2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.Mafft;
58 import org.forester.msa.Msa;
59 import org.forester.msa.MsaInferrer;
60 import org.forester.pccx.TestPccx;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyBranch;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.data.BinaryCharacters;
66 import org.forester.phylogeny.data.BranchWidth;
67 import org.forester.phylogeny.data.Confidence;
68 import org.forester.phylogeny.data.Distribution;
69 import org.forester.phylogeny.data.DomainArchitecture;
70 import org.forester.phylogeny.data.Event;
71 import org.forester.phylogeny.data.Identifier;
72 import org.forester.phylogeny.data.PhylogenyData;
73 import org.forester.phylogeny.data.Polygon;
74 import org.forester.phylogeny.data.PropertiesMap;
75 import org.forester.phylogeny.data.Property;
76 import org.forester.phylogeny.data.Property.AppliesTo;
77 import org.forester.phylogeny.data.ProteinDomain;
78 import org.forester.phylogeny.data.Taxonomy;
79 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
80 import org.forester.phylogeny.factories.PhylogenyFactory;
81 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
82 import org.forester.sdi.SDI;
83 import org.forester.sdi.SDIR;
84 import org.forester.sdi.SDIse;
85 import org.forester.sdi.TaxonomyAssigner;
86 import org.forester.sdi.TestGSDI;
87 import org.forester.sequence.BasicSequence;
88 import org.forester.sequence.Sequence;
89 import org.forester.surfacing.Protein;
90 import org.forester.surfacing.TestSurfacing;
91 import org.forester.tools.ConfidenceAssessor;
92 import org.forester.tools.SupportCount;
93 import org.forester.tools.TreeSplitMatrix;
94 import org.forester.util.AsciiHistogram;
95 import org.forester.util.BasicDescriptiveStatistics;
96 import org.forester.util.BasicTable;
97 import org.forester.util.BasicTableParser;
98 import org.forester.util.DescriptiveStatistics;
99 import org.forester.util.ForesterConstants;
100 import org.forester.util.ForesterUtil;
101 import org.forester.util.GeneralTable;
102 import org.forester.ws.uniprot.DatabaseTools;
103 import org.forester.ws.uniprot.SequenceDatabaseEntry;
104 import org.forester.ws.uniprot.UniProtTaxonomy;
105 import org.forester.ws.uniprot.UniProtWsTools;
106 import org.forester.ws.wabi.TxSearch;
107 import org.forester.ws.wabi.TxSearch.RANKS;
108 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
109 import org.forester.ws.wabi.TxSearch.TAX_RANK;
111 @SuppressWarnings( "unused")
112 public final class Test {
114 private final static double ZERO_DIFF = 1.0E-9;
115 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
116 + ForesterUtil.getFileSeparator() + "test_data"
117 + ForesterUtil.getFileSeparator();
118 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
119 + ForesterUtil.getFileSeparator() + "resources"
120 + ForesterUtil.getFileSeparator();
121 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
122 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
123 + ForesterConstants.PHYLO_XML_VERSION + "/"
124 + ForesterConstants.PHYLO_XML_XSD;
125 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
126 + ForesterConstants.PHYLO_XML_VERSION + "/"
127 + ForesterConstants.PHYLO_XML_XSD;
129 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
130 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
134 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
135 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
136 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
139 public static boolean isEqual( final double a, final double b ) {
140 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
143 public static void main( final String[] args ) {
144 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
145 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
147 Locale.setDefault( Locale.US );
148 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
151 System.out.print( "[Test if directory with files for testing exists/is readable: " );
152 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
153 System.out.println( "OK.]" );
156 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
157 System.out.println( "Testing aborted." );
160 System.out.print( "[Test if resources directory exists/is readable: " );
161 if ( testDir( PATH_TO_RESOURCES ) ) {
162 System.out.println( "OK.]" );
165 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
166 System.out.println( "Testing aborted." );
169 final long start_time = new Date().getTime();
170 System.out.print( "Hmmscan output parser: " );
171 if ( testHmmscanOutputParser() ) {
172 System.out.println( "OK." );
176 System.out.println( "failed." );
179 System.out.print( "Basic node methods: " );
180 if ( Test.testBasicNodeMethods() ) {
181 System.out.println( "OK." );
185 System.out.println( "failed." );
188 System.out.print( "Basic node construction and parsing of NHX (node level): " );
189 if ( Test.testNHXNodeParsing() ) {
190 System.out.println( "OK." );
194 System.out.println( "failed." );
197 System.out.print( "NH parsing: " );
198 if ( Test.testNHParsing() ) {
199 System.out.println( "OK." );
203 System.out.println( "failed." );
206 System.out.print( "Conversion to NHX (node level): " );
207 if ( Test.testNHXconversion() ) {
208 System.out.println( "OK." );
212 System.out.println( "failed." );
215 System.out.print( "NHX parsing: " );
216 if ( Test.testNHXParsing() ) {
217 System.out.println( "OK." );
221 System.out.println( "failed." );
224 System.out.print( "NHX parsing with quotes: " );
225 if ( Test.testNHXParsingQuotes() ) {
226 System.out.println( "OK." );
230 System.out.println( "failed." );
233 System.out.print( "Nexus characters parsing: " );
234 if ( Test.testNexusCharactersParsing() ) {
235 System.out.println( "OK." );
239 System.out.println( "failed." );
242 System.out.print( "Nexus tree parsing: " );
243 if ( Test.testNexusTreeParsing() ) {
244 System.out.println( "OK." );
248 System.out.println( "failed." );
251 System.out.print( "Nexus tree parsing (translating): " );
252 if ( Test.testNexusTreeParsingTranslating() ) {
253 System.out.println( "OK." );
257 System.out.println( "failed." );
260 System.out.print( "Nexus matrix parsing: " );
261 if ( Test.testNexusMatrixParsing() ) {
262 System.out.println( "OK." );
266 System.out.println( "failed." );
269 System.out.print( "Basic phyloXML parsing: " );
270 if ( Test.testBasicPhyloXMLparsing() ) {
271 System.out.println( "OK." );
275 System.out.println( "failed." );
278 System.out.print( "Basic phyloXML parsing (validating against schema): " );
279 if ( testBasicPhyloXMLparsingValidating() ) {
280 System.out.println( "OK." );
284 System.out.println( "failed." );
287 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
288 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
289 System.out.println( "OK." );
293 System.out.println( "failed." );
296 System.out.print( "phyloXML Distribution Element: " );
297 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
298 System.out.println( "OK." );
302 System.out.println( "failed." );
305 System.out.print( "Tol XML parsing: " );
306 if ( Test.testBasicTolXMLparsing() ) {
307 System.out.println( "OK." );
311 System.out.println( "failed." );
314 System.out.print( "Copying of node data: " );
315 if ( Test.testCopyOfNodeData() ) {
316 System.out.println( "OK." );
320 System.out.println( "failed." );
323 System.out.print( "Basic tree methods: " );
324 if ( Test.testBasicTreeMethods() ) {
325 System.out.println( "OK." );
329 System.out.println( "failed." );
332 System.out.print( "Postorder Iterator: " );
333 if ( Test.testPostOrderIterator() ) {
334 System.out.println( "OK." );
338 System.out.println( "failed." );
341 System.out.print( "Preorder Iterator: " );
342 if ( Test.testPreOrderIterator() ) {
343 System.out.println( "OK." );
347 System.out.println( "failed." );
350 System.out.print( "Levelorder Iterator: " );
351 if ( Test.testLevelOrderIterator() ) {
352 System.out.println( "OK." );
356 System.out.println( "failed." );
359 System.out.print( "Re-id methods: " );
360 if ( Test.testReIdMethods() ) {
361 System.out.println( "OK." );
365 System.out.println( "failed." );
368 System.out.print( "Methods on last external nodes: " );
369 if ( Test.testLastExternalNodeMethods() ) {
370 System.out.println( "OK." );
374 System.out.println( "failed." );
377 System.out.print( "Methods on external nodes: " );
378 if ( Test.testExternalNodeRelatedMethods() ) {
379 System.out.println( "OK." );
383 System.out.println( "failed." );
386 System.out.print( "Deletion of external nodes: " );
387 if ( Test.testDeletionOfExternalNodes() ) {
388 System.out.println( "OK." );
392 System.out.println( "failed." );
395 System.out.print( "Subtree deletion: " );
396 if ( Test.testSubtreeDeletion() ) {
397 System.out.println( "OK." );
401 System.out.println( "failed." );
404 System.out.print( "Phylogeny branch: " );
405 if ( Test.testPhylogenyBranch() ) {
406 System.out.println( "OK." );
410 System.out.println( "failed." );
413 System.out.print( "Rerooting: " );
414 if ( Test.testRerooting() ) {
415 System.out.println( "OK." );
419 System.out.println( "failed." );
422 System.out.print( "Mipoint rooting: " );
423 if ( Test.testMidpointrooting() ) {
424 System.out.println( "OK." );
428 System.out.println( "failed." );
431 System.out.print( "Support count: " );
432 if ( Test.testSupportCount() ) {
433 System.out.println( "OK." );
437 System.out.println( "failed." );
440 System.out.print( "Support transfer: " );
441 if ( Test.testSupportTransfer() ) {
442 System.out.println( "OK." );
446 System.out.println( "failed." );
449 System.out.print( "Finding of LCA: " );
450 if ( Test.testGetLCA() ) {
451 System.out.println( "OK." );
455 System.out.println( "failed." );
458 System.out.print( "Calculation of distance between nodes: " );
459 if ( Test.testGetDistance() ) {
460 System.out.println( "OK." );
464 System.out.println( "failed." );
467 System.out.print( "SDIse: " );
468 if ( Test.testSDIse() ) {
469 System.out.println( "OK." );
473 System.out.println( "failed." );
476 System.out.print( "Taxonomy assigner: " );
477 if ( Test.testTaxonomyAssigner() ) {
478 System.out.println( "OK." );
482 System.out.println( "failed." );
485 System.out.print( "SDIunrooted: " );
486 if ( Test.testSDIunrooted() ) {
487 System.out.println( "OK." );
491 System.out.println( "failed." );
494 System.out.print( "GSDI: " );
495 if ( TestGSDI.test() ) {
496 System.out.println( "OK." );
500 System.out.println( "failed." );
503 System.out.print( "Descriptive statistics: " );
504 if ( Test.testDescriptiveStatistics() ) {
505 System.out.println( "OK." );
509 System.out.println( "failed." );
512 System.out.print( "Data objects and methods: " );
513 if ( Test.testDataObjects() ) {
514 System.out.println( "OK." );
518 System.out.println( "failed." );
521 System.out.print( "Properties map: " );
522 if ( Test.testPropertiesMap() ) {
523 System.out.println( "OK." );
527 System.out.println( "failed." );
530 System.out.print( "Phylogeny reconstruction:" );
531 System.out.println();
532 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
533 System.out.println( "OK." );
537 System.out.println( "failed." );
540 System.out.print( "Analysis of domain architectures: " );
541 System.out.println();
542 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
543 System.out.println( "OK." );
547 System.out.println( "failed." );
550 System.out.print( "GO: " );
551 System.out.println();
552 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
553 System.out.println( "OK." );
557 System.out.println( "failed." );
560 System.out.print( "Modeling tools: " );
561 if ( TestPccx.test() ) {
562 System.out.println( "OK." );
566 System.out.println( "failed." );
569 System.out.print( "Split Matrix strict: " );
570 if ( Test.testSplitStrict() ) {
571 System.out.println( "OK." );
575 System.out.println( "failed." );
578 System.out.print( "Split Matrix: " );
579 if ( Test.testSplit() ) {
580 System.out.println( "OK." );
584 System.out.println( "failed." );
587 System.out.print( "Confidence Assessor: " );
588 if ( Test.testConfidenceAssessor() ) {
589 System.out.println( "OK." );
593 System.out.println( "failed." );
596 System.out.print( "Basic table: " );
597 if ( Test.testBasicTable() ) {
598 System.out.println( "OK." );
602 System.out.println( "failed." );
605 System.out.print( "General table: " );
606 if ( Test.testGeneralTable() ) {
607 System.out.println( "OK." );
611 System.out.println( "failed." );
614 System.out.print( "Amino acid sequence: " );
615 if ( Test.testAminoAcidSequence() ) {
616 System.out.println( "OK." );
620 System.out.println( "failed." );
623 System.out.print( "General MSA parser: " );
624 if ( Test.testGeneralMsaParser() ) {
625 System.out.println( "OK." );
629 System.out.println( "failed." );
632 System.out.print( "Fasta parser for msa: " );
633 if ( Test.testFastaParser() ) {
634 System.out.println( "OK." );
638 System.out.println( "failed." );
641 System.out.print( "Creation of balanced phylogeny: " );
642 if ( Test.testCreateBalancedPhylogeny() ) {
643 System.out.println( "OK." );
647 System.out.println( "failed." );
650 System.out.print( "EMBL Entry Retrieval: " );
651 if ( Test.testEmblEntryRetrieval() ) {
652 System.out.println( "OK." );
656 System.out.println( "failed." );
659 System.out.print( "Uniprot Entry Retrieval: " );
660 if ( Test.testUniprotEntryRetrieval() ) {
661 System.out.println( "OK." );
665 System.out.println( "failed." );
668 System.out.print( "Uniprot Taxonomy Search: " );
669 if ( Test.testUniprotTaxonomySearch() ) {
670 System.out.println( "OK." );
674 System.out.println( "failed." );
677 if ( Mafft.isInstalled() ) {
678 System.out.print( "MAFFT (external program): " );
679 if ( Test.testMafft() ) {
680 System.out.println( "OK." );
684 System.out.println( "failed [will not count towards failed tests]" );
687 // System.out.print( "WABI TxSearch: " );
688 // if ( Test.testWabiTxSearch() ) {
689 // System.out.println( "OK." );
694 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
696 System.out.println();
697 final Runtime rt = java.lang.Runtime.getRuntime();
698 final long free_memory = rt.freeMemory() / 1000000;
699 final long total_memory = rt.totalMemory() / 1000000;
700 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
701 + free_memory + "MB, total memory: " + total_memory + "MB)" );
702 System.out.println();
703 System.out.println( "Successful tests: " + succeeded );
704 System.out.println( "Failed tests: " + failed );
705 System.out.println();
707 System.out.println( "OK." );
710 System.out.println( "Not OK." );
712 // System.out.println();
713 // Development.setTime( true );
715 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
716 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
717 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
718 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
719 // "multifurcations_ex_1.nhx";
720 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
721 // final Phylogeny t1 = factory.create( new File( domains ), new
722 // NHXParser() )[ 0 ];
723 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
725 // catch ( final Exception e ) {
726 // e.printStackTrace();
728 // t1.getRoot().preorderPrint();
729 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
733 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
734 // + "\\AtNBSpos.nhx" ) );
736 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
737 // new NHXParser() );
738 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
739 // + "\\AtNBSpos.nhx" ) );
741 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
742 // new NHXParser() );
745 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
746 // + "\\big_tree.nhx" ) );
747 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
748 // + "\\big_tree.nhx" ) );
750 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
751 // new NHXParser() );
753 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
754 // new NHXParser() );
756 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
757 // + "\\big_tree.nhx" ) );
758 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
759 // + "\\big_tree.nhx" ) );
762 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
763 // new NHXParser() );
765 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
766 // new NHXParser() );
768 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
769 // + "\\AtNBSpos.nhx" ) );
771 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
772 // new NHXParser() );
775 // catch ( IOException e ) {
776 // // TODO Auto-generated catch block
777 // e.printStackTrace();
781 private static boolean testBasicNodeMethods() {
783 if ( PhylogenyNode.getNodeCount() != 0 ) {
786 final PhylogenyNode n1 = new PhylogenyNode();
787 final PhylogenyNode n2 = new PhylogenyNode( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
788 final PhylogenyNode n3 = new PhylogenyNode( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
789 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
790 if ( n1.isHasAssignedEvent() ) {
793 if ( PhylogenyNode.getNodeCount() != 4 ) {
796 if ( n3.getIndicator() != 0 ) {
799 if ( n3.getNumberOfExternalNodes() != 1 ) {
802 if ( !n3.isExternal() ) {
805 if ( !n3.isRoot() ) {
808 if ( !n4.getName().equals( "n4" ) ) {
812 catch ( final Exception e ) {
813 e.printStackTrace( System.out );
819 private static boolean testBasicPhyloXMLparsing() {
821 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
822 final PhyloXmlParser xml_parser = new PhyloXmlParser();
823 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
825 if ( xml_parser.getErrorCount() > 0 ) {
826 System.out.println( xml_parser.getErrorMessages().toString() );
829 if ( phylogenies_0.length != 4 ) {
832 final Phylogeny t1 = phylogenies_0[ 0 ];
833 final Phylogeny t2 = phylogenies_0[ 1 ];
834 final Phylogeny t3 = phylogenies_0[ 2 ];
835 final Phylogeny t4 = phylogenies_0[ 3 ];
836 if ( t1.getNumberOfExternalNodes() != 1 ) {
839 if ( !t1.isRooted() ) {
842 if ( t1.isRerootable() ) {
845 if ( !t1.getType().equals( "gene_tree" ) ) {
848 if ( t2.getNumberOfExternalNodes() != 2 ) {
851 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
854 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
857 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
860 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
863 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
866 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
869 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
870 .startsWith( "actgtgggggt" ) ) {
873 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
874 .startsWith( "ctgtgatgcat" ) ) {
877 if ( t3.getNumberOfExternalNodes() != 4 ) {
880 if ( !t1.getName().equals( "t1" ) ) {
883 if ( !t2.getName().equals( "t2" ) ) {
886 if ( !t3.getName().equals( "t3" ) ) {
889 if ( !t4.getName().equals( "t4" ) ) {
892 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
895 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
898 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
901 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
902 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
905 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
908 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
911 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
914 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
915 .equals( "apoptosis" ) ) {
918 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
919 .equals( "GO:0006915" ) ) {
922 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
923 .equals( "UniProtKB" ) ) {
926 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
927 .equals( "experimental" ) ) {
930 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
931 .equals( "function" ) ) {
934 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
938 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
939 .getType().equals( "ml" ) ) {
942 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
943 .equals( "apoptosis" ) ) {
946 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
947 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
950 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
951 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
954 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
955 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
958 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
959 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
962 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
963 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
966 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
967 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
970 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
971 .equals( "GO:0005829" ) ) {
974 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
975 .equals( "intracellular organelle" ) ) {
978 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
981 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
982 .equals( "UniProt link" ) ) ) {
985 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
988 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
991 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
994 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
997 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1000 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1003 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1006 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1009 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1012 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1015 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1016 // .equals( "B" ) ) {
1019 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1022 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1025 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1028 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1029 // .getConfidence() != 2144 ) {
1032 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1033 // .equals( "pfam" ) ) {
1036 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1039 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1042 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1045 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1048 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1049 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1053 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1056 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1059 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1062 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1065 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1068 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1071 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1074 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1076 // if ( xml_parser.getErrorCount() > 0 ) {
1077 // System.out.println( xml_parser.getErrorMessages().toString() );
1080 // if ( phylogenies_1.length != 2 ) {
1083 // final Phylogeny a = phylogenies_1[ 0 ];
1084 // if ( !a.getName().equals( "tree 4" ) ) {
1087 // if ( a.getNumberOfExternalNodes() != 3 ) {
1090 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1093 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1097 catch ( final Exception e ) {
1098 e.printStackTrace( System.out );
1104 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1106 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1107 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1108 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1109 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1112 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1114 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1116 if ( xml_parser.getErrorCount() > 0 ) {
1117 System.out.println( xml_parser.getErrorMessages().toString() );
1120 if ( phylogenies_0.length != 4 ) {
1123 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1124 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1125 if ( phylogenies_t1.length != 1 ) {
1128 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1129 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1132 if ( !t1_rt.isRooted() ) {
1135 if ( t1_rt.isRerootable() ) {
1138 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1141 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1142 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1143 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1144 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1147 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1150 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1153 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1156 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1157 .startsWith( "actgtgggggt" ) ) {
1160 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1161 .startsWith( "ctgtgatgcat" ) ) {
1164 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1165 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1166 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1167 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1168 if ( phylogenies_1.length != 1 ) {
1171 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1172 if ( !t3_rt.getName().equals( "t3" ) ) {
1175 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1178 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1181 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1184 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1187 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1188 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1191 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1194 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1197 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1198 .equals( "UniProtKB" ) ) {
1201 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1202 .equals( "apoptosis" ) ) {
1205 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1206 .equals( "GO:0006915" ) ) {
1209 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1210 .equals( "UniProtKB" ) ) {
1213 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1214 .equals( "experimental" ) ) {
1217 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1218 .equals( "function" ) ) {
1221 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1222 .getValue() != 1 ) {
1225 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1226 .getType().equals( "ml" ) ) {
1229 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1230 .equals( "apoptosis" ) ) {
1233 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1234 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1237 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1238 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1241 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1242 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1246 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1249 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1250 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1253 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1254 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1257 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1258 .equals( "GO:0005829" ) ) {
1261 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1262 .equals( "intracellular organelle" ) ) {
1265 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1269 .equals( "UniProt link" ) ) ) {
1272 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1275 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1278 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1279 .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." ) ) ) {
1282 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1285 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1288 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1291 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1294 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1295 .equals( "ncbi" ) ) {
1298 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1301 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1302 .getName().equals( "B" ) ) {
1305 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1306 .getFrom() != 21 ) {
1309 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1312 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1313 .getLength() != 24 ) {
1316 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1317 .getConfidence() != 2144 ) {
1320 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1321 .equals( "pfam" ) ) {
1324 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1327 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1330 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1333 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1336 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1337 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1340 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1343 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1346 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1349 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1352 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1355 if ( taxbb.getSynonyms().size() != 2 ) {
1358 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1361 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1364 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1367 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1370 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1373 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1374 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1378 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1381 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1384 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1387 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1390 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1393 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1396 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1400 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1403 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1404 .equalsIgnoreCase( "435" ) ) {
1407 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1410 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1411 .equalsIgnoreCase( "443.7" ) ) {
1414 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1417 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1420 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1421 .equalsIgnoreCase( "433" ) ) {
1425 catch ( final Exception e ) {
1426 e.printStackTrace( System.out );
1432 private static boolean testBasicPhyloXMLparsingValidating() {
1434 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1435 PhyloXmlParser xml_parser = null;
1437 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1439 catch ( final Exception e ) {
1440 // Do nothing -- means were not running from jar.
