ) {
4832 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4835 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4838 if ( !tvu3.getValue().equals( "value3" ) ) {
4841 if ( n1.getName().compareTo( "" ) != 0 ) {
4844 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4847 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4850 if ( n2.getName().compareTo( "" ) != 0 ) {
4853 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4856 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4859 final PhylogenyNode n00 = PhylogenyNode
4860 .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]" );
4861 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4864 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4867 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4870 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4873 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4876 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4879 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4882 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4885 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4886 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4889 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4890 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4893 final PhylogenyNode n13 = PhylogenyNode
4894 .createInstanceFromNhxString( "blah_12345/1-2",
4895 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4896 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4899 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
4902 final PhylogenyNode n14 = PhylogenyNode
4903 .createInstanceFromNhxString( "blah_12X45/1-2",
4904 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4905 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4908 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4911 final PhylogenyNode n15 = PhylogenyNode
4912 .createInstanceFromNhxString( "something_wicked[123]",
4913 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4914 if ( !n15.getName().equals( "something_wicked" ) ) {
4917 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4920 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4923 final PhylogenyNode n16 = PhylogenyNode
4924 .createInstanceFromNhxString( "something_wicked2[9]",
4925 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4926 if ( !n16.getName().equals( "something_wicked2" ) ) {
4929 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4932 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4935 final PhylogenyNode n17 = PhylogenyNode
4936 .createInstanceFromNhxString( "something_wicked3[a]",
4937 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4938 if ( !n17.getName().equals( "something_wicked3" ) ) {
4941 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4944 final PhylogenyNode n18 = PhylogenyNode
4945 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4946 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4949 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4952 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4956 catch ( final Exception e ) {
4957 e.printStackTrace( System.out );
4963 private static boolean testNHXParsing() {
4965 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4966 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4967 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4970 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]";
4971 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4972 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4975 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]";
4976 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4977 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4980 final Phylogeny[] p3 = factory
4981 .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]",
4983 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4986 final Phylogeny[] p4 = factory
4987 .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(]",
4989 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4992 final Phylogeny[] p5 = factory
4993 .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(((]",
4995 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4998 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)";
4999 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)";
5000 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5001 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5004 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)))";
5005 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)))";
5006 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5007 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5010 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]) ))[,,, ])))))))";
5011 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5012 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5013 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5016 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5017 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5020 final Phylogeny p10 = factory
5021 .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]",
5022 new NHXParser() )[ 0 ];
5023 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5027 catch ( final Exception e ) {
5028 e.printStackTrace( System.out );
5034 private static boolean testNHXParsingQuotes() {
5036 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5037 final NHXParser p = new NHXParser();
5038 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5039 if ( phylogenies_0.length != 5 ) {
5042 final Phylogeny phy = phylogenies_0[ 4 ];
5043 if ( phy.getNumberOfExternalNodes() != 7 ) {
5046 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5049 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5052 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5053 .getScientificName().equals( "hsapiens" ) ) {
5056 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5059 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5062 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5065 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5068 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5071 final NHXParser p1p = new NHXParser();
5072 p1p.setIgnoreQuotes( true );
5073 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5074 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5077 final NHXParser p2p = new NHXParser();
5078 p1p.setIgnoreQuotes( false );
5079 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5080 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5083 final NHXParser p3p = new NHXParser();
5084 p3p.setIgnoreQuotes( false );
5085 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5086 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5089 final NHXParser p4p = new NHXParser();
5090 p4p.setIgnoreQuotes( false );
5091 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5092 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5095 final Phylogeny p10 = factory
5096 .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]",
5097 new NHXParser() )[ 0 ];
5098 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]";
5099 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5102 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5103 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5107 final Phylogeny p12 = factory
5108 .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]",
5109 new NHXParser() )[ 0 ];
5110 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]";
5111 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5114 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5115 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5118 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;";
5119 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5122 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5123 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5127 catch ( final Exception e ) {
5128 e.printStackTrace( System.out );
5134 private static boolean testNHXParsingMB() {
5136 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5137 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5138 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5139 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5140 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5141 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5142 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5143 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5144 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5145 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5146 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5149 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5152 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5153 0.1100000000000000e+00 ) ) {
5156 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5159 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5162 final Phylogeny p2 = factory
5163 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5164 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5165 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5166 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5167 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5168 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5169 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5170 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5171 + "7.369400000000000e-02}])",
5172 new NHXParser() )[ 0 ];
5173 if ( p2.getNode( "1" ) == null ) {
5176 if ( p2.getNode( "2" ) == null ) {
5180 catch ( final Exception e ) {
5181 e.printStackTrace( System.out );
5188 private static boolean testPhylogenyBranch() {
5190 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5191 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5192 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5193 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5194 if ( !a1b1.equals( a1b1 ) ) {
5197 if ( !a1b1.equals( b1a1 ) ) {
5200 if ( !b1a1.equals( a1b1 ) ) {
5203 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5204 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5205 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5206 if ( a1_b1.equals( b1_a1 ) ) {
5209 if ( a1_b1.equals( a1_b1_ ) ) {
5212 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5213 if ( !a1_b1.equals( b1_a1_ ) ) {
5216 if ( a1_b1_.equals( b1_a1_ ) ) {
5219 if ( !a1_b1_.equals( b1_a1 ) ) {
5223 catch ( final Exception e ) {
5224 e.printStackTrace( System.out );
5230 private static boolean testPhyloXMLparsingOfDistributionElement() {
5232 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5233 PhyloXmlParser xml_parser = null;
5235 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5237 catch ( final Exception e ) {
5238 // Do nothing -- means were not running from jar.
