2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.BasicMsa;
58 import org.forester.msa.Mafft;
59 import org.forester.msa.Msa;
60 import org.forester.msa.MsaInferrer;
61 import org.forester.msa.MsaMethods;
62 import org.forester.pccx.TestPccx;
63 import org.forester.phylogeny.Phylogeny;
64 import org.forester.phylogeny.PhylogenyBranch;
65 import org.forester.phylogeny.PhylogenyMethods;
66 import org.forester.phylogeny.PhylogenyNode;
67 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
68 import org.forester.phylogeny.data.BinaryCharacters;
69 import org.forester.phylogeny.data.BranchWidth;
70 import org.forester.phylogeny.data.Confidence;
71 import org.forester.phylogeny.data.Distribution;
72 import org.forester.phylogeny.data.DomainArchitecture;
73 import org.forester.phylogeny.data.Event;
74 import org.forester.phylogeny.data.Identifier;
75 import org.forester.phylogeny.data.PhylogenyData;
76 import org.forester.phylogeny.data.PhylogenyDataUtil;
77 import org.forester.phylogeny.data.Polygon;
78 import org.forester.phylogeny.data.PropertiesMap;
79 import org.forester.phylogeny.data.Property;
80 import org.forester.phylogeny.data.Property.AppliesTo;
81 import org.forester.phylogeny.data.ProteinDomain;
82 import org.forester.phylogeny.data.Taxonomy;
83 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
84 import org.forester.phylogeny.factories.PhylogenyFactory;
85 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
86 import org.forester.protein.Protein;
87 import org.forester.sdi.SDI;
88 import org.forester.sdi.SDIR;
89 import org.forester.sdi.SDIse;
90 import org.forester.sdi.TaxonomyAssigner;
91 import org.forester.sdi.TestGSDI;
92 import org.forester.sequence.BasicSequence;
93 import org.forester.sequence.Sequence;
94 import org.forester.surfacing.TestSurfacing;
95 import org.forester.tools.ConfidenceAssessor;
96 import org.forester.tools.SupportCount;
97 import org.forester.tools.TreeSplitMatrix;
98 import org.forester.util.AsciiHistogram;
99 import org.forester.util.BasicDescriptiveStatistics;
100 import org.forester.util.BasicTable;
101 import org.forester.util.BasicTableParser;
102 import org.forester.util.DescriptiveStatistics;
103 import org.forester.util.ForesterConstants;
104 import org.forester.util.ForesterUtil;
105 import org.forester.util.GeneralTable;
106 import org.forester.util.SequenceIdParser;
107 import org.forester.ws.seqdb.SequenceDatabaseEntry;
108 import org.forester.ws.seqdb.SequenceDbWsTools;
109 import org.forester.ws.seqdb.UniProtTaxonomy;
110 import org.forester.ws.wabi.TxSearch;
111 import org.forester.ws.wabi.TxSearch.RANKS;
112 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
113 import org.forester.ws.wabi.TxSearch.TAX_RANK;
115 @SuppressWarnings( "unused")
116 public final class Test {
118 private final static double ZERO_DIFF = 1.0E-9;
119 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
120 + ForesterUtil.getFileSeparator() + "test_data"
121 + ForesterUtil.getFileSeparator();
122 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
123 + ForesterUtil.getFileSeparator() + "resources"
124 + ForesterUtil.getFileSeparator();
125 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
126 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
127 + ForesterConstants.PHYLO_XML_VERSION + "/"
128 + ForesterConstants.PHYLO_XML_XSD;
129 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
130 + ForesterConstants.PHYLO_XML_VERSION + "/"
131 + ForesterConstants.PHYLO_XML_XSD;
133 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
134 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
138 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
139 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
140 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Sequence id parsing: " );
175 if ( testSequenceIdParsing() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
181 System.exit( -1 ); //TODO FIXME remove me!! ~
184 System.out.print( "Hmmscan output parser: " );
185 if ( testHmmscanOutputParser() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Basic node methods: " );
194 if ( Test.testBasicNodeMethods() ) {
195 System.out.println( "OK." );
199 System.out.println( "failed." );
202 System.out.print( "Basic node construction and parsing of NHX (node level): " );
203 if ( Test.testNHXNodeParsing() ) {
204 System.out.println( "OK." );
208 System.out.println( "failed." );
211 System.out.print( "NH parsing: " );
212 if ( Test.testNHParsing() ) {
213 System.out.println( "OK." );
217 System.out.println( "failed." );
220 System.out.print( "Conversion to NHX (node level): " );
221 if ( Test.testNHXconversion() ) {
222 System.out.println( "OK." );
226 System.out.println( "failed." );
229 System.out.print( "NHX parsing: " );
230 if ( Test.testNHXParsing() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "NHX parsing with quotes: " );
239 if ( Test.testNHXParsingQuotes() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "NHX parsing (MrBayes): " );
248 if ( Test.testNHXParsingMB() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "Nexus characters parsing: " );
257 if ( Test.testNexusCharactersParsing() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "Nexus tree parsing: " );
266 if ( Test.testNexusTreeParsing() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "Nexus tree parsing (translating): " );
275 if ( Test.testNexusTreeParsingTranslating() ) {
276 System.out.println( "OK." );
280 System.out.println( "failed." );
283 System.out.print( "Nexus matrix parsing: " );
284 if ( Test.testNexusMatrixParsing() ) {
285 System.out.println( "OK." );
289 System.out.println( "failed." );
292 System.out.print( "Basic phyloXML parsing: " );
293 if ( Test.testBasicPhyloXMLparsing() ) {
294 System.out.println( "OK." );
298 System.out.println( "failed." );
301 System.out.print( "Basic phyloXML parsing (validating against schema): " );
302 if ( testBasicPhyloXMLparsingValidating() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
311 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "phyloXML Distribution Element: " );
320 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Tol XML parsing: " );
329 if ( Test.testBasicTolXMLparsing() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "Copying of node data: " );
338 if ( Test.testCopyOfNodeData() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "Basic tree methods: " );
347 if ( Test.testBasicTreeMethods() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "Postorder Iterator: " );
356 if ( Test.testPostOrderIterator() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "Preorder Iterator: " );
365 if ( Test.testPreOrderIterator() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "Levelorder Iterator: " );
374 if ( Test.testLevelOrderIterator() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "Re-id methods: " );
383 if ( Test.testReIdMethods() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "Methods on last external nodes: " );
392 if ( Test.testLastExternalNodeMethods() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "Methods on external nodes: " );
401 if ( Test.testExternalNodeRelatedMethods() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Deletion of external nodes: " );
410 if ( Test.testDeletionOfExternalNodes() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Subtree deletion: " );
419 if ( Test.testSubtreeDeletion() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Phylogeny branch: " );
428 if ( Test.testPhylogenyBranch() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Rerooting: " );
437 if ( Test.testRerooting() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Mipoint rooting: " );
446 if ( Test.testMidpointrooting() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Support count: " );
455 if ( Test.testSupportCount() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Support transfer: " );
464 if ( Test.testSupportTransfer() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "Finding of LCA: " );
473 if ( Test.testGetLCA() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "Calculation of distance between nodes: " );
482 if ( Test.testGetDistance() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "SDIse: " );
491 if ( Test.testSDIse() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Taxonomy assigner: " );
500 if ( Test.testTaxonomyAssigner() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "SDIunrooted: " );
509 if ( Test.testSDIunrooted() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "GSDI: " );
518 if ( TestGSDI.test() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Descriptive statistics: " );
527 if ( Test.testDescriptiveStatistics() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Data objects and methods: " );
536 if ( Test.testDataObjects() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Properties map: " );
545 if ( Test.testPropertiesMap() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Phylogeny reconstruction:" );
554 System.out.println();
555 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "Analysis of domain architectures: " );
564 System.out.println();
565 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
566 System.out.println( "OK." );
570 System.out.println( "failed." );
573 System.out.print( "GO: " );
574 System.out.println();
575 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
576 System.out.println( "OK." );
580 System.out.println( "failed." );
583 System.out.print( "Modeling tools: " );
584 if ( TestPccx.test() ) {
585 System.out.println( "OK." );
589 System.out.println( "failed." );
592 System.out.print( "Split Matrix strict: " );
593 if ( Test.testSplitStrict() ) {
594 System.out.println( "OK." );
598 System.out.println( "failed." );
601 System.out.print( "Split Matrix: " );
602 if ( Test.testSplit() ) {
603 System.out.println( "OK." );
607 System.out.println( "failed." );
610 System.out.print( "Confidence Assessor: " );
611 if ( Test.testConfidenceAssessor() ) {
612 System.out.println( "OK." );
616 System.out.println( "failed." );
619 System.out.print( "Basic table: " );
620 if ( Test.testBasicTable() ) {
621 System.out.println( "OK." );
625 System.out.println( "failed." );
628 System.out.print( "General table: " );
629 if ( Test.testGeneralTable() ) {
630 System.out.println( "OK." );
634 System.out.println( "failed." );
637 System.out.print( "Amino acid sequence: " );
638 if ( Test.testAminoAcidSequence() ) {
639 System.out.println( "OK." );
643 System.out.println( "failed." );
646 System.out.print( "General MSA parser: " );
647 if ( Test.testGeneralMsaParser() ) {
648 System.out.println( "OK." );
652 System.out.println( "failed." );
655 System.out.print( "Fasta parser for msa: " );
656 if ( Test.testFastaParser() ) {
657 System.out.println( "OK." );
661 System.out.println( "failed." );
664 System.out.print( "Creation of balanced phylogeny: " );
665 if ( Test.testCreateBalancedPhylogeny() ) {
666 System.out.println( "OK." );
670 System.out.println( "failed." );
673 System.out.print( "EMBL Entry Retrieval: " );
674 if ( Test.testEmblEntryRetrieval() ) {
675 System.out.println( "OK." );
679 System.out.println( "failed." );
682 System.out.print( "Uniprot Entry Retrieval: " );
683 if ( Test.testUniprotEntryRetrieval() ) {
684 System.out.println( "OK." );
688 System.out.println( "failed." );
691 System.out.print( "Uniprot Taxonomy Search: " );
692 if ( Test.testUniprotTaxonomySearch() ) {
693 System.out.println( "OK." );
697 System.out.println( "failed." );
700 if ( Mafft.isInstalled() ) {
701 System.out.print( "MAFFT (external program): " );
702 if ( Test.testMafft() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed [will not count towards failed tests]" );
710 System.out.print( "Next nodes with collapsed: " );
711 if ( Test.testNextNodeWithCollapsing() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
719 System.out.print( "Simple MSA quality: " );
720 if ( Test.testMsaQualityMethod() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 // System.out.print( "WABI TxSearch: " );
729 // if ( Test.testWabiTxSearch() ) {
730 // System.out.println( "OK." );
735 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
737 System.out.println();
738 final Runtime rt = java.lang.Runtime.getRuntime();
739 final long free_memory = rt.freeMemory() / 1000000;
740 final long total_memory = rt.totalMemory() / 1000000;
741 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
742 + free_memory + "MB, total memory: " + total_memory + "MB)" );
743 System.out.println();
744 System.out.println( "Successful tests: " + succeeded );
745 System.out.println( "Failed tests: " + failed );
746 System.out.println();
748 System.out.println( "OK." );
751 System.out.println( "Not OK." );
753 // System.out.println();
754 // Development.setTime( true );
756 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
757 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
758 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
759 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
760 // "multifurcations_ex_1.nhx";
761 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
762 // final Phylogeny t1 = factory.create( new File( domains ), new
763 // NHXParser() )[ 0 ];
764 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
766 // catch ( final Exception e ) {
767 // e.printStackTrace();
769 // t1.getRoot().preorderPrint();
770 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
774 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
775 // + "\\AtNBSpos.nhx" ) );
777 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
778 // new NHXParser() );
779 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
780 // + "\\AtNBSpos.nhx" ) );
782 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
783 // new NHXParser() );
786 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
787 // + "\\big_tree.nhx" ) );
788 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
789 // + "\\big_tree.nhx" ) );
791 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
792 // new NHXParser() );
794 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
795 // new NHXParser() );
797 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
798 // + "\\big_tree.nhx" ) );
799 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
800 // + "\\big_tree.nhx" ) );
803 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
804 // new NHXParser() );
806 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
807 // new NHXParser() );
809 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
810 // + "\\AtNBSpos.nhx" ) );
812 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
813 // new NHXParser() );
816 // catch ( IOException e ) {
817 // // TODO Auto-generated catch block
818 // e.printStackTrace();
822 private static boolean testBasicNodeMethods() {
824 if ( PhylogenyNode.getNodeCount() != 0 ) {
827 final PhylogenyNode n1 = new PhylogenyNode();
828 final PhylogenyNode n2 = PhylogenyNode
829 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
830 final PhylogenyNode n3 = PhylogenyNode
831 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
832 final PhylogenyNode n4 = PhylogenyNode
833 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
834 if ( n1.isHasAssignedEvent() ) {
837 if ( PhylogenyNode.getNodeCount() != 4 ) {
840 if ( n3.getIndicator() != 0 ) {
843 if ( n3.getNumberOfExternalNodes() != 1 ) {
846 if ( !n3.isExternal() ) {
849 if ( !n3.isRoot() ) {
852 if ( !n4.getName().equals( "n4" ) ) {
856 catch ( final Exception e ) {
857 e.printStackTrace( System.out );
863 private static boolean testBasicPhyloXMLparsing() {
865 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
866 final PhyloXmlParser xml_parser = new PhyloXmlParser();
867 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
869 if ( xml_parser.getErrorCount() > 0 ) {
870 System.out.println( xml_parser.getErrorMessages().toString() );
873 if ( phylogenies_0.length != 4 ) {
876 final Phylogeny t1 = phylogenies_0[ 0 ];
877 final Phylogeny t2 = phylogenies_0[ 1 ];
878 final Phylogeny t3 = phylogenies_0[ 2 ];
879 final Phylogeny t4 = phylogenies_0[ 3 ];
880 if ( t1.getNumberOfExternalNodes() != 1 ) {
883 if ( !t1.isRooted() ) {
886 if ( t1.isRerootable() ) {
889 if ( !t1.getType().equals( "gene_tree" ) ) {
892 if ( t2.getNumberOfExternalNodes() != 2 ) {
895 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
898 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
901 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
904 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
907 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
910 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
913 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
914 .startsWith( "actgtgggggt" ) ) {
917 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
918 .startsWith( "ctgtgatgcat" ) ) {
921 if ( t3.getNumberOfExternalNodes() != 4 ) {
924 if ( !t1.getName().equals( "t1" ) ) {
927 if ( !t2.getName().equals( "t2" ) ) {
930 if ( !t3.getName().equals( "t3" ) ) {
933 if ( !t4.getName().equals( "t4" ) ) {
936 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
939 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
942 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
945 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
946 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
949 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
952 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
955 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
958 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
959 .equals( "apoptosis" ) ) {
962 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
963 .equals( "GO:0006915" ) ) {
966 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
967 .equals( "UniProtKB" ) ) {
970 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
971 .equals( "experimental" ) ) {
974 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
975 .equals( "function" ) ) {
978 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
982 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
