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 = PhylogenyNode
788 .createInstanceFromNhxString( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
789 final PhylogenyNode n3 = PhylogenyNode
790 .createInstanceFromNhxString( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
791 final PhylogenyNode n4 = PhylogenyNode
792 .createInstanceFromNhxString( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
793 if ( n1.isHasAssignedEvent() ) {
796 if ( PhylogenyNode.getNodeCount() != 4 ) {
799 if ( n3.getIndicator() != 0 ) {
802 if ( n3.getNumberOfExternalNodes() != 1 ) {
805 if ( !n3.isExternal() ) {
808 if ( !n3.isRoot() ) {
811 if ( !n4.getName().equals( "n4" ) ) {
815 catch ( final Exception e ) {
816 e.printStackTrace( System.out );
822 private static boolean testBasicPhyloXMLparsing() {
824 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
825 final PhyloXmlParser xml_parser = new PhyloXmlParser();
826 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
828 if ( xml_parser.getErrorCount() > 0 ) {
829 System.out.println( xml_parser.getErrorMessages().toString() );
832 if ( phylogenies_0.length != 4 ) {
835 final Phylogeny t1 = phylogenies_0[ 0 ];
836 final Phylogeny t2 = phylogenies_0[ 1 ];
837 final Phylogeny t3 = phylogenies_0[ 2 ];
838 final Phylogeny t4 = phylogenies_0[ 3 ];
839 if ( t1.getNumberOfExternalNodes() != 1 ) {
842 if ( !t1.isRooted() ) {
845 if ( t1.isRerootable() ) {
848 if ( !t1.getType().equals( "gene_tree" ) ) {
851 if ( t2.getNumberOfExternalNodes() != 2 ) {
854 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
857 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
860 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
863 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
866 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
869 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
872 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
873 .startsWith( "actgtgggggt" ) ) {
876 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
877 .startsWith( "ctgtgatgcat" ) ) {
880 if ( t3.getNumberOfExternalNodes() != 4 ) {
883 if ( !t1.getName().equals( "t1" ) ) {
886 if ( !t2.getName().equals( "t2" ) ) {
889 if ( !t3.getName().equals( "t3" ) ) {
892 if ( !t4.getName().equals( "t4" ) ) {
895 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
898 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
901 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
904 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
905 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
908 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
911 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
914 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
917 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
918 .equals( "apoptosis" ) ) {
921 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
922 .equals( "GO:0006915" ) ) {
925 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
926 .equals( "UniProtKB" ) ) {
929 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
930 .equals( "experimental" ) ) {
933 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
934 .equals( "function" ) ) {
937 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
941 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
942 .getType().equals( "ml" ) ) {
945 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
946 .equals( "apoptosis" ) ) {
949 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
950 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
953 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
954 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
957 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
958 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
961 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
962 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
965 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
966 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
969 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
970 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
973 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
974 .equals( "GO:0005829" ) ) {
977 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
978 .equals( "intracellular organelle" ) ) {
981 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
984 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
985 .equals( "UniProt link" ) ) ) {
988 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
991 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
994 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
997 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1000 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1003 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1006 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1009 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1012 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1015 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1018 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1019 // .equals( "B" ) ) {
1022 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1025 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1028 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1031 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1032 // .getConfidence() != 2144 ) {
1035 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1036 // .equals( "pfam" ) ) {
1039 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1042 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1045 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1048 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1051 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1052 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1056 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1059 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1062 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1065 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1068 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1071 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1074 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1077 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1079 // if ( xml_parser.getErrorCount() > 0 ) {
1080 // System.out.println( xml_parser.getErrorMessages().toString() );
1083 // if ( phylogenies_1.length != 2 ) {
1086 // final Phylogeny a = phylogenies_1[ 0 ];
1087 // if ( !a.getName().equals( "tree 4" ) ) {
1090 // if ( a.getNumberOfExternalNodes() != 3 ) {
1093 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1096 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1100 catch ( final Exception e ) {
1101 e.printStackTrace( System.out );
1107 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1109 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1110 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1111 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1112 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1115 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1117 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1119 if ( xml_parser.getErrorCount() > 0 ) {
1120 System.out.println( xml_parser.getErrorMessages().toString() );
1123 if ( phylogenies_0.length != 4 ) {
1126 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1127 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1128 if ( phylogenies_t1.length != 1 ) {
1131 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1132 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1135 if ( !t1_rt.isRooted() ) {
1138 if ( t1_rt.isRerootable() ) {
1141 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1144 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1145 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1146 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1147 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1150 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1153 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1156 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1159 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1160 .startsWith( "actgtgggggt" ) ) {
1163 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1164 .startsWith( "ctgtgatgcat" ) ) {
1167 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1168 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1169 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1170 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1171 if ( phylogenies_1.length != 1 ) {
1174 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1175 if ( !t3_rt.getName().equals( "t3" ) ) {
1178 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1181 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1184 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1187 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1190 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1191 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1194 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1197 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1200 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1201 .equals( "UniProtKB" ) ) {
1204 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1205 .equals( "apoptosis" ) ) {
1208 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1209 .equals( "GO:0006915" ) ) {
1212 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1213 .equals( "UniProtKB" ) ) {
1216 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1217 .equals( "experimental" ) ) {
1220 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1221 .equals( "function" ) ) {
1224 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1225 .getValue() != 1 ) {
1228 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1229 .getType().equals( "ml" ) ) {
1232 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1233 .equals( "apoptosis" ) ) {
1236 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1237 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1241 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1244 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1245 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1249 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1253 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1256 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1257 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1261 .equals( "GO:0005829" ) ) {
1264 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1265 .equals( "intracellular organelle" ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1271 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1272 .equals( "UniProt link" ) ) ) {
1275 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1278 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1281 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1282 .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." ) ) ) {
1285 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1288 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1291 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1294 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1297 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1298 .equals( "ncbi" ) ) {
1301 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1304 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1305 .getName().equals( "B" ) ) {
1308 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1309 .getFrom() != 21 ) {
1312 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1315 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1316 .getLength() != 24 ) {
1319 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1320 .getConfidence() != 2144 ) {
1323 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1324 .equals( "pfam" ) ) {
1327 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1330 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1333 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1336 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1339 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1340 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1343 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1346 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1349 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1352 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1355 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1358 if ( taxbb.getSynonyms().size() != 2 ) {
1361 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1364 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1367 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1370 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1373 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1376 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1377 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1381 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1384 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1387 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1390 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1393 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1396 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1399 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1403 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1406 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1407 .equalsIgnoreCase( "435" ) ) {
1410 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1413 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1414 .equalsIgnoreCase( "443.7" ) ) {
1417 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1420 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1423 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1424 .equalsIgnoreCase( "433" ) ) {
1428 catch ( final Exception e ) {
1429 e.printStackTrace( System.out );
1435 private static boolean testBasicPhyloXMLparsingValidating() {
1437 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1438 PhyloXmlParser xml_parser = null;
1440 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1442 catch ( final Exception e ) {
1443 // Do nothing -- means were not running from jar.
1445 if ( xml_parser == null ) {
1446 xml_parser = new PhyloXmlParser();
1447 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1448 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1451 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1454 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1456 if ( xml_parser.getErrorCount() > 0 ) {
1457 System.out.println( xml_parser.getErrorMessages().toString() );
1460 if ( phylogenies_0.length != 4 ) {
1463 final Phylogeny t1 = phylogenies_0[ 0 ];
1464 final Phylogeny t2 = phylogenies_0[ 1 ];
1465 final Phylogeny t3 = phylogenies_0[ 2 ];
1466 final Phylogeny t4 = phylogenies_0[ 3 ];
1467 if ( !t1.getName().equals( "t1" ) ) {
1470 if ( !t2.getName().equals( "t2" ) ) {
1473 if ( !t3.getName().equals( "t3" ) ) {
1476 if ( !t4.getName().equals( "t4" ) ) {
1479 if ( t1.getNumberOfExternalNodes() != 1 ) {
1482 if ( t2.getNumberOfExternalNodes() != 2 ) {
1485 if ( t3.getNumberOfExternalNodes() != 4 ) {
1488 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1489 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1490 if ( xml_parser.getErrorCount() > 0 ) {
1491 System.out.println( "errors:" );
1492 System.out.println( xml_parser.getErrorMessages().toString() );
1495 if ( phylogenies_1.length != 4 ) {
1498 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1500 if ( xml_parser.getErrorCount() > 0 ) {
1501 System.out.println( "errors:" );
1502 System.out.println( xml_parser.getErrorMessages().toString() );
1505 if ( phylogenies_2.length != 1 ) {
1508 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1511 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1513 if ( xml_parser.getErrorCount() > 0 ) {
1514 System.out.println( xml_parser.getErrorMessages().toString() );
1517 if ( phylogenies_3.length != 2 ) {
1520 final Phylogeny a = phylogenies_3[ 0 ];
1521 if ( !a.getName().equals( "tree 4" ) ) {
1524 if ( a.getNumberOfExternalNodes() != 3 ) {
1527 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1530 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1533 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1535 if ( xml_parser.getErrorCount() > 0 ) {
1536 System.out.println( xml_parser.getErrorMessages().toString() );
1539 if ( phylogenies_4.length != 1 ) {
1542 final Phylogeny s = phylogenies_4[ 0 ];
1543 if ( s.getNumberOfExternalNodes() != 6 ) {
1546 s.getNode( "first" );
1548 s.getNode( "\"<a'b&c'd\">\"" );
1549 s.getNode( "'''\"" );
1550 s.getNode( "\"\"\"" );
1551 s.getNode( "dick & doof" );
1553 catch ( final Exception e ) {
1554 e.printStackTrace( System.out );
1560 private static boolean testBasicTable() {
1562 final BasicTable<String> t0 = new BasicTable<String>();
1563 if ( t0.getNumberOfColumns() != 0 ) {
1566 if ( t0.getNumberOfRows() != 0 ) {
1569 t0.setValue( 3, 2, "23" );
1570 t0.setValue( 10, 1, "error" );
1571 t0.setValue( 10, 1, "110" );
1572 t0.setValue( 9, 1, "19" );
1573 t0.setValue( 1, 10, "101" );
1574 t0.setValue( 10, 10, "1010" );
1575 t0.setValue( 100, 10, "10100" );
1576 t0.setValue( 0, 0, "00" );
1577 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1580 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1583 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1586 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1589 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1592 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1595 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1598 if ( t0.getNumberOfColumns() != 101 ) {
1601 if ( t0.getNumberOfRows() != 11 ) {
1604 if ( t0.getValueAsString( 49, 4 ) != null ) {
1607 final String l = ForesterUtil.getLineSeparator();
1608 final StringBuffer source = new StringBuffer();
1609 source.append( "" + l );
1610 source.append( "# 1 1 1 1 1 1 1 1" + l );
1611 source.append( " 00 01 02 03" + l );
1612 source.append( " 10 11 12 13 " + l );
1613 source.append( "20 21 22 23 " + l );
1614 source.append( " 30 31 32 33" + l );
1615 source.append( "40 41 42 43" + l );
1616 source.append( " # 1 1 1 1 1 " + l );
1617 source.append( "50 51 52 53 54" + l );
1618 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1619 if ( t1.getNumberOfColumns() != 5 ) {
1622 if ( t1.getNumberOfRows() != 6 ) {
1625 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1628 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1631 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1634 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1637 final StringBuffer source1 = new StringBuffer();
1638 source1.append( "" + l );
1639 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1640 source1.append( " 00; 01 ;02;03" + l );
1641 source1.append( " 10; 11; 12; 13 " + l );
1642 source1.append( "20; 21; 22; 23 " + l );
1643 source1.append( " 30; 31; 32; 33" + l );
1644 source1.append( "40;41;42;43" + l );
1645 source1.append( " # 1 1 1 1 1 " + l );
1646 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1647 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1648 if ( t2.getNumberOfColumns() != 5 ) {
1651 if ( t2.getNumberOfRows() != 6 ) {
1654 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1657 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1660 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1663 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1666 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1669 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1672 final StringBuffer source2 = new StringBuffer();
1673 source2.append( "" + l );
1674 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1675 source2.append( " 00; 01 ;02;03" + l );
1676 source2.append( " 10; 11; 12; 13 " + l );
1677 source2.append( "20; 21; 22; 23 " + l );
1678 source2.append( " " + l );
1679 source2.append( " 30; 31; 32; 33" + l );
1680 source2.append( "40;41;42;43" + l );
1681 source2.append( " comment: 1 1 1 1 1 " + l );
1682 source2.append( ";;;50 ; 52; 53;;54 " + l );
1683 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1688 if ( tl.size() != 2 ) {
1691 final BasicTable<String> t3 = tl.get( 0 );
1692 final BasicTable<String> t4 = tl.get( 1 );
1693 if ( t3.getNumberOfColumns() != 4 ) {
1696 if ( t3.getNumberOfRows() != 3 ) {
1699 if ( t4.getNumberOfColumns() != 4 ) {
1702 if ( t4.getNumberOfRows() != 3 ) {
1705 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1708 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1712 catch ( final Exception e ) {
1713 e.printStackTrace( System.out );
1719 private static boolean testBasicTolXMLparsing() {
1721 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1722 final TolParser parser = new TolParser();
1723 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1724 if ( parser.getErrorCount() > 0 ) {
1725 System.out.println( parser.getErrorMessages().toString() );
1728 if ( phylogenies_0.length != 1 ) {
1731 final Phylogeny t1 = phylogenies_0[ 0 ];
1732 if ( t1.getNumberOfExternalNodes() != 5 ) {
1735 if ( !t1.isRooted() ) {