5240 if ( xml_parser == null ) {
5241 xml_parser = new PhyloXmlParser();
5242 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5243 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5246 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5249 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5251 if ( xml_parser.getErrorCount() > 0 ) {
5252 System.out.println( xml_parser.getErrorMessages().toString() );
5255 if ( phylogenies_0.length != 1 ) {
5258 final Phylogeny t1 = phylogenies_0[ 0 ];
5259 PhylogenyNode n = null;
5260 Distribution d = null;
5261 n = t1.getNode( "root node" );
5262 if ( !n.getNodeData().isHasDistribution() ) {
5265 if ( n.getNodeData().getDistributions().size() != 1 ) {
5268 d = n.getNodeData().getDistribution();
5269 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5272 if ( d.getPoints().size() != 1 ) {
5275 if ( d.getPolygons() != null ) {
5278 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5281 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5284 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5287 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5290 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5293 n = t1.getNode( "node a" );
5294 if ( !n.getNodeData().isHasDistribution() ) {
5297 if ( n.getNodeData().getDistributions().size() != 2 ) {
5300 d = n.getNodeData().getDistribution( 1 );
5301 if ( !d.getDesc().equals( "San Diego" ) ) {
5304 if ( d.getPoints().size() != 1 ) {
5307 if ( d.getPolygons() != null ) {
5310 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5313 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5316 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5319 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5322 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5325 n = t1.getNode( "node bb" );
5326 if ( !n.getNodeData().isHasDistribution() ) {
5329 if ( n.getNodeData().getDistributions().size() != 1 ) {
5332 d = n.getNodeData().getDistribution( 0 );
5333 if ( d.getPoints().size() != 3 ) {
5336 if ( d.getPolygons().size() != 2 ) {
5339 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5342 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5345 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5348 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5351 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5354 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5357 Polygon p = d.getPolygons().get( 0 );
5358 if ( p.getPoints().size() != 3 ) {
5361 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5364 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5367 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5370 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5373 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5376 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5379 p = d.getPolygons().get( 1 );
5380 if ( p.getPoints().size() != 3 ) {
5383 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5386 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5389 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5393 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5394 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5395 if ( rt.length != 1 ) {
5398 final Phylogeny t1_rt = rt[ 0 ];
5399 n = t1_rt.getNode( "root node" );
5400 if ( !n.getNodeData().isHasDistribution() ) {
5403 if ( n.getNodeData().getDistributions().size() != 1 ) {
5406 d = n.getNodeData().getDistribution();
5407 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5410 if ( d.getPoints().size() != 1 ) {
5413 if ( d.getPolygons() != null ) {
5416 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5419 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5422 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5425 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5428 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5431 n = t1_rt.getNode( "node a" );
5432 if ( !n.getNodeData().isHasDistribution() ) {
5435 if ( n.getNodeData().getDistributions().size() != 2 ) {
5438 d = n.getNodeData().getDistribution( 1 );
5439 if ( !d.getDesc().equals( "San Diego" ) ) {
5442 if ( d.getPoints().size() != 1 ) {
5445 if ( d.getPolygons() != null ) {
5448 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5451 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5454 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5457 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5460 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5463 n = t1_rt.getNode( "node bb" );
5464 if ( !n.getNodeData().isHasDistribution() ) {
5467 if ( n.getNodeData().getDistributions().size() != 1 ) {
5470 d = n.getNodeData().getDistribution( 0 );
5471 if ( d.getPoints().size() != 3 ) {
5474 if ( d.getPolygons().size() != 2 ) {
5477 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5480 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5483 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5486 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5489 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5492 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5495 p = d.getPolygons().get( 0 );
5496 if ( p.getPoints().size() != 3 ) {
5499 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5502 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5505 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5508 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5511 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5514 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5517 p = d.getPolygons().get( 1 );
5518 if ( p.getPoints().size() != 3 ) {
5521 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5524 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5527 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5531 catch ( final Exception e ) {
5532 e.printStackTrace( System.out );
5538 private static boolean testPostOrderIterator() {
5540 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5541 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5542 PhylogenyNodeIterator it0;
5543 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5546 for( it0.reset(); it0.hasNext(); ) {
5549 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5550 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5551 if ( !it.next().getName().equals( "A" ) ) {
5554 if ( !it.next().getName().equals( "B" ) ) {
5557 if ( !it.next().getName().equals( "ab" ) ) {
5560 if ( !it.next().getName().equals( "C" ) ) {
5563 if ( !it.next().getName().equals( "D" ) ) {
5566 if ( !it.next().getName().equals( "cd" ) ) {
5569 if ( !it.next().getName().equals( "abcd" ) ) {
5572 if ( !it.next().getName().equals( "E" ) ) {
5575 if ( !it.next().getName().equals( "F" ) ) {
5578 if ( !it.next().getName().equals( "ef" ) ) {
5581 if ( !it.next().getName().equals( "G" ) ) {
5584 if ( !it.next().getName().equals( "H" ) ) {
5587 if ( !it.next().getName().equals( "gh" ) ) {
5590 if ( !it.next().getName().equals( "efgh" ) ) {
5593 if ( !it.next().getName().equals( "r" ) ) {
5596 if ( it.hasNext() ) {
5600 catch ( final Exception e ) {
5601 e.printStackTrace( System.out );
5607 private static boolean testPreOrderIterator() {
5609 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5610 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5611 PhylogenyNodeIterator it0;
5612 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5615 for( it0.reset(); it0.hasNext(); ) {
5618 PhylogenyNodeIterator it = t0.iteratorPreorder();
5619 if ( !it.next().getName().equals( "r" ) ) {
5622 if ( !it.next().getName().equals( "ab" ) ) {
5625 if ( !it.next().getName().equals( "A" ) ) {
5628 if ( !it.next().getName().equals( "B" ) ) {
5631 if ( !it.next().getName().equals( "cd" ) ) {
5634 if ( !it.next().getName().equals( "C" ) ) {
5637 if ( !it.next().getName().equals( "D" ) ) {
5640 if ( it.hasNext() ) {
5643 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5644 it = t1.iteratorPreorder();
5645 if ( !it.next().getName().equals( "r" ) ) {
5648 if ( !it.next().getName().equals( "abcd" ) ) {
5651 if ( !it.next().getName().equals( "ab" ) ) {
5654 if ( !it.next().getName().equals( "A" ) ) {
5657 if ( !it.next().getName().equals( "B" ) ) {
5660 if ( !it.next().getName().equals( "cd" ) ) {
5663 if ( !it.next().getName().equals( "C" ) ) {
5666 if ( !it.next().getName().equals( "D" ) ) {
5669 if ( !it.next().getName().equals( "efgh" ) ) {
5672 if ( !it.next().getName().equals( "ef" ) ) {
5675 if ( !it.next().getName().equals( "E" ) ) {
5678 if ( !it.next().getName().equals( "F" ) ) {
5681 if ( !it.next().getName().equals( "gh" ) ) {
5684 if ( !it.next().getName().equals( "G" ) ) {
5687 if ( !it.next().getName().equals( "H" ) ) {
5690 if ( it.hasNext() ) {
5694 catch ( final Exception e ) {
5695 e.printStackTrace( System.out );
5701 private static boolean testPropertiesMap() {
5703 final PropertiesMap pm = new PropertiesMap();
5704 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5705 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5706 final Property p2 = new Property( "something:else",
5708 "improbable:research",
5711 pm.addProperty( p0 );
5712 pm.addProperty( p1 );
5713 pm.addProperty( p2 );
5714 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5717 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5720 if ( pm.getProperties().size() != 3 ) {
5723 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5726 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5729 if ( pm.getProperties().size() != 3 ) {
5732 pm.removeProperty( "dimensions:diameter" );
5733 if ( pm.getProperties().size() != 2 ) {
5736 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5739 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5743 catch ( final Exception e ) {
5744 e.printStackTrace( System.out );
5750 private static boolean testReIdMethods() {
5752 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5753 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5754 final int count = PhylogenyNode.getNodeCount();
5756 if ( p.getNode( "r" ).getId() != count ) {
5759 if ( p.getNode( "A" ).getId() != count + 1 ) {
5762 if ( p.getNode( "B" ).getId() != count + 1 ) {
5765 if ( p.getNode( "C" ).getId() != count + 1 ) {
5768 if ( p.getNode( "1" ).getId() != count + 2 ) {
5771 if ( p.getNode( "2" ).getId() != count + 2 ) {
5774 if ( p.getNode( "3" ).getId() != count + 2 ) {
5777 if ( p.getNode( "4" ).getId() != count + 2 ) {
5780 if ( p.getNode( "5" ).getId() != count + 2 ) {
5783 if ( p.getNode( "6" ).getId() != count + 2 ) {
5786 if ( p.getNode( "a" ).getId() != count + 3 ) {
5789 if ( p.getNode( "b" ).getId() != count + 3 ) {
5792 if ( p.getNode( "X" ).getId() != count + 4 ) {
5795 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5798 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5802 catch ( final Exception e ) {
5803 e.printStackTrace( System.out );
5809 private static boolean testRerooting() {
5811 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5812 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",
5813 new NHXParser() )[ 0 ];