983 .getType().equals( "ml" ) ) {
986 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
987 .equals( "apoptosis" ) ) {
990 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
991 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
994 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
995 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
998 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
999 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1002 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1003 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1006 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1007 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1010 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1011 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1014 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1015 .equals( "GO:0005829" ) ) {
1018 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1019 .equals( "intracellular organelle" ) ) {
1022 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1025 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1026 .equals( "UniProt link" ) ) ) {
1029 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1032 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1035 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1038 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1041 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1044 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1047 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1050 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1053 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1056 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1059 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1060 // .equals( "B" ) ) {
1063 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1066 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1069 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1072 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1073 // .getConfidence() != 2144 ) {
1076 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1077 // .equals( "pfam" ) ) {
1080 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1083 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1086 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1089 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1092 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1093 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1097 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1100 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1103 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1106 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1109 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1112 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1115 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1118 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1120 // if ( xml_parser.getErrorCount() > 0 ) {
1121 // System.out.println( xml_parser.getErrorMessages().toString() );
1124 // if ( phylogenies_1.length != 2 ) {
1127 // final Phylogeny a = phylogenies_1[ 0 ];
1128 // if ( !a.getName().equals( "tree 4" ) ) {
1131 // if ( a.getNumberOfExternalNodes() != 3 ) {
1134 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1137 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1141 catch ( final Exception e ) {
1142 e.printStackTrace( System.out );
1148 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1150 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1151 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1152 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1153 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1156 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1158 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1160 if ( xml_parser.getErrorCount() > 0 ) {
1161 System.out.println( xml_parser.getErrorMessages().toString() );
1164 if ( phylogenies_0.length != 4 ) {
1167 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1168 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1169 if ( phylogenies_t1.length != 1 ) {
1172 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1173 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1176 if ( !t1_rt.isRooted() ) {
1179 if ( t1_rt.isRerootable() ) {
1182 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1185 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1186 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1187 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1188 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1191 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1194 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1197 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1200 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1201 .startsWith( "actgtgggggt" ) ) {
1204 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1205 .startsWith( "ctgtgatgcat" ) ) {
1208 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1209 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1210 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1211 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1212 if ( phylogenies_1.length != 1 ) {
1215 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1216 if ( !t3_rt.getName().equals( "t3" ) ) {
1219 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1222 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1225 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1228 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1231 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1232 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1235 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1238 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1241 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1242 .equals( "UniProtKB" ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1246 .equals( "apoptosis" ) ) {
1249 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1250 .equals( "GO:0006915" ) ) {
1253 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1254 .equals( "UniProtKB" ) ) {
1257 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1258 .equals( "experimental" ) ) {
1261 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1262 .equals( "function" ) ) {
1265 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1266 .getValue() != 1 ) {
1269 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1270 .getType().equals( "ml" ) ) {
1273 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1274 .equals( "apoptosis" ) ) {
1277 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1278 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1281 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1282 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1285 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1286 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1289 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1290 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1293 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1294 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1297 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1298 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1301 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1302 .equals( "GO:0005829" ) ) {
1305 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1306 .equals( "intracellular organelle" ) ) {
1309 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1312 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1313 .equals( "UniProt link" ) ) ) {
1316 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1319 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1322 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1323 .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." ) ) ) {
1326 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1329 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1332 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1335 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1338 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1339 .equals( "ncbi" ) ) {
1342 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1345 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1346 .getName().equals( "B" ) ) {
1349 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1350 .getFrom() != 21 ) {
1353 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1356 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1357 .getLength() != 24 ) {
1360 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1361 .getConfidence() != 2144 ) {
1364 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1365 .equals( "pfam" ) ) {
1368 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1371 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1374 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1377 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1380 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1381 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1384 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1387 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1390 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1393 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1396 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1399 if ( taxbb.getSynonyms().size() != 2 ) {
1402 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1405 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1408 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1411 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1414 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1417 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1418 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1422 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1425 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1428 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1431 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1434 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1437 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1440 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1444 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1447 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1448 .equalsIgnoreCase( "435" ) ) {
1451 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1454 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1455 .equalsIgnoreCase( "443.7" ) ) {
1458 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1461 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1464 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1465 .equalsIgnoreCase( "433" ) ) {
1469 catch ( final Exception e ) {
1470 e.printStackTrace( System.out );
1476 private static boolean testBasicPhyloXMLparsingValidating() {
1478 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1479 PhyloXmlParser xml_parser = null;
1481 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1483 catch ( final Exception e ) {
1484 // Do nothing -- means were not running from jar.
1486 if ( xml_parser == null ) {
1487 xml_parser = new PhyloXmlParser();
1488 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1489 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1492 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1495 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1497 if ( xml_parser.getErrorCount() > 0 ) {
1498 System.out.println( xml_parser.getErrorMessages().toString() );
1501 if ( phylogenies_0.length != 4 ) {
1504 final Phylogeny t1 = phylogenies_0[ 0 ];
1505 final Phylogeny t2 = phylogenies_0[ 1 ];
1506 final Phylogeny t3 = phylogenies_0[ 2 ];
1507 final Phylogeny t4 = phylogenies_0[ 3 ];
1508 if ( !t1.getName().equals( "t1" ) ) {
1511 if ( !t2.getName().equals( "t2" ) ) {
1514 if ( !t3.getName().equals( "t3" ) ) {
1517 if ( !t4.getName().equals( "t4" ) ) {
1520 if ( t1.getNumberOfExternalNodes() != 1 ) {
1523 if ( t2.getNumberOfExternalNodes() != 2 ) {
1526 if ( t3.getNumberOfExternalNodes() != 4 ) {
1529 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1530 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1531 if ( xml_parser.getErrorCount() > 0 ) {
1532 System.out.println( "errors:" );
1533 System.out.println( xml_parser.getErrorMessages().toString() );
1536 if ( phylogenies_1.length != 4 ) {
1539 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1541 if ( xml_parser.getErrorCount() > 0 ) {
1542 System.out.println( "errors:" );
1543 System.out.println( xml_parser.getErrorMessages().toString() );
1546 if ( phylogenies_2.length != 1 ) {
1549 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1552 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1554 if ( xml_parser.getErrorCount() > 0 ) {
1555 System.out.println( xml_parser.getErrorMessages().toString() );
1558 if ( phylogenies_3.length != 2 ) {
1561 final Phylogeny a = phylogenies_3[ 0 ];
1562 if ( !a.getName().equals( "tree 4" ) ) {
1565 if ( a.getNumberOfExternalNodes() != 3 ) {
1568 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1571 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1574 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1576 if ( xml_parser.getErrorCount() > 0 ) {
1577 System.out.println( xml_parser.getErrorMessages().toString() );
1580 if ( phylogenies_4.length != 1 ) {
1583 final Phylogeny s = phylogenies_4[ 0 ];
1584 if ( s.getNumberOfExternalNodes() != 6 ) {
1587 s.getNode( "first" );
1589 s.getNode( "\"<a'b&c'd\">\"" );
1590 s.getNode( "'''\"" );
1591 s.getNode( "\"\"\"" );
1592 s.getNode( "dick & doof" );
1594 catch ( final Exception e ) {
1595 e.printStackTrace( System.out );
1601 private static boolean testBasicTable() {
1603 final BasicTable<String> t0 = new BasicTable<String>();
1604 if ( t0.getNumberOfColumns() != 0 ) {
1607 if ( t0.getNumberOfRows() != 0 ) {
1610 t0.setValue( 3, 2, "23" );
1611 t0.setValue( 10, 1, "error" );
1612 t0.setValue( 10, 1, "110" );
1613 t0.setValue( 9, 1, "19" );
1614 t0.setValue( 1, 10, "101" );
1615 t0.setValue( 10, 10, "1010" );
1616 t0.setValue( 100, 10, "10100" );
1617 t0.setValue( 0, 0, "00" );
1618 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1621 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1624 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1627 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1630 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1633 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1636 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1639 if ( t0.getNumberOfColumns() != 101 ) {
1642 if ( t0.getNumberOfRows() != 11 ) {
1645 if ( t0.getValueAsString( 49, 4 ) != null ) {
1648 final String l = ForesterUtil.getLineSeparator();
1649 final StringBuffer source = new StringBuffer();
1650 source.append( "" + l );
1651 source.append( "# 1 1 1 1 1 1 1 1" + l );
1652 source.append( " 00 01 02 03" + l );
1653 source.append( " 10 11 12 13 " + l );
1654 source.append( "20 21 22 23 " + l );
1655 source.append( " 30 31 32 33" + l );
1656 source.append( "40 41 42 43" + l );
1657 source.append( " # 1 1 1 1 1 " + l );
1658 source.append( "50 51 52 53 54" + l );
1659 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1660 if ( t1.getNumberOfColumns() != 5 ) {
1663 if ( t1.getNumberOfRows() != 6 ) {
1666 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1669 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1672 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1675 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1678 final StringBuffer source1 = new StringBuffer();
1679 source1.append( "" + l );
1680 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1681 source1.append( " 00; 01 ;02;03" + l );
1682 source1.append( " 10; 11; 12; 13 " + l );
1683 source1.append( "20; 21; 22; 23 " + l );
1684 source1.append( " 30; 31; 32; 33" + l );
1685 source1.append( "40;41;42;43" + l );
1686 source1.append( " # 1 1 1 1 1 " + l );
1687 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1688 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1689 if ( t2.getNumberOfColumns() != 5 ) {
1692 if ( t2.getNumberOfRows() != 6 ) {
1695 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1698 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1701 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1704 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1707 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1710 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1713 final StringBuffer source2 = new StringBuffer();
1714 source2.append( "" + l );
1715 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1716 source2.append( " 00; 01 ;02;03" + l );
1717 source2.append( " 10; 11; 12; 13 " + l );
1718 source2.append( "20; 21; 22; 23 " + l );
1719 source2.append( " " + l );
1720 source2.append( " 30; 31; 32; 33" + l );
1721 source2.append( "40;41;42;43" + l );
1722 source2.append( " comment: 1 1 1 1 1 " + l );
1723 source2.append( ";;;50 ; 52; 53;;54 " + l );
1724 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1729 if ( tl.size() != 2 ) {
1732 final BasicTable<String> t3 = tl.get( 0 );
1733 final BasicTable<String> t4 = tl.get( 1 );
1734 if ( t3.getNumberOfColumns() != 4 ) {
1737 if ( t3.getNumberOfRows() != 3 ) {
1740 if ( t4.getNumberOfColumns() != 4 ) {
1743 if ( t4.getNumberOfRows() != 3 ) {
1746 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1749 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1753 catch ( final Exception e ) {
1754 e.printStackTrace( System.out );
1760 private static boolean testBasicTolXMLparsing() {
1762 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1763 final TolParser parser = new TolParser();
1764 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1765 if ( parser.getErrorCount() > 0 ) {
1766 System.out.println( parser.getErrorMessages().toString() );
1769 if ( phylogenies_0.length != 1 ) {
1772 final Phylogeny t1 = phylogenies_0[ 0 ];