1442 if ( xml_parser == null ) {
1443 xml_parser = new PhyloXmlParser();
1444 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1445 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1448 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1451 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1453 if ( xml_parser.getErrorCount() > 0 ) {
1454 System.out.println( xml_parser.getErrorMessages().toString() );
1457 if ( phylogenies_0.length != 4 ) {
1460 final Phylogeny t1 = phylogenies_0[ 0 ];
1461 final Phylogeny t2 = phylogenies_0[ 1 ];
1462 final Phylogeny t3 = phylogenies_0[ 2 ];
1463 final Phylogeny t4 = phylogenies_0[ 3 ];
1464 if ( !t1.getName().equals( "t1" ) ) {
1467 if ( !t2.getName().equals( "t2" ) ) {
1470 if ( !t3.getName().equals( "t3" ) ) {
1473 if ( !t4.getName().equals( "t4" ) ) {
1476 if ( t1.getNumberOfExternalNodes() != 1 ) {
1479 if ( t2.getNumberOfExternalNodes() != 2 ) {
1482 if ( t3.getNumberOfExternalNodes() != 4 ) {
1485 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1486 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1487 if ( xml_parser.getErrorCount() > 0 ) {
1488 System.out.println( "errors:" );
1489 System.out.println( xml_parser.getErrorMessages().toString() );
1492 if ( phylogenies_1.length != 4 ) {
1495 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1497 if ( xml_parser.getErrorCount() > 0 ) {
1498 System.out.println( "errors:" );
1499 System.out.println( xml_parser.getErrorMessages().toString() );
1502 if ( phylogenies_2.length != 1 ) {
1505 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1508 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1510 if ( xml_parser.getErrorCount() > 0 ) {
1511 System.out.println( xml_parser.getErrorMessages().toString() );
1514 if ( phylogenies_3.length != 2 ) {
1517 final Phylogeny a = phylogenies_3[ 0 ];
1518 if ( !a.getName().equals( "tree 4" ) ) {
1521 if ( a.getNumberOfExternalNodes() != 3 ) {
1524 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1527 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1530 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1532 if ( xml_parser.getErrorCount() > 0 ) {
1533 System.out.println( xml_parser.getErrorMessages().toString() );
1536 if ( phylogenies_4.length != 1 ) {
1539 final Phylogeny s = phylogenies_4[ 0 ];
1540 if ( s.getNumberOfExternalNodes() != 6 ) {
1543 s.getNode( "first" );
1545 s.getNode( "\"<a'b&c'd\">\"" );
1546 s.getNode( "'''\"" );
1547 s.getNode( "\"\"\"" );
1548 s.getNode( "dick & doof" );
1550 catch ( final Exception e ) {
1551 e.printStackTrace( System.out );
1557 private static boolean testBasicTable() {
1559 final BasicTable<String> t0 = new BasicTable<String>();
1560 if ( t0.getNumberOfColumns() != 0 ) {
1563 if ( t0.getNumberOfRows() != 0 ) {
1566 t0.setValue( 3, 2, "23" );
1567 t0.setValue( 10, 1, "error" );
1568 t0.setValue( 10, 1, "110" );
1569 t0.setValue( 9, 1, "19" );
1570 t0.setValue( 1, 10, "101" );
1571 t0.setValue( 10, 10, "1010" );
1572 t0.setValue( 100, 10, "10100" );
1573 t0.setValue( 0, 0, "00" );
1574 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1577 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1580 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1583 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1586 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1589 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1592 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1595 if ( t0.getNumberOfColumns() != 101 ) {
1598 if ( t0.getNumberOfRows() != 11 ) {
1601 if ( t0.getValueAsString( 49, 4 ) != null ) {
1604 final String l = ForesterUtil.getLineSeparator();
1605 final StringBuffer source = new StringBuffer();
1606 source.append( "" + l );
1607 source.append( "# 1 1 1 1 1 1 1 1" + l );
1608 source.append( " 00 01 02 03" + l );
1609 source.append( " 10 11 12 13 " + l );
1610 source.append( "20 21 22 23 " + l );
1611 source.append( " 30 31 32 33" + l );
1612 source.append( "40 41 42 43" + l );
1613 source.append( " # 1 1 1 1 1 " + l );
1614 source.append( "50 51 52 53 54" + l );
1615 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1616 if ( t1.getNumberOfColumns() != 5 ) {
1619 if ( t1.getNumberOfRows() != 6 ) {
1622 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1625 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1628 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1631 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1634 final StringBuffer source1 = new StringBuffer();
1635 source1.append( "" + l );
1636 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1637 source1.append( " 00; 01 ;02;03" + l );
1638 source1.append( " 10; 11; 12; 13 " + l );
1639 source1.append( "20; 21; 22; 23 " + l );
1640 source1.append( " 30; 31; 32; 33" + l );
1641 source1.append( "40;41;42;43" + l );
1642 source1.append( " # 1 1 1 1 1 " + l );
1643 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1644 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1645 if ( t2.getNumberOfColumns() != 5 ) {
1648 if ( t2.getNumberOfRows() != 6 ) {
1651 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1654 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1657 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1660 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1663 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1666 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1669 final StringBuffer source2 = new StringBuffer();
1670 source2.append( "" + l );
1671 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1672 source2.append( " 00; 01 ;02;03" + l );
1673 source2.append( " 10; 11; 12; 13 " + l );
1674 source2.append( "20; 21; 22; 23 " + l );
1675 source2.append( " " + l );
1676 source2.append( " 30; 31; 32; 33" + l );
1677 source2.append( "40;41;42;43" + l );
1678 source2.append( " comment: 1 1 1 1 1 " + l );
1679 source2.append( ";;;50 ; 52; 53;;54 " + l );
1680 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1685 if ( tl.size() != 2 ) {
1688 final BasicTable<String> t3 = tl.get( 0 );
1689 final BasicTable<String> t4 = tl.get( 1 );
1690 if ( t3.getNumberOfColumns() != 4 ) {
1693 if ( t3.getNumberOfRows() != 3 ) {
1696 if ( t4.getNumberOfColumns() != 4 ) {
1699 if ( t4.getNumberOfRows() != 3 ) {
1702 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1705 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1709 catch ( final Exception e ) {
1710 e.printStackTrace( System.out );
1716 private static boolean testBasicTolXMLparsing() {
1718 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1719 final TolParser parser = new TolParser();
1720 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1721 if ( parser.getErrorCount() > 0 ) {
1722 System.out.println( parser.getErrorMessages().toString() );
1725 if ( phylogenies_0.length != 1 ) {
1728 final Phylogeny t1 = phylogenies_0[ 0 ];
1729 if ( t1.getNumberOfExternalNodes() != 5 ) {
1732 if ( !t1.isRooted() ) {
1735 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1738 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1741 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1744 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1747 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1748 if ( parser.getErrorCount() > 0 ) {
1749 System.out.println( parser.getErrorMessages().toString() );
1752 if ( phylogenies_1.length != 1 ) {
1755 final Phylogeny t2 = phylogenies_1[ 0 ];
1756 if ( t2.getNumberOfExternalNodes() != 664 ) {
1759 if ( !t2.isRooted() ) {
1762 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1765 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1768 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1771 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1774 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1777 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1778 .equals( "Aquifex" ) ) {
1781 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1782 if ( parser.getErrorCount() > 0 ) {
1783 System.out.println( parser.getErrorMessages().toString() );
1786 if ( phylogenies_2.length != 1 ) {
1789 final Phylogeny t3 = phylogenies_2[ 0 ];
1790 if ( t3.getNumberOfExternalNodes() != 184 ) {
1793 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1796 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1799 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1802 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1803 if ( parser.getErrorCount() > 0 ) {
1804 System.out.println( parser.getErrorMessages().toString() );
1807 if ( phylogenies_3.length != 1 ) {
1810 final Phylogeny t4 = phylogenies_3[ 0 ];
1811 if ( t4.getNumberOfExternalNodes() != 1 ) {
1814 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1817 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1820 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1823 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1824 if ( parser.getErrorCount() > 0 ) {
1825 System.out.println( parser.getErrorMessages().toString() );
1828 if ( phylogenies_4.length != 1 ) {
1831 final Phylogeny t5 = phylogenies_4[ 0 ];
1832 if ( t5.getNumberOfExternalNodes() != 13 ) {
1835 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1838 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1841 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1845 catch ( final Exception e ) {
1846 e.printStackTrace( System.out );
1852 private static boolean testBasicTreeMethods() {
1854 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1855 final Phylogeny t1 = factory.create();
1856 if ( !t1.isEmpty() ) {
1859 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1860 if ( t2.getNumberOfExternalNodes() != 4 ) {
1863 if ( t2.getHeight() != 8.5 ) {
1866 if ( !t2.isCompletelyBinary() ) {
1869 if ( t2.isEmpty() ) {
1872 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1873 if ( t3.getNumberOfExternalNodes() != 5 ) {
1876 if ( t3.getHeight() != 11 ) {
1879 if ( t3.isCompletelyBinary() ) {
1882 final PhylogenyNode n = t3.getNode( "ABC" );
1883 PhylogenyNodeIterator it;
1884 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1887 for( it.reset(); it.hasNext(); ) {
1890 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1891 if ( !it2.next().getName().equals( "A" ) ) {
1894 if ( !it2.next().getName().equals( "B" ) ) {
1897 if ( !it2.next().getName().equals( "C" ) ) {
1900 if ( it2.hasNext() ) {
1903 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 ];
1904 if ( t4.getNumberOfExternalNodes() != 9 ) {
1907 if ( t4.getHeight() != 11 ) {
1910 if ( t4.isCompletelyBinary() ) {
1913 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)" );
1914 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1915 if ( t5.getNumberOfExternalNodes() != 8 ) {
1918 if ( t5.getHeight() != 15 ) {
1921 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)" );
1922 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1923 if ( t6.getHeight() != 15 ) {
1926 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)" );
1927 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1928 if ( t7.getHeight() != 15 ) {
1931 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)" );
1932 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1933 if ( t8.getNumberOfExternalNodes() != 10 ) {
1936 if ( t8.getHeight() != 15 ) {
1939 final char[] a9 = new char[] {};
1940 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1941 if ( t9.getHeight() != 0 ) {
1944 final char[] a10 = new char[] { 'a', ':', '6' };
1945 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1946 if ( t10.getHeight() != 6 ) {
1950 catch ( final Exception e ) {
1951 e.printStackTrace( System.out );
1957 private static boolean testConfidenceAssessor() {
1959 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1960 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1961 final Phylogeny[] ev0 = factory
1962 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1964 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1965 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1968 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1971 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1972 final Phylogeny[] ev1 = factory
1973 .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)));",
1975 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1976 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1979 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1982 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1983 final Phylogeny[] ev_b = factory
1984 .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",
1986 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1987 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
1988 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1991 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1995 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1996 final Phylogeny[] ev1x = factory
1997 .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)));",
1999 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2000 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2003 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2006 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2007 final Phylogeny[] ev_bx = factory
2008 .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",
2010 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2011 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2014 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2018 final Phylogeny[] t2 = factory
2019 .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);",
2021 final Phylogeny[] ev2 = factory
2022 .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);",
2024 for( final Phylogeny target : t2 ) {
2025 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2028 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2029 new NHXParser() )[ 0 ];
2030 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2031 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2032 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2035 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2038 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2042 catch ( final Exception e ) {
2043 e.printStackTrace();
2049 private static boolean testCopyOfNodeData() {
2051 final PhylogenyNode n1 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2052 final PhylogenyNode n2 = n1.copyNodeData();
2053 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2057 catch ( final Exception e ) {
2058 e.printStackTrace();
2064 private static boolean testDataObjects() {
2066 final Confidence s0 = new Confidence();
2067 final Confidence s1 = new Confidence();
2068 if ( !s0.isEqual( s1 ) ) {
2071 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2072 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2073 if ( s2.isEqual( s1 ) ) {
2076 if ( !s2.isEqual( s3 ) ) {
2079 final Confidence s4 = ( Confidence ) s3.copy();
2080 if ( !s4.isEqual( s3 ) ) {
2087 final Taxonomy t1 = new Taxonomy();
2088 final Taxonomy t2 = new Taxonomy();
2089 final Taxonomy t3 = new Taxonomy();
2090 final Taxonomy t4 = new Taxonomy();
2091 final Taxonomy t5 = new Taxonomy();
2092 t1.setIdentifier( new Identifier( "ecoli" ) );
2093 t1.setTaxonomyCode( "ECOLI" );
2094 t1.setScientificName( "E. coli" );
2095 t1.setCommonName( "coli" );
2096 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2097 if ( !t1.isEqual( t0 ) ) {
2100 t2.setIdentifier( new Identifier( "ecoli" ) );
2101 t2.setTaxonomyCode( "other" );
2102 t2.setScientificName( "what" );
2103 t2.setCommonName( "something" );
2104 if ( !t1.isEqual( t2 ) ) {
2107 t2.setIdentifier( new Identifier( "nemve" ) );
2108 if ( t1.isEqual( t2 ) ) {
2111 t1.setIdentifier( null );
2112 t3.setTaxonomyCode( "ECOLI" );
2113 t3.setScientificName( "what" );
2114 t3.setCommonName( "something" );
2115 if ( !t1.isEqual( t3 ) ) {
2118 t1.setIdentifier( null );
2119 t1.setTaxonomyCode( "" );
2120 t4.setScientificName( "E. ColI" );
2121 t4.setCommonName( "something" );
2122 if ( !t1.isEqual( t4 ) ) {
2125 t4.setScientificName( "B. subtilis" );
2126 t4.setCommonName( "something" );
2127 if ( t1.isEqual( t4 ) ) {
2130 t1.setIdentifier( null );
2131 t1.setTaxonomyCode( "" );
2132 t1.setScientificName( "" );
2133 t5.setCommonName( "COLI" );
2134 if ( !t1.isEqual( t5 ) ) {
2137 t5.setCommonName( "vibrio" );
2138 if ( t1.isEqual( t5 ) ) {
2143 final Identifier id0 = new Identifier( "123", "pfam" );
2144 final Identifier id1 = ( Identifier ) id0.copy();
2145 if ( !id1.isEqual( id1 ) ) {
2148 if ( !id1.isEqual( id0 ) ) {
2151 if ( !id0.isEqual( id1 ) ) {
2158 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2159 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2160 if ( !pd1.isEqual( pd1 ) ) {
2163 if ( !pd1.isEqual( pd0 ) ) {
2168 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2169 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2170 if ( !pd3.isEqual( pd3 ) ) {
2173 if ( !pd2.isEqual( pd3 ) ) {
2176 if ( !pd0.isEqual( pd3 ) ) {
2181 // DomainArchitecture
2182 // ------------------
2183 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2184 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2185 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2186 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2187 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2188 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2193 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2194 if ( ds0.getNumberOfDomains() != 4 ) {
2197 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2198 if ( !ds0.isEqual( ds0 ) ) {
2201 if ( !ds0.isEqual( ds1 ) ) {
2204 if ( ds1.getNumberOfDomains() != 4 ) {
2207 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2212 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2213 if ( ds0.isEqual( ds2 ) ) {
2219 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2220 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2221 System.out.println( ds3.toNHX() );
2224 if ( ds3.getNumberOfDomains() != 3 ) {
2229 final Event e1 = new Event( Event.EventType.fusion );
2230 if ( e1.isDuplication() ) {
2233 if ( !e1.isFusion() ) {
2236 if ( !e1.asText().toString().equals( "fusion" ) ) {
2239 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2242 final Event e11 = new Event( Event.EventType.fusion );
2243 if ( !e11.isEqual( e1 ) ) {
2246 if ( !e11.toNHX().toString().equals( "" ) ) {
2249 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2250 if ( e2.isDuplication() ) {
2253 if ( !e2.isSpeciationOrDuplication() ) {
2256 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2259 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2262 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2265 if ( e11.isEqual( e2 ) ) {
2268 final Event e2c = ( Event ) e2.copy();
2269 if ( !e2c.isEqual( e2 ) ) {
2272 Event e3 = new Event( 1, 2, 3 );
2273 if ( e3.isDuplication() ) {
2276 if ( e3.isSpeciation() ) {
2279 if ( e3.isGeneLoss() ) {
2282 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2285 final Event e3c = ( Event ) e3.copy();
2286 final Event e3cc = ( Event ) e3c.copy();
2287 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2291 if ( !e3c.isEqual( e3cc ) ) {
2294 Event e4 = new Event( 1, 2, 3 );
2295 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2298 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2301 final Event e4c = ( Event ) e4.copy();
2303 final Event e4cc = ( Event ) e4c.copy();
2304 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2307 if ( !e4c.isEqual( e4cc ) ) {
2310 final Event e5 = new Event();
2311 if ( !e5.isUnassigned() ) {
2314 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2317 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2320 final Event e6 = new Event( 1, 0, 0 );
2321 if ( !e6.asText().toString().equals( "duplication" ) ) {
2324 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2327 final Event e7 = new Event( 0, 1, 0 );
2328 if ( !e7.asText().toString().equals( "speciation" ) ) {
2331 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2334 final Event e8 = new Event( 0, 0, 1 );
2335 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2338 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2342 catch ( final Exception e ) {
2343 e.printStackTrace( System.out );
2349 private static boolean testDeletionOfExternalNodes() {
2351 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2352 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2353 final PhylogenyWriter w = new PhylogenyWriter();
2354 if ( t0.isEmpty() ) {
2357 if ( t0.getNumberOfExternalNodes() != 1 ) {
2360 t0.deleteSubtree( t0.getNode( "A" ), false );
2361 if ( t0.getNumberOfExternalNodes() != 0 ) {
2364 if ( !t0.isEmpty() ) {
2367 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2368 if ( t1.getNumberOfExternalNodes() != 2 ) {
2371 t1.deleteSubtree( t1.getNode( "A" ), false );
2372 if ( t1.getNumberOfExternalNodes() != 1 ) {
2375 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2378 t1.deleteSubtree( t1.getNode( "B" ), false );
2379 if ( t1.getNumberOfExternalNodes() != 1 ) {
2382 t1.deleteSubtree( t1.getNode( "r" ), false );
2383 if ( !t1.isEmpty() ) {
2386 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2387 if ( t2.getNumberOfExternalNodes() != 3 ) {
2390 t2.deleteSubtree( t2.getNode( "B" ), false );
2391 if ( t2.getNumberOfExternalNodes() != 2 ) {
2394 t2.toNewHampshireX();
2395 PhylogenyNode n = t2.getNode( "A" );
2396 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2399 t2.deleteSubtree( t2.getNode( "A" ), false );
2400 if ( t2.getNumberOfExternalNodes() != 2 ) {
2403 t2.deleteSubtree( t2.getNode( "C" ), true );
2404 if ( t2.getNumberOfExternalNodes() != 1 ) {
2407 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2408 if ( t3.getNumberOfExternalNodes() != 4 ) {
2411 t3.deleteSubtree( t3.getNode( "B" ), true );
2412 if ( t3.getNumberOfExternalNodes() != 3 ) {
2415 n = t3.getNode( "A" );
2416 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2419 n = n.getNextExternalNode();
2420 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2423 t3.deleteSubtree( t3.getNode( "A" ), true );
2424 if ( t3.getNumberOfExternalNodes() != 2 ) {
2427 n = t3.getNode( "C" );
2428 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2431 t3.deleteSubtree( t3.getNode( "C" ), true );
2432 if ( t3.getNumberOfExternalNodes() != 1 ) {
2435 t3.deleteSubtree( t3.getNode( "D" ), true );
2436 if ( t3.getNumberOfExternalNodes() != 0 ) {
2439 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2440 if ( t4.getNumberOfExternalNodes() != 6 ) {
2443 t4.deleteSubtree( t4.getNode( "B2" ), true );
2444 if ( t4.getNumberOfExternalNodes() != 5 ) {
2447 String s = w.toNewHampshire( t4, false, true ).toString();
2448 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2451 t4.deleteSubtree( t4.getNode( "B11" ), true );
2452 if ( t4.getNumberOfExternalNodes() != 4 ) {
2455 t4.deleteSubtree( t4.getNode( "C" ), true );
2456 if ( t4.getNumberOfExternalNodes() != 3 ) {