5814 if ( !t1.isRooted() ) {
5817 t1.reRoot( t1.getNode( "D" ) );
5818 t1.reRoot( t1.getNode( "CD" ) );
5819 t1.reRoot( t1.getNode( "A" ) );
5820 t1.reRoot( t1.getNode( "B" ) );
5821 t1.reRoot( t1.getNode( "AB" ) );
5822 t1.reRoot( t1.getNode( "D" ) );
5823 t1.reRoot( t1.getNode( "C" ) );
5824 t1.reRoot( t1.getNode( "CD" ) );
5825 t1.reRoot( t1.getNode( "A" ) );
5826 t1.reRoot( t1.getNode( "B" ) );
5827 t1.reRoot( t1.getNode( "AB" ) );
5828 t1.reRoot( t1.getNode( "D" ) );
5829 t1.reRoot( t1.getNode( "D" ) );
5830 t1.reRoot( t1.getNode( "C" ) );
5831 t1.reRoot( t1.getNode( "A" ) );
5832 t1.reRoot( t1.getNode( "B" ) );
5833 t1.reRoot( t1.getNode( "AB" ) );
5834 t1.reRoot( t1.getNode( "C" ) );
5835 t1.reRoot( t1.getNode( "D" ) );
5836 t1.reRoot( t1.getNode( "CD" ) );
5837 t1.reRoot( t1.getNode( "D" ) );
5838 t1.reRoot( t1.getNode( "A" ) );
5839 t1.reRoot( t1.getNode( "B" ) );
5840 t1.reRoot( t1.getNode( "AB" ) );
5841 t1.reRoot( t1.getNode( "C" ) );
5842 t1.reRoot( t1.getNode( "D" ) );
5843 t1.reRoot( t1.getNode( "CD" ) );
5844 t1.reRoot( t1.getNode( "D" ) );
5845 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5848 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5851 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5854 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5857 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5860 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5863 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",
5864 new NHXParser() )[ 0 ];
5865 t2.reRoot( t2.getNode( "A" ) );
5866 t2.reRoot( t2.getNode( "D" ) );
5867 t2.reRoot( t2.getNode( "ABC" ) );
5868 t2.reRoot( t2.getNode( "A" ) );
5869 t2.reRoot( t2.getNode( "B" ) );
5870 t2.reRoot( t2.getNode( "D" ) );
5871 t2.reRoot( t2.getNode( "C" ) );
5872 t2.reRoot( t2.getNode( "ABC" ) );
5873 t2.reRoot( t2.getNode( "A" ) );
5874 t2.reRoot( t2.getNode( "B" ) );
5875 t2.reRoot( t2.getNode( "AB" ) );
5876 t2.reRoot( t2.getNode( "AB" ) );
5877 t2.reRoot( t2.getNode( "D" ) );
5878 t2.reRoot( t2.getNode( "C" ) );
5879 t2.reRoot( t2.getNode( "B" ) );
5880 t2.reRoot( t2.getNode( "AB" ) );
5881 t2.reRoot( t2.getNode( "D" ) );
5882 t2.reRoot( t2.getNode( "D" ) );
5883 t2.reRoot( t2.getNode( "ABC" ) );
5884 t2.reRoot( t2.getNode( "A" ) );
5885 t2.reRoot( t2.getNode( "B" ) );
5886 t2.reRoot( t2.getNode( "AB" ) );
5887 t2.reRoot( t2.getNode( "D" ) );
5888 t2.reRoot( t2.getNode( "C" ) );
5889 t2.reRoot( t2.getNode( "ABC" ) );
5890 t2.reRoot( t2.getNode( "A" ) );
5891 t2.reRoot( t2.getNode( "B" ) );
5892 t2.reRoot( t2.getNode( "AB" ) );
5893 t2.reRoot( t2.getNode( "D" ) );
5894 t2.reRoot( t2.getNode( "D" ) );
5895 t2.reRoot( t2.getNode( "C" ) );
5896 t2.reRoot( t2.getNode( "A" ) );
5897 t2.reRoot( t2.getNode( "B" ) );
5898 t2.reRoot( t2.getNode( "AB" ) );
5899 t2.reRoot( t2.getNode( "C" ) );
5900 t2.reRoot( t2.getNode( "D" ) );
5901 t2.reRoot( t2.getNode( "ABC" ) );
5902 t2.reRoot( t2.getNode( "D" ) );
5903 t2.reRoot( t2.getNode( "A" ) );
5904 t2.reRoot( t2.getNode( "B" ) );
5905 t2.reRoot( t2.getNode( "AB" ) );
5906 t2.reRoot( t2.getNode( "C" ) );
5907 t2.reRoot( t2.getNode( "D" ) );
5908 t2.reRoot( t2.getNode( "ABC" ) );
5909 t2.reRoot( t2.getNode( "D" ) );
5910 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5913 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5916 t2.reRoot( t2.getNode( "ABC" ) );
5917 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5920 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5923 t2.reRoot( t2.getNode( "AB" ) );
5924 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5927 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5930 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5933 t2.reRoot( t2.getNode( "AB" ) );
5934 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5937 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5940 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5943 t2.reRoot( t2.getNode( "D" ) );
5944 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5947 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5950 t2.reRoot( t2.getNode( "ABC" ) );
5951 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5954 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5957 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5958 new NHXParser() )[ 0 ];
5959 t3.reRoot( t3.getNode( "B" ) );
5960 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5963 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5966 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5969 t3.reRoot( t3.getNode( "B" ) );
5970 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5973 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5976 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5979 t3.reRoot( t3.getRoot() );
5980 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5983 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5986 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5990 catch ( final Exception e ) {
5991 e.printStackTrace( System.out );
5997 private static boolean testSDIse() {
5999 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6000 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6001 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6002 gene1.setRooted( true );
6003 species1.setRooted( true );
6004 final SDI sdi = new SDIse( gene1, species1 );
6005 if ( !gene1.getRoot().isDuplication() ) {
6008 final Phylogeny species2 = factory
6009 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6010 new NHXParser() )[ 0 ];
6011 final Phylogeny gene2 = factory
6012 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6013 new NHXParser() )[ 0 ];
6014 species2.setRooted( true );
6015 gene2.setRooted( true );
6016 final SDI sdi2 = new SDIse( gene2, species2 );
6017 if ( sdi2.getDuplicationsSum() != 0 ) {
6020 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6023 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6026 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6029 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6032 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6035 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6038 final Phylogeny species3 = factory
6039 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6040 new NHXParser() )[ 0 ];
6041 final Phylogeny gene3 = factory
6042 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6043 new NHXParser() )[ 0 ];
6044 species3.setRooted( true );
6045 gene3.setRooted( true );
6046 final SDI sdi3 = new SDIse( gene3, species3 );
6047 if ( sdi3.getDuplicationsSum() != 1 ) {
6050 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6053 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6056 final Phylogeny species4 = factory
6057 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6058 new NHXParser() )[ 0 ];
6059 final Phylogeny gene4 = factory
6060 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6061 new NHXParser() )[ 0 ];
6062 species4.setRooted( true );
6063 gene4.setRooted( true );
6064 final SDI sdi4 = new SDIse( gene4, species4 );
6065 if ( sdi4.getDuplicationsSum() != 1 ) {
6068 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6071 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6074 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6077 if ( species4.getNumberOfExternalNodes() != 6 ) {
6080 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6083 final Phylogeny species5 = factory
6084 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6085 new NHXParser() )[ 0 ];
6086 final Phylogeny gene5 = factory
6087 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6088 new NHXParser() )[ 0 ];
6089 species5.setRooted( true );
6090 gene5.setRooted( true );
6091 final SDI sdi5 = new SDIse( gene5, species5 );
6092 if ( sdi5.getDuplicationsSum() != 2 ) {
6095 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6098 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6101 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6104 if ( species5.getNumberOfExternalNodes() != 6 ) {
6107 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6110 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6111 // Conjecture for Comparing Molecular Phylogenies"
6112 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6113 final Phylogeny species6 = factory
6114 .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,"
6115 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6116 new NHXParser() )[ 0 ];
6117 final Phylogeny gene6 = factory
6118 .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,"
6119 + "((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,"
6120 + "(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;",
6121 new NHXParser() )[ 0 ];
6122 species6.setRooted( true );
6123 gene6.setRooted( true );
6124 final SDI sdi6 = new SDIse( gene6, species6 );
6125 if ( sdi6.getDuplicationsSum() != 3 ) {
6128 if ( !gene6.getNode( "r" ).isDuplication() ) {
6131 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6134 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6137 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6140 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6143 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6146 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6149 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6152 sdi6.computeMappingCostL();
6153 if ( sdi6.computeMappingCostL() != 17 ) {
6156 if ( species6.getNumberOfExternalNodes() != 9 ) {
6159 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6162 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6163 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6164 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6165 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6166 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6167 species7.setRooted( true );
6168 final Phylogeny gene7_1 = Test
6169 .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])" );
6170 gene7_1.setRooted( true );
6171 final SDI sdi7 = new SDIse( gene7_1, species7 );
6172 if ( sdi7.getDuplicationsSum() != 0 ) {
6175 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6178 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6181 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6184 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6187 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6190 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6193 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6196 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6199 final Phylogeny gene7_2 = Test
6200 .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])" );
6201 gene7_2.setRooted( true );
6202 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6203 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6206 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6209 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6212 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6215 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6218 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6221 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6224 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6227 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6230 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6234 catch ( final Exception e ) {