1773 if ( t1.getNumberOfExternalNodes() != 5 ) {
1776 if ( !t1.isRooted() ) {
1779 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1782 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1785 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1788 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1791 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1792 if ( parser.getErrorCount() > 0 ) {
1793 System.out.println( parser.getErrorMessages().toString() );
1796 if ( phylogenies_1.length != 1 ) {
1799 final Phylogeny t2 = phylogenies_1[ 0 ];
1800 if ( t2.getNumberOfExternalNodes() != 664 ) {
1803 if ( !t2.isRooted() ) {
1806 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1809 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1812 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1815 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1818 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1821 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1822 .equals( "Aquifex" ) ) {
1825 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1826 if ( parser.getErrorCount() > 0 ) {
1827 System.out.println( parser.getErrorMessages().toString() );
1830 if ( phylogenies_2.length != 1 ) {
1833 final Phylogeny t3 = phylogenies_2[ 0 ];
1834 if ( t3.getNumberOfExternalNodes() != 184 ) {
1837 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1840 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1843 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1846 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1847 if ( parser.getErrorCount() > 0 ) {
1848 System.out.println( parser.getErrorMessages().toString() );
1851 if ( phylogenies_3.length != 1 ) {
1854 final Phylogeny t4 = phylogenies_3[ 0 ];
1855 if ( t4.getNumberOfExternalNodes() != 1 ) {
1858 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1861 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1864 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1867 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1868 if ( parser.getErrorCount() > 0 ) {
1869 System.out.println( parser.getErrorMessages().toString() );
1872 if ( phylogenies_4.length != 1 ) {
1875 final Phylogeny t5 = phylogenies_4[ 0 ];
1876 if ( t5.getNumberOfExternalNodes() != 13 ) {
1879 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1882 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1885 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1889 catch ( final Exception e ) {
1890 e.printStackTrace( System.out );
1896 private static boolean testBasicTreeMethods() {
1898 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1899 final Phylogeny t1 = factory.create();
1900 if ( !t1.isEmpty() ) {
1903 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1904 if ( t2.getNumberOfExternalNodes() != 4 ) {
1907 if ( t2.getHeight() != 8.5 ) {
1910 if ( !t2.isCompletelyBinary() ) {
1913 if ( t2.isEmpty() ) {
1916 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1917 if ( t3.getNumberOfExternalNodes() != 5 ) {
1920 if ( t3.getHeight() != 11 ) {
1923 if ( t3.isCompletelyBinary() ) {
1926 final PhylogenyNode n = t3.getNode( "ABC" );
1927 PhylogenyNodeIterator it;
1928 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1931 for( it.reset(); it.hasNext(); ) {
1934 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1935 if ( !it2.next().getName().equals( "A" ) ) {
1938 if ( !it2.next().getName().equals( "B" ) ) {
1941 if ( !it2.next().getName().equals( "C" ) ) {
1944 if ( it2.hasNext() ) {
1947 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 ];
1948 if ( t4.getNumberOfExternalNodes() != 9 ) {
1951 if ( t4.getHeight() != 11 ) {
1954 if ( t4.isCompletelyBinary() ) {
1957 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)" );
1958 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1959 if ( t5.getNumberOfExternalNodes() != 8 ) {
1962 if ( t5.getHeight() != 15 ) {
1965 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)" );
1966 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1967 if ( t6.getHeight() != 15 ) {
1970 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)" );
1971 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1972 if ( t7.getHeight() != 15 ) {
1975 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)" );
1976 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1977 if ( t8.getNumberOfExternalNodes() != 10 ) {
1980 if ( t8.getHeight() != 15 ) {
1983 final char[] a9 = new char[] {};
1984 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1985 if ( t9.getHeight() != 0 ) {
1988 final char[] a10 = new char[] { 'a', ':', '6' };
1989 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1990 if ( t10.getHeight() != 6 ) {
1994 catch ( final Exception e ) {
1995 e.printStackTrace( System.out );
2001 private static boolean testConfidenceAssessor() {
2003 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2004 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2005 final Phylogeny[] ev0 = factory
2006 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2008 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2009 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2012 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2015 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2016 final Phylogeny[] ev1 = factory
2017 .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)));",
2019 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2020 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2023 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2026 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2027 final Phylogeny[] ev_b = factory
2028 .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",
2030 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2031 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2032 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2035 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2039 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2040 final Phylogeny[] ev1x = factory
2041 .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)));",
2043 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2044 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2047 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2050 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2051 final Phylogeny[] ev_bx = factory
2052 .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",
2054 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2055 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2058 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2062 final Phylogeny[] t2 = factory
2063 .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);",
2065 final Phylogeny[] ev2 = factory
2066 .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);",
2068 for( final Phylogeny target : t2 ) {
2069 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2072 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2073 new NHXParser() )[ 0 ];
2074 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2075 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2076 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2079 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2082 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2086 catch ( final Exception e ) {
2087 e.printStackTrace();
2093 private static boolean testCopyOfNodeData() {
2095 final PhylogenyNode n1 = PhylogenyNode
2096 .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]" );
2097 final PhylogenyNode n2 = n1.copyNodeData();
2098 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2102 catch ( final Exception e ) {
2103 e.printStackTrace();
2109 private static boolean testDataObjects() {
2111 final Confidence s0 = new Confidence();
2112 final Confidence s1 = new Confidence();
2113 if ( !s0.isEqual( s1 ) ) {
2116 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2117 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2118 if ( s2.isEqual( s1 ) ) {
2121 if ( !s2.isEqual( s3 ) ) {
2124 final Confidence s4 = ( Confidence ) s3.copy();
2125 if ( !s4.isEqual( s3 ) ) {
2132 final Taxonomy t1 = new Taxonomy();
2133 final Taxonomy t2 = new Taxonomy();
2134 final Taxonomy t3 = new Taxonomy();
2135 final Taxonomy t4 = new Taxonomy();
2136 final Taxonomy t5 = new Taxonomy();
2137 t1.setIdentifier( new Identifier( "ecoli" ) );
2138 t1.setTaxonomyCode( "ECOLI" );
2139 t1.setScientificName( "E. coli" );
2140 t1.setCommonName( "coli" );
2141 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2142 if ( !t1.isEqual( t0 ) ) {
2145 t2.setIdentifier( new Identifier( "ecoli" ) );
2146 t2.setTaxonomyCode( "other" );
2147 t2.setScientificName( "what" );
2148 t2.setCommonName( "something" );
2149 if ( !t1.isEqual( t2 ) ) {
2152 t2.setIdentifier( new Identifier( "nemve" ) );
2153 if ( t1.isEqual( t2 ) ) {
2156 t1.setIdentifier( null );
2157 t3.setTaxonomyCode( "ECOLI" );
2158 t3.setScientificName( "what" );
2159 t3.setCommonName( "something" );
2160 if ( !t1.isEqual( t3 ) ) {
2163 t1.setIdentifier( null );
2164 t1.setTaxonomyCode( "" );
2165 t4.setScientificName( "E. ColI" );
2166 t4.setCommonName( "something" );
2167 if ( !t1.isEqual( t4 ) ) {
2170 t4.setScientificName( "B. subtilis" );
2171 t4.setCommonName( "something" );
2172 if ( t1.isEqual( t4 ) ) {
2175 t1.setIdentifier( null );
2176 t1.setTaxonomyCode( "" );
2177 t1.setScientificName( "" );
2178 t5.setCommonName( "COLI" );
2179 if ( !t1.isEqual( t5 ) ) {
2182 t5.setCommonName( "vibrio" );
2183 if ( t1.isEqual( t5 ) ) {
2188 final Identifier id0 = new Identifier( "123", "pfam" );
2189 final Identifier id1 = ( Identifier ) id0.copy();
2190 if ( !id1.isEqual( id1 ) ) {
2193 if ( !id1.isEqual( id0 ) ) {
2196 if ( !id0.isEqual( id1 ) ) {
2203 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2204 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2205 if ( !pd1.isEqual( pd1 ) ) {
2208 if ( !pd1.isEqual( pd0 ) ) {
2213 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2214 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2215 if ( !pd3.isEqual( pd3 ) ) {
2218 if ( !pd2.isEqual( pd3 ) ) {
2221 if ( !pd0.isEqual( pd3 ) ) {
2226 // DomainArchitecture
2227 // ------------------
2228 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2229 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2230 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2231 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2232 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2233 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2238 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2239 if ( ds0.getNumberOfDomains() != 4 ) {
2242 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2243 if ( !ds0.isEqual( ds0 ) ) {
2246 if ( !ds0.isEqual( ds1 ) ) {
2249 if ( ds1.getNumberOfDomains() != 4 ) {
2252 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2257 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2258 if ( ds0.isEqual( ds2 ) ) {
2264 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2265 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2266 System.out.println( ds3.toNHX() );
2269 if ( ds3.getNumberOfDomains() != 3 ) {
2274 final Event e1 = new Event( Event.EventType.fusion );
2275 if ( e1.isDuplication() ) {
2278 if ( !e1.isFusion() ) {
2281 if ( !e1.asText().toString().equals( "fusion" ) ) {
2284 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2287 final Event e11 = new Event( Event.EventType.fusion );
2288 if ( !e11.isEqual( e1 ) ) {
2291 if ( !e11.toNHX().toString().equals( "" ) ) {
2294 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2295 if ( e2.isDuplication() ) {
2298 if ( !e2.isSpeciationOrDuplication() ) {
2301 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2304 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2307 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2310 if ( e11.isEqual( e2 ) ) {
2313 final Event e2c = ( Event ) e2.copy();
2314 if ( !e2c.isEqual( e2 ) ) {
2317 Event e3 = new Event( 1, 2, 3 );
2318 if ( e3.isDuplication() ) {
2321 if ( e3.isSpeciation() ) {
2324 if ( e3.isGeneLoss() ) {
2327 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2330 final Event e3c = ( Event ) e3.copy();
2331 final Event e3cc = ( Event ) e3c.copy();
2332 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2336 if ( !e3c.isEqual( e3cc ) ) {
2339 Event e4 = new Event( 1, 2, 3 );
2340 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2343 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2346 final Event e4c = ( Event ) e4.copy();
2348 final Event e4cc = ( Event ) e4c.copy();
2349 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2352 if ( !e4c.isEqual( e4cc ) ) {
2355 final Event e5 = new Event();
2356 if ( !e5.isUnassigned() ) {
2359 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2362 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2365 final Event e6 = new Event( 1, 0, 0 );
2366 if ( !e6.asText().toString().equals( "duplication" ) ) {
2369 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2372 final Event e7 = new Event( 0, 1, 0 );
2373 if ( !e7.asText().toString().equals( "speciation" ) ) {
2376 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2379 final Event e8 = new Event( 0, 0, 1 );
2380 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2383 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2387 catch ( final Exception e ) {
2388 e.printStackTrace( System.out );
2394 private static boolean testDeletionOfExternalNodes() {
2396 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2397 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2398 final PhylogenyWriter w = new PhylogenyWriter();
2399 if ( t0.isEmpty() ) {
2402 if ( t0.getNumberOfExternalNodes() != 1 ) {
2405 t0.deleteSubtree( t0.getNode( "A" ), false );
2406 if ( t0.getNumberOfExternalNodes() != 0 ) {
2409 if ( !t0.isEmpty() ) {
2412 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2413 if ( t1.getNumberOfExternalNodes() != 2 ) {
2416 t1.deleteSubtree( t1.getNode( "A" ), false );
2417 if ( t1.getNumberOfExternalNodes() != 1 ) {
2420 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2423 t1.deleteSubtree( t1.getNode( "B" ), false );
2424 if ( t1.getNumberOfExternalNodes() != 1 ) {
2427 t1.deleteSubtree( t1.getNode( "r" ), false );
2428 if ( !t1.isEmpty() ) {
2431 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2432 if ( t2.getNumberOfExternalNodes() != 3 ) {
2435 t2.deleteSubtree( t2.getNode( "B" ), false );
2436 if ( t2.getNumberOfExternalNodes() != 2 ) {
2439 t2.toNewHampshireX();
2440 PhylogenyNode n = t2.getNode( "A" );
2441 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2444 t2.deleteSubtree( t2.getNode( "A" ), false );
2445 if ( t2.getNumberOfExternalNodes() != 2 ) {
2448 t2.deleteSubtree( t2.getNode( "C" ), true );
2449 if ( t2.getNumberOfExternalNodes() != 1 ) {
2452 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2453 if ( t3.getNumberOfExternalNodes() != 4 ) {
2456 t3.deleteSubtree( t3.getNode( "B" ), true );
2457 if ( t3.getNumberOfExternalNodes() != 3 ) {
2460 n = t3.getNode( "A" );
2461 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2464 n = n.getNextExternalNode();
2465 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2468 t3.deleteSubtree( t3.getNode( "A" ), true );
2469 if ( t3.getNumberOfExternalNodes() != 2 ) {
2472 n = t3.getNode( "C" );
2473 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2476 t3.deleteSubtree( t3.getNode( "C" ), true );
2477 if ( t3.getNumberOfExternalNodes() != 1 ) {
2480 t3.deleteSubtree( t3.getNode( "D" ), true );
2481 if ( t3.getNumberOfExternalNodes() != 0 ) {
2484 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2485 if ( t4.getNumberOfExternalNodes() != 6 ) {
2488 t4.deleteSubtree( t4.getNode( "B2" ), true );
2489 if ( t4.getNumberOfExternalNodes() != 5 ) {
2492 String s = w.toNewHampshire( t4, false, true ).toString();
2493 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2496 t4.deleteSubtree( t4.getNode( "B11" ), true );
2497 if ( t4.getNumberOfExternalNodes() != 4 ) {
2500 t4.deleteSubtree( t4.getNode( "C" ), true );
2501 if ( t4.getNumberOfExternalNodes() != 3 ) {
2504 n = t4.getNode( "A" );
2505 n = n.getNextExternalNode();
2506 if ( !n.getName().equals( "B12" ) ) {
2509 n = n.getNextExternalNode();
2510 if ( !n.getName().equals( "D" ) ) {
2513 s = w.toNewHampshire( t4, false, true ).toString();
2514 if ( !s.equals( "((A,B12),D);" ) ) {
2517 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2518 t5.deleteSubtree( t5.getNode( "A" ), true );
2519 if ( t5.getNumberOfExternalNodes() != 5 ) {
2522 s = w.toNewHampshire( t5, false, true ).toString();
2523 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2526 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2527 t6.deleteSubtree( t6.getNode( "B11" ), true );
2528 if ( t6.getNumberOfExternalNodes() != 5 ) {
2531 s = w.toNewHampshire( t6, false, false ).toString();
2532 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2535 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2536 t7.deleteSubtree( t7.getNode( "B12" ), true );
2537 if ( t7.getNumberOfExternalNodes() != 5 ) {
2540 s = w.toNewHampshire( t7, false, true ).toString();
2541 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2544 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2545 t8.deleteSubtree( t8.getNode( "B2" ), true );
2546 if ( t8.getNumberOfExternalNodes() != 5 ) {
2549 s = w.toNewHampshire( t8, false, false ).toString();
2550 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2553 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2554 t9.deleteSubtree( t9.getNode( "C" ), true );
2555 if ( t9.getNumberOfExternalNodes() != 5 ) {
2558 s = w.toNewHampshire( t9, false, true ).toString();
2559 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2562 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2563 t10.deleteSubtree( t10.getNode( "D" ), true );
2564 if ( t10.getNumberOfExternalNodes() != 5 ) {
2567 s = w.toNewHampshire( t10, false, true ).toString();
2568 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2571 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2572 t11.deleteSubtree( t11.getNode( "A" ), true );