2459 n = t4.getNode( "A" );
2460 n = n.getNextExternalNode();
2461 if ( !n.getName().equals( "B12" ) ) {
2464 n = n.getNextExternalNode();
2465 if ( !n.getName().equals( "D" ) ) {
2468 s = w.toNewHampshire( t4, false, true ).toString();
2469 if ( !s.equals( "((A,B12),D);" ) ) {
2472 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2473 t5.deleteSubtree( t5.getNode( "A" ), true );
2474 if ( t5.getNumberOfExternalNodes() != 5 ) {
2477 s = w.toNewHampshire( t5, false, true ).toString();
2478 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2481 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2482 t6.deleteSubtree( t6.getNode( "B11" ), true );
2483 if ( t6.getNumberOfExternalNodes() != 5 ) {
2486 s = w.toNewHampshire( t6, false, false ).toString();
2487 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2490 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2491 t7.deleteSubtree( t7.getNode( "B12" ), true );
2492 if ( t7.getNumberOfExternalNodes() != 5 ) {
2495 s = w.toNewHampshire( t7, false, true ).toString();
2496 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2499 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2500 t8.deleteSubtree( t8.getNode( "B2" ), true );
2501 if ( t8.getNumberOfExternalNodes() != 5 ) {
2504 s = w.toNewHampshire( t8, false, false ).toString();
2505 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2508 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2509 t9.deleteSubtree( t9.getNode( "C" ), true );
2510 if ( t9.getNumberOfExternalNodes() != 5 ) {
2513 s = w.toNewHampshire( t9, false, true ).toString();
2514 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2517 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2518 t10.deleteSubtree( t10.getNode( "D" ), true );
2519 if ( t10.getNumberOfExternalNodes() != 5 ) {
2522 s = w.toNewHampshire( t10, false, true ).toString();
2523 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2526 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2527 t11.deleteSubtree( t11.getNode( "A" ), true );
2528 if ( t11.getNumberOfExternalNodes() != 2 ) {
2531 s = w.toNewHampshire( t11, false, true ).toString();
2532 if ( !s.equals( "(B,C);" ) ) {
2535 t11.deleteSubtree( t11.getNode( "C" ), true );
2536 if ( t11.getNumberOfExternalNodes() != 1 ) {
2539 s = w.toNewHampshire( t11, false, false ).toString();
2540 if ( !s.equals( "B;" ) ) {
2543 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2544 t12.deleteSubtree( t12.getNode( "B2" ), true );
2545 if ( t12.getNumberOfExternalNodes() != 8 ) {
2548 s = w.toNewHampshire( t12, false, true ).toString();
2549 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2552 t12.deleteSubtree( t12.getNode( "B3" ), true );
2553 if ( t12.getNumberOfExternalNodes() != 7 ) {
2556 s = w.toNewHampshire( t12, false, true ).toString();
2557 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2560 t12.deleteSubtree( t12.getNode( "C3" ), true );
2561 if ( t12.getNumberOfExternalNodes() != 6 ) {
2564 s = w.toNewHampshire( t12, false, true ).toString();
2565 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2568 t12.deleteSubtree( t12.getNode( "A1" ), true );
2569 if ( t12.getNumberOfExternalNodes() != 5 ) {
2572 s = w.toNewHampshire( t12, false, true ).toString();
2573 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2576 t12.deleteSubtree( t12.getNode( "B1" ), true );
2577 if ( t12.getNumberOfExternalNodes() != 4 ) {
2580 s = w.toNewHampshire( t12, false, true ).toString();
2581 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2584 t12.deleteSubtree( t12.getNode( "A3" ), true );
2585 if ( t12.getNumberOfExternalNodes() != 3 ) {
2588 s = w.toNewHampshire( t12, false, true ).toString();
2589 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2592 t12.deleteSubtree( t12.getNode( "A2" ), true );
2593 if ( t12.getNumberOfExternalNodes() != 2 ) {
2596 s = w.toNewHampshire( t12, false, true ).toString();
2597 if ( !s.equals( "(C1,C2);" ) ) {
2600 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2601 t13.deleteSubtree( t13.getNode( "D" ), true );
2602 if ( t13.getNumberOfExternalNodes() != 4 ) {
2605 s = w.toNewHampshire( t13, false, true ).toString();
2606 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2609 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2610 t14.deleteSubtree( t14.getNode( "E" ), true );
2611 if ( t14.getNumberOfExternalNodes() != 5 ) {
2614 s = w.toNewHampshire( t14, false, true ).toString();
2615 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2618 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2619 t15.deleteSubtree( t15.getNode( "B2" ), true );
2620 if ( t15.getNumberOfExternalNodes() != 11 ) {
2623 t15.deleteSubtree( t15.getNode( "B1" ), true );
2624 if ( t15.getNumberOfExternalNodes() != 10 ) {
2627 t15.deleteSubtree( t15.getNode( "B3" ), true );
2628 if ( t15.getNumberOfExternalNodes() != 9 ) {
2631 t15.deleteSubtree( t15.getNode( "B4" ), true );
2632 if ( t15.getNumberOfExternalNodes() != 8 ) {
2635 t15.deleteSubtree( t15.getNode( "A1" ), true );
2636 if ( t15.getNumberOfExternalNodes() != 7 ) {
2639 t15.deleteSubtree( t15.getNode( "C4" ), true );
2640 if ( t15.getNumberOfExternalNodes() != 6 ) {
2644 catch ( final Exception e ) {
2645 e.printStackTrace( System.out );
2651 private static boolean testDescriptiveStatistics() {
2653 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2654 dss1.addValue( 82 );
2655 dss1.addValue( 78 );
2656 dss1.addValue( 70 );
2657 dss1.addValue( 58 );
2658 dss1.addValue( 42 );
2659 if ( dss1.getN() != 5 ) {
2662 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2665 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2668 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2671 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2674 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2677 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2680 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2683 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2686 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2689 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2692 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2695 dss1.addValue( 123 );
2696 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2699 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2702 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2705 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2706 dss2.addValue( -1.85 );
2707 dss2.addValue( 57.5 );
2708 dss2.addValue( 92.78 );
2709 dss2.addValue( 57.78 );
2710 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2713 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2716 final double[] a = dss2.getDataAsDoubleArray();
2717 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2720 dss2.addValue( -100 );
2721 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2724 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2727 final double[] ds = new double[ 14 ];
2742 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2743 if ( bins.length != 4 ) {
2746 if ( bins[ 0 ] != 2 ) {
2749 if ( bins[ 1 ] != 3 ) {
2752 if ( bins[ 2 ] != 4 ) {
2755 if ( bins[ 3 ] != 5 ) {
2758 final double[] ds1 = new double[ 9 ];
2768 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2769 if ( bins1.length != 4 ) {
2772 if ( bins1[ 0 ] != 2 ) {
2775 if ( bins1[ 1 ] != 3 ) {
2778 if ( bins1[ 2 ] != 0 ) {
2781 if ( bins1[ 3 ] != 4 ) {
2784 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2785 if ( bins1_1.length != 3 ) {
2788 if ( bins1_1[ 0 ] != 3 ) {
2791 if ( bins1_1[ 1 ] != 2 ) {
2794 if ( bins1_1[ 2 ] != 4 ) {
2797 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2798 if ( bins1_2.length != 3 ) {
2801 if ( bins1_2[ 0 ] != 2 ) {
2804 if ( bins1_2[ 1 ] != 2 ) {
2807 if ( bins1_2[ 2 ] != 2 ) {
2810 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2824 dss3.addValue( 10 );
2825 dss3.addValue( 10 );
2826 dss3.addValue( 10 );
2827 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2828 histo.toStringBuffer( 10, '=', 40, 5 );
2829 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2831 catch ( final Exception e ) {
2832 e.printStackTrace( System.out );
2838 private static boolean testDir( final String file ) {
2840 final File f = new File( file );
2841 if ( !f.exists() ) {
2844 if ( !f.isDirectory() ) {
2847 if ( !f.canRead() ) {
2851 catch ( final Exception e ) {
2857 private static boolean testExternalNodeRelatedMethods() {
2859 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2860 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2861 PhylogenyNode n = t1.getNode( "A" );
2862 n = n.getNextExternalNode();
2863 if ( !n.getName().equals( "B" ) ) {
2866 n = n.getNextExternalNode();
2867 if ( !n.getName().equals( "C" ) ) {
2870 n = n.getNextExternalNode();
2871 if ( !n.getName().equals( "D" ) ) {
2874 n = t1.getNode( "B" );
2875 while ( !n.isLastExternalNode() ) {
2876 n = n.getNextExternalNode();
2878 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2879 n = t2.getNode( "A" );
2880 n = n.getNextExternalNode();
2881 if ( !n.getName().equals( "B" ) ) {
2884 n = n.getNextExternalNode();
2885 if ( !n.getName().equals( "C" ) ) {
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "D" ) ) {
2892 n = t2.getNode( "B" );
2893 while ( !n.isLastExternalNode() ) {
2894 n = n.getNextExternalNode();
2896 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2897 n = t3.getNode( "A" );
2898 n = n.getNextExternalNode();
2899 if ( !n.getName().equals( "B" ) ) {
2902 n = n.getNextExternalNode();
2903 if ( !n.getName().equals( "C" ) ) {
2906 n = n.getNextExternalNode();
2907 if ( !n.getName().equals( "D" ) ) {
2910 n = n.getNextExternalNode();
2911 if ( !n.getName().equals( "E" ) ) {
2914 n = n.getNextExternalNode();
2915 if ( !n.getName().equals( "F" ) ) {
2918 n = n.getNextExternalNode();
2919 if ( !n.getName().equals( "G" ) ) {
2922 n = n.getNextExternalNode();
2923 if ( !n.getName().equals( "H" ) ) {
2926 n = t3.getNode( "B" );
2927 while ( !n.isLastExternalNode() ) {
2928 n = n.getNextExternalNode();
2930 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2931 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2932 final PhylogenyNode node = iter.next();
2934 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2935 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2936 final PhylogenyNode node = iter.next();
2939 catch ( final Exception e ) {
2940 e.printStackTrace( System.out );
2946 private static boolean testGeneralTable() {
2948 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2949 t0.setValue( 3, 2, "23" );
2950 t0.setValue( 10, 1, "error" );
2951 t0.setValue( 10, 1, "110" );
2952 t0.setValue( 9, 1, "19" );
2953 t0.setValue( 1, 10, "101" );
2954 t0.setValue( 10, 10, "1010" );
2955 t0.setValue( 100, 10, "10100" );
2956 t0.setValue( 0, 0, "00" );
2957 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2960 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2963 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2966 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2969 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2972 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2975 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2978 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2981 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2984 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2985 t1.setValue( "3", "2", "23" );
2986 t1.setValue( "10", "1", "error" );
2987 t1.setValue( "10", "1", "110" );
2988 t1.setValue( "9", "1", "19" );
2989 t1.setValue( "1", "10", "101" );
2990 t1.setValue( "10", "10", "1010" );
2991 t1.setValue( "100", "10", "10100" );
2992 t1.setValue( "0", "0", "00" );
2993 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2994 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2997 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3000 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3003 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3006 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3009 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3012 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3015 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3018 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3021 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3025 catch ( final Exception e ) {
3026 e.printStackTrace( System.out );
3032 private static boolean testGetDistance() {
3034 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3035 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",
3036 new NHXParser() )[ 0 ];
3037 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3038 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3041 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3044 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3047 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3050 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3053 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3056 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3059 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3062 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3065 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3068 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3071 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3074 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3077 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3080 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3083 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3086 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3089 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3092 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3095 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3098 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3101 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3104 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3107 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3110 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3113 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3116 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3119 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3122 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3125 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3128 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3131 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",
3132 new NHXParser() )[ 0 ];
3133 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3136 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3139 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3142 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3145 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3148 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3151 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3154 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3157 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3160 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3163 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3167 catch ( final Exception e ) {
3168 e.printStackTrace( System.out );
3174 private static boolean testGetLCA() {
3176 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3177 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3178 new NHXParser() )[ 0 ];
3179 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3180 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3181 if ( !A.getName().equals( "A" ) ) {
3184 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3185 if ( !gh.getName().equals( "gh" ) ) {
3188 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3189 if ( !ab.getName().equals( "ab" ) ) {
3192 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3193 if ( !ab2.getName().equals( "ab" ) ) {
3196 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3197 if ( !gh2.getName().equals( "gh" ) ) {
3200 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3201 if ( !gh3.getName().equals( "gh" ) ) {
3204 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3205 if ( !abc.getName().equals( "abc" ) ) {
3208 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3209 if ( !abc2.getName().equals( "abc" ) ) {
3212 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3213 if ( !abcd.getName().equals( "abcd" ) ) {
3216 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3217 if ( !abcd2.getName().equals( "abcd" ) ) {
3220 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3221 if ( !abcdef.getName().equals( "abcdef" ) ) {
3224 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3225 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3228 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3229 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3232 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3233 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3236 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3237 if ( !abcde.getName().equals( "abcde" ) ) {
3240 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3241 if ( !abcde2.getName().equals( "abcde" ) ) {
3244 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3245 if ( !r.getName().equals( "abcdefgh" ) ) {
3248 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3249 if ( !r2.getName().equals( "abcdefgh" ) ) {
3252 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3253 if ( !r3.getName().equals( "abcdefgh" ) ) {
3256 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3257 if ( !abcde3.getName().equals( "abcde" ) ) {
3260 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3261 if ( !abcde4.getName().equals( "abcde" ) ) {
3264 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3265 if ( !ab3.getName().equals( "ab" ) ) {
3268 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3269 if ( !ab4.getName().equals( "ab" ) ) {
3272 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3273 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3274 if ( !cd.getName().equals( "cd" ) ) {
3277 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3278 if ( !cd2.getName().equals( "cd" ) ) {
3281 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3282 if ( !cde.getName().equals( "cde" ) ) {
3285 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3286 if ( !cde2.getName().equals( "cde" ) ) {
3289 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3290 if ( !cdef.getName().equals( "cdef" ) ) {
3293 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3294 if ( !cdef2.getName().equals( "cdef" ) ) {
3297 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3298 if ( !cdef3.getName().equals( "cdef" ) ) {
3301 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3302 if ( !rt.getName().equals( "r" ) ) {
3305 final Phylogeny p3 = factory
3306 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3307 new NHXParser() )[ 0 ];
3308 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3309 if ( !bc_3.getName().equals( "bc" ) ) {
3312 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3313 if ( !ac_3.getName().equals( "abc" ) ) {
3316 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3317 if ( !ad_3.getName().equals( "abcde" ) ) {
3320 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3321 if ( !af_3.getName().equals( "abcdef" ) ) {
3324 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3325 if ( !ag_3.getName().equals( "" ) ) {
3328 if ( !ag_3.isRoot() ) {
3331 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3332 if ( !al_3.getName().equals( "" ) ) {
3335 if ( !al_3.isRoot() ) {
3338 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3339 if ( !kl_3.getName().equals( "" ) ) {
3342 if ( !kl_3.isRoot() ) {
3345 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3346 if ( !fl_3.getName().equals( "" ) ) {
3349 if ( !fl_3.isRoot() ) {
3352 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3353 if ( !gk_3.getName().equals( "ghijk" ) ) {
3356 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3357 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3358 if ( !r_4.getName().equals( "r" ) ) {
3361 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3362 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3363 if ( !r_5.getName().equals( "root" ) ) {
3366 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3367 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3368 if ( !r_6.getName().equals( "rot" ) ) {
3371 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3372 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3373 if ( !r_7.getName().equals( "rott" ) ) {
3377 catch ( final Exception e ) {
3378 e.printStackTrace( System.out );
3384 private static boolean testHmmscanOutputParser() {
3385 final String test_dir = Test.PATH_TO_TEST_DATA;
3387 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3388 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3390 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3391 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3392 final List<Protein> domain_collections = parser2.parse();
3393 if ( parser2.getProteinsEncountered() != 4 ) {
3396 if ( domain_collections.size() != 4 ) {
3399 if ( parser2.getDomainsEncountered() != 69 ) {
3402 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3405 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3408 final Protein p1 = domain_collections.get( 0 );
3409 if ( p1.getNumberOfProteinDomains() != 15 ) {
3412 final Protein p4 = domain_collections.get( 3 );
3413 if ( p4.getNumberOfProteinDomains() != 1 ) {
3416 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3419 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3422 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3425 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3428 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3431 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3434 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3437 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3440 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3444 catch ( final Exception e ) {
3445 e.printStackTrace( System.out );
3451 private static boolean testLastExternalNodeMethods() {
3453 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3454 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3455 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3456 final PhylogenyNode n1 = t0.getNode( "A" );
3457 if ( n1.isLastExternalNode() ) {
3460 final PhylogenyNode n2 = t0.getNode( "B" );
3461 if ( n2.isLastExternalNode() ) {
3464 final PhylogenyNode n3 = t0.getNode( "C" );
3465 if ( n3.isLastExternalNode() ) {
3468 final PhylogenyNode n4 = t0.getNode( "D" );
3469 if ( !n4.isLastExternalNode() ) {
3473 catch ( final Exception e ) {
3474 e.printStackTrace( System.out );
3480 private static boolean testLevelOrderIterator() {