6240 private static boolean testSDIunrooted() {
6242 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6243 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6244 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6245 final Iterator<PhylogenyBranch> iter = l.iterator();
6246 PhylogenyBranch br = iter.next();
6247 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6250 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6254 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6257 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6261 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6264 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6268 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6271 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6275 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6278 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6282 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6285 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6289 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6292 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6296 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6299 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6303 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6306 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6310 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6313 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6317 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6320 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6324 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6327 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6331 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6334 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6338 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6341 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6345 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6348 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6351 if ( iter.hasNext() ) {
6354 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6355 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6356 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6358 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6361 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6365 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6368 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6372 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6375 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6378 if ( iter1.hasNext() ) {
6381 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6382 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6383 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6385 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6388 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6392 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6395 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6399 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6402 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6405 if ( iter2.hasNext() ) {
6408 final Phylogeny species0 = factory
6409 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6410 new NHXParser() )[ 0 ];
6411 final Phylogeny gene1 = factory
6412 .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])",
6413 new NHXParser() )[ 0 ];
6414 species0.setRooted( true );
6415 gene1.setRooted( true );
6416 final SDIR sdi_unrooted = new SDIR();
6417 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6418 if ( sdi_unrooted.getCount() != 1 ) {
6421 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6424 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6427 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6430 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6433 final Phylogeny gene2 = factory
6434 .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])",
6435 new NHXParser() )[ 0 ];
6436 gene2.setRooted( true );
6437 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6438 if ( sdi_unrooted.getCount() != 1 ) {
6441 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6444 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6447 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6450 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6453 final Phylogeny species6 = factory
6454 .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,"
6455 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6456 new NHXParser() )[ 0 ];
6457 final Phylogeny gene6 = factory
6458 .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],"
6459 + "(((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],"
6460 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6461 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6462 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6463 new NHXParser() )[ 0 ];
6464 species6.setRooted( true );
6465 gene6.setRooted( true );
6466 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6467 if ( sdi_unrooted.getCount() != 1 ) {
6470 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6473 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6476 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6479 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6482 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6485 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6488 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6491 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6494 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6497 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6500 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6503 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6507 final Phylogeny species7 = factory
6508 .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,"
6509 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6510 new NHXParser() )[ 0 ];
6511 final Phylogeny gene7 = factory
6512 .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],"
6513 + "(((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],"
6514 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6515 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6516 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6517 new NHXParser() )[ 0 ];
6518 species7.setRooted( true );
6519 gene7.setRooted( true );
6520 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6521 if ( sdi_unrooted.getCount() != 1 ) {
6524 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6527 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6530 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6533 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6536 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6539 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6542 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6545 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6548 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6551 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6554 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6557 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6561 final Phylogeny species8 = factory
6562 .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,"
6563 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6564 new NHXParser() )[ 0 ];
6565 final Phylogeny gene8 = factory
6566 .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],"
6567 + "(((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],"
6568 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6569 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6570 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6571 new NHXParser() )[ 0 ];
6572 species8.setRooted( true );
6573 gene8.setRooted( true );
6574 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6575 if ( sdi_unrooted.getCount() != 1 ) {
6578 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6581 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6584 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6587 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6590 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6593 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6596 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6599 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6602 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6605 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6608 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6611 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6616 catch ( final Exception e ) {
6617 e.printStackTrace( System.out );
6623 private static boolean testSplit() {
6625 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6626 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6627 //Archaeopteryx.createApplication( p0 );
6628 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6629 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6630 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6631 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6632 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6633 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6634 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6635 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6636 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6637 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6638 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6639 // System.out.println( s0.toString() );
6641 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6644 if ( s0.match( query_nodes ) ) {
6647 query_nodes = new HashSet<PhylogenyNode>();
6648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6655 if ( !s0.match( query_nodes ) ) {
6659 query_nodes = new HashSet<PhylogenyNode>();
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6663 if ( !s0.match( query_nodes ) ) {
6667 query_nodes = new HashSet<PhylogenyNode>();
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6672 if ( !s0.match( query_nodes ) ) {
6676 query_nodes = new HashSet<PhylogenyNode>();
6677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6681 if ( !s0.match( query_nodes ) ) {
6685 query_nodes = new HashSet<PhylogenyNode>();
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6689 if ( !s0.match( query_nodes ) ) {
6693 query_nodes = new HashSet<PhylogenyNode>();
6694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6696 if ( !s0.match( query_nodes ) ) {
6700 query_nodes = new HashSet<PhylogenyNode>();
6701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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 if ( !s0.match( query_nodes ) ) {
6718 query_nodes = new HashSet<PhylogenyNode>();
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6723 if ( !s0.match( query_nodes ) ) {