2573 if ( t11.getNumberOfExternalNodes() != 2 ) {
2576 s = w.toNewHampshire( t11, false, true ).toString();
2577 if ( !s.equals( "(B,C);" ) ) {
2580 t11.deleteSubtree( t11.getNode( "C" ), true );
2581 if ( t11.getNumberOfExternalNodes() != 1 ) {
2584 s = w.toNewHampshire( t11, false, false ).toString();
2585 if ( !s.equals( "B;" ) ) {
2588 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2589 t12.deleteSubtree( t12.getNode( "B2" ), true );
2590 if ( t12.getNumberOfExternalNodes() != 8 ) {
2593 s = w.toNewHampshire( t12, false, true ).toString();
2594 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2597 t12.deleteSubtree( t12.getNode( "B3" ), true );
2598 if ( t12.getNumberOfExternalNodes() != 7 ) {
2601 s = w.toNewHampshire( t12, false, true ).toString();
2602 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2605 t12.deleteSubtree( t12.getNode( "C3" ), true );
2606 if ( t12.getNumberOfExternalNodes() != 6 ) {
2609 s = w.toNewHampshire( t12, false, true ).toString();
2610 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2613 t12.deleteSubtree( t12.getNode( "A1" ), true );
2614 if ( t12.getNumberOfExternalNodes() != 5 ) {
2617 s = w.toNewHampshire( t12, false, true ).toString();
2618 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2621 t12.deleteSubtree( t12.getNode( "B1" ), true );
2622 if ( t12.getNumberOfExternalNodes() != 4 ) {
2625 s = w.toNewHampshire( t12, false, true ).toString();
2626 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2629 t12.deleteSubtree( t12.getNode( "A3" ), true );
2630 if ( t12.getNumberOfExternalNodes() != 3 ) {
2633 s = w.toNewHampshire( t12, false, true ).toString();
2634 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2637 t12.deleteSubtree( t12.getNode( "A2" ), true );
2638 if ( t12.getNumberOfExternalNodes() != 2 ) {
2641 s = w.toNewHampshire( t12, false, true ).toString();
2642 if ( !s.equals( "(C1,C2);" ) ) {
2645 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2646 t13.deleteSubtree( t13.getNode( "D" ), true );
2647 if ( t13.getNumberOfExternalNodes() != 4 ) {
2650 s = w.toNewHampshire( t13, false, true ).toString();
2651 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2654 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2655 t14.deleteSubtree( t14.getNode( "E" ), true );
2656 if ( t14.getNumberOfExternalNodes() != 5 ) {
2659 s = w.toNewHampshire( t14, false, true ).toString();
2660 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2663 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2664 t15.deleteSubtree( t15.getNode( "B2" ), true );
2665 if ( t15.getNumberOfExternalNodes() != 11 ) {
2668 t15.deleteSubtree( t15.getNode( "B1" ), true );
2669 if ( t15.getNumberOfExternalNodes() != 10 ) {
2672 t15.deleteSubtree( t15.getNode( "B3" ), true );
2673 if ( t15.getNumberOfExternalNodes() != 9 ) {
2676 t15.deleteSubtree( t15.getNode( "B4" ), true );
2677 if ( t15.getNumberOfExternalNodes() != 8 ) {
2680 t15.deleteSubtree( t15.getNode( "A1" ), true );
2681 if ( t15.getNumberOfExternalNodes() != 7 ) {
2684 t15.deleteSubtree( t15.getNode( "C4" ), true );
2685 if ( t15.getNumberOfExternalNodes() != 6 ) {
2689 catch ( final Exception e ) {
2690 e.printStackTrace( System.out );
2696 private static boolean testDescriptiveStatistics() {
2698 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2699 dss1.addValue( 82 );
2700 dss1.addValue( 78 );
2701 dss1.addValue( 70 );
2702 dss1.addValue( 58 );
2703 dss1.addValue( 42 );
2704 if ( dss1.getN() != 5 ) {
2707 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2710 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2713 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2716 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2719 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2722 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2725 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2728 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2731 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2734 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2737 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2740 dss1.addValue( 123 );
2741 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2744 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2747 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2750 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2751 dss2.addValue( -1.85 );
2752 dss2.addValue( 57.5 );
2753 dss2.addValue( 92.78 );
2754 dss2.addValue( 57.78 );
2755 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2758 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2761 final double[] a = dss2.getDataAsDoubleArray();
2762 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2765 dss2.addValue( -100 );
2766 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2769 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2772 final double[] ds = new double[ 14 ];
2787 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2788 if ( bins.length != 4 ) {
2791 if ( bins[ 0 ] != 2 ) {
2794 if ( bins[ 1 ] != 3 ) {
2797 if ( bins[ 2 ] != 4 ) {
2800 if ( bins[ 3 ] != 5 ) {
2803 final double[] ds1 = new double[ 9 ];
2813 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2814 if ( bins1.length != 4 ) {
2817 if ( bins1[ 0 ] != 2 ) {
2820 if ( bins1[ 1 ] != 3 ) {
2823 if ( bins1[ 2 ] != 0 ) {
2826 if ( bins1[ 3 ] != 4 ) {
2829 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2830 if ( bins1_1.length != 3 ) {
2833 if ( bins1_1[ 0 ] != 3 ) {
2836 if ( bins1_1[ 1 ] != 2 ) {
2839 if ( bins1_1[ 2 ] != 4 ) {
2842 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2843 if ( bins1_2.length != 3 ) {
2846 if ( bins1_2[ 0 ] != 2 ) {
2849 if ( bins1_2[ 1 ] != 2 ) {
2852 if ( bins1_2[ 2 ] != 2 ) {
2855 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2869 dss3.addValue( 10 );
2870 dss3.addValue( 10 );
2871 dss3.addValue( 10 );
2872 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2873 histo.toStringBuffer( 10, '=', 40, 5 );
2874 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2876 catch ( final Exception e ) {
2877 e.printStackTrace( System.out );
2883 private static boolean testDir( final String file ) {
2885 final File f = new File( file );
2886 if ( !f.exists() ) {
2889 if ( !f.isDirectory() ) {
2892 if ( !f.canRead() ) {
2896 catch ( final Exception e ) {
2902 private static boolean testExternalNodeRelatedMethods() {
2904 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2905 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2906 PhylogenyNode n = t1.getNode( "A" );
2907 n = n.getNextExternalNode();
2908 if ( !n.getName().equals( "B" ) ) {
2911 n = n.getNextExternalNode();
2912 if ( !n.getName().equals( "C" ) ) {
2915 n = n.getNextExternalNode();
2916 if ( !n.getName().equals( "D" ) ) {
2919 n = t1.getNode( "B" );
2920 while ( !n.isLastExternalNode() ) {
2921 n = n.getNextExternalNode();
2923 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2924 n = t2.getNode( "A" );
2925 n = n.getNextExternalNode();
2926 if ( !n.getName().equals( "B" ) ) {
2929 n = n.getNextExternalNode();
2930 if ( !n.getName().equals( "C" ) ) {
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "D" ) ) {
2937 n = t2.getNode( "B" );
2938 while ( !n.isLastExternalNode() ) {
2939 n = n.getNextExternalNode();
2941 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2942 n = t3.getNode( "A" );
2943 n = n.getNextExternalNode();
2944 if ( !n.getName().equals( "B" ) ) {
2947 n = n.getNextExternalNode();
2948 if ( !n.getName().equals( "C" ) ) {
2951 n = n.getNextExternalNode();
2952 if ( !n.getName().equals( "D" ) ) {
2955 n = n.getNextExternalNode();
2956 if ( !n.getName().equals( "E" ) ) {
2959 n = n.getNextExternalNode();
2960 if ( !n.getName().equals( "F" ) ) {
2963 n = n.getNextExternalNode();
2964 if ( !n.getName().equals( "G" ) ) {
2967 n = n.getNextExternalNode();
2968 if ( !n.getName().equals( "H" ) ) {
2971 n = t3.getNode( "B" );
2972 while ( !n.isLastExternalNode() ) {
2973 n = n.getNextExternalNode();
2975 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2976 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2977 final PhylogenyNode node = iter.next();
2979 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2980 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2981 final PhylogenyNode node = iter.next();
2984 catch ( final Exception e ) {
2985 e.printStackTrace( System.out );
2991 private static boolean testGeneralTable() {
2993 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2994 t0.setValue( 3, 2, "23" );
2995 t0.setValue( 10, 1, "error" );
2996 t0.setValue( 10, 1, "110" );
2997 t0.setValue( 9, 1, "19" );
2998 t0.setValue( 1, 10, "101" );
2999 t0.setValue( 10, 10, "1010" );
3000 t0.setValue( 100, 10, "10100" );
3001 t0.setValue( 0, 0, "00" );
3002 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
3005 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
3008 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
3011 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
3014 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
3017 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
3020 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3023 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3026 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3029 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3030 t1.setValue( "3", "2", "23" );
3031 t1.setValue( "10", "1", "error" );
3032 t1.setValue( "10", "1", "110" );
3033 t1.setValue( "9", "1", "19" );
3034 t1.setValue( "1", "10", "101" );
3035 t1.setValue( "10", "10", "1010" );
3036 t1.setValue( "100", "10", "10100" );
3037 t1.setValue( "0", "0", "00" );
3038 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3039 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3042 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3045 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3048 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3051 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3054 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3057 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3060 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3063 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3066 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3070 catch ( final Exception e ) {
3071 e.printStackTrace( System.out );
3077 private static boolean testGetDistance() {
3079 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3080 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",
3081 new NHXParser() )[ 0 ];
3082 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3083 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3086 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3089 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3092 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3095 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3098 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3101 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3104 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3107 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3110 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3113 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3116 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3119 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3122 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3125 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3128 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3131 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3134 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3137 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3140 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3143 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3146 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3149 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3152 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3155 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3158 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3161 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3164 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3167 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3170 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3173 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3176 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",
3177 new NHXParser() )[ 0 ];
3178 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3181 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3184 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3187 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3190 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3193 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3196 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3199 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3202 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3205 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3208 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3212 catch ( final Exception e ) {
3213 e.printStackTrace( System.out );
3219 private static boolean testGetLCA() {
3221 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3222 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3223 new NHXParser() )[ 0 ];
3224 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3225 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3226 if ( !A.getName().equals( "A" ) ) {
3229 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3230 if ( !gh.getName().equals( "gh" ) ) {
3233 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3234 if ( !ab.getName().equals( "ab" ) ) {
3237 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3238 if ( !ab2.getName().equals( "ab" ) ) {
3241 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3242 if ( !gh2.getName().equals( "gh" ) ) {
3245 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3246 if ( !gh3.getName().equals( "gh" ) ) {
3249 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3250 if ( !abc.getName().equals( "abc" ) ) {
3253 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3254 if ( !abc2.getName().equals( "abc" ) ) {
3257 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3258 if ( !abcd.getName().equals( "abcd" ) ) {
3261 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3262 if ( !abcd2.getName().equals( "abcd" ) ) {
3265 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3266 if ( !abcdef.getName().equals( "abcdef" ) ) {
3269 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3270 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3273 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3274 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3277 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3278 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3281 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3282 if ( !abcde.getName().equals( "abcde" ) ) {
3285 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3286 if ( !abcde2.getName().equals( "abcde" ) ) {
3289 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3290 if ( !r.getName().equals( "abcdefgh" ) ) {
3293 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3294 if ( !r2.getName().equals( "abcdefgh" ) ) {
3297 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3298 if ( !r3.getName().equals( "abcdefgh" ) ) {
3301 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3302 if ( !abcde3.getName().equals( "abcde" ) ) {
3305 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3306 if ( !abcde4.getName().equals( "abcde" ) ) {
3309 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3310 if ( !ab3.getName().equals( "ab" ) ) {
3313 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3314 if ( !ab4.getName().equals( "ab" ) ) {
3317 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3318 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3319 if ( !cd.getName().equals( "cd" ) ) {
3322 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3323 if ( !cd2.getName().equals( "cd" ) ) {
3326 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3327 if ( !cde.getName().equals( "cde" ) ) {
3330 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3331 if ( !cde2.getName().equals( "cde" ) ) {
3334 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3335 if ( !cdef.getName().equals( "cdef" ) ) {
3338 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3339 if ( !cdef2.getName().equals( "cdef" ) ) {
3342 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3343 if ( !cdef3.getName().equals( "cdef" ) ) {
3346 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3347 if ( !rt.getName().equals( "r" ) ) {
3350 final Phylogeny p3 = factory
3351 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3352 new NHXParser() )[ 0 ];
3353 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3354 if ( !bc_3.getName().equals( "bc" ) ) {
3357 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3358 if ( !ac_3.getName().equals( "abc" ) ) {
3361 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3362 if ( !ad_3.getName().equals( "abcde" ) ) {
3365 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3366 if ( !af_3.getName().equals( "abcdef" ) ) {
3369 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3370 if ( !ag_3.getName().equals( "" ) ) {
3373 if ( !ag_3.isRoot() ) {
3376 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3377 if ( !al_3.getName().equals( "" ) ) {
3380 if ( !al_3.isRoot() ) {
3383 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3384 if ( !kl_3.getName().equals( "" ) ) {
3387 if ( !kl_3.isRoot() ) {
3390 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3391 if ( !fl_3.getName().equals( "" ) ) {
3394 if ( !fl_3.isRoot() ) {
3397 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3398 if ( !gk_3.getName().equals( "ghijk" ) ) {