3482 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3483 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3484 PhylogenyNodeIterator it0;
3485 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3488 for( it0.reset(); it0.hasNext(); ) {
3491 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3492 if ( !it.next().getName().equals( "r" ) ) {
3495 if ( !it.next().getName().equals( "ab" ) ) {
3498 if ( !it.next().getName().equals( "cd" ) ) {
3501 if ( !it.next().getName().equals( "A" ) ) {
3504 if ( !it.next().getName().equals( "B" ) ) {
3507 if ( !it.next().getName().equals( "C" ) ) {
3510 if ( !it.next().getName().equals( "D" ) ) {
3513 if ( it.hasNext() ) {
3516 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",
3517 new NHXParser() )[ 0 ];
3518 PhylogenyNodeIterator it2;
3519 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3522 for( it2.reset(); it2.hasNext(); ) {
3525 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3526 if ( !it3.next().getName().equals( "r" ) ) {
3529 if ( !it3.next().getName().equals( "abc" ) ) {
3532 if ( !it3.next().getName().equals( "defg" ) ) {
3535 if ( !it3.next().getName().equals( "A" ) ) {
3538 if ( !it3.next().getName().equals( "B" ) ) {
3541 if ( !it3.next().getName().equals( "C" ) ) {
3544 if ( !it3.next().getName().equals( "D" ) ) {
3547 if ( !it3.next().getName().equals( "E" ) ) {
3550 if ( !it3.next().getName().equals( "F" ) ) {
3553 if ( !it3.next().getName().equals( "G" ) ) {
3556 if ( !it3.next().getName().equals( "1" ) ) {
3559 if ( !it3.next().getName().equals( "2" ) ) {
3562 if ( !it3.next().getName().equals( "3" ) ) {
3565 if ( !it3.next().getName().equals( "4" ) ) {
3568 if ( !it3.next().getName().equals( "5" ) ) {
3571 if ( !it3.next().getName().equals( "6" ) ) {
3574 if ( !it3.next().getName().equals( "f1" ) ) {
3577 if ( !it3.next().getName().equals( "f2" ) ) {
3580 if ( !it3.next().getName().equals( "f3" ) ) {
3583 if ( !it3.next().getName().equals( "a" ) ) {
3586 if ( !it3.next().getName().equals( "b" ) ) {
3589 if ( !it3.next().getName().equals( "f21" ) ) {
3592 if ( !it3.next().getName().equals( "X" ) ) {
3595 if ( !it3.next().getName().equals( "Y" ) ) {
3598 if ( !it3.next().getName().equals( "Z" ) ) {
3601 if ( it3.hasNext() ) {
3604 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3605 PhylogenyNodeIterator it4;
3606 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3609 for( it4.reset(); it4.hasNext(); ) {
3612 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3613 if ( !it5.next().getName().equals( "r" ) ) {
3616 if ( !it5.next().getName().equals( "A" ) ) {
3619 if ( !it5.next().getName().equals( "B" ) ) {
3622 if ( !it5.next().getName().equals( "C" ) ) {
3625 if ( !it5.next().getName().equals( "D" ) ) {
3628 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3629 PhylogenyNodeIterator it6;
3630 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3633 for( it6.reset(); it6.hasNext(); ) {
3636 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3637 if ( !it7.next().getName().equals( "A" ) ) {
3640 if ( it.hasNext() ) {
3644 catch ( final Exception e ) {
3645 e.printStackTrace( System.out );
3651 private static boolean testMidpointrooting() {
3653 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3654 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",
3655 new NHXParser() )[ 0 ];
3656 if ( !t1.isRooted() ) {
3659 PhylogenyMethods.midpointRoot( t1 );
3660 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3663 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3666 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3669 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3672 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3675 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3678 t1.reRoot( t1.getNode( "A" ) );
3679 PhylogenyMethods.midpointRoot( t1 );
3680 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3683 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3686 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3689 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3692 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3695 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3699 catch ( final Exception e ) {
3700 e.printStackTrace( System.out );
3706 private static boolean testNexusCharactersParsing() {
3708 final NexusCharactersParser parser = new NexusCharactersParser();
3709 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3711 String[] labels = parser.getCharStateLabels();
3712 if ( labels.length != 7 ) {
3715 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3718 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3721 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3724 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3727 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3730 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3733 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3736 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3738 labels = parser.getCharStateLabels();
3739 if ( labels.length != 7 ) {
3742 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3745 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3748 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3751 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3754 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3757 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3760 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3764 catch ( final Exception e ) {
3765 e.printStackTrace( System.out );
3771 private static boolean testNexusMatrixParsing() {
3773 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3774 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3776 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3777 if ( m.getNumberOfCharacters() != 9 ) {
3780 if ( m.getNumberOfIdentifiers() != 5 ) {
3783 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3786 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3789 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3792 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3795 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3798 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3801 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3804 // if ( labels.length != 7 ) {
3807 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3810 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3813 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3816 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3819 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3822 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3825 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3828 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3830 // labels = parser.getCharStateLabels();
3831 // if ( labels.length != 7 ) {
3834 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3837 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3840 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3843 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3846 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3849 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3852 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3856 catch ( final Exception e ) {
3857 e.printStackTrace( System.out );
3863 private static boolean testNexusTreeParsing() {
3865 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3866 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3867 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3868 if ( phylogenies.length != 1 ) {
3871 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3874 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3878 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3879 if ( phylogenies.length != 1 ) {
3882 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3885 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3889 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3890 if ( phylogenies.length != 1 ) {
3893 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3896 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3899 if ( phylogenies[ 0 ].isRooted() ) {
3903 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3904 if ( phylogenies.length != 18 ) {
3907 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3910 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3913 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3916 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3919 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3922 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3925 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3928 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3931 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3934 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3937 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3940 if ( phylogenies[ 8 ].isRooted() ) {
3943 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3946 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3949 if ( !phylogenies[ 9 ].isRooted() ) {
3952 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3955 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3958 if ( !phylogenies[ 10 ].isRooted() ) {
3961 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3964 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3967 if ( phylogenies[ 11 ].isRooted() ) {
3970 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
3973 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
3976 if ( !phylogenies[ 12 ].isRooted() ) {
3979 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
3982 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
3985 if ( !phylogenies[ 13 ].isRooted() ) {
3988 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
3991 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
3994 if ( !phylogenies[ 14 ].isRooted() ) {
3997 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4000 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4003 if ( phylogenies[ 15 ].isRooted() ) {
4006 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4009 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4012 if ( !phylogenies[ 16 ].isRooted() ) {
4015 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4018 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4021 if ( phylogenies[ 17 ].isRooted() ) {
4024 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4028 catch ( final Exception e ) {
4029 e.printStackTrace( System.out );
4035 private static boolean testNexusTreeParsingTranslating() {
4037 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4038 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4039 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4040 if ( phylogenies.length != 1 ) {
4043 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4046 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4049 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4052 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4055 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4056 .equals( "Aranaeus" ) ) {
4060 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4061 if ( phylogenies.length != 3 ) {
4064 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4067 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4070 if ( phylogenies[ 0 ].isRooted() ) {
4073 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4076 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4079 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4080 .equals( "Aranaeus" ) ) {
4083 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4086 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4089 if ( phylogenies[ 1 ].isRooted() ) {
4092 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4095 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4098 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4099 .equals( "Aranaeus" ) ) {
4102 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4105 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4108 if ( !phylogenies[ 2 ].isRooted() ) {
4111 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4114 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4117 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4118 .equals( "Aranaeus" ) ) {
4122 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4123 if ( phylogenies.length != 3 ) {
4126 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4129 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4132 if ( phylogenies[ 0 ].isRooted() ) {
4135 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4138 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4141 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4142 .equals( "Aranaeus" ) ) {
4145 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4148 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4151 if ( phylogenies[ 1 ].isRooted() ) {
4154 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4157 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4160 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4161 .equals( "Aranaeus" ) ) {
4164 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4167 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4170 if ( !phylogenies[ 2 ].isRooted() ) {
4173 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4176 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4179 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4180 .equals( "Aranaeus" ) ) {
4184 catch ( final Exception e ) {
4185 e.printStackTrace( System.out );
4191 private static boolean testNHParsing() {
4193 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4194 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4195 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4198 final NHXParser nhxp = new NHXParser();
4199 nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
4200 nhxp.setReplaceUnderscores( true );
4201 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4202 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4205 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4208 final Phylogeny p1b = factory
4209 .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 ",
4210 new NHXParser() )[ 0 ];
4211 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4214 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4217 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4218 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4219 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4220 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4221 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4222 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4223 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4224 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4225 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4226 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4227 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4228 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4229 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4231 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4234 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4237 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4240 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4243 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4244 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4245 final String p16_S = "((A,B),C)";
4246 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4247 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4250 final String p17_S = "(C,(A,B))";
4251 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4252 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4255 final String p18_S = "((A,B),(C,D))";
4256 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4257 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4260 final String p19_S = "(((A,B),C),D)";
4261 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4262 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4265 final String p20_S = "(A,(B,(C,D)))";
4266 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4267 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4270 final String p21_S = "(A,(B,(C,(D,E))))";
4271 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4272 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4275 final String p22_S = "((((A,B),C),D),E)";
4276 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4277 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4280 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4281 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4282 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4285 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4286 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4287 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4290 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4291 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4292 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4293 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4296 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4299 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4300 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4301 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4302 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4303 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4304 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4305 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4306 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4307 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4308 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4311 final String p26_S = "(A,B)ab";
4312 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4313 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4316 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4317 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4319 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4322 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4323 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4324 final String p28_S3 = "(A,B)ab";
4325 final String p28_S4 = "((((A,B),C),D),;E;)";
4326 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4328 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4331 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4334 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4337 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4340 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";
4341 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4342 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4345 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";
4346 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4347 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4350 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4351 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4352 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4355 final String p33_S = "A";
4356 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4357 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4360 final String p34_S = "B;";
4361 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4362 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4365 final String p35_S = "B:0.2";
4366 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4367 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4370 final String p36_S = "(A)";
4371 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4372 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4375 final String p37_S = "((A))";
4376 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4377 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4380 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4381 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4382 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4385 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4386 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4387 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4390 final String p40_S = "(A,B,C)";
4391 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4392 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4395 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4396 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4397 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4400 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4401 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4402 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4405 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)";
4406 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4407 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4410 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)))";
4411 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4412 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4415 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4416 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4417 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4420 final String p46_S = "";
4421 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4422 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4426 catch ( final Exception e ) {
4427 e.printStackTrace( System.out );
4433 private static boolean testNHXconversion() {
4435 final PhylogenyNode n1 = new PhylogenyNode();
4436 final PhylogenyNode n2 = new PhylogenyNode( "" );
4437 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4438 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4439 final PhylogenyNode n5 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4440 final PhylogenyNode n6 = new PhylogenyNode( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4441 if ( !n1.toNewHampshireX().equals( "" ) ) {
4444 if ( !n2.toNewHampshireX().equals( "" ) ) {
4447 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4450 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4453 if ( !n5.toNewHampshireX()
4454 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56.0:W=2.0:C=10.20.30]" ) ) {
4457 if ( !n6.toNewHampshireX()
4458 .equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100.0:W=2.0:C=0.0.0]" ) ) {
4462 catch ( final Exception e ) {
4463 e.printStackTrace( System.out );
4469 private static boolean testNHXNodeParsing() {
4471 final PhylogenyNode n1 = new PhylogenyNode();
4472 final PhylogenyNode n2 = new PhylogenyNode( "" );
4473 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4474 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4475 final PhylogenyNode n5 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
4476 if ( !n3.getName().equals( "n3" ) ) {
4479 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4482 if ( n3.isDuplication() ) {
4485 if ( n3.isHasAssignedEvent() ) {