6727 query_nodes = new HashSet<PhylogenyNode>();
6728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6730 if ( s0.match( query_nodes ) ) {
6734 query_nodes = new HashSet<PhylogenyNode>();
6735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6739 if ( s0.match( query_nodes ) ) {
6743 query_nodes = new HashSet<PhylogenyNode>();
6744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6745 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
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( "B" ) );
6756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6757 if ( s0.match( query_nodes ) ) {
6761 query_nodes = new HashSet<PhylogenyNode>();
6762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6764 if ( s0.match( query_nodes ) ) {
6768 query_nodes = new HashSet<PhylogenyNode>();
6769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6770 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6771 if ( s0.match( query_nodes ) ) {
6775 query_nodes = new HashSet<PhylogenyNode>();
6776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6777 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6778 if ( s0.match( query_nodes ) ) {
6782 query_nodes = new HashSet<PhylogenyNode>();
6783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6784 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6785 if ( s0.match( query_nodes ) ) {
6789 query_nodes = new HashSet<PhylogenyNode>();
6790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6791 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6792 if ( s0.match( query_nodes ) ) {
6796 query_nodes = new HashSet<PhylogenyNode>();
6797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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( "F" ) );
6806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6807 if ( s0.match( query_nodes ) ) {
6811 query_nodes = new HashSet<PhylogenyNode>();
6812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
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 if ( s0.match( query_nodes ) ) {
6827 query_nodes = new HashSet<PhylogenyNode>();
6828 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6829 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6832 if ( s0.match( query_nodes ) ) {
6836 // query_nodes = new HashSet<PhylogenyNode>();
6837 // query_nodes.add( new PhylogenyNode( "X" ) );
6838 // query_nodes.add( new PhylogenyNode( "Y" ) );
6839 // query_nodes.add( new PhylogenyNode( "A" ) );
6840 // query_nodes.add( new PhylogenyNode( "B" ) );
6841 // query_nodes.add( new PhylogenyNode( "C" ) );
6842 // query_nodes.add( new PhylogenyNode( "D" ) );
6843 // query_nodes.add( new PhylogenyNode( "E" ) );
6844 // query_nodes.add( new PhylogenyNode( "F" ) );
6845 // query_nodes.add( new PhylogenyNode( "G" ) );
6846 // if ( !s0.match( query_nodes ) ) {
6849 // query_nodes = new HashSet<PhylogenyNode>();
6850 // query_nodes.add( new PhylogenyNode( "X" ) );
6851 // query_nodes.add( new PhylogenyNode( "Y" ) );
6852 // query_nodes.add( new PhylogenyNode( "A" ) );
6853 // query_nodes.add( new PhylogenyNode( "B" ) );
6854 // query_nodes.add( new PhylogenyNode( "C" ) );
6855 // if ( !s0.match( query_nodes ) ) {
6859 // query_nodes = new HashSet<PhylogenyNode>();
6860 // query_nodes.add( new PhylogenyNode( "X" ) );
6861 // query_nodes.add( new PhylogenyNode( "Y" ) );
6862 // query_nodes.add( new PhylogenyNode( "D" ) );
6863 // query_nodes.add( new PhylogenyNode( "E" ) );
6864 // query_nodes.add( new PhylogenyNode( "F" ) );
6865 // query_nodes.add( new PhylogenyNode( "G" ) );
6866 // if ( !s0.match( query_nodes ) ) {
6870 // query_nodes = new HashSet<PhylogenyNode>();
6871 // query_nodes.add( new PhylogenyNode( "X" ) );
6872 // query_nodes.add( new PhylogenyNode( "Y" ) );
6873 // query_nodes.add( new PhylogenyNode( "A" ) );
6874 // query_nodes.add( new PhylogenyNode( "B" ) );
6875 // query_nodes.add( new PhylogenyNode( "C" ) );
6876 // query_nodes.add( new PhylogenyNode( "D" ) );
6877 // if ( !s0.match( query_nodes ) ) {
6881 // query_nodes = new HashSet<PhylogenyNode>();
6882 // query_nodes.add( new PhylogenyNode( "X" ) );
6883 // query_nodes.add( new PhylogenyNode( "Y" ) );
6884 // query_nodes.add( new PhylogenyNode( "E" ) );
6885 // query_nodes.add( new PhylogenyNode( "F" ) );
6886 // query_nodes.add( new PhylogenyNode( "G" ) );
6887 // if ( !s0.match( query_nodes ) ) {
6891 // query_nodes = new HashSet<PhylogenyNode>();
6892 // query_nodes.add( new PhylogenyNode( "X" ) );
6893 // query_nodes.add( new PhylogenyNode( "Y" ) );
6894 // query_nodes.add( new PhylogenyNode( "F" ) );
6895 // query_nodes.add( new PhylogenyNode( "G" ) );
6896 // if ( !s0.match( query_nodes ) ) {
6900 query_nodes = new HashSet<PhylogenyNode>();
6901 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6905 if ( s0.match( query_nodes ) ) {
6909 query_nodes = new HashSet<PhylogenyNode>();
6910 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6914 if ( s0.match( query_nodes ) ) {
6917 ///////////////////////////
6919 query_nodes = new HashSet<PhylogenyNode>();
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6924 if ( s0.match( query_nodes ) ) {
6928 query_nodes = new HashSet<PhylogenyNode>();
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6933 if ( s0.match( query_nodes ) ) {
6937 query_nodes = new HashSet<PhylogenyNode>();
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6942 if ( s0.match( query_nodes ) ) {
6946 query_nodes = new HashSet<PhylogenyNode>();
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6951 if ( s0.match( query_nodes ) ) {
6955 query_nodes = new HashSet<PhylogenyNode>();
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6960 if ( s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6968 if ( s0.match( query_nodes ) ) {
6972 query_nodes = new HashSet<PhylogenyNode>();
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6978 if ( s0.match( query_nodes ) ) {
6982 query_nodes = new HashSet<PhylogenyNode>();
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6988 if ( s0.match( query_nodes ) ) {
6992 query_nodes = new HashSet<PhylogenyNode>();
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6998 if ( s0.match( query_nodes ) ) {
7002 query_nodes = new HashSet<PhylogenyNode>();
7003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7009 if ( s0.match( query_nodes ) ) {
7013 catch ( final Exception e ) {
7014 e.printStackTrace();
7020 private static boolean testSplitStrict() {
7022 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7023 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7024 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7025 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7026 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7027 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7028 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7029 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7030 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7031 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7032 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7033 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7036 if ( s0.match( query_nodes ) ) {
7039 query_nodes = new HashSet<PhylogenyNode>();
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7047 if ( !s0.match( query_nodes ) ) {
7051 query_nodes = new HashSet<PhylogenyNode>();
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7055 if ( !s0.match( query_nodes ) ) {
7059 query_nodes = new HashSet<PhylogenyNode>();
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7064 if ( !s0.match( query_nodes ) ) {
7068 query_nodes = new HashSet<PhylogenyNode>();
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7073 if ( !s0.match( query_nodes ) ) {
7077 query_nodes = new HashSet<PhylogenyNode>();
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7081 if ( !s0.match( query_nodes ) ) {
7085 query_nodes = new HashSet<PhylogenyNode>();
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7088 if ( !s0.match( query_nodes ) ) {
7092 query_nodes = new HashSet<PhylogenyNode>();
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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 if ( !s0.match( query_nodes ) ) {
7110 query_nodes = new HashSet<PhylogenyNode>();
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7115 if ( !s0.match( query_nodes ) ) {
7119 query_nodes = new HashSet<PhylogenyNode>();
7120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7122 if ( s0.match( query_nodes ) ) {
7126 query_nodes = new HashSet<PhylogenyNode>();
7127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7131 if ( s0.match( query_nodes ) ) {
7135 query_nodes = new HashSet<PhylogenyNode>();
7136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7137 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
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( "B" ) );
7148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7149 if ( s0.match( query_nodes ) ) {
7153 query_nodes = new HashSet<PhylogenyNode>();
7154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7156 if ( s0.match( query_nodes ) ) {
7160 query_nodes = new HashSet<PhylogenyNode>();
7161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7162 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7163 if ( s0.match( query_nodes ) ) {
7167 query_nodes = new HashSet<PhylogenyNode>();
7168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7169 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7170 if ( s0.match( query_nodes ) ) {
7174 query_nodes = new HashSet<PhylogenyNode>();
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7177 if ( s0.match( query_nodes ) ) {
7181 query_nodes = new HashSet<PhylogenyNode>();
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7184 if ( s0.match( query_nodes ) ) {
7188 query_nodes = new HashSet<PhylogenyNode>();
7189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
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( "F" ) );
7198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7199 if ( s0.match( query_nodes ) ) {
7203 query_nodes = new HashSet<PhylogenyNode>();
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
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 if ( s0.match( query_nodes ) ) {
7219 query_nodes = new HashSet<PhylogenyNode>();
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7224 if ( s0.match( query_nodes ) ) {
7228 catch ( final Exception e ) {
7229 e.printStackTrace();
7235 private static boolean testSubtreeDeletion() {
7237 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7238 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7239 t1.deleteSubtree( t1.getNode( "A" ), false );
7240 if ( t1.getNumberOfExternalNodes() != 5 ) {
7243 t1.toNewHampshireX();
7244 t1.deleteSubtree( t1.getNode( "E" ), false );
7245 if ( t1.getNumberOfExternalNodes() != 4 ) {
7248 t1.toNewHampshireX();
7249 t1.deleteSubtree( t1.getNode( "F" ), false );
7250 if ( t1.getNumberOfExternalNodes() != 3 ) {
7253 t1.toNewHampshireX();
7254 t1.deleteSubtree( t1.getNode( "D" ), false );
7255 t1.toNewHampshireX();