1738 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1741 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1744 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1747 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1750 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1751 if ( parser.getErrorCount() > 0 ) {
1752 System.out.println( parser.getErrorMessages().toString() );
1755 if ( phylogenies_1.length != 1 ) {
1758 final Phylogeny t2 = phylogenies_1[ 0 ];
1759 if ( t2.getNumberOfExternalNodes() != 664 ) {
1762 if ( !t2.isRooted() ) {
1765 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1768 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1771 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1774 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1777 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1780 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1781 .equals( "Aquifex" ) ) {
1784 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1785 if ( parser.getErrorCount() > 0 ) {
1786 System.out.println( parser.getErrorMessages().toString() );
1789 if ( phylogenies_2.length != 1 ) {
1792 final Phylogeny t3 = phylogenies_2[ 0 ];
1793 if ( t3.getNumberOfExternalNodes() != 184 ) {
1796 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1799 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1802 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1805 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1806 if ( parser.getErrorCount() > 0 ) {
1807 System.out.println( parser.getErrorMessages().toString() );
1810 if ( phylogenies_3.length != 1 ) {
1813 final Phylogeny t4 = phylogenies_3[ 0 ];
1814 if ( t4.getNumberOfExternalNodes() != 1 ) {
1817 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1820 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1823 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1826 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1827 if ( parser.getErrorCount() > 0 ) {
1828 System.out.println( parser.getErrorMessages().toString() );
1831 if ( phylogenies_4.length != 1 ) {
1834 final Phylogeny t5 = phylogenies_4[ 0 ];
1835 if ( t5.getNumberOfExternalNodes() != 13 ) {
1838 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1841 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1844 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1848 catch ( final Exception e ) {
1849 e.printStackTrace( System.out );
1855 private static boolean testBasicTreeMethods() {
1857 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1858 final Phylogeny t1 = factory.create();
1859 if ( !t1.isEmpty() ) {
1862 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1863 if ( t2.getNumberOfExternalNodes() != 4 ) {
1866 if ( t2.getHeight() != 8.5 ) {
1869 if ( !t2.isCompletelyBinary() ) {
1872 if ( t2.isEmpty() ) {
1875 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1876 if ( t3.getNumberOfExternalNodes() != 5 ) {
1879 if ( t3.getHeight() != 11 ) {
1882 if ( t3.isCompletelyBinary() ) {
1885 final PhylogenyNode n = t3.getNode( "ABC" );
1886 PhylogenyNodeIterator it;
1887 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1890 for( it.reset(); it.hasNext(); ) {
1893 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1894 if ( !it2.next().getName().equals( "A" ) ) {
1897 if ( !it2.next().getName().equals( "B" ) ) {
1900 if ( !it2.next().getName().equals( "C" ) ) {
1903 if ( it2.hasNext() ) {
1906 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 ];
1907 if ( t4.getNumberOfExternalNodes() != 9 ) {
1910 if ( t4.getHeight() != 11 ) {
1913 if ( t4.isCompletelyBinary() ) {
1916 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)" );
1917 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1918 if ( t5.getNumberOfExternalNodes() != 8 ) {
1921 if ( t5.getHeight() != 15 ) {
1924 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)" );
1925 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1926 if ( t6.getHeight() != 15 ) {
1929 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)" );
1930 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1931 if ( t7.getHeight() != 15 ) {
1934 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)" );
1935 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1936 if ( t8.getNumberOfExternalNodes() != 10 ) {
1939 if ( t8.getHeight() != 15 ) {
1942 final char[] a9 = new char[] {};
1943 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1944 if ( t9.getHeight() != 0 ) {
1947 final char[] a10 = new char[] { 'a', ':', '6' };
1948 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1949 if ( t10.getHeight() != 6 ) {
1953 catch ( final Exception e ) {
1954 e.printStackTrace( System.out );
1960 private static boolean testConfidenceAssessor() {
1962 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1963 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1964 final Phylogeny[] ev0 = factory
1965 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1967 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1968 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1971 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1974 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1975 final Phylogeny[] ev1 = factory
1976 .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)));",
1978 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1979 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1982 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1985 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1986 final Phylogeny[] ev_b = factory
1987 .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",
1989 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1990 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
1991 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1994 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1998 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1999 final Phylogeny[] ev1x = factory
2000 .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)));",
2002 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2003 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2006 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2009 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2010 final Phylogeny[] ev_bx = factory
2011 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2013 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2014 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2017 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2021 final Phylogeny[] t2 = factory
2022 .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);",
2024 final Phylogeny[] ev2 = factory
2025 .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);",
2027 for( final Phylogeny target : t2 ) {
2028 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2031 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2032 new NHXParser() )[ 0 ];
2033 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2034 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2035 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2038 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2041 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2045 catch ( final Exception e ) {
2046 e.printStackTrace();
2052 private static boolean testCopyOfNodeData() {
2054 final PhylogenyNode n1 = PhylogenyNode
2055 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2056 final PhylogenyNode n2 = n1.copyNodeData();
2057 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2061 catch ( final Exception e ) {
2062 e.printStackTrace();
2068 private static boolean testDataObjects() {
2070 final Confidence s0 = new Confidence();
2071 final Confidence s1 = new Confidence();
2072 if ( !s0.isEqual( s1 ) ) {
2075 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2076 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2077 if ( s2.isEqual( s1 ) ) {
2080 if ( !s2.isEqual( s3 ) ) {
2083 final Confidence s4 = ( Confidence ) s3.copy();
2084 if ( !s4.isEqual( s3 ) ) {
2091 final Taxonomy t1 = new Taxonomy();
2092 final Taxonomy t2 = new Taxonomy();
2093 final Taxonomy t3 = new Taxonomy();
2094 final Taxonomy t4 = new Taxonomy();
2095 final Taxonomy t5 = new Taxonomy();
2096 t1.setIdentifier( new Identifier( "ecoli" ) );
2097 t1.setTaxonomyCode( "ECOLI" );
2098 t1.setScientificName( "E. coli" );
2099 t1.setCommonName( "coli" );
2100 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2101 if ( !t1.isEqual( t0 ) ) {
2104 t2.setIdentifier( new Identifier( "ecoli" ) );
2105 t2.setTaxonomyCode( "other" );
2106 t2.setScientificName( "what" );
2107 t2.setCommonName( "something" );
2108 if ( !t1.isEqual( t2 ) ) {
2111 t2.setIdentifier( new Identifier( "nemve" ) );
2112 if ( t1.isEqual( t2 ) ) {
2115 t1.setIdentifier( null );
2116 t3.setTaxonomyCode( "ECOLI" );
2117 t3.setScientificName( "what" );
2118 t3.setCommonName( "something" );
2119 if ( !t1.isEqual( t3 ) ) {
2122 t1.setIdentifier( null );
2123 t1.setTaxonomyCode( "" );
2124 t4.setScientificName( "E. ColI" );
2125 t4.setCommonName( "something" );
2126 if ( !t1.isEqual( t4 ) ) {
2129 t4.setScientificName( "B. subtilis" );
2130 t4.setCommonName( "something" );
2131 if ( t1.isEqual( t4 ) ) {
2134 t1.setIdentifier( null );
2135 t1.setTaxonomyCode( "" );
2136 t1.setScientificName( "" );
2137 t5.setCommonName( "COLI" );
2138 if ( !t1.isEqual( t5 ) ) {
2141 t5.setCommonName( "vibrio" );
2142 if ( t1.isEqual( t5 ) ) {
2147 final Identifier id0 = new Identifier( "123", "pfam" );
2148 final Identifier id1 = ( Identifier ) id0.copy();
2149 if ( !id1.isEqual( id1 ) ) {
2152 if ( !id1.isEqual( id0 ) ) {
2155 if ( !id0.isEqual( id1 ) ) {
2162 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2163 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2164 if ( !pd1.isEqual( pd1 ) ) {
2167 if ( !pd1.isEqual( pd0 ) ) {
2172 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2173 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2174 if ( !pd3.isEqual( pd3 ) ) {
2177 if ( !pd2.isEqual( pd3 ) ) {
2180 if ( !pd0.isEqual( pd3 ) ) {
2185 // DomainArchitecture
2186 // ------------------
2187 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2188 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2189 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2190 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2191 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2192 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2197 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2198 if ( ds0.getNumberOfDomains() != 4 ) {
2201 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2202 if ( !ds0.isEqual( ds0 ) ) {
2205 if ( !ds0.isEqual( ds1 ) ) {
2208 if ( ds1.getNumberOfDomains() != 4 ) {
2211 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2216 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2217 if ( ds0.isEqual( ds2 ) ) {
2223 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2224 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2225 System.out.println( ds3.toNHX() );
2228 if ( ds3.getNumberOfDomains() != 3 ) {
2233 final Event e1 = new Event( Event.EventType.fusion );
2234 if ( e1.isDuplication() ) {
2237 if ( !e1.isFusion() ) {
2240 if ( !e1.asText().toString().equals( "fusion" ) ) {
2243 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2246 final Event e11 = new Event( Event.EventType.fusion );
2247 if ( !e11.isEqual( e1 ) ) {
2250 if ( !e11.toNHX().toString().equals( "" ) ) {
2253 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2254 if ( e2.isDuplication() ) {
2257 if ( !e2.isSpeciationOrDuplication() ) {
2260 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2263 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2266 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2269 if ( e11.isEqual( e2 ) ) {
2272 final Event e2c = ( Event ) e2.copy();
2273 if ( !e2c.isEqual( e2 ) ) {
2276 Event e3 = new Event( 1, 2, 3 );
2277 if ( e3.isDuplication() ) {
2280 if ( e3.isSpeciation() ) {
2283 if ( e3.isGeneLoss() ) {
2286 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2289 final Event e3c = ( Event ) e3.copy();
2290 final Event e3cc = ( Event ) e3c.copy();
2291 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2295 if ( !e3c.isEqual( e3cc ) ) {
2298 Event e4 = new Event( 1, 2, 3 );
2299 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2302 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2305 final Event e4c = ( Event ) e4.copy();
2307 final Event e4cc = ( Event ) e4c.copy();
2308 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2311 if ( !e4c.isEqual( e4cc ) ) {
2314 final Event e5 = new Event();
2315 if ( !e5.isUnassigned() ) {
2318 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2321 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2324 final Event e6 = new Event( 1, 0, 0 );
2325 if ( !e6.asText().toString().equals( "duplication" ) ) {
2328 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2331 final Event e7 = new Event( 0, 1, 0 );
2332 if ( !e7.asText().toString().equals( "speciation" ) ) {
2335 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2338 final Event e8 = new Event( 0, 0, 1 );
2339 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2342 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2346 catch ( final Exception e ) {
2347 e.printStackTrace( System.out );
2353 private static boolean testDeletionOfExternalNodes() {
2355 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2356 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2357 final PhylogenyWriter w = new PhylogenyWriter();
2358 if ( t0.isEmpty() ) {
2361 if ( t0.getNumberOfExternalNodes() != 1 ) {
2364 t0.deleteSubtree( t0.getNode( "A" ), false );
2365 if ( t0.getNumberOfExternalNodes() != 0 ) {
2368 if ( !t0.isEmpty() ) {
2371 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2372 if ( t1.getNumberOfExternalNodes() != 2 ) {
2375 t1.deleteSubtree( t1.getNode( "A" ), false );
2376 if ( t1.getNumberOfExternalNodes() != 1 ) {
2379 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2382 t1.deleteSubtree( t1.getNode( "B" ), false );
2383 if ( t1.getNumberOfExternalNodes() != 1 ) {
2386 t1.deleteSubtree( t1.getNode( "r" ), false );
2387 if ( !t1.isEmpty() ) {
2390 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2391 if ( t2.getNumberOfExternalNodes() != 3 ) {
2394 t2.deleteSubtree( t2.getNode( "B" ), false );
2395 if ( t2.getNumberOfExternalNodes() != 2 ) {
2398 t2.toNewHampshireX();
2399 PhylogenyNode n = t2.getNode( "A" );
2400 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2403 t2.deleteSubtree( t2.getNode( "A" ), false );
2404 if ( t2.getNumberOfExternalNodes() != 2 ) {
2407 t2.deleteSubtree( t2.getNode( "C" ), true );
2408 if ( t2.getNumberOfExternalNodes() != 1 ) {
2411 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2412 if ( t3.getNumberOfExternalNodes() != 4 ) {
2415 t3.deleteSubtree( t3.getNode( "B" ), true );
2416 if ( t3.getNumberOfExternalNodes() != 3 ) {
2419 n = t3.getNode( "A" );
2420 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2423 n = n.getNextExternalNode();
2424 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2427 t3.deleteSubtree( t3.getNode( "A" ), true );
2428 if ( t3.getNumberOfExternalNodes() != 2 ) {
2431 n = t3.getNode( "C" );
2432 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2435 t3.deleteSubtree( t3.getNode( "C" ), true );
2436 if ( t3.getNumberOfExternalNodes() != 1 ) {
2439 t3.deleteSubtree( t3.getNode( "D" ), true );
2440 if ( t3.getNumberOfExternalNodes() != 0 ) {
2443 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2444 if ( t4.getNumberOfExternalNodes() != 6 ) {
2447 t4.deleteSubtree( t4.getNode( "B2" ), true );
2448 if ( t4.getNumberOfExternalNodes() != 5 ) {
2451 String s = w.toNewHampshire( t4, false, true ).toString();
2452 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2455 t4.deleteSubtree( t4.getNode( "B11" ), true );
2456 if ( t4.getNumberOfExternalNodes() != 4 ) {
2459 t4.deleteSubtree( t4.getNode( "C" ), true );
2460 if ( t4.getNumberOfExternalNodes() != 3 ) {
2463 n = t4.getNode( "A" );
2464 n = n.getNextExternalNode();
2465 if ( !n.getName().equals( "B12" ) ) {
2468 n = n.getNextExternalNode();
2469 if ( !n.getName().equals( "D" ) ) {
2472 s = w.toNewHampshire( t4, false, true ).toString();
2473 if ( !s.equals( "((A,B12),D);" ) ) {
2476 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2477 t5.deleteSubtree( t5.getNode( "A" ), true );
2478 if ( t5.getNumberOfExternalNodes() != 5 ) {
2481 s = w.toNewHampshire( t5, false, true ).toString();
2482 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2485 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2486 t6.deleteSubtree( t6.getNode( "B11" ), true );
2487 if ( t6.getNumberOfExternalNodes() != 5 ) {
2490 s = w.toNewHampshire( t6, false, false ).toString();
2491 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2494 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2495 t7.deleteSubtree( t7.getNode( "B12" ), true );
2496 if ( t7.getNumberOfExternalNodes() != 5 ) {
2499 s = w.toNewHampshire( t7, false, true ).toString();
2500 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2503 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2504 t8.deleteSubtree( t8.getNode( "B2" ), true );
2505 if ( t8.getNumberOfExternalNodes() != 5 ) {
2508 s = w.toNewHampshire( t8, false, false ).toString();
2509 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2512 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2513 t9.deleteSubtree( t9.getNode( "C" ), true );
2514 if ( t9.getNumberOfExternalNodes() != 5 ) {
2517 s = w.toNewHampshire( t9, false, true ).toString();
2518 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2521 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2522 t10.deleteSubtree( t10.getNode( "D" ), true );
2523 if ( t10.getNumberOfExternalNodes() != 5 ) {
2526 s = w.toNewHampshire( t10, false, true ).toString();
2527 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2530 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2531 t11.deleteSubtree( t11.getNode( "A" ), true );
2532 if ( t11.getNumberOfExternalNodes() != 2 ) {
2535 s = w.toNewHampshire( t11, false, true ).toString();
2536 if ( !s.equals( "(B,C);" ) ) {
2539 t11.deleteSubtree( t11.getNode( "C" ), true );
2540 if ( t11.getNumberOfExternalNodes() != 1 ) {
2543 s = w.toNewHampshire( t11, false, false ).toString();
2544 if ( !s.equals( "B;" ) ) {
2547 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2548 t12.deleteSubtree( t12.getNode( "B2" ), true );
2549 if ( t12.getNumberOfExternalNodes() != 8 ) {
2552 s = w.toNewHampshire( t12, false, true ).toString();
2553 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2556 t12.deleteSubtree( t12.getNode( "B3" ), true );
2557 if ( t12.getNumberOfExternalNodes() != 7 ) {
2560 s = w.toNewHampshire( t12, false, true ).toString();
2561 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2564 t12.deleteSubtree( t12.getNode( "C3" ), true );
2565 if ( t12.getNumberOfExternalNodes() != 6 ) {
2568 s = w.toNewHampshire( t12, false, true ).toString();
2569 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2572 t12.deleteSubtree( t12.getNode( "A1" ), true );
2573 if ( t12.getNumberOfExternalNodes() != 5 ) {
2576 s = w.toNewHampshire( t12, false, true ).toString();
2577 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2580 t12.deleteSubtree( t12.getNode( "B1" ), true );
2581 if ( t12.getNumberOfExternalNodes() != 4 ) {
2584 s = w.toNewHampshire( t12, false, true ).toString();
2585 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2588 t12.deleteSubtree( t12.getNode( "A3" ), true );
2589 if ( t12.getNumberOfExternalNodes() != 3 ) {
2592 s = w.toNewHampshire( t12, false, true ).toString();
2593 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2596 t12.deleteSubtree( t12.getNode( "A2" ), true );
2597 if ( t12.getNumberOfExternalNodes() != 2 ) {
2600 s = w.toNewHampshire( t12, false, true ).toString();
2601 if ( !s.equals( "(C1,C2);" ) ) {
2604 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2605 t13.deleteSubtree( t13.getNode( "D" ), true );
2606 if ( t13.getNumberOfExternalNodes() != 4 ) {
2609 s = w.toNewHampshire( t13, false, true ).toString();
2610 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2613 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2614 t14.deleteSubtree( t14.getNode( "E" ), true );
2615 if ( t14.getNumberOfExternalNodes() != 5 ) {
2618 s = w.toNewHampshire( t14, false, true ).toString();
2619 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2622 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2623 t15.deleteSubtree( t15.getNode( "B2" ), true );
2624 if ( t15.getNumberOfExternalNodes() != 11 ) {
2627 t15.deleteSubtree( t15.getNode( "B1" ), true );
2628 if ( t15.getNumberOfExternalNodes() != 10 ) {
2631 t15.deleteSubtree( t15.getNode( "B3" ), true );
2632 if ( t15.getNumberOfExternalNodes() != 9 ) {
2635 t15.deleteSubtree( t15.getNode( "B4" ), true );
2636 if ( t15.getNumberOfExternalNodes() != 8 ) {
2639 t15.deleteSubtree( t15.getNode( "A1" ), true );
2640 if ( t15.getNumberOfExternalNodes() != 7 ) {
2643 t15.deleteSubtree( t15.getNode( "C4" ), true );
2644 if ( t15.getNumberOfExternalNodes() != 6 ) {
2648 catch ( final Exception e ) {
2649 e.printStackTrace( System.out );
2655 private static boolean testDescriptiveStatistics() {
2657 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2658 dss1.addValue( 82 );
2659 dss1.addValue( 78 );
2660 dss1.addValue( 70 );
2661 dss1.addValue( 58 );
2662 dss1.addValue( 42 );