4488 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4491 if ( !n4.getName().equals( "n4" ) ) {
4494 if ( n4.getDistanceToParent() != 0.01 ) {
4497 if ( !n5.getName().equals( "n5" ) ) {
4500 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4503 if ( n5.getDistanceToParent() != 0.1 ) {
4506 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4509 if ( !n5.isDuplication() ) {
4512 if ( !n5.isHasAssignedEvent() ) {
4515 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4518 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4521 final PhylogenyNode n8 = new PhylogenyNode( "n8_ECOLI/12:0.01",
4522 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4523 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4526 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4529 final PhylogenyNode n9 = new PhylogenyNode( "n9_ECOLI/12=12:0.01",
4530 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4531 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4534 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4537 final PhylogenyNode n10 = new PhylogenyNode( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4538 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4541 final PhylogenyNode n20 = new PhylogenyNode( "n20_ECOLI/1-2",
4542 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4543 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4546 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4549 final PhylogenyNode n20x = new PhylogenyNode( "n20_ECOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4550 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4553 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4556 final PhylogenyNode n20xx = new PhylogenyNode( "n20_eCOL1/1-2",
4557 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4558 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4561 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4564 final PhylogenyNode n20xxx = new PhylogenyNode( "n20_ecoli/1-2",
4565 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4566 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4569 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4572 final PhylogenyNode n20xxxx = new PhylogenyNode( "n20_Ecoli/1-2",
4573 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4574 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4577 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4580 final PhylogenyNode n21 = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4581 if ( !n21.getName().equals( "n21_PIG" ) ) {
4584 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4587 final PhylogenyNode n21x = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4588 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4591 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4594 final PhylogenyNode n22 = new PhylogenyNode( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4595 if ( !n22.getName().equals( "n22/PIG" ) ) {
4598 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4601 final PhylogenyNode n23 = new PhylogenyNode( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4602 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4605 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4608 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4609 final PhylogenyNode a = new PhylogenyNode( "n10_ECOLI/1-2",
4610 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4611 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4614 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4617 final PhylogenyNode b = new PhylogenyNode( "n10_ECOLI1/1-2",
4618 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4619 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4622 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4625 final PhylogenyNode c = new PhylogenyNode( "n10_RATAF12/1000-2000",
4626 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4627 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4630 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4633 final PhylogenyNode d = new PhylogenyNode( "n10_RAT1/1-2",
4634 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4635 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4638 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4641 final PhylogenyNode e = new PhylogenyNode( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4642 if ( !e.getName().equals( "n10_RAT1" ) ) {
4645 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4649 final PhylogenyNode n11 = new PhylogenyNode( "n111111_ECOLI/jdj:0.4",
4650 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4651 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4654 if ( n11.getDistanceToParent() != 0.4 ) {
4657 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4660 final PhylogenyNode n12 = new PhylogenyNode( "n111111-ECOLI---/jdj:0.4",
4661 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4662 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4665 if ( n12.getDistanceToParent() != 0.4 ) {
4668 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4671 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4672 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4673 if ( !tvu1.getRef().equals( "tag1" ) ) {
4676 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4679 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4682 if ( !tvu1.getValue().equals( "value1" ) ) {
4685 if ( !tvu3.getRef().equals( "tag3" ) ) {
4688 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4691 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4694 if ( !tvu3.getValue().equals( "value3" ) ) {
4697 if ( n1.getName().compareTo( "" ) != 0 ) {
4700 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4703 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4706 if ( n2.getName().compareTo( "" ) != 0 ) {
4709 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4712 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4715 final PhylogenyNode n00 = new PhylogenyNode( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4716 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4719 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4722 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4725 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4728 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4731 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4734 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4737 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4740 final PhylogenyNode nx = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4741 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4744 final PhylogenyNode nx2 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4745 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4748 final PhylogenyNode n13 = new PhylogenyNode( "blah_12345/1-2",
4749 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4750 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4753 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4756 final PhylogenyNode n14 = new PhylogenyNode( "blah_12X45/1-2",
4757 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4758 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4761 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4764 final PhylogenyNode n15 = new PhylogenyNode( "something_wicked[123]",
4765 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4766 if ( !n15.getName().equals( "something_wicked" ) ) {
4769 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4772 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4775 final PhylogenyNode n16 = new PhylogenyNode( "something_wicked2[9]",
4776 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4777 if ( !n16.getName().equals( "something_wicked2" ) ) {
4780 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4783 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4786 final PhylogenyNode n17 = new PhylogenyNode( "something_wicked3[a]",
4787 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4788 if ( !n17.getName().equals( "something_wicked3" ) ) {
4791 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4794 final PhylogenyNode n18 = new PhylogenyNode( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4795 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4798 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4801 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4805 catch ( final Exception e ) {
4806 e.printStackTrace( System.out );
4812 private static boolean testNHXParsing() {
4814 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4815 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4816 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4819 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]";
4820 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4821 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4824 final String p2b_S = "(((((((A:0.2[&NHX:S=qwerty]):0.2[&:S=uiop]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
4825 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4826 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4829 final Phylogeny[] p3 = factory
4830 .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]",
4832 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4835 final Phylogeny[] p4 = factory
4836 .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(]",
4838 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4841 final Phylogeny[] p5 = factory
4842 .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(((]",
4844 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4847 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)";
4848 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)";
4849 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4850 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4853 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)))";
4854 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)))";
4855 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4856 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4859 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]) ))[,,, ])))))))";
4860 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4861 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4862 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4865 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4866 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4869 final Phylogeny p10 = factory
4870 .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]",
4871 new NHXParser() )[ 0 ];
4872 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4876 catch ( final Exception e ) {
4877 e.printStackTrace( System.out );
4883 private static boolean testNHXParsingQuotes() {
4885 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4886 final NHXParser p = new NHXParser();
4887 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4888 if ( phylogenies_0.length != 5 ) {
4891 final Phylogeny phy = phylogenies_0[ 4 ];
4892 if ( phy.getNumberOfExternalNodes() != 7 ) {
4895 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4898 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4901 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4902 .getScientificName().equals( "hsapiens" ) ) {
4905 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4908 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4911 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4914 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4917 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4920 final NHXParser p1p = new NHXParser();
4921 p1p.setIgnoreQuotes( true );
4922 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4923 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4926 final NHXParser p2p = new NHXParser();
4927 p1p.setIgnoreQuotes( false );
4928 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4929 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4932 final NHXParser p3p = new NHXParser();
4933 p3p.setIgnoreQuotes( false );
4934 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4935 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4938 final NHXParser p4p = new NHXParser();
4939 p4p.setIgnoreQuotes( false );
4940 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4941 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4944 final Phylogeny p10 = factory
4945 .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]",
4946 new NHXParser() )[ 0 ];
4947 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
4948 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
4951 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
4952 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
4956 final Phylogeny p12 = factory
4957 .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]",
4958 new NHXParser() )[ 0 ];
4959 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
4960 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
4963 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
4964 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
4967 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;";
4968 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
4971 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
4972 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
4976 catch ( final Exception e ) {
4977 e.printStackTrace( System.out );
4983 private static boolean testPhylogenyBranch() {
4985 final PhylogenyNode a1 = new PhylogenyNode( "a" );
4986 final PhylogenyNode b1 = new PhylogenyNode( "b" );
4987 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
4988 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
4989 if ( !a1b1.equals( a1b1 ) ) {
4992 if ( !a1b1.equals( b1a1 ) ) {
4995 if ( !b1a1.equals( a1b1 ) ) {
4998 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
4999 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5000 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5001 if ( a1_b1.equals( b1_a1 ) ) {
5004 if ( a1_b1.equals( a1_b1_ ) ) {
5007 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5008 if ( !a1_b1.equals( b1_a1_ ) ) {
5011 if ( a1_b1_.equals( b1_a1_ ) ) {
5014 if ( !a1_b1_.equals( b1_a1 ) ) {
5018 catch ( final Exception e ) {
5019 e.printStackTrace( System.out );
5025 private static boolean testPhyloXMLparsingOfDistributionElement() {
5027 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5028 PhyloXmlParser xml_parser = null;
5030 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5032 catch ( final Exception e ) {
5033 // Do nothing -- means were not running from jar.
5035 if ( xml_parser == null ) {
5036 xml_parser = new PhyloXmlParser();
5037 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5038 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5041 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5044 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5046 if ( xml_parser.getErrorCount() > 0 ) {
5047 System.out.println( xml_parser.getErrorMessages().toString() );
5050 if ( phylogenies_0.length != 1 ) {
5053 final Phylogeny t1 = phylogenies_0[ 0 ];
5054 PhylogenyNode n = null;
5055 Distribution d = null;
5056 n = t1.getNode( "root node" );
5057 if ( !n.getNodeData().isHasDistribution() ) {
5060 if ( n.getNodeData().getDistributions().size() != 1 ) {
5063 d = n.getNodeData().getDistribution();
5064 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5067 if ( d.getPoints().size() != 1 ) {
5070 if ( d.getPolygons() != null ) {
5073 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5076 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5079 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5082 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5085 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5088 n = t1.getNode( "node a" );
5089 if ( !n.getNodeData().isHasDistribution() ) {
5092 if ( n.getNodeData().getDistributions().size() != 2 ) {
5095 d = n.getNodeData().getDistribution( 1 );
5096 if ( !d.getDesc().equals( "San Diego" ) ) {
5099 if ( d.getPoints().size() != 1 ) {
5102 if ( d.getPolygons() != null ) {
5105 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5108 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5111 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5114 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5117 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5120 n = t1.getNode( "node bb" );
5121 if ( !n.getNodeData().isHasDistribution() ) {
5124 if ( n.getNodeData().getDistributions().size() != 1 ) {
5127 d = n.getNodeData().getDistribution( 0 );
5128 if ( d.getPoints().size() != 3 ) {
5131 if ( d.getPolygons().size() != 2 ) {
5134 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5137 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5140 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5143 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5146 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5149 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5152 Polygon p = d.getPolygons().get( 0 );
5153 if ( p.getPoints().size() != 3 ) {
5156 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5159 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5162 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5165 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5168 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5171 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5174 p = d.getPolygons().get( 1 );
5175 if ( p.getPoints().size() != 3 ) {
5178 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5181 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5184 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5188 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5189 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5190 if ( rt.length != 1 ) {
5193 final Phylogeny t1_rt = rt[ 0 ];
5194 n = t1_rt.getNode( "root node" );
5195 if ( !n.getNodeData().isHasDistribution() ) {
5198 if ( n.getNodeData().getDistributions().size() != 1 ) {
5201 d = n.getNodeData().getDistribution();
5202 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5205 if ( d.getPoints().size() != 1 ) {
5208 if ( d.getPolygons() != null ) {
5211 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5214 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5217 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5220 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5223 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5226 n = t1_rt.getNode( "node a" );
5227 if ( !n.getNodeData().isHasDistribution() ) {
5230 if ( n.getNodeData().getDistributions().size() != 2 ) {
5233 d = n.getNodeData().getDistribution( 1 );
5234 if ( !d.getDesc().equals( "San Diego" ) ) {
5237 if ( d.getPoints().size() != 1 ) {
5240 if ( d.getPolygons() != null ) {
5243 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5246 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5249 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5252 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5255 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5258 n = t1_rt.getNode( "node bb" );
5259 if ( !n.getNodeData().isHasDistribution() ) {
5262 if ( n.getNodeData().getDistributions().size() != 1 ) {
5265 d = n.getNodeData().getDistribution( 0 );
5266 if ( d.getPoints().size() != 3 ) {
5269 if ( d.getPolygons().size() != 2 ) {
5272 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5275 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5278 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5281 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5284 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5287 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5290 p = d.getPolygons().get( 0 );
5291 if ( p.getPoints().size() != 3 ) {
5294 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5297 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5300 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5303 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5306 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5309 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5312 p = d.getPolygons().get( 1 );
5313 if ( p.getPoints().size() != 3 ) {
5316 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5319 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5322 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5326 catch ( final Exception e ) {
5327 e.printStackTrace( System.out );
5333 private static boolean testPostOrderIterator() {
5335 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5336 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5337 PhylogenyNodeIterator it0;
5338 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5341 for( it0.reset(); it0.hasNext(); ) {
5344 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5345 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5346 if ( !it.next().getName().equals( "A" ) ) {
5349 if ( !it.next().getName().equals( "B" ) ) {
5352 if ( !it.next().getName().equals( "ab" ) ) {
5355 if ( !it.next().getName().equals( "C" ) ) {
5358 if ( !it.next().getName().equals( "D" ) ) {
5361 if ( !it.next().getName().equals( "cd" ) ) {
5364 if ( !it.next().getName().equals( "abcd" ) ) {
5367 if ( !it.next().getName().equals( "E" ) ) {
5370 if ( !it.next().getName().equals( "F" ) ) {
5373 if ( !it.next().getName().equals( "ef" ) ) {
5376 if ( !it.next().getName().equals( "G" ) ) {
5379 if ( !it.next().getName().equals( "H" ) ) {
5382 if ( !it.next().getName().equals( "gh" ) ) {
5385 if ( !it.next().getName().equals( "efgh" ) ) {
5388 if ( !it.next().getName().equals( "r" ) ) {
5391 if ( it.hasNext() ) {
5395 catch ( final Exception e ) {
5396 e.printStackTrace( System.out );
5402 private static boolean testPreOrderIterator() {
5404 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5405 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5406 PhylogenyNodeIterator it0;
5407 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5410 for( it0.reset(); it0.hasNext(); ) {
5413 PhylogenyNodeIterator it = t0.iteratorPreorder();
5414 if ( !it.next().getName().equals( "r" ) ) {
5417 if ( !it.next().getName().equals( "ab" ) ) {
5420 if ( !it.next().getName().equals( "A" ) ) {
5423 if ( !it.next().getName().equals( "B" ) ) {
5426 if ( !it.next().getName().equals( "cd" ) ) {
5429 if ( !it.next().getName().equals( "C" ) ) {
5432 if ( !it.next().getName().equals( "D" ) ) {
5435 if ( it.hasNext() ) {
5438 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5439 it = t1.iteratorPreorder();
5440 if ( !it.next().getName().equals( "r" ) ) {
5443 if ( !it.next().getName().equals( "abcd" ) ) {
5446 if ( !it.next().getName().equals( "ab" ) ) {
5449 if ( !it.next().getName().equals( "A" ) ) {
5452 if ( !it.next().getName().equals( "B" ) ) {
5455 if ( !it.next().getName().equals( "cd" ) ) {
5458 if ( !it.next().getName().equals( "C" ) ) {
5461 if ( !it.next().getName().equals( "D" ) ) {
5464 if ( !it.next().getName().equals( "efgh" ) ) {