7256 if ( t1.getNumberOfExternalNodes() != 3 ) {
7259 t1.deleteSubtree( t1.getNode( "def" ), false );
7260 t1.toNewHampshireX();
7261 if ( t1.getNumberOfExternalNodes() != 2 ) {
7264 t1.deleteSubtree( t1.getNode( "B" ), false );
7265 t1.toNewHampshireX();
7266 if ( t1.getNumberOfExternalNodes() != 1 ) {
7269 t1.deleteSubtree( t1.getNode( "C" ), false );
7270 t1.toNewHampshireX();
7271 if ( t1.getNumberOfExternalNodes() != 1 ) {
7274 t1.deleteSubtree( t1.getNode( "abc" ), false );
7275 t1.toNewHampshireX();
7276 if ( t1.getNumberOfExternalNodes() != 1 ) {
7279 t1.deleteSubtree( t1.getNode( "r" ), false );
7280 if ( t1.getNumberOfExternalNodes() != 0 ) {
7283 if ( !t1.isEmpty() ) {
7286 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7287 t2.deleteSubtree( t2.getNode( "A" ), false );
7288 t2.toNewHampshireX();
7289 if ( t2.getNumberOfExternalNodes() != 5 ) {
7292 t2.deleteSubtree( t2.getNode( "abc" ), false );
7293 t2.toNewHampshireX();
7294 if ( t2.getNumberOfExternalNodes() != 3 ) {
7297 t2.deleteSubtree( t2.getNode( "def" ), false );
7298 t2.toNewHampshireX();
7299 if ( t2.getNumberOfExternalNodes() != 1 ) {
7303 catch ( final Exception e ) {
7304 e.printStackTrace( System.out );
7310 private static boolean testSupportCount() {
7312 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7313 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7314 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7315 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7316 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7317 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7318 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7320 SupportCount.count( t0_1, phylogenies_1, true, false );
7321 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7322 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7323 + "(((((A,B),C),D),E),((F,G),X))"
7324 + "(((((A,Y),B),C),D),((F,G),E))"
7325 + "(((((A,B),C),D),E),(F,G))"
7326 + "(((((A,B),C),D),E),(F,G))"
7327 + "(((((A,B),C),D),E),(F,G))"
7328 + "(((((A,B),C),D),E),(F,G),Z)"
7329 + "(((((A,B),C),D),E),(F,G))"
7330 + "((((((A,B),C),D),E),F),G)"
7331 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7333 SupportCount.count( t0_2, phylogenies_2, true, false );
7334 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7335 while ( it.hasNext() ) {
7336 final PhylogenyNode n = it.next();
7337 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7341 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7342 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7343 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7344 SupportCount.count( t0_3, phylogenies_3, true, false );
7345 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7346 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7349 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7352 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7355 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7358 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7361 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7364 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7367 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7370 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7373 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7376 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7377 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7378 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7379 SupportCount.count( t0_4, phylogenies_4, true, false );
7380 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7381 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7384 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7387 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7390 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7393 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7396 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7399 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7402 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7405 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7408 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7411 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7412 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7413 double d = SupportCount.compare( b1, a, true, true, true );
7414 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7417 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7418 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7419 d = SupportCount.compare( b2, a, true, true, true );
7420 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7423 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7424 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7425 d = SupportCount.compare( b3, a, true, true, true );
7426 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7429 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7430 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7431 d = SupportCount.compare( b4, a, true, true, false );
7432 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7436 catch ( final Exception e ) {
7437 e.printStackTrace( System.out );
7443 private static boolean testSupportTransfer() {
7445 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7446 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)",
7447 new NHXParser() )[ 0 ];
7448 final Phylogeny p2 = factory
7449 .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 ];
7450 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7453 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7456 support_transfer.moveBranchLengthsToBootstrap( p1 );
7457 support_transfer.transferSupportValues( p1, p2 );
7458 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7461 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7464 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7467 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7470 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7473 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7476 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7479 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7483 catch ( final Exception e ) {
7484 e.printStackTrace( System.out );
7490 private static boolean testUniprotTaxonomySearch() {
7492 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7494 if ( results.size() != 1 ) {
7497 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7500 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7503 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7506 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7509 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7513 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7514 if ( results.size() != 1 ) {
7517 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7520 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7523 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7526 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7529 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7533 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7534 if ( results.size() != 1 ) {
7537 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7540 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7543 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7546 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7549 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7553 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7554 if ( results.size() != 1 ) {
7557 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7560 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7563 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7566 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7569 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7572 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7575 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7578 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7579 .equals( "Nematostella vectensis" ) ) {
7580 System.out.println( results.get( 0 ).getLineage() );
7584 catch ( final IOException e ) {
7585 System.out.println();
7586 System.out.println( "the following might be due to absence internet connection:" );
7587 e.printStackTrace( System.out );
7590 catch ( final Exception e ) {
7596 private static boolean testEmblEntryRetrieval() {
7597 //The format for GenBank Accession numbers are:
7598 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7599 //Protein: 3 letters + 5 numerals
7600 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7601 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7604 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7607 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7610 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7613 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7616 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7619 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7622 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7625 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7628 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7631 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7634 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7637 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7643 private static boolean testUniprotEntryRetrieval() {
7644 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7647 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7650 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7653 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7656 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7659 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7662 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7665 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7668 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7671 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7674 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7677 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7680 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7684 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7685 if ( !entry.getAccession().equals( "P12345" ) ) {
7688 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7691 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7694 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7697 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7701 catch ( final IOException e ) {
7702 System.out.println();
7703 System.out.println( "the following might be due to absence internet connection:" );
7704 e.printStackTrace( System.out );
7707 catch ( final Exception e ) {
7713 private static boolean testWabiTxSearch() {
7716 result = TxSearch.searchSimple( "nematostella" );
7717 result = TxSearch.getTxId( "nematostella" );
7718 if ( !result.equals( "45350" ) ) {
7721 result = TxSearch.getTxName( "45350" );
7722 if ( !result.equals( "Nematostella" ) ) {
7725 result = TxSearch.getTxId( "nematostella vectensis" );