2663 if ( dss1.getN() != 5 ) {
2666 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2669 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2672 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2675 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2678 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2681 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2684 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2687 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2690 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2693 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2696 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2699 dss1.addValue( 123 );
2700 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2703 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2706 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2709 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2710 dss2.addValue( -1.85 );
2711 dss2.addValue( 57.5 );
2712 dss2.addValue( 92.78 );
2713 dss2.addValue( 57.78 );
2714 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2717 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2720 final double[] a = dss2.getDataAsDoubleArray();
2721 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2724 dss2.addValue( -100 );
2725 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2728 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2731 final double[] ds = new double[ 14 ];
2746 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2747 if ( bins.length != 4 ) {
2750 if ( bins[ 0 ] != 2 ) {
2753 if ( bins[ 1 ] != 3 ) {
2756 if ( bins[ 2 ] != 4 ) {
2759 if ( bins[ 3 ] != 5 ) {
2762 final double[] ds1 = new double[ 9 ];
2772 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2773 if ( bins1.length != 4 ) {
2776 if ( bins1[ 0 ] != 2 ) {
2779 if ( bins1[ 1 ] != 3 ) {
2782 if ( bins1[ 2 ] != 0 ) {
2785 if ( bins1[ 3 ] != 4 ) {
2788 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2789 if ( bins1_1.length != 3 ) {
2792 if ( bins1_1[ 0 ] != 3 ) {
2795 if ( bins1_1[ 1 ] != 2 ) {
2798 if ( bins1_1[ 2 ] != 4 ) {
2801 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2802 if ( bins1_2.length != 3 ) {
2805 if ( bins1_2[ 0 ] != 2 ) {
2808 if ( bins1_2[ 1 ] != 2 ) {
2811 if ( bins1_2[ 2 ] != 2 ) {
2814 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2828 dss3.addValue( 10 );
2829 dss3.addValue( 10 );
2830 dss3.addValue( 10 );
2831 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2832 histo.toStringBuffer( 10, '=', 40, 5 );
2833 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2835 catch ( final Exception e ) {
2836 e.printStackTrace( System.out );
2842 private static boolean testDir( final String file ) {
2844 final File f = new File( file );
2845 if ( !f.exists() ) {
2848 if ( !f.isDirectory() ) {
2851 if ( !f.canRead() ) {
2855 catch ( final Exception e ) {
2861 private static boolean testExternalNodeRelatedMethods() {
2863 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2864 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2865 PhylogenyNode n = t1.getNode( "A" );
2866 n = n.getNextExternalNode();
2867 if ( !n.getName().equals( "B" ) ) {
2870 n = n.getNextExternalNode();
2871 if ( !n.getName().equals( "C" ) ) {
2874 n = n.getNextExternalNode();
2875 if ( !n.getName().equals( "D" ) ) {
2878 n = t1.getNode( "B" );
2879 while ( !n.isLastExternalNode() ) {
2880 n = n.getNextExternalNode();
2882 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2883 n = t2.getNode( "A" );
2884 n = n.getNextExternalNode();
2885 if ( !n.getName().equals( "B" ) ) {
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "C" ) ) {
2892 n = n.getNextExternalNode();
2893 if ( !n.getName().equals( "D" ) ) {
2896 n = t2.getNode( "B" );
2897 while ( !n.isLastExternalNode() ) {
2898 n = n.getNextExternalNode();
2900 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2901 n = t3.getNode( "A" );
2902 n = n.getNextExternalNode();
2903 if ( !n.getName().equals( "B" ) ) {
2906 n = n.getNextExternalNode();
2907 if ( !n.getName().equals( "C" ) ) {
2910 n = n.getNextExternalNode();
2911 if ( !n.getName().equals( "D" ) ) {
2914 n = n.getNextExternalNode();
2915 if ( !n.getName().equals( "E" ) ) {
2918 n = n.getNextExternalNode();
2919 if ( !n.getName().equals( "F" ) ) {
2922 n = n.getNextExternalNode();
2923 if ( !n.getName().equals( "G" ) ) {
2926 n = n.getNextExternalNode();
2927 if ( !n.getName().equals( "H" ) ) {
2930 n = t3.getNode( "B" );
2931 while ( !n.isLastExternalNode() ) {
2932 n = n.getNextExternalNode();
2934 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2935 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2936 final PhylogenyNode node = iter.next();
2938 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2939 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2940 final PhylogenyNode node = iter.next();
2943 catch ( final Exception e ) {
2944 e.printStackTrace( System.out );
2950 private static boolean testGeneralTable() {
2952 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2953 t0.setValue( 3, 2, "23" );
2954 t0.setValue( 10, 1, "error" );
2955 t0.setValue( 10, 1, "110" );
2956 t0.setValue( 9, 1, "19" );
2957 t0.setValue( 1, 10, "101" );
2958 t0.setValue( 10, 10, "1010" );
2959 t0.setValue( 100, 10, "10100" );
2960 t0.setValue( 0, 0, "00" );
2961 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2964 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2967 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2970 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2973 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2976 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2979 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2982 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2985 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2988 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2989 t1.setValue( "3", "2", "23" );
2990 t1.setValue( "10", "1", "error" );
2991 t1.setValue( "10", "1", "110" );
2992 t1.setValue( "9", "1", "19" );
2993 t1.setValue( "1", "10", "101" );
2994 t1.setValue( "10", "10", "1010" );
2995 t1.setValue( "100", "10", "10100" );
2996 t1.setValue( "0", "0", "00" );
2997 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2998 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3001 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3004 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3007 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3010 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3013 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3016 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3019 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3022 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3025 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3029 catch ( final Exception e ) {
3030 e.printStackTrace( System.out );
3036 private static boolean testGetDistance() {
3038 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3039 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",
3040 new NHXParser() )[ 0 ];
3041 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3042 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3045 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3048 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3051 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3054 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3057 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3060 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3063 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3066 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3069 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3072 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3075 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3078 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3081 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3084 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3087 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3090 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3093 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3096 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3099 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3102 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3105 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3108 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3111 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3114 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3117 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3120 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3123 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3126 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3129 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3132 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3135 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",
3136 new NHXParser() )[ 0 ];
3137 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3140 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3143 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3146 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3149 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3152 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3155 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3158 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3161 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3164 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3167 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3171 catch ( final Exception e ) {
3172 e.printStackTrace( System.out );
3178 private static boolean testGetLCA() {
3180 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3181 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3182 new NHXParser() )[ 0 ];
3183 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3184 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3185 if ( !A.getName().equals( "A" ) ) {
3188 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3189 if ( !gh.getName().equals( "gh" ) ) {
3192 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3193 if ( !ab.getName().equals( "ab" ) ) {
3196 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3197 if ( !ab2.getName().equals( "ab" ) ) {
3200 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3201 if ( !gh2.getName().equals( "gh" ) ) {
3204 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3205 if ( !gh3.getName().equals( "gh" ) ) {
3208 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3209 if ( !abc.getName().equals( "abc" ) ) {
3212 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3213 if ( !abc2.getName().equals( "abc" ) ) {
3216 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3217 if ( !abcd.getName().equals( "abcd" ) ) {
3220 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3221 if ( !abcd2.getName().equals( "abcd" ) ) {
3224 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3225 if ( !abcdef.getName().equals( "abcdef" ) ) {
3228 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3229 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3232 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3233 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3236 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3237 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3240 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3241 if ( !abcde.getName().equals( "abcde" ) ) {
3244 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3245 if ( !abcde2.getName().equals( "abcde" ) ) {
3248 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3249 if ( !r.getName().equals( "abcdefgh" ) ) {
3252 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3253 if ( !r2.getName().equals( "abcdefgh" ) ) {
3256 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3257 if ( !r3.getName().equals( "abcdefgh" ) ) {
3260 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3261 if ( !abcde3.getName().equals( "abcde" ) ) {
3264 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3265 if ( !abcde4.getName().equals( "abcde" ) ) {
3268 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3269 if ( !ab3.getName().equals( "ab" ) ) {
3272 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3273 if ( !ab4.getName().equals( "ab" ) ) {
3276 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3277 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3278 if ( !cd.getName().equals( "cd" ) ) {
3281 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3282 if ( !cd2.getName().equals( "cd" ) ) {
3285 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3286 if ( !cde.getName().equals( "cde" ) ) {
3289 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3290 if ( !cde2.getName().equals( "cde" ) ) {
3293 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3294 if ( !cdef.getName().equals( "cdef" ) ) {
3297 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3298 if ( !cdef2.getName().equals( "cdef" ) ) {
3301 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3302 if ( !cdef3.getName().equals( "cdef" ) ) {
3305 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3306 if ( !rt.getName().equals( "r" ) ) {
3309 final Phylogeny p3 = factory
3310 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3311 new NHXParser() )[ 0 ];
3312 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3313 if ( !bc_3.getName().equals( "bc" ) ) {
3316 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3317 if ( !ac_3.getName().equals( "abc" ) ) {
3320 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3321 if ( !ad_3.getName().equals( "abcde" ) ) {
3324 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3325 if ( !af_3.getName().equals( "abcdef" ) ) {
3328 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3329 if ( !ag_3.getName().equals( "" ) ) {
3332 if ( !ag_3.isRoot() ) {
3335 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3336 if ( !al_3.getName().equals( "" ) ) {
3339 if ( !al_3.isRoot() ) {
3342 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3343 if ( !kl_3.getName().equals( "" ) ) {
3346 if ( !kl_3.isRoot() ) {
3349 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3350 if ( !fl_3.getName().equals( "" ) ) {
3353 if ( !fl_3.isRoot() ) {
3356 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3357 if ( !gk_3.getName().equals( "ghijk" ) ) {
3360 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3361 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3362 if ( !r_4.getName().equals( "r" ) ) {
3365 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3366 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3367 if ( !r_5.getName().equals( "root" ) ) {
3370 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3371 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3372 if ( !r_6.getName().equals( "rot" ) ) {
3375 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3376 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3377 if ( !r_7.getName().equals( "rott" ) ) {
3381 catch ( final Exception e ) {
3382 e.printStackTrace( System.out );
3388 private static boolean testHmmscanOutputParser() {
3389 final String test_dir = Test.PATH_TO_TEST_DATA;
3391 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3392 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3394 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3395 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3396 final List<Protein> domain_collections = parser2.parse();
3397 if ( parser2.getProteinsEncountered() != 4 ) {
3400 if ( domain_collections.size() != 4 ) {
3403 if ( parser2.getDomainsEncountered() != 69 ) {
3406 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3409 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3412 final Protein p1 = domain_collections.get( 0 );
3413 if ( p1.getNumberOfProteinDomains() != 15 ) {
3416 final Protein p4 = domain_collections.get( 3 );
3417 if ( p4.getNumberOfProteinDomains() != 1 ) {
3420 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3423 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3426 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3429 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3432 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3435 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3438 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3441 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3444 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3448 catch ( final Exception e ) {
3449 e.printStackTrace( System.out );
3455 private static boolean testLastExternalNodeMethods() {
3457 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3458 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3459 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3460 final PhylogenyNode n1 = t0.getNode( "A" );
3461 if ( n1.isLastExternalNode() ) {
3464 final PhylogenyNode n2 = t0.getNode( "B" );
3465 if ( n2.isLastExternalNode() ) {
3468 final PhylogenyNode n3 = t0.getNode( "C" );
3469 if ( n3.isLastExternalNode() ) {
3472 final PhylogenyNode n4 = t0.getNode( "D" );
3473 if ( !n4.isLastExternalNode() ) {
3477 catch ( final Exception e ) {
3478 e.printStackTrace( System.out );
3484 private static boolean testLevelOrderIterator() {
3486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3487 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3488 PhylogenyNodeIterator it0;
3489 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3492 for( it0.reset(); it0.hasNext(); ) {
3495 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3496 if ( !it.next().getName().equals( "r" ) ) {
3499 if ( !it.next().getName().equals( "ab" ) ) {
3502 if ( !it.next().getName().equals( "cd" ) ) {
3505 if ( !it.next().getName().equals( "A" ) ) {
3508 if ( !it.next().getName().equals( "B" ) ) {
3511 if ( !it.next().getName().equals( "C" ) ) {
3514 if ( !it.next().getName().equals( "D" ) ) {
3517 if ( it.hasNext() ) {
3520 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",
3521 new NHXParser() )[ 0 ];
3522 PhylogenyNodeIterator it2;
3523 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3526 for( it2.reset(); it2.hasNext(); ) {
3529 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3530 if ( !it3.next().getName().equals( "r" ) ) {
3533 if ( !it3.next().getName().equals( "abc" ) ) {
3536 if ( !it3.next().getName().equals( "defg" ) ) {
3539 if ( !it3.next().getName().equals( "A" ) ) {
3542 if ( !it3.next().getName().equals( "B" ) ) {
3545 if ( !it3.next().getName().equals( "C" ) ) {
3548 if ( !it3.next().getName().equals( "D" ) ) {
3551 if ( !it3.next().getName().equals( "E" ) ) {
3554 if ( !it3.next().getName().equals( "F" ) ) {
3557 if ( !it3.next().getName().equals( "G" ) ) {
3560 if ( !it3.next().getName().equals( "1" ) ) {
3563 if ( !it3.next().getName().equals( "2" ) ) {
3566 if ( !it3.next().getName().equals( "3" ) ) {
3569 if ( !it3.next().getName().equals( "4" ) ) {
3572 if ( !it3.next().getName().equals( "5" ) ) {
3575 if ( !it3.next().getName().equals( "6" ) ) {
3578 if ( !it3.next().getName().equals( "f1" ) ) {
3581 if ( !it3.next().getName().equals( "f2" ) ) {
3584 if ( !it3.next().getName().equals( "f3" ) ) {
3587 if ( !it3.next().getName().equals( "a" ) ) {
3590 if ( !it3.next().getName().equals( "b" ) ) {
3593 if ( !it3.next().getName().equals( "f21" ) ) {
3596 if ( !it3.next().getName().equals( "X" ) ) {
3599 if ( !it3.next().getName().equals( "Y" ) ) {
3602 if ( !it3.next().getName().equals( "Z" ) ) {
3605 if ( it3.hasNext() ) {
3608 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3609 PhylogenyNodeIterator it4;
3610 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3613 for( it4.reset(); it4.hasNext(); ) {
3616 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3617 if ( !it5.next().getName().equals( "r" ) ) {
3620 if ( !it5.next().getName().equals( "A" ) ) {
3623 if ( !it5.next().getName().equals( "B" ) ) {
3626 if ( !it5.next().getName().equals( "C" ) ) {
3629 if ( !it5.next().getName().equals( "D" ) ) {
3632 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3633 PhylogenyNodeIterator it6;
3634 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3637 for( it6.reset(); it6.hasNext(); ) {
3640 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3641 if ( !it7.next().getName().equals( "A" ) ) {
3644 if ( it.hasNext() ) {
3648 catch ( final Exception e ) {
3649 e.printStackTrace( System.out );
3655 private static boolean testMidpointrooting() {
3657 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3658 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",
3659 new NHXParser() )[ 0 ];
3660 if ( !t1.isRooted() ) {
3663 PhylogenyMethods.midpointRoot( t1 );
3664 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3667 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3670 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3673 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3676 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3679 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3682 t1.reRoot( t1.getNode( "A" ) );
3683 PhylogenyMethods.midpointRoot( t1 );