5467 if ( !it.next().getName().equals( "ef" ) ) {
5470 if ( !it.next().getName().equals( "E" ) ) {
5473 if ( !it.next().getName().equals( "F" ) ) {
5476 if ( !it.next().getName().equals( "gh" ) ) {
5479 if ( !it.next().getName().equals( "G" ) ) {
5482 if ( !it.next().getName().equals( "H" ) ) {
5485 if ( it.hasNext() ) {
5489 catch ( final Exception e ) {
5490 e.printStackTrace( System.out );
5496 private static boolean testPropertiesMap() {
5498 final PropertiesMap pm = new PropertiesMap();
5499 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5500 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5501 final Property p2 = new Property( "something:else",
5503 "improbable:research",
5506 pm.addProperty( p0 );
5507 pm.addProperty( p1 );
5508 pm.addProperty( p2 );
5509 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5512 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5515 if ( pm.getProperties().size() != 3 ) {
5518 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5521 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5524 if ( pm.getProperties().size() != 3 ) {
5527 pm.removeProperty( "dimensions:diameter" );
5528 if ( pm.getProperties().size() != 2 ) {
5531 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5534 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5538 catch ( final Exception e ) {
5539 e.printStackTrace( System.out );
5545 private static boolean testReIdMethods() {
5547 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5548 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5549 final int count = PhylogenyNode.getNodeCount();
5551 if ( p.getNode( "r" ).getId() != count ) {
5554 if ( p.getNode( "A" ).getId() != count + 1 ) {
5557 if ( p.getNode( "B" ).getId() != count + 1 ) {
5560 if ( p.getNode( "C" ).getId() != count + 1 ) {
5563 if ( p.getNode( "1" ).getId() != count + 2 ) {
5566 if ( p.getNode( "2" ).getId() != count + 2 ) {
5569 if ( p.getNode( "3" ).getId() != count + 2 ) {
5572 if ( p.getNode( "4" ).getId() != count + 2 ) {
5575 if ( p.getNode( "5" ).getId() != count + 2 ) {
5578 if ( p.getNode( "6" ).getId() != count + 2 ) {
5581 if ( p.getNode( "a" ).getId() != count + 3 ) {
5584 if ( p.getNode( "b" ).getId() != count + 3 ) {
5587 if ( p.getNode( "X" ).getId() != count + 4 ) {
5590 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5593 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5597 catch ( final Exception e ) {
5598 e.printStackTrace( System.out );
5604 private static boolean testRerooting() {
5606 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5607 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",
5608 new NHXParser() )[ 0 ];
5609 if ( !t1.isRooted() ) {
5612 t1.reRoot( t1.getNode( "D" ) );
5613 t1.reRoot( t1.getNode( "CD" ) );
5614 t1.reRoot( t1.getNode( "A" ) );
5615 t1.reRoot( t1.getNode( "B" ) );
5616 t1.reRoot( t1.getNode( "AB" ) );
5617 t1.reRoot( t1.getNode( "D" ) );
5618 t1.reRoot( t1.getNode( "C" ) );
5619 t1.reRoot( t1.getNode( "CD" ) );
5620 t1.reRoot( t1.getNode( "A" ) );
5621 t1.reRoot( t1.getNode( "B" ) );
5622 t1.reRoot( t1.getNode( "AB" ) );
5623 t1.reRoot( t1.getNode( "D" ) );
5624 t1.reRoot( t1.getNode( "D" ) );
5625 t1.reRoot( t1.getNode( "C" ) );
5626 t1.reRoot( t1.getNode( "A" ) );
5627 t1.reRoot( t1.getNode( "B" ) );
5628 t1.reRoot( t1.getNode( "AB" ) );
5629 t1.reRoot( t1.getNode( "C" ) );
5630 t1.reRoot( t1.getNode( "D" ) );
5631 t1.reRoot( t1.getNode( "CD" ) );
5632 t1.reRoot( t1.getNode( "D" ) );
5633 t1.reRoot( t1.getNode( "A" ) );
5634 t1.reRoot( t1.getNode( "B" ) );
5635 t1.reRoot( t1.getNode( "AB" ) );
5636 t1.reRoot( t1.getNode( "C" ) );
5637 t1.reRoot( t1.getNode( "D" ) );
5638 t1.reRoot( t1.getNode( "CD" ) );
5639 t1.reRoot( t1.getNode( "D" ) );
5640 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5643 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5646 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5649 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5652 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5655 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5658 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",
5659 new NHXParser() )[ 0 ];
5660 t2.reRoot( t2.getNode( "A" ) );
5661 t2.reRoot( t2.getNode( "D" ) );
5662 t2.reRoot( t2.getNode( "ABC" ) );
5663 t2.reRoot( t2.getNode( "A" ) );
5664 t2.reRoot( t2.getNode( "B" ) );
5665 t2.reRoot( t2.getNode( "D" ) );
5666 t2.reRoot( t2.getNode( "C" ) );
5667 t2.reRoot( t2.getNode( "ABC" ) );
5668 t2.reRoot( t2.getNode( "A" ) );
5669 t2.reRoot( t2.getNode( "B" ) );
5670 t2.reRoot( t2.getNode( "AB" ) );
5671 t2.reRoot( t2.getNode( "AB" ) );
5672 t2.reRoot( t2.getNode( "D" ) );
5673 t2.reRoot( t2.getNode( "C" ) );
5674 t2.reRoot( t2.getNode( "B" ) );
5675 t2.reRoot( t2.getNode( "AB" ) );
5676 t2.reRoot( t2.getNode( "D" ) );
5677 t2.reRoot( t2.getNode( "D" ) );
5678 t2.reRoot( t2.getNode( "ABC" ) );
5679 t2.reRoot( t2.getNode( "A" ) );
5680 t2.reRoot( t2.getNode( "B" ) );
5681 t2.reRoot( t2.getNode( "AB" ) );
5682 t2.reRoot( t2.getNode( "D" ) );
5683 t2.reRoot( t2.getNode( "C" ) );
5684 t2.reRoot( t2.getNode( "ABC" ) );
5685 t2.reRoot( t2.getNode( "A" ) );
5686 t2.reRoot( t2.getNode( "B" ) );
5687 t2.reRoot( t2.getNode( "AB" ) );
5688 t2.reRoot( t2.getNode( "D" ) );
5689 t2.reRoot( t2.getNode( "D" ) );
5690 t2.reRoot( t2.getNode( "C" ) );
5691 t2.reRoot( t2.getNode( "A" ) );
5692 t2.reRoot( t2.getNode( "B" ) );
5693 t2.reRoot( t2.getNode( "AB" ) );
5694 t2.reRoot( t2.getNode( "C" ) );
5695 t2.reRoot( t2.getNode( "D" ) );
5696 t2.reRoot( t2.getNode( "ABC" ) );
5697 t2.reRoot( t2.getNode( "D" ) );
5698 t2.reRoot( t2.getNode( "A" ) );
5699 t2.reRoot( t2.getNode( "B" ) );
5700 t2.reRoot( t2.getNode( "AB" ) );
5701 t2.reRoot( t2.getNode( "C" ) );
5702 t2.reRoot( t2.getNode( "D" ) );
5703 t2.reRoot( t2.getNode( "ABC" ) );
5704 t2.reRoot( t2.getNode( "D" ) );
5705 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5708 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5711 t2.reRoot( t2.getNode( "ABC" ) );
5712 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5715 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5718 t2.reRoot( t2.getNode( "AB" ) );
5719 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5722 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5725 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5728 t2.reRoot( t2.getNode( "AB" ) );
5729 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5732 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5735 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5738 t2.reRoot( t2.getNode( "D" ) );
5739 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5742 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5745 t2.reRoot( t2.getNode( "ABC" ) );
5746 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5749 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5752 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5753 new NHXParser() )[ 0 ];
5754 t3.reRoot( t3.getNode( "B" ) );
5755 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5758 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5761 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5764 t3.reRoot( t3.getNode( "B" ) );
5765 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5768 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5771 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5774 t3.reRoot( t3.getRoot() );
5775 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5778 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5781 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5785 catch ( final Exception e ) {
5786 e.printStackTrace( System.out );
5792 private static boolean testSDIse() {
5794 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5795 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5796 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5797 gene1.setRooted( true );
5798 species1.setRooted( true );
5799 final SDI sdi = new SDIse( gene1, species1 );
5800 if ( !gene1.getRoot().isDuplication() ) {
5803 final Phylogeny species2 = factory
5804 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5805 new NHXParser() )[ 0 ];
5806 final Phylogeny gene2 = factory
5807 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5808 new NHXParser() )[ 0 ];
5809 species2.setRooted( true );
5810 gene2.setRooted( true );
5811 final SDI sdi2 = new SDIse( gene2, species2 );
5812 if ( sdi2.getDuplicationsSum() != 0 ) {
5815 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5818 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5821 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5824 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5827 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5830 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5833 final Phylogeny species3 = factory
5834 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5835 new NHXParser() )[ 0 ];
5836 final Phylogeny gene3 = factory
5837 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5838 new NHXParser() )[ 0 ];
5839 species3.setRooted( true );
5840 gene3.setRooted( true );
5841 final SDI sdi3 = new SDIse( gene3, species3 );
5842 if ( sdi3.getDuplicationsSum() != 1 ) {
5845 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5848 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5851 final Phylogeny species4 = factory
5852 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5853 new NHXParser() )[ 0 ];
5854 final Phylogeny gene4 = factory
5855 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5856 new NHXParser() )[ 0 ];
5857 species4.setRooted( true );
5858 gene4.setRooted( true );
5859 final SDI sdi4 = new SDIse( gene4, species4 );
5860 if ( sdi4.getDuplicationsSum() != 1 ) {
5863 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5866 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5869 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5872 if ( species4.getNumberOfExternalNodes() != 6 ) {
5875 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5878 final Phylogeny species5 = factory
5879 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5880 new NHXParser() )[ 0 ];
5881 final Phylogeny gene5 = factory
5882 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5883 new NHXParser() )[ 0 ];
5884 species5.setRooted( true );
5885 gene5.setRooted( true );
5886 final SDI sdi5 = new SDIse( gene5, species5 );
5887 if ( sdi5.getDuplicationsSum() != 2 ) {
5890 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5893 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5896 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5899 if ( species5.getNumberOfExternalNodes() != 6 ) {
5902 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5905 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5906 // Conjecture for Comparing Molecular Phylogenies"
5907 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5908 final Phylogeny species6 = factory
5909 .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,"
5910 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5911 new NHXParser() )[ 0 ];
5912 final Phylogeny gene6 = factory
5913 .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,"
5914 + "((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,"
5915 + "(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;",
5916 new NHXParser() )[ 0 ];
5917 species6.setRooted( true );
5918 gene6.setRooted( true );
5919 final SDI sdi6 = new SDIse( gene6, species6 );
5920 if ( sdi6.getDuplicationsSum() != 3 ) {
5923 if ( !gene6.getNode( "r" ).isDuplication() ) {
5926 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
5929 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
5932 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
5935 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
5938 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
5941 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
5944 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
5947 sdi6.computeMappingCostL();
5948 if ( sdi6.computeMappingCostL() != 17 ) {
5951 if ( species6.getNumberOfExternalNodes() != 9 ) {
5954 if ( gene6.getNumberOfExternalNodes() != 9 ) {
5957 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
5958 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
5959 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
5960 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
5961 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
5962 species7.setRooted( true );
5963 final Phylogeny gene7_1 = Test
5964 .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])" );
5965 gene7_1.setRooted( true );
5966 final SDI sdi7 = new SDIse( gene7_1, species7 );
5967 if ( sdi7.getDuplicationsSum() != 0 ) {
5970 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
5973 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
5976 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
5979 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
5982 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
5985 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
5988 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
5991 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
5994 final Phylogeny gene7_2 = Test
5995 .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])" );
5996 gene7_2.setRooted( true );
5997 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
5998 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6001 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6004 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6007 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6010 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6013 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6016 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6019 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6022 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6025 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6029 catch ( final Exception e ) {
6035 private static boolean testSDIunrooted() {
6037 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6038 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6039 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6040 final Iterator<PhylogenyBranch> iter = l.iterator();
6041 PhylogenyBranch br = iter.next();
6042 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6045 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6049 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6052 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6056 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6059 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6063 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6066 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6070 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6073 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6077 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6080 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6084 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6087 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6091 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6094 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6098 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6101 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6105 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6108 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6112 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6115 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6119 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6122 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6126 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6129 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6133 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6136 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6140 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6143 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6146 if ( iter.hasNext() ) {
6149 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6150 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6151 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6153 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6156 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6160 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6163 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6167 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6170 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6173 if ( iter1.hasNext() ) {
6176 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6177 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6178 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6180 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6183 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6187 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6190 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6194 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6197 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6200 if ( iter2.hasNext() ) {
6203 final Phylogeny species0 = factory
6204 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6205 new NHXParser() )[ 0 ];
6206 final Phylogeny gene1 = factory
6207 .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])",
6208 new NHXParser() )[ 0 ];
6209 species0.setRooted( true );
6210 gene1.setRooted( true );
6211 final SDIR sdi_unrooted = new SDIR();
6212 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6213 if ( sdi_unrooted.getCount() != 1 ) {
6216 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6219 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6222 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6225 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6228 final Phylogeny gene2 = factory
6229 .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])",
6230 new NHXParser() )[ 0 ];
6231 gene2.setRooted( true );
6232 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6233 if ( sdi_unrooted.getCount() != 1 ) {
6236 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6239 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6242 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6245 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6248 final Phylogeny species6 = factory
6249 .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,"
6250 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6251 new NHXParser() )[ 0 ];
6252 final Phylogeny gene6 = factory
6253 .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],"
6254 + "(((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],"
6255 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6256 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6257 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6258 new NHXParser() )[ 0 ];
6259 species6.setRooted( true );
6260 gene6.setRooted( true );
6261 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6262 if ( sdi_unrooted.getCount() != 1 ) {
6265 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6268 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6271 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6274 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6277 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6280 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6283 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6286 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6289 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6292 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6295 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6298 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6302 final Phylogeny species7 = factory
6303 .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,"
6304 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6305 new NHXParser() )[ 0 ];
6306 final Phylogeny gene7 = factory
6307 .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],"
6308 + "(((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],"
6309 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6310 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6311 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6312 new NHXParser() )[ 0 ];
6313 species7.setRooted( true );
6314 gene7.setRooted( true );
6315 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6316 if ( sdi_unrooted.getCount() != 1 ) {
6319 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6322 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6325 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6328 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6331 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6334 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6337 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6340 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6343 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6346 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6349 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6352 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6356 final Phylogeny species8 = factory
6357 .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,"
6358 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6359 new NHXParser() )[ 0 ];
6360 final Phylogeny gene8 = factory
6361 .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],"
6362 + "(((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],"
6363 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6364 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6365 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6366 new NHXParser() )[ 0 ];
6367 species8.setRooted( true );
6368 gene8.setRooted( true );
6369 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6370 if ( sdi_unrooted.getCount() != 1 ) {
6373 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6376 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6379 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6382 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6385 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6388 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6391 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6394 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6397 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6400 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6403 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6406 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6411 catch ( final Exception e ) {
6412 e.printStackTrace( System.out );
6418 private static boolean testSplit() {
6420 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6421 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6422 //Archaeopteryx.createApplication( p0 );