3401 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3402 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3403 if ( !r_4.getName().equals( "r" ) ) {
3406 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3407 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3408 if ( !r_5.getName().equals( "root" ) ) {
3411 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3412 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3413 if ( !r_6.getName().equals( "rot" ) ) {
3416 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3417 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3418 if ( !r_7.getName().equals( "rott" ) ) {
3422 catch ( final Exception e ) {
3423 e.printStackTrace( System.out );
3429 private static boolean testHmmscanOutputParser() {
3430 final String test_dir = Test.PATH_TO_TEST_DATA;
3432 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3433 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3435 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3436 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3437 final List<Protein> proteins = parser2.parse();
3438 if ( parser2.getProteinsEncountered() != 4 ) {
3441 if ( proteins.size() != 4 ) {
3444 if ( parser2.getDomainsEncountered() != 69 ) {
3447 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3450 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3453 final Protein p1 = proteins.get( 0 );
3454 if ( p1.getNumberOfProteinDomains() != 15 ) {
3457 if ( p1.getLength() != 850 ) {
3460 final Protein p2 = proteins.get( 1 );
3461 if ( p2.getNumberOfProteinDomains() != 51 ) {
3464 if ( p2.getLength() != 1291 ) {
3467 final Protein p3 = proteins.get( 2 );
3468 if ( p3.getNumberOfProteinDomains() != 2 ) {
3471 final Protein p4 = proteins.get( 3 );
3472 if ( p4.getNumberOfProteinDomains() != 1 ) {
3475 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3478 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3481 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3484 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3487 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3490 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3493 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3496 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3499 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3503 catch ( final Exception e ) {
3504 e.printStackTrace( System.out );
3510 private static boolean testLastExternalNodeMethods() {
3512 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3513 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3514 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3515 final PhylogenyNode n1 = t0.getNode( "A" );
3516 if ( n1.isLastExternalNode() ) {
3519 final PhylogenyNode n2 = t0.getNode( "B" );
3520 if ( n2.isLastExternalNode() ) {
3523 final PhylogenyNode n3 = t0.getNode( "C" );
3524 if ( n3.isLastExternalNode() ) {
3527 final PhylogenyNode n4 = t0.getNode( "D" );
3528 if ( !n4.isLastExternalNode() ) {
3532 catch ( final Exception e ) {
3533 e.printStackTrace( System.out );
3539 private static boolean testLevelOrderIterator() {
3541 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3542 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3543 PhylogenyNodeIterator it0;
3544 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3547 for( it0.reset(); it0.hasNext(); ) {
3550 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3551 if ( !it.next().getName().equals( "r" ) ) {
3554 if ( !it.next().getName().equals( "ab" ) ) {
3557 if ( !it.next().getName().equals( "cd" ) ) {
3560 if ( !it.next().getName().equals( "A" ) ) {
3563 if ( !it.next().getName().equals( "B" ) ) {
3566 if ( !it.next().getName().equals( "C" ) ) {
3569 if ( !it.next().getName().equals( "D" ) ) {
3572 if ( it.hasNext() ) {
3575 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",
3576 new NHXParser() )[ 0 ];
3577 PhylogenyNodeIterator it2;
3578 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3581 for( it2.reset(); it2.hasNext(); ) {
3584 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3585 if ( !it3.next().getName().equals( "r" ) ) {
3588 if ( !it3.next().getName().equals( "abc" ) ) {
3591 if ( !it3.next().getName().equals( "defg" ) ) {
3594 if ( !it3.next().getName().equals( "A" ) ) {
3597 if ( !it3.next().getName().equals( "B" ) ) {
3600 if ( !it3.next().getName().equals( "C" ) ) {
3603 if ( !it3.next().getName().equals( "D" ) ) {
3606 if ( !it3.next().getName().equals( "E" ) ) {
3609 if ( !it3.next().getName().equals( "F" ) ) {
3612 if ( !it3.next().getName().equals( "G" ) ) {
3615 if ( !it3.next().getName().equals( "1" ) ) {
3618 if ( !it3.next().getName().equals( "2" ) ) {
3621 if ( !it3.next().getName().equals( "3" ) ) {
3624 if ( !it3.next().getName().equals( "4" ) ) {
3627 if ( !it3.next().getName().equals( "5" ) ) {
3630 if ( !it3.next().getName().equals( "6" ) ) {
3633 if ( !it3.next().getName().equals( "f1" ) ) {
3636 if ( !it3.next().getName().equals( "f2" ) ) {
3639 if ( !it3.next().getName().equals( "f3" ) ) {
3642 if ( !it3.next().getName().equals( "a" ) ) {
3645 if ( !it3.next().getName().equals( "b" ) ) {
3648 if ( !it3.next().getName().equals( "f21" ) ) {
3651 if ( !it3.next().getName().equals( "X" ) ) {
3654 if ( !it3.next().getName().equals( "Y" ) ) {
3657 if ( !it3.next().getName().equals( "Z" ) ) {
3660 if ( it3.hasNext() ) {
3663 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3664 PhylogenyNodeIterator it4;
3665 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3668 for( it4.reset(); it4.hasNext(); ) {
3671 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3672 if ( !it5.next().getName().equals( "r" ) ) {
3675 if ( !it5.next().getName().equals( "A" ) ) {
3678 if ( !it5.next().getName().equals( "B" ) ) {
3681 if ( !it5.next().getName().equals( "C" ) ) {
3684 if ( !it5.next().getName().equals( "D" ) ) {
3687 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3688 PhylogenyNodeIterator it6;
3689 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3692 for( it6.reset(); it6.hasNext(); ) {
3695 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3696 if ( !it7.next().getName().equals( "A" ) ) {
3699 if ( it.hasNext() ) {
3703 catch ( final Exception e ) {
3704 e.printStackTrace( System.out );
3710 private static boolean testMidpointrooting() {
3712 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3713 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",
3714 new NHXParser() )[ 0 ];
3715 if ( !t1.isRooted() ) {
3718 PhylogenyMethods.midpointRoot( t1 );
3719 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3722 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3725 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3728 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3731 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3734 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3737 t1.reRoot( t1.getNode( "A" ) );
3738 PhylogenyMethods.midpointRoot( t1 );
3739 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3742 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3745 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3748 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3751 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3754 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3758 catch ( final Exception e ) {
3759 e.printStackTrace( System.out );
3765 private static boolean testNexusCharactersParsing() {
3767 final NexusCharactersParser parser = new NexusCharactersParser();
3768 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3770 String[] labels = parser.getCharStateLabels();
3771 if ( labels.length != 7 ) {
3774 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3777 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3780 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3783 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3786 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3789 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3792 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3795 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3797 labels = parser.getCharStateLabels();
3798 if ( labels.length != 7 ) {
3801 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3804 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3807 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3810 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3813 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3816 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3819 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3823 catch ( final Exception e ) {
3824 e.printStackTrace( System.out );
3830 private static boolean testNexusMatrixParsing() {
3832 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3833 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3835 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3836 if ( m.getNumberOfCharacters() != 9 ) {
3839 if ( m.getNumberOfIdentifiers() != 5 ) {
3842 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3845 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3848 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3851 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3854 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3857 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3860 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3863 // if ( labels.length != 7 ) {
3866 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3869 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3872 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3875 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3878 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3881 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3884 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3887 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3889 // labels = parser.getCharStateLabels();
3890 // if ( labels.length != 7 ) {
3893 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3896 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3899 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3902 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3905 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3908 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3911 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3915 catch ( final Exception e ) {
3916 e.printStackTrace( System.out );
3922 private static boolean testNexusTreeParsing() {
3924 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3925 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3926 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3927 if ( phylogenies.length != 1 ) {
3930 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3933 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3937 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3938 if ( phylogenies.length != 1 ) {
3941 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3944 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3948 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3949 if ( phylogenies.length != 1 ) {
3952 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3955 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3958 if ( phylogenies[ 0 ].isRooted() ) {
3962 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3963 if ( phylogenies.length != 18 ) {
3966 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3969 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3972 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3975 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3978 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3981 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3984 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3987 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3990 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3993 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3996 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3999 if ( phylogenies[ 8 ].isRooted() ) {
4002 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4005 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4008 if ( !phylogenies[ 9 ].isRooted() ) {
4011 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4014 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4017 if ( !phylogenies[ 10 ].isRooted() ) {
4020 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4023 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4026 if ( phylogenies[ 11 ].isRooted() ) {
4029 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4032 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4035 if ( !phylogenies[ 12 ].isRooted() ) {
4038 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4041 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4044 if ( !phylogenies[ 13 ].isRooted() ) {
4047 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4050 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4053 if ( !phylogenies[ 14 ].isRooted() ) {
4056 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4059 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4062 if ( phylogenies[ 15 ].isRooted() ) {
4065 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4068 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4071 if ( !phylogenies[ 16 ].isRooted() ) {
4074 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4077 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4080 if ( phylogenies[ 17 ].isRooted() ) {
4083 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4087 catch ( final Exception e ) {
4088 e.printStackTrace( System.out );
4094 private static boolean testNexusTreeParsingTranslating() {
4096 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4097 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4098 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4099 if ( phylogenies.length != 1 ) {
4102 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4105 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4108 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4111 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4114 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4115 .equals( "Aranaeus" ) ) {
4119 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4120 if ( phylogenies.length != 3 ) {
4123 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4126 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4129 if ( phylogenies[ 0 ].isRooted() ) {
4132 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4135 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4138 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4139 .equals( "Aranaeus" ) ) {
4142 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4145 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4148 if ( phylogenies[ 1 ].isRooted() ) {
4151 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4154 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4157 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4158 .equals( "Aranaeus" ) ) {
4161 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4164 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4167 if ( !phylogenies[ 2 ].isRooted() ) {
4170 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4173 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4176 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4177 .equals( "Aranaeus" ) ) {
4181 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4182 if ( phylogenies.length != 3 ) {
4185 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4188 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4191 if ( phylogenies[ 0 ].isRooted() ) {
4194 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4197 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4200 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4201 .equals( "Aranaeus" ) ) {
4204 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4207 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4210 if ( phylogenies[ 1 ].isRooted() ) {
4213 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4216 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4219 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4220 .equals( "Aranaeus" ) ) {
4223 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4226 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4229 if ( !phylogenies[ 2 ].isRooted() ) {
4232 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4235 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4238 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4239 .equals( "Aranaeus" ) ) {
4243 catch ( final Exception e ) {
4244 e.printStackTrace( System.out );
4250 private static boolean testNHParsing() {
4252 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4253 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4254 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4257 final NHXParser nhxp = new NHXParser();
4258 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4259 nhxp.setReplaceUnderscores( true );
4260 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4261 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4264 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4267 final Phylogeny p1b = factory
4268 .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 ",
4269 new NHXParser() )[ 0 ];
4270 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4273 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4276 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4277 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4278 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4279 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4280 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4281 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4282 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4283 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4284 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4285 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4286 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4287 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4288 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4290 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4293 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4296 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4299 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4302 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4303 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4304 final String p16_S = "((A,B),C)";