3684 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3687 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3690 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3693 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3696 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3699 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3703 catch ( final Exception e ) {
3704 e.printStackTrace( System.out );
3710 private static boolean testNexusCharactersParsing() {
3712 final NexusCharactersParser parser = new NexusCharactersParser();
3713 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3715 String[] labels = parser.getCharStateLabels();
3716 if ( labels.length != 7 ) {
3719 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3722 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3725 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3728 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3731 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3734 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3737 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3740 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3742 labels = parser.getCharStateLabels();
3743 if ( labels.length != 7 ) {
3746 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3749 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3752 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3755 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3758 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3761 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3764 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3768 catch ( final Exception e ) {
3769 e.printStackTrace( System.out );
3775 private static boolean testNexusMatrixParsing() {
3777 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3778 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3780 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3781 if ( m.getNumberOfCharacters() != 9 ) {
3784 if ( m.getNumberOfIdentifiers() != 5 ) {
3787 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3790 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3793 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3796 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3799 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3802 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3805 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3808 // if ( labels.length != 7 ) {
3811 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3814 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3817 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3820 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3823 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3826 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3829 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3832 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3834 // labels = parser.getCharStateLabels();
3835 // if ( labels.length != 7 ) {
3838 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3841 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3844 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3847 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3850 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3853 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3856 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3860 catch ( final Exception e ) {
3861 e.printStackTrace( System.out );
3867 private static boolean testNexusTreeParsing() {
3869 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3870 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3871 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3872 if ( phylogenies.length != 1 ) {
3875 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3878 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3882 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3883 if ( phylogenies.length != 1 ) {
3886 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3889 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3893 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3894 if ( phylogenies.length != 1 ) {
3897 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3900 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3903 if ( phylogenies[ 0 ].isRooted() ) {
3907 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3908 if ( phylogenies.length != 18 ) {
3911 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3914 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3917 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3920 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3923 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3926 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3929 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3932 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3935 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3938 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3941 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3944 if ( phylogenies[ 8 ].isRooted() ) {
3947 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3950 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3953 if ( !phylogenies[ 9 ].isRooted() ) {
3956 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3959 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3962 if ( !phylogenies[ 10 ].isRooted() ) {
3965 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3968 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3971 if ( phylogenies[ 11 ].isRooted() ) {
3974 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
3977 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
3980 if ( !phylogenies[ 12 ].isRooted() ) {
3983 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
3986 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
3989 if ( !phylogenies[ 13 ].isRooted() ) {
3992 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
3995 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
3998 if ( !phylogenies[ 14 ].isRooted() ) {
4001 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4004 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4007 if ( phylogenies[ 15 ].isRooted() ) {
4010 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4013 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4016 if ( !phylogenies[ 16 ].isRooted() ) {
4019 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4022 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4025 if ( phylogenies[ 17 ].isRooted() ) {
4028 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4032 catch ( final Exception e ) {
4033 e.printStackTrace( System.out );
4039 private static boolean testNexusTreeParsingTranslating() {
4041 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4042 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4043 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4044 if ( phylogenies.length != 1 ) {
4047 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4050 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4053 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4056 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4059 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4060 .equals( "Aranaeus" ) ) {
4064 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4065 if ( phylogenies.length != 3 ) {
4068 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4071 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4074 if ( phylogenies[ 0 ].isRooted() ) {
4077 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4080 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4083 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4084 .equals( "Aranaeus" ) ) {
4087 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4090 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4093 if ( phylogenies[ 1 ].isRooted() ) {
4096 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4099 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4102 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4103 .equals( "Aranaeus" ) ) {
4106 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4109 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4112 if ( !phylogenies[ 2 ].isRooted() ) {
4115 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4118 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4121 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4122 .equals( "Aranaeus" ) ) {
4126 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4127 if ( phylogenies.length != 3 ) {
4130 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4133 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4136 if ( phylogenies[ 0 ].isRooted() ) {
4139 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4142 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4145 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4146 .equals( "Aranaeus" ) ) {
4149 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4152 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4155 if ( phylogenies[ 1 ].isRooted() ) {
4158 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4161 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4164 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4165 .equals( "Aranaeus" ) ) {
4168 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4171 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4174 if ( !phylogenies[ 2 ].isRooted() ) {
4177 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4180 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4183 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4184 .equals( "Aranaeus" ) ) {
4188 catch ( final Exception e ) {
4189 e.printStackTrace( System.out );
4195 private static boolean testNHParsing() {
4197 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4198 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4199 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4202 final NHXParser nhxp = new NHXParser();
4203 nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
4204 nhxp.setReplaceUnderscores( true );
4205 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4206 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4209 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4212 final Phylogeny p1b = factory
4213 .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 ",
4214 new NHXParser() )[ 0 ];
4215 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4218 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4221 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4222 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4223 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4224 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4225 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4226 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4227 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4228 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4229 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4230 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4231 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4232 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4233 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4235 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4238 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4241 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4244 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4247 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4248 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4249 final String p16_S = "((A,B),C)";
4250 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4251 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4254 final String p17_S = "(C,(A,B))";
4255 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4256 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4259 final String p18_S = "((A,B),(C,D))";
4260 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4261 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4264 final String p19_S = "(((A,B),C),D)";
4265 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4266 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4269 final String p20_S = "(A,(B,(C,D)))";
4270 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4271 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4274 final String p21_S = "(A,(B,(C,(D,E))))";
4275 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4276 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4279 final String p22_S = "((((A,B),C),D),E)";
4280 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4281 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4284 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4285 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4286 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4289 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4290 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4291 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4294 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4295 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4296 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4297 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4300 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4303 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4304 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4305 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4306 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4307 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4308 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4309 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4310 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4311 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4312 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4315 final String p26_S = "(A,B)ab";
4316 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4317 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4320 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4321 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4323 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4326 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4327 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4328 final String p28_S3 = "(A,B)ab";
4329 final String p28_S4 = "((((A,B),C),D),;E;)";
4330 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4332 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4335 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4338 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4341 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4344 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";
4345 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4346 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4349 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";
4350 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4351 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4354 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4355 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4356 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4359 final String p33_S = "A";
4360 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4361 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4364 final String p34_S = "B;";
4365 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4366 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4369 final String p35_S = "B:0.2";
4370 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4371 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4374 final String p36_S = "(A)";
4375 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4376 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4379 final String p37_S = "((A))";
4380 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4381 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4384 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4385 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4386 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4389 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4390 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4391 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4394 final String p40_S = "(A,B,C)";
4395 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4396 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4399 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4400 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4401 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4404 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4405 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4406 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4409 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)";
4410 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4411 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4414 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)))";
4415 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4416 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4419 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4420 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4421 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4424 final String p46_S = "";
4425 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4426 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4430 catch ( final Exception e ) {
4431 e.printStackTrace( System.out );
4437 private static boolean testNHXconversion() {
4439 final PhylogenyNode n1 = new PhylogenyNode();
4440 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4441 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4442 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4443 final PhylogenyNode n5 = PhylogenyNode
4444 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4445 final PhylogenyNode n6 = PhylogenyNode
4446 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4447 if ( !n1.toNewHampshireX().equals( "" ) ) {
4450 if ( !n2.toNewHampshireX().equals( "" ) ) {
4453 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4456 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4459 if ( !n5.toNewHampshireX()
4460 .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]" ) ) {
4463 if ( !n6.toNewHampshireX()
4464 .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]" ) ) {
4468 catch ( final Exception e ) {
4469 e.printStackTrace( System.out );
4475 private static boolean testNHXNodeParsing() {
4477 final PhylogenyNode n1 = new PhylogenyNode();
4478 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4479 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4480 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4481 final PhylogenyNode n5 = PhylogenyNode
4482 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
4483 if ( !n3.getName().equals( "n3" ) ) {
4486 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4489 if ( n3.isDuplication() ) {
4492 if ( n3.isHasAssignedEvent() ) {
4495 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4498 if ( !n4.getName().equals( "n4" ) ) {
4501 if ( n4.getDistanceToParent() != 0.01 ) {
4504 if ( !n5.getName().equals( "n5" ) ) {
4507 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4510 if ( n5.getDistanceToParent() != 0.1 ) {
4513 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4516 if ( !n5.isDuplication() ) {
4519 if ( !n5.isHasAssignedEvent() ) {
4522 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4525 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4528 final PhylogenyNode n8 = PhylogenyNode
4529 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4530 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4533 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4536 final PhylogenyNode n9 = PhylogenyNode
4537 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4538 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4539 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4542 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4545 final PhylogenyNode n10 = PhylogenyNode
4546 .createInstanceFromNhxString( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4547 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4550 final PhylogenyNode n20 = PhylogenyNode
4551 .createInstanceFromNhxString( "n20_ECOLI/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4552 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4555 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4558 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
4559 ForesterUtil.TAXONOMY_EXTRACTION.YES );
4560 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4563 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4566 final PhylogenyNode n20xx = PhylogenyNode
4567 .createInstanceFromNhxString( "n20_eCOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4568 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4571 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4574 final PhylogenyNode n20xxx = PhylogenyNode
4575 .createInstanceFromNhxString( "n20_ecoli/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4576 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4579 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4582 final PhylogenyNode n20xxxx = PhylogenyNode