6423 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6424 ex.add( new PhylogenyNode( "A" ) );
6425 ex.add( new PhylogenyNode( "B" ) );
6426 ex.add( new PhylogenyNode( "C" ) );
6427 ex.add( new PhylogenyNode( "D" ) );
6428 ex.add( new PhylogenyNode( "E" ) );
6429 ex.add( new PhylogenyNode( "F" ) );
6430 ex.add( new PhylogenyNode( "G" ) );
6431 ex.add( new PhylogenyNode( "X" ) );
6432 ex.add( new PhylogenyNode( "Y" ) );
6433 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6434 // System.out.println( s0.toString() );
6436 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6437 query_nodes.add( new PhylogenyNode( "A" ) );
6438 query_nodes.add( new PhylogenyNode( "B" ) );
6439 if ( s0.match( query_nodes ) ) {
6442 query_nodes = new HashSet<PhylogenyNode>();
6443 query_nodes.add( new PhylogenyNode( "A" ) );
6444 query_nodes.add( new PhylogenyNode( "B" ) );
6445 query_nodes.add( new PhylogenyNode( "C" ) );
6446 query_nodes.add( new PhylogenyNode( "D" ) );
6447 query_nodes.add( new PhylogenyNode( "E" ) );
6448 query_nodes.add( new PhylogenyNode( "F" ) );
6449 query_nodes.add( new PhylogenyNode( "G" ) );
6450 if ( !s0.match( query_nodes ) ) {
6454 query_nodes = new HashSet<PhylogenyNode>();
6455 query_nodes.add( new PhylogenyNode( "A" ) );
6456 query_nodes.add( new PhylogenyNode( "B" ) );
6457 query_nodes.add( new PhylogenyNode( "C" ) );
6458 if ( !s0.match( query_nodes ) ) {
6462 query_nodes = new HashSet<PhylogenyNode>();
6463 query_nodes.add( new PhylogenyNode( "D" ) );
6464 query_nodes.add( new PhylogenyNode( "E" ) );
6465 query_nodes.add( new PhylogenyNode( "F" ) );
6466 query_nodes.add( new PhylogenyNode( "G" ) );
6467 if ( !s0.match( query_nodes ) ) {
6471 query_nodes = new HashSet<PhylogenyNode>();
6472 query_nodes.add( new PhylogenyNode( "A" ) );
6473 query_nodes.add( new PhylogenyNode( "B" ) );
6474 query_nodes.add( new PhylogenyNode( "C" ) );
6475 query_nodes.add( new PhylogenyNode( "D" ) );
6476 if ( !s0.match( query_nodes ) ) {
6480 query_nodes = new HashSet<PhylogenyNode>();
6481 query_nodes.add( new PhylogenyNode( "E" ) );
6482 query_nodes.add( new PhylogenyNode( "F" ) );
6483 query_nodes.add( new PhylogenyNode( "G" ) );
6484 if ( !s0.match( query_nodes ) ) {
6488 query_nodes = new HashSet<PhylogenyNode>();
6489 query_nodes.add( new PhylogenyNode( "F" ) );
6490 query_nodes.add( new PhylogenyNode( "G" ) );
6491 if ( !s0.match( query_nodes ) ) {
6495 query_nodes = new HashSet<PhylogenyNode>();
6496 query_nodes.add( new PhylogenyNode( "E" ) );
6497 query_nodes.add( new PhylogenyNode( "D" ) );
6498 query_nodes.add( new PhylogenyNode( "C" ) );
6499 query_nodes.add( new PhylogenyNode( "B" ) );
6500 query_nodes.add( new PhylogenyNode( "A" ) );
6501 if ( !s0.match( query_nodes ) ) {
6505 query_nodes = new HashSet<PhylogenyNode>();
6506 query_nodes.add( new PhylogenyNode( "F" ) );
6507 query_nodes.add( new PhylogenyNode( "G" ) );
6508 query_nodes.add( new PhylogenyNode( "E" ) );
6509 if ( !s0.match( query_nodes ) ) {
6513 query_nodes = new HashSet<PhylogenyNode>();
6514 query_nodes.add( new PhylogenyNode( "F" ) );
6515 query_nodes.add( new PhylogenyNode( "G" ) );
6516 query_nodes.add( new PhylogenyNode( "E" ) );
6517 query_nodes.add( new PhylogenyNode( "D" ) );
6518 if ( !s0.match( query_nodes ) ) {
6522 query_nodes = new HashSet<PhylogenyNode>();
6523 query_nodes.add( new PhylogenyNode( "F" ) );
6524 query_nodes.add( new PhylogenyNode( "A" ) );
6525 if ( s0.match( query_nodes ) ) {
6529 query_nodes = new HashSet<PhylogenyNode>();
6530 query_nodes.add( new PhylogenyNode( "A" ) );
6531 query_nodes.add( new PhylogenyNode( "E" ) );
6532 query_nodes.add( new PhylogenyNode( "B" ) );
6533 query_nodes.add( new PhylogenyNode( "C" ) );
6534 if ( s0.match( query_nodes ) ) {
6538 query_nodes = new HashSet<PhylogenyNode>();
6539 query_nodes.add( new PhylogenyNode( "F" ) );
6540 query_nodes.add( new PhylogenyNode( "G" ) );
6541 query_nodes.add( new PhylogenyNode( "E" ) );
6542 query_nodes.add( new PhylogenyNode( "D" ) );
6543 query_nodes.add( new PhylogenyNode( "C" ) );
6544 if ( s0.match( query_nodes ) ) {
6548 query_nodes = new HashSet<PhylogenyNode>();
6549 query_nodes.add( new PhylogenyNode( "A" ) );
6550 query_nodes.add( new PhylogenyNode( "B" ) );
6551 query_nodes.add( new PhylogenyNode( "D" ) );
6552 if ( s0.match( query_nodes ) ) {
6556 query_nodes = new HashSet<PhylogenyNode>();
6557 query_nodes.add( new PhylogenyNode( "A" ) );
6558 query_nodes.add( new PhylogenyNode( "D" ) );
6559 if ( s0.match( query_nodes ) ) {
6563 query_nodes = new HashSet<PhylogenyNode>();
6564 query_nodes.add( new PhylogenyNode( "A" ) );
6565 query_nodes.add( new PhylogenyNode( "B" ) );
6566 if ( s0.match( query_nodes ) ) {
6570 query_nodes = new HashSet<PhylogenyNode>();
6571 query_nodes.add( new PhylogenyNode( "A" ) );
6572 query_nodes.add( new PhylogenyNode( "C" ) );
6573 if ( s0.match( query_nodes ) ) {
6577 query_nodes = new HashSet<PhylogenyNode>();
6578 query_nodes.add( new PhylogenyNode( "A" ) );
6579 query_nodes.add( new PhylogenyNode( "E" ) );
6580 if ( s0.match( query_nodes ) ) {
6584 query_nodes = new HashSet<PhylogenyNode>();
6585 query_nodes.add( new PhylogenyNode( "A" ) );
6586 query_nodes.add( new PhylogenyNode( "F" ) );
6587 if ( s0.match( query_nodes ) ) {
6591 query_nodes = new HashSet<PhylogenyNode>();
6592 query_nodes.add( new PhylogenyNode( "A" ) );
6593 query_nodes.add( new PhylogenyNode( "G" ) );
6594 if ( s0.match( query_nodes ) ) {
6598 query_nodes = new HashSet<PhylogenyNode>();
6599 query_nodes.add( new PhylogenyNode( "A" ) );
6600 query_nodes.add( new PhylogenyNode( "F" ) );
6601 query_nodes.add( new PhylogenyNode( "G" ) );
6602 if ( s0.match( query_nodes ) ) {
6606 query_nodes = new HashSet<PhylogenyNode>();
6607 query_nodes.add( new PhylogenyNode( "A" ) );
6608 query_nodes.add( new PhylogenyNode( "B" ) );
6609 query_nodes.add( new PhylogenyNode( "D" ) );
6610 if ( s0.match( query_nodes ) ) {
6614 query_nodes = new HashSet<PhylogenyNode>();
6615 query_nodes.add( new PhylogenyNode( "E" ) );
6616 query_nodes.add( new PhylogenyNode( "D" ) );
6617 query_nodes.add( new PhylogenyNode( "A" ) );
6618 if ( s0.match( query_nodes ) ) {
6622 query_nodes = new HashSet<PhylogenyNode>();
6623 query_nodes.add( new PhylogenyNode( "E" ) );
6624 query_nodes.add( new PhylogenyNode( "D" ) );
6625 query_nodes.add( new PhylogenyNode( "A" ) );
6626 query_nodes.add( new PhylogenyNode( "G" ) );
6627 if ( s0.match( query_nodes ) ) {
6631 // query_nodes = new HashSet<PhylogenyNode>();
6632 // query_nodes.add( new PhylogenyNode( "X" ) );
6633 // query_nodes.add( new PhylogenyNode( "Y" ) );
6634 // query_nodes.add( new PhylogenyNode( "A" ) );
6635 // query_nodes.add( new PhylogenyNode( "B" ) );
6636 // query_nodes.add( new PhylogenyNode( "C" ) );
6637 // query_nodes.add( new PhylogenyNode( "D" ) );
6638 // query_nodes.add( new PhylogenyNode( "E" ) );
6639 // query_nodes.add( new PhylogenyNode( "F" ) );
6640 // query_nodes.add( new PhylogenyNode( "G" ) );
6641 // if ( !s0.match( query_nodes ) ) {
6644 // query_nodes = new HashSet<PhylogenyNode>();
6645 // query_nodes.add( new PhylogenyNode( "X" ) );
6646 // query_nodes.add( new PhylogenyNode( "Y" ) );
6647 // query_nodes.add( new PhylogenyNode( "A" ) );
6648 // query_nodes.add( new PhylogenyNode( "B" ) );
6649 // query_nodes.add( new PhylogenyNode( "C" ) );
6650 // if ( !s0.match( query_nodes ) ) {
6654 // query_nodes = new HashSet<PhylogenyNode>();
6655 // query_nodes.add( new PhylogenyNode( "X" ) );
6656 // query_nodes.add( new PhylogenyNode( "Y" ) );
6657 // query_nodes.add( new PhylogenyNode( "D" ) );
6658 // query_nodes.add( new PhylogenyNode( "E" ) );
6659 // query_nodes.add( new PhylogenyNode( "F" ) );
6660 // query_nodes.add( new PhylogenyNode( "G" ) );
6661 // if ( !s0.match( query_nodes ) ) {
6665 // query_nodes = new HashSet<PhylogenyNode>();
6666 // query_nodes.add( new PhylogenyNode( "X" ) );
6667 // query_nodes.add( new PhylogenyNode( "Y" ) );
6668 // query_nodes.add( new PhylogenyNode( "A" ) );
6669 // query_nodes.add( new PhylogenyNode( "B" ) );
6670 // query_nodes.add( new PhylogenyNode( "C" ) );
6671 // query_nodes.add( new PhylogenyNode( "D" ) );
6672 // if ( !s0.match( query_nodes ) ) {
6676 // query_nodes = new HashSet<PhylogenyNode>();
6677 // query_nodes.add( new PhylogenyNode( "X" ) );
6678 // query_nodes.add( new PhylogenyNode( "Y" ) );
6679 // query_nodes.add( new PhylogenyNode( "E" ) );
6680 // query_nodes.add( new PhylogenyNode( "F" ) );
6681 // query_nodes.add( new PhylogenyNode( "G" ) );
6682 // if ( !s0.match( query_nodes ) ) {
6686 // query_nodes = new HashSet<PhylogenyNode>();
6687 // query_nodes.add( new PhylogenyNode( "X" ) );
6688 // query_nodes.add( new PhylogenyNode( "Y" ) );
6689 // query_nodes.add( new PhylogenyNode( "F" ) );
6690 // query_nodes.add( new PhylogenyNode( "G" ) );
6691 // if ( !s0.match( query_nodes ) ) {
6695 query_nodes = new HashSet<PhylogenyNode>();
6696 query_nodes.add( new PhylogenyNode( "X" ) );
6697 query_nodes.add( new PhylogenyNode( "Y" ) );
6698 query_nodes.add( new PhylogenyNode( "E" ) );
6699 query_nodes.add( new PhylogenyNode( "G" ) );
6700 if ( s0.match( query_nodes ) ) {
6704 query_nodes = new HashSet<PhylogenyNode>();
6705 query_nodes.add( new PhylogenyNode( "X" ) );
6706 query_nodes.add( new PhylogenyNode( "Y" ) );
6707 query_nodes.add( new PhylogenyNode( "A" ) );
6708 query_nodes.add( new PhylogenyNode( "B" ) );
6709 if ( s0.match( query_nodes ) ) {
6712 ///////////////////////////
6714 query_nodes = new HashSet<PhylogenyNode>();
6715 query_nodes.add( new PhylogenyNode( "X" ) );
6716 query_nodes.add( new PhylogenyNode( "Y" ) );
6717 query_nodes.add( new PhylogenyNode( "A" ) );
6718 query_nodes.add( new PhylogenyNode( "D" ) );
6719 if ( s0.match( query_nodes ) ) {
6723 query_nodes = new HashSet<PhylogenyNode>();
6724 query_nodes.add( new PhylogenyNode( "X" ) );
6725 query_nodes.add( new PhylogenyNode( "Y" ) );
6726 query_nodes.add( new PhylogenyNode( "A" ) );
6727 query_nodes.add( new PhylogenyNode( "B" ) );
6728 if ( s0.match( query_nodes ) ) {
6732 query_nodes = new HashSet<PhylogenyNode>();
6733 query_nodes.add( new PhylogenyNode( "X" ) );
6734 query_nodes.add( new PhylogenyNode( "Y" ) );
6735 query_nodes.add( new PhylogenyNode( "A" ) );
6736 query_nodes.add( new PhylogenyNode( "C" ) );
6737 if ( s0.match( query_nodes ) ) {
6741 query_nodes = new HashSet<PhylogenyNode>();
6742 query_nodes.add( new PhylogenyNode( "X" ) );
6743 query_nodes.add( new PhylogenyNode( "Y" ) );
6744 query_nodes.add( new PhylogenyNode( "A" ) );
6745 query_nodes.add( new PhylogenyNode( "E" ) );
6746 if ( s0.match( query_nodes ) ) {
6750 query_nodes = new HashSet<PhylogenyNode>();
6751 query_nodes.add( new PhylogenyNode( "X" ) );
6752 query_nodes.add( new PhylogenyNode( "Y" ) );
6753 query_nodes.add( new PhylogenyNode( "A" ) );
6754 query_nodes.add( new PhylogenyNode( "F" ) );
6755 if ( s0.match( query_nodes ) ) {
6759 query_nodes = new HashSet<PhylogenyNode>();
6760 query_nodes.add( new PhylogenyNode( "Y" ) );
6761 query_nodes.add( new PhylogenyNode( "A" ) );
6762 query_nodes.add( new PhylogenyNode( "G" ) );
6763 if ( s0.match( query_nodes ) ) {
6767 query_nodes = new HashSet<PhylogenyNode>();
6768 query_nodes.add( new PhylogenyNode( "X" ) );
6769 query_nodes.add( new PhylogenyNode( "Y" ) );
6770 query_nodes.add( new PhylogenyNode( "A" ) );
6771 query_nodes.add( new PhylogenyNode( "F" ) );
6772 query_nodes.add( new PhylogenyNode( "G" ) );
6773 if ( s0.match( query_nodes ) ) {
6777 query_nodes = new HashSet<PhylogenyNode>();
6778 query_nodes.add( new PhylogenyNode( "X" ) );
6779 query_nodes.add( new PhylogenyNode( "Y" ) );
6780 query_nodes.add( new PhylogenyNode( "A" ) );
6781 query_nodes.add( new PhylogenyNode( "B" ) );
6782 query_nodes.add( new PhylogenyNode( "D" ) );
6783 if ( s0.match( query_nodes ) ) {
6787 query_nodes = new HashSet<PhylogenyNode>();
6788 query_nodes.add( new PhylogenyNode( "X" ) );
6789 query_nodes.add( new PhylogenyNode( "Y" ) );
6790 query_nodes.add( new PhylogenyNode( "E" ) );
6791 query_nodes.add( new PhylogenyNode( "D" ) );
6792 query_nodes.add( new PhylogenyNode( "A" ) );
6793 if ( s0.match( query_nodes ) ) {
6797 query_nodes = new HashSet<PhylogenyNode>();
6798 query_nodes.add( new PhylogenyNode( "X" ) );
6799 query_nodes.add( new PhylogenyNode( "Y" ) );
6800 query_nodes.add( new PhylogenyNode( "E" ) );
6801 query_nodes.add( new PhylogenyNode( "D" ) );
6802 query_nodes.add( new PhylogenyNode( "A" ) );
6803 query_nodes.add( new PhylogenyNode( "G" ) );
6804 if ( s0.match( query_nodes ) ) {
6808 catch ( final Exception e ) {
6809 e.printStackTrace();
6815 private static boolean testSplitStrict() {
6817 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6818 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6819 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6820 ex.add( new PhylogenyNode( "A" ) );
6821 ex.add( new PhylogenyNode( "B" ) );
6822 ex.add( new PhylogenyNode( "C" ) );
6823 ex.add( new PhylogenyNode( "D" ) );
6824 ex.add( new PhylogenyNode( "E" ) );
6825 ex.add( new PhylogenyNode( "F" ) );
6826 ex.add( new PhylogenyNode( "G" ) );
6827 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6828 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6829 query_nodes.add( new PhylogenyNode( "A" ) );
6830 query_nodes.add( new PhylogenyNode( "B" ) );
6831 if ( s0.match( query_nodes ) ) {
6834 query_nodes = new HashSet<PhylogenyNode>();
6835 query_nodes.add( new PhylogenyNode( "A" ) );
6836 query_nodes.add( new PhylogenyNode( "B" ) );
6837 query_nodes.add( new PhylogenyNode( "C" ) );
6838 query_nodes.add( new PhylogenyNode( "D" ) );
6839 query_nodes.add( new PhylogenyNode( "E" ) );
6840 query_nodes.add( new PhylogenyNode( "F" ) );
6841 query_nodes.add( new PhylogenyNode( "G" ) );
6842 if ( !s0.match( query_nodes ) ) {
6846 query_nodes = new HashSet<PhylogenyNode>();
6847 query_nodes.add( new PhylogenyNode( "A" ) );
6848 query_nodes.add( new PhylogenyNode( "B" ) );
6849 query_nodes.add( new PhylogenyNode( "C" ) );
6850 if ( !s0.match( query_nodes ) ) {
6854 query_nodes = new HashSet<PhylogenyNode>();
6855 query_nodes.add( new PhylogenyNode( "D" ) );
6856 query_nodes.add( new PhylogenyNode( "E" ) );
6857 query_nodes.add( new PhylogenyNode( "F" ) );
6858 query_nodes.add( new PhylogenyNode( "G" ) );
6859 if ( !s0.match( query_nodes ) ) {
6863 query_nodes = new HashSet<PhylogenyNode>();
6864 query_nodes.add( new PhylogenyNode( "A" ) );
6865 query_nodes.add( new PhylogenyNode( "B" ) );
6866 query_nodes.add( new PhylogenyNode( "C" ) );
6867 query_nodes.add( new PhylogenyNode( "D" ) );
6868 if ( !s0.match( query_nodes ) ) {
6872 query_nodes = new HashSet<PhylogenyNode>();
6873 query_nodes.add( new PhylogenyNode( "E" ) );
6874 query_nodes.add( new PhylogenyNode( "F" ) );
6875 query_nodes.add( new PhylogenyNode( "G" ) );
6876 if ( !s0.match( query_nodes ) ) {
6880 query_nodes = new HashSet<PhylogenyNode>();
6881 query_nodes.add( new PhylogenyNode( "F" ) );
6882 query_nodes.add( new PhylogenyNode( "G" ) );
6883 if ( !s0.match( query_nodes ) ) {
6887 query_nodes = new HashSet<PhylogenyNode>();
6888 query_nodes.add( new PhylogenyNode( "E" ) );
6889 query_nodes.add( new PhylogenyNode( "D" ) );
6890 query_nodes.add( new PhylogenyNode( "C" ) );
6891 query_nodes.add( new PhylogenyNode( "B" ) );
6892 query_nodes.add( new PhylogenyNode( "A" ) );
6893 if ( !s0.match( query_nodes ) ) {
6897 query_nodes = new HashSet<PhylogenyNode>();
6898 query_nodes.add( new PhylogenyNode( "F" ) );
6899 query_nodes.add( new PhylogenyNode( "G" ) );
6900 query_nodes.add( new PhylogenyNode( "E" ) );
6901 if ( !s0.match( query_nodes ) ) {
6905 query_nodes = new HashSet<PhylogenyNode>();
6906 query_nodes.add( new PhylogenyNode( "F" ) );
6907 query_nodes.add( new PhylogenyNode( "G" ) );
6908 query_nodes.add( new PhylogenyNode( "E" ) );
6909 query_nodes.add( new PhylogenyNode( "D" ) );
6910 if ( !s0.match( query_nodes ) ) {
6914 query_nodes = new HashSet<PhylogenyNode>();
6915 query_nodes.add( new PhylogenyNode( "F" ) );
6916 query_nodes.add( new PhylogenyNode( "A" ) );
6917 if ( s0.match( query_nodes ) ) {
6921 query_nodes = new HashSet<PhylogenyNode>();
6922 query_nodes.add( new PhylogenyNode( "A" ) );
6923 query_nodes.add( new PhylogenyNode( "E" ) );
6924 query_nodes.add( new PhylogenyNode( "B" ) );
6925 query_nodes.add( new PhylogenyNode( "C" ) );
6926 if ( s0.match( query_nodes ) ) {
6930 query_nodes = new HashSet<PhylogenyNode>();
6931 query_nodes.add( new PhylogenyNode( "F" ) );
6932 query_nodes.add( new PhylogenyNode( "G" ) );
6933 query_nodes.add( new PhylogenyNode( "E" ) );
6934 query_nodes.add( new PhylogenyNode( "D" ) );
6935 query_nodes.add( new PhylogenyNode( "C" ) );
6936 if ( s0.match( query_nodes ) ) {
6940 query_nodes = new HashSet<PhylogenyNode>();
6941 query_nodes.add( new PhylogenyNode( "A" ) );
6942 query_nodes.add( new PhylogenyNode( "B" ) );
6943 query_nodes.add( new PhylogenyNode( "D" ) );
6944 if ( s0.match( query_nodes ) ) {
6948 query_nodes = new HashSet<PhylogenyNode>();
6949 query_nodes.add( new PhylogenyNode( "A" ) );
6950 query_nodes.add( new PhylogenyNode( "D" ) );
6951 if ( s0.match( query_nodes ) ) {
6955 query_nodes = new HashSet<PhylogenyNode>();
6956 query_nodes.add( new PhylogenyNode( "A" ) );
6957 query_nodes.add( new PhylogenyNode( "B" ) );
6958 if ( s0.match( query_nodes ) ) {
6962 query_nodes = new HashSet<PhylogenyNode>();
6963 query_nodes.add( new PhylogenyNode( "A" ) );
6964 query_nodes.add( new PhylogenyNode( "C" ) );
6965 if ( s0.match( query_nodes ) ) {
6969 query_nodes = new HashSet<PhylogenyNode>();
6970 query_nodes.add( new PhylogenyNode( "A" ) );
6971 query_nodes.add( new PhylogenyNode( "E" ) );
6972 if ( s0.match( query_nodes ) ) {
6976 query_nodes = new HashSet<PhylogenyNode>();
6977 query_nodes.add( new PhylogenyNode( "A" ) );
6978 query_nodes.add( new PhylogenyNode( "F" ) );
6979 if ( s0.match( query_nodes ) ) {
6983 query_nodes = new HashSet<PhylogenyNode>();
6984 query_nodes.add( new PhylogenyNode( "A" ) );
6985 query_nodes.add( new PhylogenyNode( "G" ) );
6986 if ( s0.match( query_nodes ) ) {
6990 query_nodes = new HashSet<PhylogenyNode>();
6991 query_nodes.add( new PhylogenyNode( "A" ) );
6992 query_nodes.add( new PhylogenyNode( "F" ) );
6993 query_nodes.add( new PhylogenyNode( "G" ) );
6994 if ( s0.match( query_nodes ) ) {
6998 query_nodes = new HashSet<PhylogenyNode>();
6999 query_nodes.add( new PhylogenyNode( "A" ) );
7000 query_nodes.add( new PhylogenyNode( "B" ) );
7001 query_nodes.add( new PhylogenyNode( "D" ) );
7002 if ( s0.match( query_nodes ) ) {
7006 query_nodes = new HashSet<PhylogenyNode>();
7007 query_nodes.add( new PhylogenyNode( "E" ) );
7008 query_nodes.add( new PhylogenyNode( "D" ) );
7009 query_nodes.add( new PhylogenyNode( "A" ) );
7010 if ( s0.match( query_nodes ) ) {
7014 query_nodes = new HashSet<PhylogenyNode>();
7015 query_nodes.add( new PhylogenyNode( "E" ) );
7016 query_nodes.add( new PhylogenyNode( "D" ) );
7017 query_nodes.add( new PhylogenyNode( "A" ) );
7018 query_nodes.add( new PhylogenyNode( "G" ) );
7019 if ( s0.match( query_nodes ) ) {
7023 catch ( final Exception e ) {
7024 e.printStackTrace();
7030 private static boolean testSubtreeDeletion() {
7032 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7033 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7034 t1.deleteSubtree( t1.getNode( "A" ), false );
7035 if ( t1.getNumberOfExternalNodes() != 5 ) {
7038 t1.toNewHampshireX();
7039 t1.deleteSubtree( t1.getNode( "E" ), false );
7040 if ( t1.getNumberOfExternalNodes() != 4 ) {
7043 t1.toNewHampshireX();
7044 t1.deleteSubtree( t1.getNode( "F" ), false );
7045 if ( t1.getNumberOfExternalNodes() != 3 ) {
7048 t1.toNewHampshireX();
7049 t1.deleteSubtree( t1.getNode( "D" ), false );
7050 t1.toNewHampshireX();
7051 if ( t1.getNumberOfExternalNodes() != 3 ) {
7054 t1.deleteSubtree( t1.getNode( "def" ), false );
7055 t1.toNewHampshireX();
7056 if ( t1.getNumberOfExternalNodes() != 2 ) {
7059 t1.deleteSubtree( t1.getNode( "B" ), false );
7060 t1.toNewHampshireX();
7061 if ( t1.getNumberOfExternalNodes() != 1 ) {
7064 t1.deleteSubtree( t1.getNode( "C" ), false );
7065 t1.toNewHampshireX();
7066 if ( t1.getNumberOfExternalNodes() != 1 ) {
7069 t1.deleteSubtree( t1.getNode( "abc" ), false );
7070 t1.toNewHampshireX();
7071 if ( t1.getNumberOfExternalNodes() != 1 ) {
7074 t1.deleteSubtree( t1.getNode( "r" ), false );
7075 if ( t1.getNumberOfExternalNodes() != 0 ) {
7078 if ( !t1.isEmpty() ) {
7081 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7082 t2.deleteSubtree( t2.getNode( "A" ), false );
7083 t2.toNewHampshireX();
7084 if ( t2.getNumberOfExternalNodes() != 5 ) {
7087 t2.deleteSubtree( t2.getNode( "abc" ), false );
7088 t2.toNewHampshireX();
7089 if ( t2.getNumberOfExternalNodes() != 3 ) {
7092 t2.deleteSubtree( t2.getNode( "def" ), false );
7093 t2.toNewHampshireX();
7094 if ( t2.getNumberOfExternalNodes() != 1 ) {
7098 catch ( final Exception e ) {
7099 e.printStackTrace( System.out );
7105 private static boolean testSupportCount() {
7107 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7108 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7109 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7110 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7111 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7112 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7113 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7115 SupportCount.count( t0_1, phylogenies_1, true, false );
7116 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7117 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7118 + "(((((A,B),C),D),E),((F,G),X))"
7119 + "(((((A,Y),B),C),D),((F,G),E))"
7120 + "(((((A,B),C),D),E),(F,G))"
7121 + "(((((A,B),C),D),E),(F,G))"
7122 + "(((((A,B),C),D),E),(F,G))"
7123 + "(((((A,B),C),D),E),(F,G),Z)"
7124 + "(((((A,B),C),D),E),(F,G))"
7125 + "((((((A,B),C),D),E),F),G)"
7126 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7128 SupportCount.count( t0_2, phylogenies_2, true, false );
7129 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7130 while ( it.hasNext() ) {
7131 final PhylogenyNode n = it.next();
7132 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7136 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7137 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7138 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7139 SupportCount.count( t0_3, phylogenies_3, true, false );
7140 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7141 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7144 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7147 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7150 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7153 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7156 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7159 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7162 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7165 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7168 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7171 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7172 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7173 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7174 SupportCount.count( t0_4, phylogenies_4, true, false );