4305 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4306 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4309 final String p17_S = "(C,(A,B))";
4310 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4311 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4314 final String p18_S = "((A,B),(C,D))";
4315 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4316 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4319 final String p19_S = "(((A,B),C),D)";
4320 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4321 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4324 final String p20_S = "(A,(B,(C,D)))";
4325 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4326 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4329 final String p21_S = "(A,(B,(C,(D,E))))";
4330 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4331 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4334 final String p22_S = "((((A,B),C),D),E)";
4335 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4336 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4339 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4340 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4341 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4344 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4345 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4346 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4349 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4350 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4351 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4352 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4355 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4358 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4359 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4360 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4361 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4362 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4363 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4364 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4365 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4366 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4367 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4370 final String p26_S = "(A,B)ab";
4371 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4372 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4375 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4376 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4378 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4381 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4382 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4383 final String p28_S3 = "(A,B)ab";
4384 final String p28_S4 = "((((A,B),C),D),;E;)";
4385 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4387 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4390 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4393 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4396 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4399 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";
4400 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4401 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4404 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";
4405 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4406 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4409 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4410 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4411 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4414 final String p33_S = "A";
4415 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4416 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4419 final String p34_S = "B;";
4420 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4421 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4424 final String p35_S = "B:0.2";
4425 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4426 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4429 final String p36_S = "(A)";
4430 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4431 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4434 final String p37_S = "((A))";
4435 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4436 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4439 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4440 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4441 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4444 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4445 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4446 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4449 final String p40_S = "(A,B,C)";
4450 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4451 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4454 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4455 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4456 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4459 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4460 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4461 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4464 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)";
4465 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4466 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4469 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)))";
4470 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4471 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4474 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4475 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4476 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4479 final String p46_S = "";
4480 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4481 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4484 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4485 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4488 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4489 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4492 final Phylogeny p49 = factory
4493 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4494 new NHXParser() )[ 0 ];
4495 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4498 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4499 if ( p50.getNode( "A" ) == null ) {
4502 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4503 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4506 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4509 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4510 .equals( "((A,B)88:2.0,C);" ) ) {
4513 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4514 if ( p51.getNode( "A(A" ) == null ) {
4517 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4518 if ( p52.getNode( "A(A" ) == null ) {
4521 final Phylogeny p53 = factory
4522 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4523 new NHXParser() )[ 0 ];
4524 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4528 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4529 if ( p54.getNode( "A" ) == null ) {
4532 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4533 .equals( "((A,B)[88],C);" ) ) {
4537 catch ( final Exception e ) {
4538 e.printStackTrace( System.out );
4544 private static boolean testNHXconversion() {
4546 final PhylogenyNode n1 = new PhylogenyNode();
4547 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4548 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4549 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4550 final PhylogenyNode n5 = PhylogenyNode
4551 .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]" );
4552 final PhylogenyNode n6 = PhylogenyNode
4553 .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]" );
4554 if ( !n1.toNewHampshireX().equals( "" ) ) {
4557 if ( !n2.toNewHampshireX().equals( "" ) ) {
4560 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4563 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4566 if ( !n5.toNewHampshireX()
4567 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4570 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4574 catch ( final Exception e ) {
4575 e.printStackTrace( System.out );
4581 private static boolean testNHXNodeParsing() {
4583 final PhylogenyNode n1 = new PhylogenyNode();
4584 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4585 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4586 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4587 final PhylogenyNode n5 = PhylogenyNode
4588 .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]" );
4589 if ( !n3.getName().equals( "n3" ) ) {
4592 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4595 if ( n3.isDuplication() ) {
4598 if ( n3.isHasAssignedEvent() ) {
4601 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4604 if ( !n4.getName().equals( "n4" ) ) {
4607 if ( n4.getDistanceToParent() != 0.01 ) {
4610 if ( !n5.getName().equals( "n5" ) ) {
4613 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4616 if ( n5.getDistanceToParent() != 0.1 ) {
4619 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4622 if ( !n5.isDuplication() ) {
4625 if ( !n5.isHasAssignedEvent() ) {
4628 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4631 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4634 final PhylogenyNode n8 = PhylogenyNode
4635 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4636 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4637 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4640 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4643 final PhylogenyNode n9 = PhylogenyNode
4644 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4645 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4646 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4649 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4652 final PhylogenyNode n10 = PhylogenyNode
4653 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4654 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4657 final PhylogenyNode n20 = PhylogenyNode
4658 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4659 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4662 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4665 final PhylogenyNode n20x = PhylogenyNode
4666 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4667 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4670 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4673 final PhylogenyNode n20xx = PhylogenyNode
4674 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4675 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4678 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4681 final PhylogenyNode n20xxx = PhylogenyNode
4682 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4683 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4686 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4689 final PhylogenyNode n20xxxx = PhylogenyNode
4690 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4691 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4694 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4697 final PhylogenyNode n21 = PhylogenyNode
4698 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4699 if ( !n21.getName().equals( "n21_PIG" ) ) {
4702 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4705 final PhylogenyNode n21x = PhylogenyNode
4706 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4707 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4710 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4713 final PhylogenyNode n22 = PhylogenyNode
4714 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4715 if ( !n22.getName().equals( "n22/PIG" ) ) {
4718 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4721 final PhylogenyNode n23 = PhylogenyNode
4722 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4723 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4726 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4729 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4730 final PhylogenyNode a = PhylogenyNode
4731 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4732 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4733 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4736 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4739 final PhylogenyNode b = PhylogenyNode
4740 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4741 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4742 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4745 if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
4748 final PhylogenyNode c = PhylogenyNode
4749 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4750 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4751 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4754 if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
4757 final PhylogenyNode c1 = PhylogenyNode
4758 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4759 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4760 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4763 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4766 final PhylogenyNode c2 = PhylogenyNode
4767 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4768 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4769 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4772 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4775 final PhylogenyNode d = PhylogenyNode
4776 .createInstanceFromNhxString( "n10_RAT1/1-2",
4777 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4778 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4781 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4784 final PhylogenyNode e = PhylogenyNode
4785 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4786 if ( !e.getName().equals( "n10_RAT1" ) ) {
4789 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4793 final PhylogenyNode n11 = PhylogenyNode
4794 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4795 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4796 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4799 if ( n11.getDistanceToParent() != 0.4 ) {
4802 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4805 final PhylogenyNode n12 = PhylogenyNode
4806 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4807 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4808 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4811 if ( n12.getDistanceToParent() != 0.4 ) {
4814 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4817 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4818 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4819 if ( !tvu1.getRef().equals( "tag1" ) ) {
4822 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4825 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4828 if ( !tvu1.getValue().equals( "value1" ) ) {
4831 if ( !tvu3.getRef().equals( "tag3" ) ) {
4834 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4837 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4840 if ( !tvu3.getValue().equals( "value3" ) ) {
4843 if ( n1.getName().compareTo( "" ) != 0 ) {
4846 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4849 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4852 if ( n2.getName().compareTo( "" ) != 0 ) {
4855 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4858 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4861 final PhylogenyNode n00 = PhylogenyNode
4862 .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]" );
4863 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4866 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4869 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4872 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4875 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4878 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4881 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4884 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4887 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4888 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4891 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4892 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4895 final PhylogenyNode n13 = PhylogenyNode
4896 .createInstanceFromNhxString( "blah_12345/1-2",
4897 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4898 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4901 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4904 final PhylogenyNode n14 = PhylogenyNode
4905 .createInstanceFromNhxString( "blah_12X45/1-2",
4906 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4907 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4910 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4913 final PhylogenyNode n15 = PhylogenyNode
4914 .createInstanceFromNhxString( "something_wicked[123]",
4915 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4916 if ( !n15.getName().equals( "something_wicked" ) ) {
4919 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4922 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4925 final PhylogenyNode n16 = PhylogenyNode
4926 .createInstanceFromNhxString( "something_wicked2[9]",
4927 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4928 if ( !n16.getName().equals( "something_wicked2" ) ) {
4931 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4934 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4937 final PhylogenyNode n17 = PhylogenyNode
4938 .createInstanceFromNhxString( "something_wicked3[a]",