7726 if ( !result.equals( "45351" ) ) {
7729 result = TxSearch.getTxName( "45351" );
7730 if ( !result.equals( "Nematostella vectensis" ) ) {
7733 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7734 if ( !result.equals( "536089" ) ) {
7737 result = TxSearch.getTxName( "536089" );
7738 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7741 final List<String> queries = new ArrayList<String>();
7742 queries.add( "Campylobacter coli" );
7743 queries.add( "Escherichia coli" );
7744 queries.add( "Arabidopsis" );
7745 queries.add( "Trichoplax" );
7746 queries.add( "Samanea saman" );
7747 queries.add( "Kluyveromyces marxianus" );
7748 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7749 queries.add( "Bornavirus parrot/PDD/2008" );
7750 final List<RANKS> ranks = new ArrayList<RANKS>();
7751 ranks.add( RANKS.SUPERKINGDOM );
7752 ranks.add( RANKS.KINGDOM );
7753 ranks.add( RANKS.FAMILY );
7754 ranks.add( RANKS.GENUS );
7755 ranks.add( RANKS.TRIBE );
7756 result = TxSearch.searchLineage( queries, ranks );
7757 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7758 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7760 catch ( final Exception e ) {
7761 System.out.println();
7762 System.out.println( "the following might be due to absence internet connection:" );
7763 e.printStackTrace( System.out );
7769 private static boolean testAminoAcidSequence() {
7771 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7772 if ( aa1.getLength() != 13 ) {
7775 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7778 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7781 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7784 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7785 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7788 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7789 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7792 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7793 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7797 catch ( final Exception e ) {
7798 e.printStackTrace();
7804 private static boolean testCreateBalancedPhylogeny() {
7806 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7807 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7810 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7813 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7814 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7817 if ( p1.getNumberOfExternalNodes() != 100 ) {
7821 catch ( final Exception e ) {
7822 e.printStackTrace();
7828 private static boolean testFastaParser() {
7830 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7833 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7836 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7837 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7840 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7843 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7846 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7849 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7852 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7856 catch ( final Exception e ) {
7857 e.printStackTrace();
7863 private static boolean testGeneralMsaParser() {
7865 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7866 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7867 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
7868 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7869 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7870 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7871 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7872 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7873 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7876 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7879 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7882 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7885 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7888 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7891 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7894 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7897 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7900 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7903 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7906 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7909 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7910 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7913 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7916 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7919 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7920 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7923 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7926 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7929 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7930 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7933 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7936 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7940 catch ( final Exception e ) {
7941 e.printStackTrace();
7947 private static boolean testMafft() {
7949 final List<String> opts = new ArrayList<String>();
7950 opts.add( "--maxiterate" );
7952 opts.add( "--localpair" );
7953 opts.add( "--quiet" );
7955 final MsaInferrer mafft = Mafft.createInstance();
7956 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
7957 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
7960 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
7964 catch ( final Exception e ) {
7965 e.printStackTrace( System.out );
7971 private static boolean testNextNodeWithCollapsing() {
7973 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7975 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
7976 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
7977 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
7978 t0.getNode( "cd" ).setCollapse( true );
7979 t0.getNode( "cde" ).setCollapse( true );
7980 n = t0.getFirstExternalNode();
7981 while ( n != null ) {
7983 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
7985 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
7988 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
7991 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
7994 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
7997 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8000 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8004 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8005 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8006 t1.getNode( "ab" ).setCollapse( true );
8007 t1.getNode( "cd" ).setCollapse( true );
8008 t1.getNode( "cde" ).setCollapse( true );
8009 n = t1.getNode( "ab" );
8010 ext = new ArrayList<PhylogenyNode>();
8011 while ( n != null ) {
8013 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8015 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8018 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8021 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8024 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8027 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8033 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8034 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8035 t2.getNode( "ab" ).setCollapse( true );
8036 t2.getNode( "cd" ).setCollapse( true );
8037 t2.getNode( "cde" ).setCollapse( true );
8038 t2.getNode( "c" ).setCollapse( true );
8039 t2.getNode( "d" ).setCollapse( true );
8040 t2.getNode( "e" ).setCollapse( true );
8041 t2.getNode( "gh" ).setCollapse( true );
8042 n = t2.getNode( "ab" );
8043 ext = new ArrayList<PhylogenyNode>();
8044 while ( n != null ) {
8046 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8048 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8051 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8054 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8057 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8063 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8064 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8065 t3.getNode( "ab" ).setCollapse( true );
8066 t3.getNode( "cd" ).setCollapse( true );
8067 t3.getNode( "cde" ).setCollapse( true );
8068 t3.getNode( "c" ).setCollapse( true );
8069 t3.getNode( "d" ).setCollapse( true );
8070 t3.getNode( "e" ).setCollapse( true );
8071 t3.getNode( "gh" ).setCollapse( true );
8072 t3.getNode( "fgh" ).setCollapse( true );
8073 n = t3.getNode( "ab" );
8074 ext = new ArrayList<PhylogenyNode>();
8075 while ( n != null ) {
8077 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8079 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8082 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8085 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8091 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8092 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8093 t4.getNode( "ab" ).setCollapse( true );
8094 t4.getNode( "cd" ).setCollapse( true );
8095 t4.getNode( "cde" ).setCollapse( true );
8096 t4.getNode( "c" ).setCollapse( true );
8097 t4.getNode( "d" ).setCollapse( true );
8098 t4.getNode( "e" ).setCollapse( true );
8099 t4.getNode( "gh" ).setCollapse( true );
8100 t4.getNode( "fgh" ).setCollapse( true );
8101 t4.getNode( "abcdefgh" ).setCollapse( true );
8102 n = t4.getNode( "abcdefgh" );
8103 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8108 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8109 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8111 n = t5.getFirstExternalNode();
8112 while ( n != null ) {
8114 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8116 if ( ext.size() != 8 ) {
8119 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8122 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8125 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8128 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8131 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8134 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8137 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8140 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8145 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8146 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8148 t6.getNode( "ab" ).setCollapse( true );
8149 n = t6.getNode( "ab" );
8150 while ( n != null ) {
8152 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8154 if ( ext.size() != 7 ) {
8157 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8160 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8163 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8166 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8169 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8172 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8175 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8180 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8181 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8183 t7.getNode( "cd" ).setCollapse( true );
8184 n = t7.getNode( "a" );
8185 while ( n != null ) {