4583 .createInstanceFromNhxString( "n20_Ecoli/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4584 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4587 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4590 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
4591 ForesterUtil.TAXONOMY_EXTRACTION.YES );
4592 if ( !n21.getName().equals( "n21_PIG" ) ) {
4595 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4598 final PhylogenyNode n21x = PhylogenyNode
4599 .createInstanceFromNhxString( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4600 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4603 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4606 final PhylogenyNode n22 = PhylogenyNode
4607 .createInstanceFromNhxString( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4608 if ( !n22.getName().equals( "n22/PIG" ) ) {
4611 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4614 final PhylogenyNode n23 = PhylogenyNode
4615 .createInstanceFromNhxString( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4616 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4619 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4622 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4623 final PhylogenyNode a = PhylogenyNode
4624 .createInstanceFromNhxString( "n10_ECOLI/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4625 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4628 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4631 final PhylogenyNode b = PhylogenyNode
4632 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4633 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4634 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4637 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4640 final PhylogenyNode c = PhylogenyNode
4641 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4642 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4643 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4646 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4649 final PhylogenyNode d = PhylogenyNode
4650 .createInstanceFromNhxString( "n10_RAT1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4651 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4654 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4657 final PhylogenyNode e = PhylogenyNode
4658 .createInstanceFromNhxString( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4659 if ( !e.getName().equals( "n10_RAT1" ) ) {
4662 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4666 final PhylogenyNode n11 = PhylogenyNode
4667 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4668 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4669 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4672 if ( n11.getDistanceToParent() != 0.4 ) {
4675 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4678 final PhylogenyNode n12 = PhylogenyNode
4679 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4680 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4681 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4684 if ( n12.getDistanceToParent() != 0.4 ) {
4687 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4690 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4691 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4692 if ( !tvu1.getRef().equals( "tag1" ) ) {
4695 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4698 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4701 if ( !tvu1.getValue().equals( "value1" ) ) {
4704 if ( !tvu3.getRef().equals( "tag3" ) ) {
4707 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4710 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4713 if ( !tvu3.getValue().equals( "value3" ) ) {
4716 if ( n1.getName().compareTo( "" ) != 0 ) {
4719 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4722 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4725 if ( n2.getName().compareTo( "" ) != 0 ) {
4728 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4731 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4734 final PhylogenyNode n00 = PhylogenyNode
4735 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4736 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4739 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4742 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4745 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4748 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4751 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4754 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4757 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4760 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4761 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4764 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4765 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4768 final PhylogenyNode n13 = PhylogenyNode
4769 .createInstanceFromNhxString( "blah_12345/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4770 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4773 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4776 final PhylogenyNode n14 = PhylogenyNode
4777 .createInstanceFromNhxString( "blah_12X45/1-2", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4778 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4781 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4784 final PhylogenyNode n15 = PhylogenyNode
4785 .createInstanceFromNhxString( "something_wicked[123]",
4786 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4787 if ( !n15.getName().equals( "something_wicked" ) ) {
4790 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4793 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4796 final PhylogenyNode n16 = PhylogenyNode
4797 .createInstanceFromNhxString( "something_wicked2[9]",
4798 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4799 if ( !n16.getName().equals( "something_wicked2" ) ) {
4802 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4805 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4808 final PhylogenyNode n17 = PhylogenyNode
4809 .createInstanceFromNhxString( "something_wicked3[a]",
4810 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4811 if ( !n17.getName().equals( "something_wicked3" ) ) {
4814 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4817 final PhylogenyNode n18 = PhylogenyNode
4818 .createInstanceFromNhxString( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4819 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4822 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4825 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4829 catch ( final Exception e ) {
4830 e.printStackTrace( System.out );
4836 private static boolean testNHXParsing() {
4838 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4839 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4840 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4843 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]";
4844 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4845 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4848 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]";
4849 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4850 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4853 final Phylogeny[] p3 = factory
4854 .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]",
4856 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4859 final Phylogeny[] p4 = factory
4860 .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(]",
4862 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4865 final Phylogeny[] p5 = factory
4866 .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(((]",
4868 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4871 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)";
4872 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)";
4873 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4874 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4877 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)))";
4878 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)))";
4879 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4880 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4883 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]) ))[,,, ])))))))";
4884 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4885 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4886 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4889 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4890 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]" ) ) {
4893 final Phylogeny p10 = factory
4894 .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]",
4895 new NHXParser() )[ 0 ];
4896 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]" ) ) {
4900 catch ( final Exception e ) {
4901 e.printStackTrace( System.out );
4907 private static boolean testNHXParsingQuotes() {
4909 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4910 final NHXParser p = new NHXParser();
4911 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4912 if ( phylogenies_0.length != 5 ) {
4915 final Phylogeny phy = phylogenies_0[ 4 ];
4916 if ( phy.getNumberOfExternalNodes() != 7 ) {
4919 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4922 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4925 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4926 .getScientificName().equals( "hsapiens" ) ) {
4929 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4932 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4935 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4938 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4941 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4944 final NHXParser p1p = new NHXParser();
4945 p1p.setIgnoreQuotes( true );
4946 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4947 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4950 final NHXParser p2p = new NHXParser();
4951 p1p.setIgnoreQuotes( false );
4952 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4953 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4956 final NHXParser p3p = new NHXParser();
4957 p3p.setIgnoreQuotes( false );
4958 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4959 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4962 final NHXParser p4p = new NHXParser();
4963 p4p.setIgnoreQuotes( false );
4964 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4965 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4968 final Phylogeny p10 = factory
4969 .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]",
4970 new NHXParser() )[ 0 ];
4971 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]";
4972 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
4975 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
4976 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
4980 final Phylogeny p12 = factory
4981 .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]",
4982 new NHXParser() )[ 0 ];
4983 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]";
4984 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
4987 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
4988 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
4991 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;";
4992 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
4995 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
4996 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5000 catch ( final Exception e ) {
5001 e.printStackTrace( System.out );
5007 private static boolean testPhylogenyBranch() {
5009 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5010 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5011 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5012 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5013 if ( !a1b1.equals( a1b1 ) ) {
5016 if ( !a1b1.equals( b1a1 ) ) {
5019 if ( !b1a1.equals( a1b1 ) ) {
5022 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5023 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5024 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5025 if ( a1_b1.equals( b1_a1 ) ) {
5028 if ( a1_b1.equals( a1_b1_ ) ) {
5031 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5032 if ( !a1_b1.equals( b1_a1_ ) ) {
5035 if ( a1_b1_.equals( b1_a1_ ) ) {
5038 if ( !a1_b1_.equals( b1_a1 ) ) {
5042 catch ( final Exception e ) {
5043 e.printStackTrace( System.out );
5049 private static boolean testPhyloXMLparsingOfDistributionElement() {
5051 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5052 PhyloXmlParser xml_parser = null;
5054 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5056 catch ( final Exception e ) {
5057 // Do nothing -- means were not running from jar.
5059 if ( xml_parser == null ) {
5060 xml_parser = new PhyloXmlParser();
5061 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5062 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5065 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5068 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5070 if ( xml_parser.getErrorCount() > 0 ) {
5071 System.out.println( xml_parser.getErrorMessages().toString() );
5074 if ( phylogenies_0.length != 1 ) {
5077 final Phylogeny t1 = phylogenies_0[ 0 ];
5078 PhylogenyNode n = null;
5079 Distribution d = null;
5080 n = t1.getNode( "root node" );
5081 if ( !n.getNodeData().isHasDistribution() ) {
5084 if ( n.getNodeData().getDistributions().size() != 1 ) {
5087 d = n.getNodeData().getDistribution();
5088 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5091 if ( d.getPoints().size() != 1 ) {
5094 if ( d.getPolygons() != null ) {
5097 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5100 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5103 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5106 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5109 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5112 n = t1.getNode( "node a" );
5113 if ( !n.getNodeData().isHasDistribution() ) {
5116 if ( n.getNodeData().getDistributions().size() != 2 ) {
5119 d = n.getNodeData().getDistribution( 1 );
5120 if ( !d.getDesc().equals( "San Diego" ) ) {
5123 if ( d.getPoints().size() != 1 ) {
5126 if ( d.getPolygons() != null ) {
5129 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5132 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5135 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5138 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5141 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5144 n = t1.getNode( "node bb" );
5145 if ( !n.getNodeData().isHasDistribution() ) {
5148 if ( n.getNodeData().getDistributions().size() != 1 ) {
5151 d = n.getNodeData().getDistribution( 0 );
5152 if ( d.getPoints().size() != 3 ) {
5155 if ( d.getPolygons().size() != 2 ) {
5158 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5161 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5164 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5167 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5170 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5173 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5176 Polygon p = d.getPolygons().get( 0 );
5177 if ( p.getPoints().size() != 3 ) {
5180 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5183 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5186 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5189 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5192 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5195 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5198 p = d.getPolygons().get( 1 );
5199 if ( p.getPoints().size() != 3 ) {
5202 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5205 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5208 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5212 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5213 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5214 if ( rt.length != 1 ) {
5217 final Phylogeny t1_rt = rt[ 0 ];
5218 n = t1_rt.getNode( "root node" );
5219 if ( !n.getNodeData().isHasDistribution() ) {
5222 if ( n.getNodeData().getDistributions().size() != 1 ) {
5225 d = n.getNodeData().getDistribution();
5226 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5229 if ( d.getPoints().size() != 1 ) {
5232 if ( d.getPolygons() != null ) {
5235 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5238 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5241 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5244 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5247 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5250 n = t1_rt.getNode( "node a" );
5251 if ( !n.getNodeData().isHasDistribution() ) {
5254 if ( n.getNodeData().getDistributions().size() != 2 ) {
5257 d = n.getNodeData().getDistribution( 1 );
5258 if ( !d.getDesc().equals( "San Diego" ) ) {
5261 if ( d.getPoints().size() != 1 ) {
5264 if ( d.getPolygons() != null ) {
5267 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5270 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5273 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5276 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5279 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5282 n = t1_rt.getNode( "node bb" );
5283 if ( !n.getNodeData().isHasDistribution() ) {
5286 if ( n.getNodeData().getDistributions().size() != 1 ) {
5289 d = n.getNodeData().getDistribution( 0 );
5290 if ( d.getPoints().size() != 3 ) {
5293 if ( d.getPolygons().size() != 2 ) {
5296 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5299 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5302 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5305 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5308 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5311 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5314 p = d.getPolygons().get( 0 );
5315 if ( p.getPoints().size() != 3 ) {
5318 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5321 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5324 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5327 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5330 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5333 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5336 p = d.getPolygons().get( 1 );
5337 if ( p.getPoints().size() != 3 ) {
5340 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5343 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5346 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5350 catch ( final Exception e ) {
5351 e.printStackTrace( System.out );
5357 private static boolean testPostOrderIterator() {
5359 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5360 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5361 PhylogenyNodeIterator it0;
5362 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5365 for( it0.reset(); it0.hasNext(); ) {
5368 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5369 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5370 if ( !it.next().getName().equals( "A" ) ) {
5373 if ( !it.next().getName().equals( "B" ) ) {
5376 if ( !it.next().getName().equals( "ab" ) ) {
5379 if ( !it.next().getName().equals( "C" ) ) {
5382 if ( !it.next().getName().equals( "D" ) ) {
5385 if ( !it.next().getName().equals( "cd" ) ) {
5388 if ( !it.next().getName().equals( "abcd" ) ) {
5391 if ( !it.next().getName().equals( "E" ) ) {
5394 if ( !it.next().getName().equals( "F" ) ) {
5397 if ( !it.next().getName().equals( "ef" ) ) {
5400 if ( !it.next().getName().equals( "G" ) ) {
5403 if ( !it.next().getName().equals( "H" ) ) {
5406 if ( !it.next().getName().equals( "gh" ) ) {
5409 if ( !it.next().getName().equals( "efgh" ) ) {
5412 if ( !it.next().getName().equals( "r" ) ) {
5415 if ( it.hasNext() ) {
5419 catch ( final Exception e ) {
5420 e.printStackTrace( System.out );
5426 private static boolean testPreOrderIterator() {
5428 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5429 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5430 PhylogenyNodeIterator it0;
5431 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5434 for( it0.reset(); it0.hasNext(); ) {
5437 PhylogenyNodeIterator it = t0.iteratorPreorder();
5438 if ( !it.next().getName().equals( "r" ) ) {
5441 if ( !it.next().getName().equals( "ab" ) ) {
5444 if ( !it.next().getName().equals( "A" ) ) {
5447 if ( !it.next().getName().equals( "B" ) ) {
5450 if ( !it.next().getName().equals( "cd" ) ) {
5453 if ( !it.next().getName().equals( "C" ) ) {
5456 if ( !it.next().getName().equals( "D" ) ) {
5459 if ( it.hasNext() ) {
5462 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5463 it = t1.iteratorPreorder();
5464 if ( !it.next().getName().equals( "r" ) ) {
5467 if ( !it.next().getName().equals( "abcd" ) ) {
5470 if ( !it.next().getName().equals( "ab" ) ) {
5473 if ( !it.next().getName().equals( "A" ) ) {
5476 if ( !it.next().getName().equals( "B" ) ) {
5479 if ( !it.next().getName().equals( "cd" ) ) {
5482 if ( !it.next().getName().equals( "C" ) ) {
5485 if ( !it.next().getName().equals( "D" ) ) {
5488 if ( !it.next().getName().equals( "efgh" ) ) {
5491 if ( !it.next().getName().equals( "ef" ) ) {
5494 if ( !it.next().getName().equals( "E" ) ) {
5497 if ( !it.next().getName().equals( "F" ) ) {
5500 if ( !it.next().getName().equals( "gh" ) ) {
5503 if ( !it.next().getName().equals( "G" ) ) {
5506 if ( !it.next().getName().equals( "H" ) ) {