7175 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7176 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7179 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7182 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7185 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7188 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7191 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7194 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7197 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7200 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7203 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7206 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7207 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7208 double d = SupportCount.compare( b1, a, true, true, true );
7209 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7212 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7213 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7214 d = SupportCount.compare( b2, a, true, true, true );
7215 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7218 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7219 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7220 d = SupportCount.compare( b3, a, true, true, true );
7221 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7224 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7225 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7226 d = SupportCount.compare( b4, a, true, true, false );
7227 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7231 catch ( final Exception e ) {
7232 e.printStackTrace( System.out );
7238 private static boolean testSupportTransfer() {
7240 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7241 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)",
7242 new NHXParser() )[ 0 ];
7243 final Phylogeny p2 = factory
7244 .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 ];
7245 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7248 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7251 support_transfer.moveBranchLengthsToBootstrap( p1 );
7252 support_transfer.transferSupportValues( p1, p2 );
7253 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7256 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7259 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7262 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7265 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7268 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7271 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7274 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7278 catch ( final Exception e ) {
7279 e.printStackTrace( System.out );
7285 private static boolean testTaxonomyAssigner() {
7287 String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]";
7288 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7289 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7290 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7291 s0.setRooted( true );
7292 g0.setRooted( true );
7293 TaxonomyAssigner.execute( g0, s0 );
7294 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7297 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7300 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7303 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7304 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7305 g0.setRooted( true );
7306 TaxonomyAssigner.execute( g0, s0 );
7307 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7310 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7313 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7316 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7317 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7318 g0.setRooted( true );
7319 TaxonomyAssigner.execute( g0, s0 );
7320 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7323 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7326 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7329 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7330 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7331 g0.setRooted( true );
7332 TaxonomyAssigner.execute( g0, s0 );
7333 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7336 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7339 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7342 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7343 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7344 g0.setRooted( true );
7345 TaxonomyAssigner.execute( g0, s0 );
7346 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7349 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7352 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7355 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7356 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7357 g0.setRooted( true );
7358 TaxonomyAssigner.execute( g0, s0 );
7359 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7362 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7365 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7368 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7369 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7370 g0.setRooted( true );
7371 TaxonomyAssigner.execute( g0, s0 );
7372 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7375 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7378 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7381 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7382 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7383 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7384 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7385 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7386 s0.setRooted( true );
7387 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7388 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7389 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7390 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7391 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7392 g0.setRooted( true );
7393 TaxonomyAssigner.execute( g0, s0 );
7394 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7397 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7400 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7403 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7406 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7409 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7410 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7411 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7412 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7413 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7414 g0.setRooted( true );
7415 TaxonomyAssigner.execute( g0, s0 );
7416 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7419 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7422 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7425 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7428 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7431 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7432 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7433 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7434 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7435 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7436 g0.setRooted( true );
7437 TaxonomyAssigner.execute( g0, s0 );
7438 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7441 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7444 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7447 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7450 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7453 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7454 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7455 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7456 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7457 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7458 g0.setRooted( true );
7459 TaxonomyAssigner.execute( g0, s0 );
7460 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7463 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7466 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7469 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7472 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7475 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7476 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7477 g0.setRooted( true );
7478 TaxonomyAssigner.execute( g0, s0 );
7479 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7482 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7485 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7488 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7489 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7490 g0.setRooted( true );
7491 TaxonomyAssigner.execute( g0, s0 );
7492 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7495 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7498 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7501 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7502 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7503 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7504 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7505 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7506 g0.setRooted( true );
7507 TaxonomyAssigner.execute( g0, s0 );
7508 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7511 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7514 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7517 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7520 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7523 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7526 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7529 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7530 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7531 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7532 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7533 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7534 g0.setRooted( true );
7535 TaxonomyAssigner.execute( g0, s0 );
7536 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7539 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7542 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7545 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7548 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7551 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7554 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7557 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7558 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7559 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7560 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7561 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7562 g0.setRooted( true );
7563 TaxonomyAssigner.execute( g0, s0 );
7564 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7567 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7570 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7573 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7576 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7579 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7582 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7585 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7586 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7587 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7588 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7589 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7590 g0.setRooted( true );
7591 TaxonomyAssigner.execute( g0, s0 );
7592 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7595 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7598 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7601 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7604 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7607 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7610 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7613 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7614 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7615 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7616 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7617 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7618 s0.setRooted( true );
7619 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7620 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7621 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7622 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7623 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7624 g0.setRooted( true );
7625 TaxonomyAssigner.execute( g0, s0 );
7626 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7629 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7633 catch ( final Exception e ) {
7634 e.printStackTrace( System.out );
7640 private static boolean testUniprotTaxonomySearch() {
7642 List<UniProtTaxonomy> results = UniProtWsTools
7643 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7644 if ( results.size() != 1 ) {
7647 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7650 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7653 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7656 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7659 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7663 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7664 if ( results.size() != 1 ) {
7667 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7670 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7673 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7676 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7679 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7683 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7684 if ( results.size() != 1 ) {
7687 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7690 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7693 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7696 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7699 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7703 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7704 if ( results.size() != 1 ) {
7707 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7710 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7713 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7716 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7719 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7722 if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) {
7725 if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) {
7728 if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) {
7732 catch ( final IOException e ) {
7733 System.out.println();
7734 System.out.println( "the following might be due to absence internet connection:" );
7735 e.printStackTrace( System.out );
7738 catch ( final Exception e ) {
7744 private static boolean testEmblEntryRetrieval() {
7745 //The format for GenBank Accession numbers are:
7746 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7747 //Protein: 3 letters + 5 numerals
7748 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7749 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7752 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7755 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7758 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7761 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7764 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7767 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7770 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7773 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7776 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7779 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7782 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7785 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7791 private static boolean testUniprotEntryRetrieval() {
7792 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7795 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7798 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7801 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7804 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7807 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7810 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7813 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7816 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7819 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7822 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7825 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7828 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7832 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7833 if ( !entry.getAccession().equals( "P12345" ) ) {
7836 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7839 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7842 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7845 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7849 catch ( final IOException e ) {
7850 System.out.println();
7851 System.out.println( "the following might be due to absence internet connection:" );
7852 e.printStackTrace( System.out );
7855 catch ( final Exception e ) {
7861 private static boolean testWabiTxSearch() {
7864 result = TxSearch.searchSimple( "nematostella" );
7865 result = TxSearch.getTxId( "nematostella" );
7866 if ( !result.equals( "45350" ) ) {
7869 result = TxSearch.getTxName( "45350" );
7870 if ( !result.equals( "Nematostella" ) ) {
7873 result = TxSearch.getTxId( "nematostella vectensis" );
7874 if ( !result.equals( "45351" ) ) {
7877 result = TxSearch.getTxName( "45351" );
7878 if ( !result.equals( "Nematostella vectensis" ) ) {
7881 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7882 if ( !result.equals( "536089" ) ) {
7885 result = TxSearch.getTxName( "536089" );
7886 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7889 final List<String> queries = new ArrayList<String>();
7890 queries.add( "Campylobacter coli" );
7891 queries.add( "Escherichia coli" );
7892 queries.add( "Arabidopsis" );
7893 queries.add( "Trichoplax" );
7894 queries.add( "Samanea saman" );
7895 queries.add( "Kluyveromyces marxianus" );
7896 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7897 queries.add( "Bornavirus parrot/PDD/2008" );
7898 final List<RANKS> ranks = new ArrayList<RANKS>();
7899 ranks.add( RANKS.SUPERKINGDOM );
7900 ranks.add( RANKS.KINGDOM );
7901 ranks.add( RANKS.FAMILY );
7902 ranks.add( RANKS.GENUS );
7903 ranks.add( RANKS.TRIBE );
7904 result = TxSearch.searchLineage( queries, ranks );
7905 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7906 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7908 catch ( final Exception e ) {
7909 System.out.println();
7910 System.out.println( "the following might be due to absence internet connection:" );
7911 e.printStackTrace( System.out );
7917 private static boolean testAminoAcidSequence() {
7919 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7920 if ( aa1.getLength() != 13 ) {
7923 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7926 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7929 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7932 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7933 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7936 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7937 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7940 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7941 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7945 catch ( final Exception e ) {
7946 e.printStackTrace();
7952 private static boolean testCreateBalancedPhylogeny() {
7954 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7955 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7958 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7961 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7962 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7965 if ( p1.getNumberOfExternalNodes() != 100 ) {
7969 catch ( final Exception e ) {
7970 e.printStackTrace();
7976 private static boolean testFastaParser() {
7978 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7981 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7984 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7985 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7988 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7991 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7994 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7997 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8000 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8004 catch ( final Exception e ) {
8005 e.printStackTrace();
8011 private static boolean testGeneralMsaParser() {
8013 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8014 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8015 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8016 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8017 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8018 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8019 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8020 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8021 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8022 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8025 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8028 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8031 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8032 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8035 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8038 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8041 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8042 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8045 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8048 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8052 catch ( final Exception e ) {
8053 e.printStackTrace();
8059 private static boolean testMafft() {
8061 final List<String> opts = new ArrayList<String>();
8062 opts.add( "--maxiterate" );
8064 opts.add( "--localpair" );
8065 opts.add( "--quiet" );
8067 final MsaInferrer mafft = Mafft.createInstance();
8068 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8069 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8073 catch ( final Exception e ) {
8074 e.printStackTrace( System.out );