8187 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8189 if ( ext.size() != 7 ) {
8192 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8195 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8198 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8201 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8204 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8207 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8210 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8215 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8216 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8218 t8.getNode( "cd" ).setCollapse( true );
8219 t8.getNode( "c" ).setCollapse( true );
8220 t8.getNode( "d" ).setCollapse( true );
8221 n = t8.getNode( "a" );
8222 while ( n != null ) {
8224 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8226 if ( ext.size() != 7 ) {
8229 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8232 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8235 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8236 System.out.println( "2 fail" );
8239 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8242 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8245 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8248 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8253 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8254 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8256 t9.getNode( "gh" ).setCollapse( true );
8257 n = t9.getNode( "a" );
8258 while ( n != null ) {
8260 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8262 if ( ext.size() != 7 ) {
8265 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8268 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8271 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8274 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8277 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8280 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8283 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8288 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8289 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8291 t10.getNode( "gh" ).setCollapse( true );
8292 t10.getNode( "g" ).setCollapse( true );
8293 t10.getNode( "h" ).setCollapse( true );
8294 n = t10.getNode( "a" );
8295 while ( n != null ) {
8297 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8299 if ( ext.size() != 7 ) {
8302 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8305 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8308 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8311 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8314 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8317 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8320 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8325 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8326 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8328 t11.getNode( "gh" ).setCollapse( true );
8329 t11.getNode( "fgh" ).setCollapse( true );
8330 n = t11.getNode( "a" );
8331 while ( n != null ) {
8333 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8335 if ( ext.size() != 6 ) {
8338 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8341 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8344 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8347 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8350 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8353 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8358 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8359 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8361 t12.getNode( "gh" ).setCollapse( true );
8362 t12.getNode( "fgh" ).setCollapse( true );
8363 t12.getNode( "g" ).setCollapse( true );
8364 t12.getNode( "h" ).setCollapse( true );
8365 t12.getNode( "f" ).setCollapse( true );
8366 n = t12.getNode( "a" );
8367 while ( n != null ) {
8369 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8371 if ( ext.size() != 6 ) {
8374 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8377 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8380 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8383 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8386 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8389 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8394 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8395 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8397 t13.getNode( "ab" ).setCollapse( true );
8398 t13.getNode( "b" ).setCollapse( true );
8399 t13.getNode( "fgh" ).setCollapse( true );
8400 t13.getNode( "gh" ).setCollapse( true );
8401 n = t13.getNode( "ab" );
8402 while ( n != null ) {
8404 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8406 if ( ext.size() != 5 ) {
8409 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8412 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8415 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8418 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8421 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8426 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8427 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8429 t14.getNode( "ab" ).setCollapse( true );
8430 t14.getNode( "a" ).setCollapse( true );
8431 t14.getNode( "fgh" ).setCollapse( true );
8432 t14.getNode( "gh" ).setCollapse( true );
8433 n = t14.getNode( "ab" );
8434 while ( n != null ) {
8436 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8438 if ( ext.size() != 5 ) {
8441 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8444 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8447 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8450 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8453 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8458 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" );
8459 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8461 t15.getNode( "ab" ).setCollapse( true );
8462 t15.getNode( "a" ).setCollapse( true );
8463 t15.getNode( "fgh" ).setCollapse( true );
8464 t15.getNode( "gh" ).setCollapse( true );
8465 n = t15.getNode( "ab" );
8466 while ( n != null ) {
8468 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8470 if ( ext.size() != 6 ) {
8473 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8476 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8479 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8482 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8485 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8488 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8493 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" );
8494 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8496 t16.getNode( "ab" ).setCollapse( true );
8497 t16.getNode( "a" ).setCollapse( true );
8498 t16.getNode( "fgh" ).setCollapse( true );
8499 t16.getNode( "gh" ).setCollapse( true );
8500 t16.getNode( "cd" ).setCollapse( true );
8501 t16.getNode( "cde" ).setCollapse( true );
8502 t16.getNode( "d" ).setCollapse( true );
8503 t16.getNode( "x" ).setCollapse( true );
8504 n = t16.getNode( "ab" );
8505 while ( n != null ) {
8507 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8509 if ( ext.size() != 4 ) {
8512 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8515 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8518 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8521 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8525 catch ( final Exception e ) {
8526 e.printStackTrace( System.out );
8532 private static boolean testMsaQualityMethod() {
8534 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8535 final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
8536 final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
8537 final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
8538 final List<Sequence> l = new ArrayList<Sequence>();
8543 final Msa msa = BasicMsa.createInstance( l );
8544 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8547 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8550 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8553 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8557 catch ( final Exception e ) {
8558 e.printStackTrace( System.out );
8564 private static boolean testSequenceIdParsing() {
8566 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8567 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8568 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8570 System.out.println( "value =" + id.getValue() );
8571 System.out.println( "provider=" + id.getProvider() );
8576 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8577 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8578 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8580 System.out.println( "value =" + id.getValue() );
8581 System.out.println( "provider=" + id.getProvider() );
8586 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8587 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8588 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8590 System.out.println( "value =" + id.getValue() );
8591 System.out.println( "provider=" + id.getProvider() );
8596 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8597 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8598 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8600 System.out.println( "value =" + id.getValue() );
8601 System.out.println( "provider=" + id.getProvider() );
8606 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8607 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8608 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8610 System.out.println( "value =" + id.getValue() );
8611 System.out.println( "provider=" + id.getProvider() );
8616 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8617 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8618 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8620 System.out.println( "value =" + id.getValue() );
8621 System.out.println( "provider=" + id.getProvider() );
8626 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8627 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8628 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8630 System.out.println( "value =" + id.getValue() );
8631 System.out.println( "provider=" + id.getProvider() );
8636 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8637 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8638 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8640 System.out.println( "value =" + id.getValue() );
8641 System.out.println( "provider=" + id.getProvider() );
8646 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8647 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8648 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8650 System.out.println( "value =" + id.getValue() );
8651 System.out.println( "provider=" + id.getProvider() );
8656 id = SequenceIdParser.parse( "XP_12345" );
8660 // lcl_91970_unknown_
8662 catch ( final Exception e ) {
8663 e.printStackTrace( System.out );