5509 if ( it.hasNext() ) {
5513 catch ( final Exception e ) {
5514 e.printStackTrace( System.out );
5520 private static boolean testPropertiesMap() {
5522 final PropertiesMap pm = new PropertiesMap();
5523 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5524 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5525 final Property p2 = new Property( "something:else",
5527 "improbable:research",
5530 pm.addProperty( p0 );
5531 pm.addProperty( p1 );
5532 pm.addProperty( p2 );
5533 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5536 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5539 if ( pm.getProperties().size() != 3 ) {
5542 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5545 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5548 if ( pm.getProperties().size() != 3 ) {
5551 pm.removeProperty( "dimensions:diameter" );
5552 if ( pm.getProperties().size() != 2 ) {
5555 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5558 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5562 catch ( final Exception e ) {
5563 e.printStackTrace( System.out );
5569 private static boolean testReIdMethods() {
5571 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5572 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5573 final int count = PhylogenyNode.getNodeCount();
5575 if ( p.getNode( "r" ).getId() != count ) {
5578 if ( p.getNode( "A" ).getId() != count + 1 ) {
5581 if ( p.getNode( "B" ).getId() != count + 1 ) {
5584 if ( p.getNode( "C" ).getId() != count + 1 ) {
5587 if ( p.getNode( "1" ).getId() != count + 2 ) {
5590 if ( p.getNode( "2" ).getId() != count + 2 ) {
5593 if ( p.getNode( "3" ).getId() != count + 2 ) {
5596 if ( p.getNode( "4" ).getId() != count + 2 ) {
5599 if ( p.getNode( "5" ).getId() != count + 2 ) {
5602 if ( p.getNode( "6" ).getId() != count + 2 ) {
5605 if ( p.getNode( "a" ).getId() != count + 3 ) {
5608 if ( p.getNode( "b" ).getId() != count + 3 ) {
5611 if ( p.getNode( "X" ).getId() != count + 4 ) {
5614 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5617 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5621 catch ( final Exception e ) {
5622 e.printStackTrace( System.out );
5628 private static boolean testRerooting() {
5630 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5631 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",
5632 new NHXParser() )[ 0 ];
5633 if ( !t1.isRooted() ) {
5636 t1.reRoot( t1.getNode( "D" ) );
5637 t1.reRoot( t1.getNode( "CD" ) );
5638 t1.reRoot( t1.getNode( "A" ) );
5639 t1.reRoot( t1.getNode( "B" ) );
5640 t1.reRoot( t1.getNode( "AB" ) );
5641 t1.reRoot( t1.getNode( "D" ) );
5642 t1.reRoot( t1.getNode( "C" ) );
5643 t1.reRoot( t1.getNode( "CD" ) );
5644 t1.reRoot( t1.getNode( "A" ) );
5645 t1.reRoot( t1.getNode( "B" ) );
5646 t1.reRoot( t1.getNode( "AB" ) );
5647 t1.reRoot( t1.getNode( "D" ) );
5648 t1.reRoot( t1.getNode( "D" ) );
5649 t1.reRoot( t1.getNode( "C" ) );
5650 t1.reRoot( t1.getNode( "A" ) );
5651 t1.reRoot( t1.getNode( "B" ) );
5652 t1.reRoot( t1.getNode( "AB" ) );
5653 t1.reRoot( t1.getNode( "C" ) );
5654 t1.reRoot( t1.getNode( "D" ) );
5655 t1.reRoot( t1.getNode( "CD" ) );
5656 t1.reRoot( t1.getNode( "D" ) );
5657 t1.reRoot( t1.getNode( "A" ) );
5658 t1.reRoot( t1.getNode( "B" ) );
5659 t1.reRoot( t1.getNode( "AB" ) );
5660 t1.reRoot( t1.getNode( "C" ) );
5661 t1.reRoot( t1.getNode( "D" ) );
5662 t1.reRoot( t1.getNode( "CD" ) );
5663 t1.reRoot( t1.getNode( "D" ) );
5664 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5667 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5670 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5673 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5676 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5679 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5682 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",
5683 new NHXParser() )[ 0 ];
5684 t2.reRoot( t2.getNode( "A" ) );
5685 t2.reRoot( t2.getNode( "D" ) );
5686 t2.reRoot( t2.getNode( "ABC" ) );
5687 t2.reRoot( t2.getNode( "A" ) );
5688 t2.reRoot( t2.getNode( "B" ) );
5689 t2.reRoot( t2.getNode( "D" ) );
5690 t2.reRoot( t2.getNode( "C" ) );
5691 t2.reRoot( t2.getNode( "ABC" ) );
5692 t2.reRoot( t2.getNode( "A" ) );
5693 t2.reRoot( t2.getNode( "B" ) );
5694 t2.reRoot( t2.getNode( "AB" ) );
5695 t2.reRoot( t2.getNode( "AB" ) );
5696 t2.reRoot( t2.getNode( "D" ) );
5697 t2.reRoot( t2.getNode( "C" ) );
5698 t2.reRoot( t2.getNode( "B" ) );
5699 t2.reRoot( t2.getNode( "AB" ) );
5700 t2.reRoot( t2.getNode( "D" ) );
5701 t2.reRoot( t2.getNode( "D" ) );
5702 t2.reRoot( t2.getNode( "ABC" ) );
5703 t2.reRoot( t2.getNode( "A" ) );
5704 t2.reRoot( t2.getNode( "B" ) );
5705 t2.reRoot( t2.getNode( "AB" ) );
5706 t2.reRoot( t2.getNode( "D" ) );
5707 t2.reRoot( t2.getNode( "C" ) );
5708 t2.reRoot( t2.getNode( "ABC" ) );
5709 t2.reRoot( t2.getNode( "A" ) );
5710 t2.reRoot( t2.getNode( "B" ) );
5711 t2.reRoot( t2.getNode( "AB" ) );
5712 t2.reRoot( t2.getNode( "D" ) );
5713 t2.reRoot( t2.getNode( "D" ) );
5714 t2.reRoot( t2.getNode( "C" ) );
5715 t2.reRoot( t2.getNode( "A" ) );
5716 t2.reRoot( t2.getNode( "B" ) );
5717 t2.reRoot( t2.getNode( "AB" ) );
5718 t2.reRoot( t2.getNode( "C" ) );
5719 t2.reRoot( t2.getNode( "D" ) );
5720 t2.reRoot( t2.getNode( "ABC" ) );
5721 t2.reRoot( t2.getNode( "D" ) );
5722 t2.reRoot( t2.getNode( "A" ) );
5723 t2.reRoot( t2.getNode( "B" ) );
5724 t2.reRoot( t2.getNode( "AB" ) );
5725 t2.reRoot( t2.getNode( "C" ) );
5726 t2.reRoot( t2.getNode( "D" ) );
5727 t2.reRoot( t2.getNode( "ABC" ) );
5728 t2.reRoot( t2.getNode( "D" ) );
5729 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5732 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5735 t2.reRoot( t2.getNode( "ABC" ) );
5736 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5739 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5742 t2.reRoot( t2.getNode( "AB" ) );
5743 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5746 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5749 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5752 t2.reRoot( t2.getNode( "AB" ) );
5753 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5756 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5759 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5762 t2.reRoot( t2.getNode( "D" ) );
5763 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5766 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5769 t2.reRoot( t2.getNode( "ABC" ) );
5770 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5773 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5776 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5777 new NHXParser() )[ 0 ];
5778 t3.reRoot( t3.getNode( "B" ) );
5779 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5782 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5785 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5788 t3.reRoot( t3.getNode( "B" ) );
5789 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5792 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5795 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5798 t3.reRoot( t3.getRoot() );
5799 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5802 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5805 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5809 catch ( final Exception e ) {
5810 e.printStackTrace( System.out );
5816 private static boolean testSDIse() {
5818 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5819 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5820 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5821 gene1.setRooted( true );
5822 species1.setRooted( true );
5823 final SDI sdi = new SDIse( gene1, species1 );
5824 if ( !gene1.getRoot().isDuplication() ) {
5827 final Phylogeny species2 = factory
5828 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5829 new NHXParser() )[ 0 ];
5830 final Phylogeny gene2 = factory
5831 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5832 new NHXParser() )[ 0 ];
5833 species2.setRooted( true );
5834 gene2.setRooted( true );
5835 final SDI sdi2 = new SDIse( gene2, species2 );
5836 if ( sdi2.getDuplicationsSum() != 0 ) {
5839 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5842 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5845 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5848 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5851 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5854 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5857 final Phylogeny species3 = factory
5858 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5859 new NHXParser() )[ 0 ];
5860 final Phylogeny gene3 = factory
5861 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5862 new NHXParser() )[ 0 ];
5863 species3.setRooted( true );
5864 gene3.setRooted( true );
5865 final SDI sdi3 = new SDIse( gene3, species3 );
5866 if ( sdi3.getDuplicationsSum() != 1 ) {
5869 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5872 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5875 final Phylogeny species4 = factory
5876 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5877 new NHXParser() )[ 0 ];
5878 final Phylogeny gene4 = factory
5879 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5880 new NHXParser() )[ 0 ];
5881 species4.setRooted( true );
5882 gene4.setRooted( true );
5883 final SDI sdi4 = new SDIse( gene4, species4 );
5884 if ( sdi4.getDuplicationsSum() != 1 ) {
5887 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5890 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5893 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5896 if ( species4.getNumberOfExternalNodes() != 6 ) {
5899 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5902 final Phylogeny species5 = factory
5903 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5904 new NHXParser() )[ 0 ];
5905 final Phylogeny gene5 = factory
5906 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5907 new NHXParser() )[ 0 ];
5908 species5.setRooted( true );
5909 gene5.setRooted( true );
5910 final SDI sdi5 = new SDIse( gene5, species5 );
5911 if ( sdi5.getDuplicationsSum() != 2 ) {
5914 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5917 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5920 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5923 if ( species5.getNumberOfExternalNodes() != 6 ) {
5926 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5929 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5930 // Conjecture for Comparing Molecular Phylogenies"
5931 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5932 final Phylogeny species6 = factory
5933 .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,"
5934 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5935 new NHXParser() )[ 0 ];
5936 final Phylogeny gene6 = factory
5937 .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,"
5938 + "((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,"
5939 + "(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;",
5940 new NHXParser() )[ 0 ];
5941 species6.setRooted( true );
5942 gene6.setRooted( true );
5943 final SDI sdi6 = new SDIse( gene6, species6 );
5944 if ( sdi6.getDuplicationsSum() != 3 ) {
5947 if ( !gene6.getNode( "r" ).isDuplication() ) {
5950 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
5953 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
5956 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
5959 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
5962 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
5965 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
5968 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
5971 sdi6.computeMappingCostL();
5972 if ( sdi6.computeMappingCostL() != 17 ) {
5975 if ( species6.getNumberOfExternalNodes() != 9 ) {
5978 if ( gene6.getNumberOfExternalNodes() != 9 ) {
5981 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
5982 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
5983 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
5984 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
5985 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
5986 species7.setRooted( true );
5987 final Phylogeny gene7_1 = Test
5988 .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])" );
5989 gene7_1.setRooted( true );
5990 final SDI sdi7 = new SDIse( gene7_1, species7 );
5991 if ( sdi7.getDuplicationsSum() != 0 ) {
5994 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
5997 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6000 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6003 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6006 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6009 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6012 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6015 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6018 final Phylogeny gene7_2 = Test
6019 .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])" );
6020 gene7_2.setRooted( true );
6021 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6022 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6025 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6028 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6031 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6034 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6037 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6040 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6043 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6046 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6049 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6053 catch ( final Exception e ) {
6059 private static boolean testSDIunrooted() {
6061 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6062 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6063 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6064 final Iterator<PhylogenyBranch> iter = l.iterator();
6065 PhylogenyBranch br = iter.next();
6066 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6069 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6073 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6076 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6080 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6083 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6087 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6090 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6094 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6097 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6101 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6104 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6108 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6111 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6115 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6118 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6122 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6125 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6129 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6132 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6136 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6139 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6143 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6146 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6150 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6153 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6157 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6160 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6164 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6167 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6170 if ( iter.hasNext() ) {
6173 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6174 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6175 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6177 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6180 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6184 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6187 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6191 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6194 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6197 if ( iter1.hasNext() ) {
6200 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6201 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6202 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6204 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6207 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6211 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6214 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6218 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6221 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6224 if ( iter2.hasNext() ) {
6227 final Phylogeny species0 = factory
6228 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6229 new NHXParser() )[ 0 ];
6230 final Phylogeny gene1 = factory
6231 .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])",
6232 new NHXParser() )[ 0 ];
6233 species0.setRooted( true );
6234 gene1.setRooted( true );
6235 final SDIR sdi_unrooted = new SDIR();
6236 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6237 if ( sdi_unrooted.getCount() != 1 ) {
6240 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6243 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6246 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6249 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6252 final Phylogeny gene2 = factory
6253 .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])",
6254 new NHXParser() )[ 0 ];
6255 gene2.setRooted( true );
6256 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6257 if ( sdi_unrooted.getCount() != 1 ) {
6260 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6263 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6266 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6269 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6272 final Phylogeny species6 = factory
6273 .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,"
6274 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6275 new NHXParser() )[ 0 ];
6276 final Phylogeny gene6 = factory
6277 .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],"
6278 + "(((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],"
6279 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6280 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6281 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6282 new NHXParser() )[ 0 ];
6283 species6.setRooted( true );
6284 gene6.setRooted( true );
6285 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6286 if ( sdi_unrooted.getCount() != 1 ) {
6289 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6292 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6295 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6298 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6301 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6304 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6307 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6310 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6313 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6316 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6319 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6322 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6326 final Phylogeny species7 = factory
6327 .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,"
6328 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6329 new NHXParser() )[ 0 ];
6330 final Phylogeny gene7 = factory
6331 .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],"
6332 + "(((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],"
6333 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6334 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6335 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6336 new NHXParser() )[ 0 ];
6337 species7.setRooted( true );
6338 gene7.setRooted( true );
6339 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6340 if ( sdi_unrooted.getCount() != 1 ) {
6343 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6346 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6349 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6352 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6355 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6358 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6361 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6364 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6367 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6370 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6373 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6376 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6380 final Phylogeny species8 = factory
6381 .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,"
6382 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6383 new NHXParser() )[ 0 ];
6384 final Phylogeny gene8 = factory
6385 .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],"
6386 + "(((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],"
6387 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6388 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6389 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6390 new NHXParser() )[ 0 ];