4939 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4940 if ( !n17.getName().equals( "something_wicked3" ) ) {
4943 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4946 final PhylogenyNode n18 = PhylogenyNode
4947 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4948 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4951 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4954 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4958 catch ( final Exception e ) {
4959 e.printStackTrace( System.out );
4965 private static boolean testNHXParsing() {
4967 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4968 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4969 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4972 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]";
4973 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4974 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4977 final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
4978 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4979 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4982 final Phylogeny[] p3 = factory
4983 .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]",
4985 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4988 final Phylogeny[] p4 = factory
4989 .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(]",
4991 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4994 final Phylogeny[] p5 = factory
4995 .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(((]",
4997 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5000 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)";
5001 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)";
5002 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5003 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5006 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)))";
5007 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)))";
5008 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5009 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5012 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]) ))[,,, ])))))))";
5013 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5014 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5015 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5018 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5019 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5022 final Phylogeny p10 = factory
5023 .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]",
5024 new NHXParser() )[ 0 ];
5025 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5029 catch ( final Exception e ) {
5030 e.printStackTrace( System.out );
5036 private static boolean testNHXParsingQuotes() {
5038 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5039 final NHXParser p = new NHXParser();
5040 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5041 if ( phylogenies_0.length != 5 ) {
5044 final Phylogeny phy = phylogenies_0[ 4 ];
5045 if ( phy.getNumberOfExternalNodes() != 7 ) {
5048 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5051 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5054 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5055 .getScientificName().equals( "hsapiens" ) ) {
5058 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5061 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5064 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5067 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5070 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5073 final NHXParser p1p = new NHXParser();
5074 p1p.setIgnoreQuotes( true );
5075 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5076 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5079 final NHXParser p2p = new NHXParser();
5080 p1p.setIgnoreQuotes( false );
5081 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5082 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5085 final NHXParser p3p = new NHXParser();
5086 p3p.setIgnoreQuotes( false );
5087 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5088 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5091 final NHXParser p4p = new NHXParser();
5092 p4p.setIgnoreQuotes( false );
5093 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5094 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5097 final Phylogeny p10 = factory
5098 .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]",
5099 new NHXParser() )[ 0 ];
5100 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5101 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5104 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5105 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5109 final Phylogeny p12 = factory
5110 .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]",
5111 new NHXParser() )[ 0 ];
5112 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5113 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5116 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5117 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5120 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;";
5121 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5124 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5125 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5129 catch ( final Exception e ) {
5130 e.printStackTrace( System.out );
5136 private static boolean testNHXParsingMB() {
5138 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5139 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5140 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5141 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5142 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5143 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5144 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5145 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5146 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5147 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5148 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5151 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5154 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5155 0.1100000000000000e+00 ) ) {
5158 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5161 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5164 final Phylogeny p2 = factory
5165 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5166 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5167 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5168 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5169 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5170 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5171 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5172 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5173 + "7.369400000000000e-02}])",
5174 new NHXParser() )[ 0 ];
5175 if ( p2.getNode( "1" ) == null ) {
5178 if ( p2.getNode( "2" ) == null ) {
5182 catch ( final Exception e ) {
5183 e.printStackTrace( System.out );
5190 private static boolean testPhylogenyBranch() {
5192 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5193 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5194 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5195 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5196 if ( !a1b1.equals( a1b1 ) ) {
5199 if ( !a1b1.equals( b1a1 ) ) {
5202 if ( !b1a1.equals( a1b1 ) ) {
5205 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5206 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5207 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5208 if ( a1_b1.equals( b1_a1 ) ) {
5211 if ( a1_b1.equals( a1_b1_ ) ) {
5214 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5215 if ( !a1_b1.equals( b1_a1_ ) ) {
5218 if ( a1_b1_.equals( b1_a1_ ) ) {
5221 if ( !a1_b1_.equals( b1_a1 ) ) {
5225 catch ( final Exception e ) {
5226 e.printStackTrace( System.out );
5232 private static boolean testPhyloXMLparsingOfDistributionElement() {
5234 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5235 PhyloXmlParser xml_parser = null;
5237 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5239 catch ( final Exception e ) {
5240 // Do nothing -- means were not running from jar.
5242 if ( xml_parser == null ) {
5243 xml_parser = new PhyloXmlParser();
5244 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5245 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5248 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5251 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5253 if ( xml_parser.getErrorCount() > 0 ) {
5254 System.out.println( xml_parser.getErrorMessages().toString() );
5257 if ( phylogenies_0.length != 1 ) {
5260 final Phylogeny t1 = phylogenies_0[ 0 ];
5261 PhylogenyNode n = null;
5262 Distribution d = null;
5263 n = t1.getNode( "root node" );
5264 if ( !n.getNodeData().isHasDistribution() ) {
5267 if ( n.getNodeData().getDistributions().size() != 1 ) {
5270 d = n.getNodeData().getDistribution();
5271 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5274 if ( d.getPoints().size() != 1 ) {
5277 if ( d.getPolygons() != null ) {
5280 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5283 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5286 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5289 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5292 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5295 n = t1.getNode( "node a" );
5296 if ( !n.getNodeData().isHasDistribution() ) {
5299 if ( n.getNodeData().getDistributions().size() != 2 ) {
5302 d = n.getNodeData().getDistribution( 1 );
5303 if ( !d.getDesc().equals( "San Diego" ) ) {
5306 if ( d.getPoints().size() != 1 ) {
5309 if ( d.getPolygons() != null ) {
5312 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5315 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5318 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5321 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5324 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5327 n = t1.getNode( "node bb" );
5328 if ( !n.getNodeData().isHasDistribution() ) {
5331 if ( n.getNodeData().getDistributions().size() != 1 ) {
5334 d = n.getNodeData().getDistribution( 0 );
5335 if ( d.getPoints().size() != 3 ) {
5338 if ( d.getPolygons().size() != 2 ) {
5341 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5344 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5347 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5350 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5353 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5356 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5359 Polygon p = d.getPolygons().get( 0 );
5360 if ( p.getPoints().size() != 3 ) {
5363 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5366 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5369 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5372 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5375 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5378 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5381 p = d.getPolygons().get( 1 );
5382 if ( p.getPoints().size() != 3 ) {
5385 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5388 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5391 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5395 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5396 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5397 if ( rt.length != 1 ) {
5400 final Phylogeny t1_rt = rt[ 0 ];
5401 n = t1_rt.getNode( "root node" );
5402 if ( !n.getNodeData().isHasDistribution() ) {
5405 if ( n.getNodeData().getDistributions().size() != 1 ) {
5408 d = n.getNodeData().getDistribution();
5409 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5412 if ( d.getPoints().size() != 1 ) {
5415 if ( d.getPolygons() != null ) {
5418 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5421 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5424 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5427 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5430 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5433 n = t1_rt.getNode( "node a" );
5434 if ( !n.getNodeData().isHasDistribution() ) {
5437 if ( n.getNodeData().getDistributions().size() != 2 ) {
5440 d = n.getNodeData().getDistribution( 1 );
5441 if ( !d.getDesc().equals( "San Diego" ) ) {
5444 if ( d.getPoints().size() != 1 ) {
5447 if ( d.getPolygons() != null ) {
5450 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5453 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5456 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5459 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5462 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5465 n = t1_rt.getNode( "node bb" );
5466 if ( !n.getNodeData().isHasDistribution() ) {
5469 if ( n.getNodeData().getDistributions().size() != 1 ) {
5472 d = n.getNodeData().getDistribution( 0 );
5473 if ( d.getPoints().size() != 3 ) {
5476 if ( d.getPolygons().size() != 2 ) {
5479 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5482 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5485 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5488 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5491 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5494 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5497 p = d.getPolygons().get( 0 );
5498 if ( p.getPoints().size() != 3 ) {
5501 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5504 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5507 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5510 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5513 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5516 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5519 p = d.getPolygons().get( 1 );
5520 if ( p.getPoints().size() != 3 ) {
5523 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5526 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5529 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5533 catch ( final Exception e ) {
5534 e.printStackTrace( System.out );
5540 private static boolean testPostOrderIterator() {
5542 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5543 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5544 PhylogenyNodeIterator it0;
5545 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5548 for( it0.reset(); it0.hasNext(); ) {
5551 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5552 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5553 if ( !it.next().getName().equals( "A" ) ) {
5556 if ( !it.next().getName().equals( "B" ) ) {
5559 if ( !it.next().getName().equals( "ab" ) ) {
5562 if ( !it.next().getName().equals( "C" ) ) {
5565 if ( !it.next().getName().equals( "D" ) ) {
5568 if ( !it.next().getName().equals( "cd" ) ) {
5571 if ( !it.next().getName().equals( "abcd" ) ) {
5574 if ( !it.next().getName().equals( "E" ) ) {
5577 if ( !it.next().getName().equals( "F" ) ) {
5580 if ( !it.next().getName().equals( "ef" ) ) {
5583 if ( !it.next().getName().equals( "G" ) ) {
5586 if ( !it.next().getName().equals( "H" ) ) {
5589 if ( !it.next().getName().equals( "gh" ) ) {
5592 if ( !it.next().getName().equals( "efgh" ) ) {
5595 if ( !it.next().getName().equals( "r" ) ) {
5598 if ( it.hasNext() ) {
5602 catch ( final Exception e ) {
5603 e.printStackTrace( System.out );
5609 private static boolean testPreOrderIterator() {
5611 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5612 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5613 PhylogenyNodeIterator it0;
5614 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5617 for( it0.reset(); it0.hasNext(); ) {
5620 PhylogenyNodeIterator it = t0.iteratorPreorder();
5621 if ( !it.next().getName().equals( "r" ) ) {
5624 if ( !it.next().getName().equals( "ab" ) ) {
5627 if ( !it.next().getName().equals( "A" ) ) {
5630 if ( !it.next().getName().equals( "B" ) ) {
5633 if ( !it.next().getName().equals( "cd" ) ) {
5636 if ( !it.next().getName().equals( "C" ) ) {
5639 if ( !it.next().getName().equals( "D" ) ) {
5642 if ( it.hasNext() ) {
5645 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5646 it = t1.iteratorPreorder();
5647 if ( !it.next().getName().equals( "r" ) ) {
5650 if ( !it.next().getName().equals( "abcd" ) ) {
5653 if ( !it.next().getName().equals( "ab" ) ) {
5656 if ( !it.next().getName().equals( "A" ) ) {
5659 if ( !it.next().getName().equals( "B" ) ) {
5662 if ( !it.next().getName().equals( "cd" ) ) {
5665 if ( !it.next().getName().equals( "C" ) ) {
5668 if ( !it.next().getName().equals( "D" ) ) {
5671 if ( !it.next().getName().equals( "efgh" ) ) {
5674 if ( !it.next().getName().equals( "ef" ) ) {
5677 if ( !it.next().getName().equals( "E" ) ) {
5680 if ( !it.next().getName().equals( "F" ) ) {
5683 if ( !it.next().getName().equals( "gh" ) ) {
5686 if ( !it.next().getName().equals( "G" ) ) {
5689 if ( !it.next().getName().equals( "H" ) ) {
5692 if ( it.hasNext() ) {
5696 catch ( final Exception e ) {
5697 e.printStackTrace( System.out );
5703 private static boolean testPropertiesMap() {
5705 final PropertiesMap pm = new PropertiesMap();
5706 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5707 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5708 final Property p2 = new Property( "something:else",
5710 "improbable:research",
5713 pm.addProperty( p0 );
5714 pm.addProperty( p1 );
5715 pm.addProperty( p2 );
5716 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5719 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5722 if ( pm.getProperties().size() != 3 ) {
5725 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5728 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5731 if ( pm.getProperties().size() != 3 ) {
5734 pm.removeProperty( "dimensions:diameter" );
5735 if ( pm.getProperties().size() != 2 ) {
5738 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5741 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5745 catch ( final Exception e ) {
5746 e.printStackTrace( System.out );
5752 private static boolean testReIdMethods() {