6391 species8.setRooted( true );
6392 gene8.setRooted( true );
6393 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6394 if ( sdi_unrooted.getCount() != 1 ) {
6397 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6400 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6403 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6406 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6409 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6412 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6415 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6418 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6421 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6424 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6427 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6430 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6435 catch ( final Exception e ) {
6436 e.printStackTrace( System.out );
6442 private static boolean testSplit() {
6444 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6445 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6446 //Archaeopteryx.createApplication( p0 );
6447 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6448 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6449 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6450 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6451 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6452 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6453 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6454 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6455 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6456 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6457 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6458 // System.out.println( s0.toString() );
6460 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6461 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6462 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6463 if ( s0.match( query_nodes ) ) {
6466 query_nodes = new HashSet<PhylogenyNode>();
6467 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6468 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6469 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6470 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6471 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6472 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6473 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6474 if ( !s0.match( query_nodes ) ) {
6478 query_nodes = new HashSet<PhylogenyNode>();
6479 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6480 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6481 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6482 if ( !s0.match( query_nodes ) ) {
6486 query_nodes = new HashSet<PhylogenyNode>();
6487 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6488 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6489 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6490 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6491 if ( !s0.match( query_nodes ) ) {
6495 query_nodes = new HashSet<PhylogenyNode>();
6496 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6497 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6498 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6500 if ( !s0.match( query_nodes ) ) {
6504 query_nodes = new HashSet<PhylogenyNode>();
6505 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6506 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6507 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6508 if ( !s0.match( query_nodes ) ) {
6512 query_nodes = new HashSet<PhylogenyNode>();
6513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6514 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6515 if ( !s0.match( query_nodes ) ) {
6519 query_nodes = new HashSet<PhylogenyNode>();
6520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6523 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6525 if ( !s0.match( query_nodes ) ) {
6529 query_nodes = new HashSet<PhylogenyNode>();
6530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6533 if ( !s0.match( query_nodes ) ) {
6537 query_nodes = new HashSet<PhylogenyNode>();
6538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6540 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6541 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6542 if ( !s0.match( query_nodes ) ) {
6546 query_nodes = new HashSet<PhylogenyNode>();
6547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6549 if ( s0.match( query_nodes ) ) {
6553 query_nodes = new HashSet<PhylogenyNode>();
6554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6558 if ( s0.match( query_nodes ) ) {
6562 query_nodes = new HashSet<PhylogenyNode>();
6563 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6564 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6568 if ( s0.match( query_nodes ) ) {
6572 query_nodes = new HashSet<PhylogenyNode>();
6573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6576 if ( s0.match( query_nodes ) ) {
6580 query_nodes = new HashSet<PhylogenyNode>();
6581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6583 if ( s0.match( query_nodes ) ) {
6587 query_nodes = new HashSet<PhylogenyNode>();
6588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6590 if ( s0.match( query_nodes ) ) {
6594 query_nodes = new HashSet<PhylogenyNode>();
6595 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6597 if ( s0.match( query_nodes ) ) {
6601 query_nodes = new HashSet<PhylogenyNode>();
6602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6604 if ( s0.match( query_nodes ) ) {
6608 query_nodes = new HashSet<PhylogenyNode>();
6609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6611 if ( s0.match( query_nodes ) ) {
6615 query_nodes = new HashSet<PhylogenyNode>();
6616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6618 if ( s0.match( query_nodes ) ) {
6622 query_nodes = new HashSet<PhylogenyNode>();
6623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6626 if ( s0.match( query_nodes ) ) {
6630 query_nodes = new HashSet<PhylogenyNode>();
6631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6634 if ( s0.match( query_nodes ) ) {
6638 query_nodes = new HashSet<PhylogenyNode>();
6639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6642 if ( s0.match( query_nodes ) ) {
6646 query_nodes = new HashSet<PhylogenyNode>();
6647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6651 if ( s0.match( query_nodes ) ) {
6655 // query_nodes = new HashSet<PhylogenyNode>();
6656 // query_nodes.add( new PhylogenyNode( "X" ) );
6657 // query_nodes.add( new PhylogenyNode( "Y" ) );
6658 // query_nodes.add( new PhylogenyNode( "A" ) );
6659 // query_nodes.add( new PhylogenyNode( "B" ) );
6660 // query_nodes.add( new PhylogenyNode( "C" ) );
6661 // query_nodes.add( new PhylogenyNode( "D" ) );
6662 // query_nodes.add( new PhylogenyNode( "E" ) );
6663 // query_nodes.add( new PhylogenyNode( "F" ) );
6664 // query_nodes.add( new PhylogenyNode( "G" ) );
6665 // if ( !s0.match( query_nodes ) ) {
6668 // query_nodes = new HashSet<PhylogenyNode>();
6669 // query_nodes.add( new PhylogenyNode( "X" ) );
6670 // query_nodes.add( new PhylogenyNode( "Y" ) );
6671 // query_nodes.add( new PhylogenyNode( "A" ) );
6672 // query_nodes.add( new PhylogenyNode( "B" ) );
6673 // query_nodes.add( new PhylogenyNode( "C" ) );
6674 // if ( !s0.match( query_nodes ) ) {
6678 // query_nodes = new HashSet<PhylogenyNode>();
6679 // query_nodes.add( new PhylogenyNode( "X" ) );
6680 // query_nodes.add( new PhylogenyNode( "Y" ) );
6681 // query_nodes.add( new PhylogenyNode( "D" ) );
6682 // query_nodes.add( new PhylogenyNode( "E" ) );
6683 // query_nodes.add( new PhylogenyNode( "F" ) );
6684 // query_nodes.add( new PhylogenyNode( "G" ) );
6685 // if ( !s0.match( query_nodes ) ) {
6689 // query_nodes = new HashSet<PhylogenyNode>();
6690 // query_nodes.add( new PhylogenyNode( "X" ) );
6691 // query_nodes.add( new PhylogenyNode( "Y" ) );
6692 // query_nodes.add( new PhylogenyNode( "A" ) );
6693 // query_nodes.add( new PhylogenyNode( "B" ) );
6694 // query_nodes.add( new PhylogenyNode( "C" ) );
6695 // query_nodes.add( new PhylogenyNode( "D" ) );
6696 // if ( !s0.match( query_nodes ) ) {
6700 // query_nodes = new HashSet<PhylogenyNode>();
6701 // query_nodes.add( new PhylogenyNode( "X" ) );
6702 // query_nodes.add( new PhylogenyNode( "Y" ) );
6703 // query_nodes.add( new PhylogenyNode( "E" ) );
6704 // query_nodes.add( new PhylogenyNode( "F" ) );
6705 // query_nodes.add( new PhylogenyNode( "G" ) );
6706 // if ( !s0.match( query_nodes ) ) {
6710 // query_nodes = new HashSet<PhylogenyNode>();
6711 // query_nodes.add( new PhylogenyNode( "X" ) );
6712 // query_nodes.add( new PhylogenyNode( "Y" ) );
6713 // query_nodes.add( new PhylogenyNode( "F" ) );
6714 // query_nodes.add( new PhylogenyNode( "G" ) );
6715 // if ( !s0.match( query_nodes ) ) {
6719 query_nodes = new HashSet<PhylogenyNode>();
6720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6724 if ( s0.match( query_nodes ) ) {
6728 query_nodes = new HashSet<PhylogenyNode>();
6729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6733 if ( s0.match( query_nodes ) ) {
6736 ///////////////////////////
6738 query_nodes = new HashSet<PhylogenyNode>();
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6742 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6743 if ( s0.match( query_nodes ) ) {
6747 query_nodes = new HashSet<PhylogenyNode>();
6748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6752 if ( s0.match( query_nodes ) ) {
6756 query_nodes = new HashSet<PhylogenyNode>();
6757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6758 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6759 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6760 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6761 if ( s0.match( query_nodes ) ) {
6765 query_nodes = new HashSet<PhylogenyNode>();
6766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6767 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6768 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6770 if ( s0.match( query_nodes ) ) {
6774 query_nodes = new HashSet<PhylogenyNode>();
6775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6777 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6779 if ( s0.match( query_nodes ) ) {
6783 query_nodes = new HashSet<PhylogenyNode>();
6784 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6786 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6787 if ( s0.match( query_nodes ) ) {
6791 query_nodes = new HashSet<PhylogenyNode>();
6792 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6793 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6794 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6797 if ( s0.match( query_nodes ) ) {
6801 query_nodes = new HashSet<PhylogenyNode>();
6802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6807 if ( s0.match( query_nodes ) ) {
6811 query_nodes = new HashSet<PhylogenyNode>();
6812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6815 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6817 if ( s0.match( query_nodes ) ) {
6821 query_nodes = new HashSet<PhylogenyNode>();
6822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6827 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6828 if ( s0.match( query_nodes ) ) {
6832 catch ( final Exception e ) {
6833 e.printStackTrace();
6839 private static boolean testSplitStrict() {
6841 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6842 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6843 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6844 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6845 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6846 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6847 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6848 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6849 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6850 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6851 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6852 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6854 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6855 if ( s0.match( query_nodes ) ) {
6858 query_nodes = new HashSet<PhylogenyNode>();
6859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6864 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6865 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6866 if ( !s0.match( query_nodes ) ) {
6870 query_nodes = new HashSet<PhylogenyNode>();
6871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6873 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6874 if ( !s0.match( query_nodes ) ) {
6878 query_nodes = new HashSet<PhylogenyNode>();
6879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6882 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6883 if ( !s0.match( query_nodes ) ) {
6887 query_nodes = new HashSet<PhylogenyNode>();
6888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6890 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6891 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6892 if ( !s0.match( query_nodes ) ) {
6896 query_nodes = new HashSet<PhylogenyNode>();
6897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6899 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6900 if ( !s0.match( query_nodes ) ) {
6904 query_nodes = new HashSet<PhylogenyNode>();
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6907 if ( !s0.match( query_nodes ) ) {
6911 query_nodes = new HashSet<PhylogenyNode>();
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6917 if ( !s0.match( query_nodes ) ) {
6921 query_nodes = new HashSet<PhylogenyNode>();
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6925 if ( !s0.match( query_nodes ) ) {
6929 query_nodes = new HashSet<PhylogenyNode>();
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6934 if ( !s0.match( query_nodes ) ) {
6938 query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6941 if ( s0.match( query_nodes ) ) {
6945 query_nodes = new HashSet<PhylogenyNode>();
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6950 if ( s0.match( query_nodes ) ) {
6954 query_nodes = new HashSet<PhylogenyNode>();
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6960 if ( s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6968 if ( s0.match( query_nodes ) ) {
6972 query_nodes = new HashSet<PhylogenyNode>();
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6975 if ( s0.match( query_nodes ) ) {
6979 query_nodes = new HashSet<PhylogenyNode>();
6980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6982 if ( s0.match( query_nodes ) ) {
6986 query_nodes = new HashSet<PhylogenyNode>();
6987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6989 if ( s0.match( query_nodes ) ) {
6993 query_nodes = new HashSet<PhylogenyNode>();
6994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6996 if ( s0.match( query_nodes ) ) {
7000 query_nodes = new HashSet<PhylogenyNode>();
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7003 if ( s0.match( query_nodes ) ) {
7007 query_nodes = new HashSet<PhylogenyNode>();
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7010 if ( s0.match( query_nodes ) ) {
7014 query_nodes = new HashSet<PhylogenyNode>();
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7018 if ( s0.match( query_nodes ) ) {
7022 query_nodes = new HashSet<PhylogenyNode>();
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7026 if ( s0.match( query_nodes ) ) {
7030 query_nodes = new HashSet<PhylogenyNode>();
7031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7034 if ( s0.match( query_nodes ) ) {
7038 query_nodes = new HashSet<PhylogenyNode>();
7039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7043 if ( s0.match( query_nodes ) ) {
7047 catch ( final Exception e ) {
7048 e.printStackTrace();
7054 private static boolean testSubtreeDeletion() {
7056 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7057 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7058 t1.deleteSubtree( t1.getNode( "A" ), false );
7059 if ( t1.getNumberOfExternalNodes() != 5 ) {
7062 t1.toNewHampshireX();
7063 t1.deleteSubtree( t1.getNode( "E" ), false );
7064 if ( t1.getNumberOfExternalNodes() != 4 ) {
7067 t1.toNewHampshireX();
7068 t1.deleteSubtree( t1.getNode( "F" ), false );
7069 if ( t1.getNumberOfExternalNodes() != 3 ) {
7072 t1.toNewHampshireX();
7073 t1.deleteSubtree( t1.getNode( "D" ), false );
7074 t1.toNewHampshireX();
7075 if ( t1.getNumberOfExternalNodes() != 3 ) {
7078 t1.deleteSubtree( t1.getNode( "def" ), false );
7079 t1.toNewHampshireX();
7080 if ( t1.getNumberOfExternalNodes() != 2 ) {
7083 t1.deleteSubtree( t1.getNode( "B" ), false );
7084 t1.toNewHampshireX();
7085 if ( t1.getNumberOfExternalNodes() != 1 ) {
7088 t1.deleteSubtree( t1.getNode( "C" ), false );
7089 t1.toNewHampshireX();
7090 if ( t1.getNumberOfExternalNodes() != 1 ) {
7093 t1.deleteSubtree( t1.getNode( "abc" ), false );
7094 t1.toNewHampshireX();
7095 if ( t1.getNumberOfExternalNodes() != 1 ) {
7098 t1.deleteSubtree( t1.getNode( "r" ), false );
7099 if ( t1.getNumberOfExternalNodes() != 0 ) {
7102 if ( !t1.isEmpty() ) {
7105 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7106 t2.deleteSubtree( t2.getNode( "A" ), false );
7107 t2.toNewHampshireX();
7108 if ( t2.getNumberOfExternalNodes() != 5 ) {
7111 t2.deleteSubtree( t2.getNode( "abc" ), false );
7112 t2.toNewHampshireX();
7113 if ( t2.getNumberOfExternalNodes() != 3 ) {
7116 t2.deleteSubtree( t2.getNode( "def" ), false );
7117 t2.toNewHampshireX();
7118 if ( t2.getNumberOfExternalNodes() != 1 ) {
7122 catch ( final Exception e ) {
7123 e.printStackTrace( System.out );
7129 private static boolean testSupportCount() {
7131 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7132 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7133 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7134 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7135 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7136 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7137 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7139 SupportCount.count( t0_1, phylogenies_1, true, false );
7140 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7141 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7142 + "(((((A,B),C),D),E),((F,G),X))"
7143 + "(((((A,Y),B),C),D),((F,G),E))"
7144 + "(((((A,B),C),D),E),(F,G))"
7145 + "(((((A,B),C),D),E),(F,G))"
7146 + "(((((A,B),C),D),E),(F,G))"
7147 + "(((((A,B),C),D),E),(F,G),Z)"
7148 + "(((((A,B),C),D),E),(F,G))"
7149 + "((((((A,B),C),D),E),F),G)"
7150 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7152 SupportCount.count( t0_2, phylogenies_2, true, false );
7153 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7154 while ( it.hasNext() ) {
7155 final PhylogenyNode n = it.next();
7156 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7160 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7161 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7162 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7163 SupportCount.count( t0_3, phylogenies_3, true, false );
7164 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7165 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7168 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7171 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7174 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7177 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7180 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7183 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7186 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7189 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7192 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7195 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7196 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7197 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7198 SupportCount.count( t0_4, phylogenies_4, true, false );
7199 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7200 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7203 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7206 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7209 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7212 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7215 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7218 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7221 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7224 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7227 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7230 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7231 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7232 double d = SupportCount.compare( b1, a, true, true, true );
7233 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7236 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7237 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7238 d = SupportCount.compare( b2, a, true, true, true );
7239 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7242 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7243 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7244 d = SupportCount.compare( b3, a, true, true, true );
7245 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7248 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7249 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7250 d = SupportCount.compare( b4, a, true, true, false );
7251 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7255 catch ( final Exception e ) {
7256 e.printStackTrace( System.out );
7262 private static boolean testSupportTransfer() {
7264 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7265 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)",
7266 new NHXParser() )[ 0 ];
7267 final Phylogeny p2 = factory
7268 .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 ];
7269 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7272 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7275 support_transfer.moveBranchLengthsToBootstrap( p1 );
7276 support_transfer.transferSupportValues( p1, p2 );
7277 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7280 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7283 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7286 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7289 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7292 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7295 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7298 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7302 catch ( final Exception e ) {
7303 e.printStackTrace( System.out );
7309 private static boolean testTaxonomyAssigner() {
7311 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]";
7312 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7313 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7314 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7315 s0.setRooted( true );
7316 g0.setRooted( true );
7317 TaxonomyAssigner.execute( g0, s0 );
7318 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7321 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7324 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7327 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7328 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7329 g0.setRooted( true );
7330 TaxonomyAssigner.execute( g0, s0 );
7331 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7334 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7337 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7340 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7341 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7342 g0.setRooted( true );
7343 TaxonomyAssigner.execute( g0, s0 );
7344 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7347 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7350 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7353 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7354 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7355 g0.setRooted( true );
7356 TaxonomyAssigner.execute( g0, s0 );
7357 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7360 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7363 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7366 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7367 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7368 g0.setRooted( true );
7369 TaxonomyAssigner.execute( g0, s0 );
7370 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7373 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7376 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7379 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7380 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7381 g0.setRooted( true );
7382 TaxonomyAssigner.execute( g0, s0 );
7383 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7386 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7389 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7392 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7393 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7394 g0.setRooted( true );
7395 TaxonomyAssigner.execute( g0, s0 );
7396 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7399 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7402 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7405 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7406 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7407 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7408 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7409 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7410 s0.setRooted( true );
7411 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7412 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7413 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7414 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7415 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7416 g0.setRooted( true );
7417 TaxonomyAssigner.execute( g0, s0 );
7418 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7421 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7424 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7427 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7430 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7433 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7434 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7435 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7436 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7437 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7438 g0.setRooted( true );
7439 TaxonomyAssigner.execute( g0, s0 );
7440 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7443 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7446 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7449 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7452 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7455 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7456 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7457 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7458 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7459 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7460 g0.setRooted( true );
7461 TaxonomyAssigner.execute( g0, s0 );
7462 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7465 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7468 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7471 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7474 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7477 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7478 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7479 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7480 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7481 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7482 g0.setRooted( true );
7483 TaxonomyAssigner.execute( g0, s0 );
7484 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7487 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7490 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7493 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7496 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7499 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7500 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7501 g0.setRooted( true );
7502 TaxonomyAssigner.execute( g0, s0 );
7503 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7506 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7509 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7512 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7513 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7514 g0.setRooted( true );
7515 TaxonomyAssigner.execute( g0, s0 );
7516 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7519 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7522 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7525 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7526 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7527 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7528 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7529 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7530 g0.setRooted( true );
7531 TaxonomyAssigner.execute( g0, s0 );
7532 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7535 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7538 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7541 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7544 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7547 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7550 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7553 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7554 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7555 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7556 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7557 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7558 g0.setRooted( true );
7559 TaxonomyAssigner.execute( g0, s0 );
7560 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7563 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7566 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7569 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7572 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7575 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7578 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7581 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7582 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7583 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7584 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7585 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7586 g0.setRooted( true );
7587 TaxonomyAssigner.execute( g0, s0 );
7588 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7591 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7594 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7597 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7600 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7603 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7606 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7609 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7610 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7611 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7612 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7613 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7614 g0.setRooted( true );
7615 TaxonomyAssigner.execute( g0, s0 );
7616 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7619 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7622 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7625 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7628 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7631 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7634 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7637 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7638 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7639 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7640 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7641 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7642 s0.setRooted( true );
7643 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7644 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7645 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7646 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7647 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7648 g0.setRooted( true );
7649 TaxonomyAssigner.execute( g0, s0 );
7650 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7653 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7657 catch ( final Exception e ) {
7658 e.printStackTrace( System.out );
7664 private static boolean testUniprotTaxonomySearch() {
7666 List<UniProtTaxonomy> results = UniProtWsTools
7667 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7668 if ( results.size() != 1 ) {
7671 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7674 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7677 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7680 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7683 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7687 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7688 if ( results.size() != 1 ) {
7691 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7694 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7697 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7700 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7703 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7707 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7708 if ( results.size() != 1 ) {
7711 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7714 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7717 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7720 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7723 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7727 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7728 if ( results.size() != 1 ) {
7731 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7734 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7737 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7740 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7743 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7746 if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) {
7749 if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) {
7752 if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) {
7756 catch ( final IOException e ) {
7757 System.out.println();
7758 System.out.println( "the following might be due to absence internet connection:" );
7759 e.printStackTrace( System.out );
7762 catch ( final Exception e ) {
7768 private static boolean testEmblEntryRetrieval() {
7769 //The format for GenBank Accession numbers are:
7770 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7771 //Protein: 3 letters + 5 numerals
7772 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7773 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7776 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7779 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7782 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7785 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7788 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7791 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7794 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7797 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7800 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7803 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7806 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7809 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7815 private static boolean testUniprotEntryRetrieval() {
7816 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7819 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7822 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7825 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7828 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7831 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7834 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7837 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7840 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7843 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7846 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7849 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7852 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7856 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7857 if ( !entry.getAccession().equals( "P12345" ) ) {
7860 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7863 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7866 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7869 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7873 catch ( final IOException e ) {
7874 System.out.println();
7875 System.out.println( "the following might be due to absence internet connection:" );
7876 e.printStackTrace( System.out );
7879 catch ( final Exception e ) {
7885 private static boolean testWabiTxSearch() {
7888 result = TxSearch.searchSimple( "nematostella" );
7889 result = TxSearch.getTxId( "nematostella" );
7890 if ( !result.equals( "45350" ) ) {
7893 result = TxSearch.getTxName( "45350" );
7894 if ( !result.equals( "Nematostella" ) ) {
7897 result = TxSearch.getTxId( "nematostella vectensis" );
7898 if ( !result.equals( "45351" ) ) {
7901 result = TxSearch.getTxName( "45351" );
7902 if ( !result.equals( "Nematostella vectensis" ) ) {
7905 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7906 if ( !result.equals( "536089" ) ) {
7909 result = TxSearch.getTxName( "536089" );
7910 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7913 final List<String> queries = new ArrayList<String>();
7914 queries.add( "Campylobacter coli" );
7915 queries.add( "Escherichia coli" );
7916 queries.add( "Arabidopsis" );
7917 queries.add( "Trichoplax" );
7918 queries.add( "Samanea saman" );
7919 queries.add( "Kluyveromyces marxianus" );
7920 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7921 queries.add( "Bornavirus parrot/PDD/2008" );
7922 final List<RANKS> ranks = new ArrayList<RANKS>();
7923 ranks.add( RANKS.SUPERKINGDOM );
7924 ranks.add( RANKS.KINGDOM );
7925 ranks.add( RANKS.FAMILY );
7926 ranks.add( RANKS.GENUS );
7927 ranks.add( RANKS.TRIBE );
7928 result = TxSearch.searchLineage( queries, ranks );
7929 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7930 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7932 catch ( final Exception e ) {
7933 System.out.println();
7934 System.out.println( "the following might be due to absence internet connection:" );
7935 e.printStackTrace( System.out );
7941 private static boolean testAminoAcidSequence() {
7943 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7944 if ( aa1.getLength() != 13 ) {
7947 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7950 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7953 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7956 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7957 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7960 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7961 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7964 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7965 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7969 catch ( final Exception e ) {
7970 e.printStackTrace();
7976 private static boolean testCreateBalancedPhylogeny() {
7978 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7979 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7982 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7985 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7986 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7989 if ( p1.getNumberOfExternalNodes() != 100 ) {
7993 catch ( final Exception e ) {
7994 e.printStackTrace();
8000 private static boolean testFastaParser() {
8002 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8005 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8008 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8009 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8012 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8015 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8018 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8021 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8024 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8028 catch ( final Exception e ) {
8029 e.printStackTrace();
8035 private static boolean testGeneralMsaParser() {
8037 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8038 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8039 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8040 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8041 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8042 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8043 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8044 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8045 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8046 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8049 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8052 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8055 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8056 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8059 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8062 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8065 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8066 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8069 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8072 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8076 catch ( final Exception e ) {
8077 e.printStackTrace();
8083 private static boolean testMafft() {
8085 final List<String> opts = new ArrayList<String>();
8086 opts.add( "--maxiterate" );
8088 opts.add( "--localpair" );
8089 opts.add( "--quiet" );
8091 final MsaInferrer mafft = Mafft.createInstance();
8092 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8093 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8097 catch ( final Exception e ) {
8098 e.printStackTrace( System.out );