5754 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5755 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5756 final int count = PhylogenyNode.getNodeCount();
5758 if ( p.getNode( "r" ).getId() != count ) {
5761 if ( p.getNode( "A" ).getId() != count + 1 ) {
5764 if ( p.getNode( "B" ).getId() != count + 1 ) {
5767 if ( p.getNode( "C" ).getId() != count + 1 ) {
5770 if ( p.getNode( "1" ).getId() != count + 2 ) {
5773 if ( p.getNode( "2" ).getId() != count + 2 ) {
5776 if ( p.getNode( "3" ).getId() != count + 2 ) {
5779 if ( p.getNode( "4" ).getId() != count + 2 ) {
5782 if ( p.getNode( "5" ).getId() != count + 2 ) {
5785 if ( p.getNode( "6" ).getId() != count + 2 ) {
5788 if ( p.getNode( "a" ).getId() != count + 3 ) {
5791 if ( p.getNode( "b" ).getId() != count + 3 ) {
5794 if ( p.getNode( "X" ).getId() != count + 4 ) {
5797 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5800 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5804 catch ( final Exception e ) {
5805 e.printStackTrace( System.out );
5811 private static boolean testRerooting() {
5813 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5814 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",
5815 new NHXParser() )[ 0 ];
5816 if ( !t1.isRooted() ) {
5819 t1.reRoot( t1.getNode( "D" ) );
5820 t1.reRoot( t1.getNode( "CD" ) );
5821 t1.reRoot( t1.getNode( "A" ) );
5822 t1.reRoot( t1.getNode( "B" ) );
5823 t1.reRoot( t1.getNode( "AB" ) );
5824 t1.reRoot( t1.getNode( "D" ) );
5825 t1.reRoot( t1.getNode( "C" ) );
5826 t1.reRoot( t1.getNode( "CD" ) );
5827 t1.reRoot( t1.getNode( "A" ) );
5828 t1.reRoot( t1.getNode( "B" ) );
5829 t1.reRoot( t1.getNode( "AB" ) );
5830 t1.reRoot( t1.getNode( "D" ) );
5831 t1.reRoot( t1.getNode( "D" ) );
5832 t1.reRoot( t1.getNode( "C" ) );
5833 t1.reRoot( t1.getNode( "A" ) );
5834 t1.reRoot( t1.getNode( "B" ) );
5835 t1.reRoot( t1.getNode( "AB" ) );
5836 t1.reRoot( t1.getNode( "C" ) );
5837 t1.reRoot( t1.getNode( "D" ) );
5838 t1.reRoot( t1.getNode( "CD" ) );
5839 t1.reRoot( t1.getNode( "D" ) );
5840 t1.reRoot( t1.getNode( "A" ) );
5841 t1.reRoot( t1.getNode( "B" ) );
5842 t1.reRoot( t1.getNode( "AB" ) );
5843 t1.reRoot( t1.getNode( "C" ) );
5844 t1.reRoot( t1.getNode( "D" ) );
5845 t1.reRoot( t1.getNode( "CD" ) );
5846 t1.reRoot( t1.getNode( "D" ) );
5847 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5850 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5853 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5856 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5859 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5862 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5865 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",
5866 new NHXParser() )[ 0 ];
5867 t2.reRoot( t2.getNode( "A" ) );
5868 t2.reRoot( t2.getNode( "D" ) );
5869 t2.reRoot( t2.getNode( "ABC" ) );
5870 t2.reRoot( t2.getNode( "A" ) );
5871 t2.reRoot( t2.getNode( "B" ) );
5872 t2.reRoot( t2.getNode( "D" ) );
5873 t2.reRoot( t2.getNode( "C" ) );
5874 t2.reRoot( t2.getNode( "ABC" ) );
5875 t2.reRoot( t2.getNode( "A" ) );
5876 t2.reRoot( t2.getNode( "B" ) );
5877 t2.reRoot( t2.getNode( "AB" ) );
5878 t2.reRoot( t2.getNode( "AB" ) );
5879 t2.reRoot( t2.getNode( "D" ) );
5880 t2.reRoot( t2.getNode( "C" ) );
5881 t2.reRoot( t2.getNode( "B" ) );
5882 t2.reRoot( t2.getNode( "AB" ) );
5883 t2.reRoot( t2.getNode( "D" ) );
5884 t2.reRoot( t2.getNode( "D" ) );
5885 t2.reRoot( t2.getNode( "ABC" ) );
5886 t2.reRoot( t2.getNode( "A" ) );
5887 t2.reRoot( t2.getNode( "B" ) );
5888 t2.reRoot( t2.getNode( "AB" ) );
5889 t2.reRoot( t2.getNode( "D" ) );
5890 t2.reRoot( t2.getNode( "C" ) );
5891 t2.reRoot( t2.getNode( "ABC" ) );
5892 t2.reRoot( t2.getNode( "A" ) );
5893 t2.reRoot( t2.getNode( "B" ) );
5894 t2.reRoot( t2.getNode( "AB" ) );
5895 t2.reRoot( t2.getNode( "D" ) );
5896 t2.reRoot( t2.getNode( "D" ) );
5897 t2.reRoot( t2.getNode( "C" ) );
5898 t2.reRoot( t2.getNode( "A" ) );
5899 t2.reRoot( t2.getNode( "B" ) );
5900 t2.reRoot( t2.getNode( "AB" ) );
5901 t2.reRoot( t2.getNode( "C" ) );
5902 t2.reRoot( t2.getNode( "D" ) );
5903 t2.reRoot( t2.getNode( "ABC" ) );
5904 t2.reRoot( t2.getNode( "D" ) );
5905 t2.reRoot( t2.getNode( "A" ) );
5906 t2.reRoot( t2.getNode( "B" ) );
5907 t2.reRoot( t2.getNode( "AB" ) );
5908 t2.reRoot( t2.getNode( "C" ) );
5909 t2.reRoot( t2.getNode( "D" ) );
5910 t2.reRoot( t2.getNode( "ABC" ) );
5911 t2.reRoot( t2.getNode( "D" ) );
5912 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5915 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5918 t2.reRoot( t2.getNode( "ABC" ) );
5919 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5922 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5925 t2.reRoot( t2.getNode( "AB" ) );
5926 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5929 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5932 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5935 t2.reRoot( t2.getNode( "AB" ) );
5936 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5939 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5942 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5945 t2.reRoot( t2.getNode( "D" ) );
5946 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5949 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5952 t2.reRoot( t2.getNode( "ABC" ) );
5953 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5956 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5959 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5960 new NHXParser() )[ 0 ];
5961 t3.reRoot( t3.getNode( "B" ) );
5962 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5965 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5968 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5971 t3.reRoot( t3.getNode( "B" ) );
5972 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5975 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5978 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5981 t3.reRoot( t3.getRoot() );
5982 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5985 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5988 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5992 catch ( final Exception e ) {
5993 e.printStackTrace( System.out );
5999 private static boolean testSDIse() {
6001 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6002 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6003 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6004 gene1.setRooted( true );
6005 species1.setRooted( true );
6006 final SDI sdi = new SDIse( gene1, species1 );
6007 if ( !gene1.getRoot().isDuplication() ) {
6010 final Phylogeny species2 = factory
6011 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6012 new NHXParser() )[ 0 ];
6013 final Phylogeny gene2 = factory
6014 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6015 new NHXParser() )[ 0 ];
6016 species2.setRooted( true );
6017 gene2.setRooted( true );
6018 final SDI sdi2 = new SDIse( gene2, species2 );
6019 if ( sdi2.getDuplicationsSum() != 0 ) {
6022 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6025 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6028 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6031 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6034 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6037 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6040 final Phylogeny species3 = factory
6041 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6042 new NHXParser() )[ 0 ];
6043 final Phylogeny gene3 = factory
6044 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6045 new NHXParser() )[ 0 ];
6046 species3.setRooted( true );
6047 gene3.setRooted( true );
6048 final SDI sdi3 = new SDIse( gene3, species3 );
6049 if ( sdi3.getDuplicationsSum() != 1 ) {
6052 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6055 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6058 final Phylogeny species4 = factory
6059 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6060 new NHXParser() )[ 0 ];
6061 final Phylogeny gene4 = factory
6062 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6063 new NHXParser() )[ 0 ];
6064 species4.setRooted( true );
6065 gene4.setRooted( true );
6066 final SDI sdi4 = new SDIse( gene4, species4 );
6067 if ( sdi4.getDuplicationsSum() != 1 ) {
6070 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6073 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6076 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6079 if ( species4.getNumberOfExternalNodes() != 6 ) {
6082 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6085 final Phylogeny species5 = factory
6086 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6087 new NHXParser() )[ 0 ];
6088 final Phylogeny gene5 = factory
6089 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6090 new NHXParser() )[ 0 ];
6091 species5.setRooted( true );
6092 gene5.setRooted( true );
6093 final SDI sdi5 = new SDIse( gene5, species5 );
6094 if ( sdi5.getDuplicationsSum() != 2 ) {
6097 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6100 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6103 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6106 if ( species5.getNumberOfExternalNodes() != 6 ) {
6109 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6112 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6113 // Conjecture for Comparing Molecular Phylogenies"
6114 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6115 final Phylogeny species6 = factory
6116 .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,"
6117 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6118 new NHXParser() )[ 0 ];
6119 final Phylogeny gene6 = factory
6120 .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,"
6121 + "((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,"
6122 + "(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;",
6123 new NHXParser() )[ 0 ];
6124 species6.setRooted( true );
6125 gene6.setRooted( true );
6126 final SDI sdi6 = new SDIse( gene6, species6 );
6127 if ( sdi6.getDuplicationsSum() != 3 ) {
6130 if ( !gene6.getNode( "r" ).isDuplication() ) {
6133 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6136 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6139 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6142 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6145 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6148 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6151 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6154 sdi6.computeMappingCostL();
6155 if ( sdi6.computeMappingCostL() != 17 ) {
6158 if ( species6.getNumberOfExternalNodes() != 9 ) {
6161 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6164 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6165 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6166 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6167 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6168 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6169 species7.setRooted( true );
6170 final Phylogeny gene7_1 = Test
6171 .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])" );
6172 gene7_1.setRooted( true );
6173 final SDI sdi7 = new SDIse( gene7_1, species7 );
6174 if ( sdi7.getDuplicationsSum() != 0 ) {
6177 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6180 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6183 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6186 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6189 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6192 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6195 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6198 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6201 final Phylogeny gene7_2 = Test
6202 .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])" );
6203 gene7_2.setRooted( true );
6204 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6205 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6208 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6211 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6214 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6217 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6220 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6223 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6226 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6229 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6232 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6236 catch ( final Exception e ) {
6242 private static boolean testSDIunrooted() {
6244 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6245 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6246 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6247 final Iterator<PhylogenyBranch> iter = l.iterator();
6248 PhylogenyBranch br = iter.next();
6249 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6252 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6256 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6259 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6263 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6266 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6270 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6273 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6277 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6280 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6284 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6287 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6291 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6294 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6298 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6301 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6305 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6308 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6312 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6315 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6319 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6322 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6326 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6329 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6333 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6336 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6340 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6343 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6347 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6350 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6353 if ( iter.hasNext() ) {
6356 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6357 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6358 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6360 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6363 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6367 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6370 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6374 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6377 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6380 if ( iter1.hasNext() ) {
6383 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6384 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6385 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6387 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6390 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6394 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6397 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6401 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6404 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6407 if ( iter2.hasNext() ) {
6410 final Phylogeny species0 = factory
6411 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6412 new NHXParser() )[ 0 ];
6413 final Phylogeny gene1 = factory
6414 .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])",
6415 new NHXParser() )[ 0 ];
6416 species0.setRooted( true );
6417 gene1.setRooted( true );
6418 final SDIR sdi_unrooted = new SDIR();
6419 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6420 if ( sdi_unrooted.getCount() != 1 ) {
6423 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6426 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6429 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6432 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6435 final Phylogeny gene2 = factory
6436 .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])",
6437 new NHXParser() )[ 0 ];
6438 gene2.setRooted( true );
6439 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6440 if ( sdi_unrooted.getCount() != 1 ) {
6443 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6446 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6449 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6452 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6455 final Phylogeny species6 = factory
6456 .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,"
6457 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6458 new NHXParser() )[ 0 ];
6459 final Phylogeny gene6 = factory
6460 .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],"
6461 + "(((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],"
6462 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6463 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6464 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6465 new NHXParser() )[ 0 ];
6466 species6.setRooted( true );
6467 gene6.setRooted( true );
6468 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6469 if ( sdi_unrooted.getCount() != 1 ) {
6472 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6475 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6478 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6481 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6484 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6487 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6490 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6493 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6496 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6499 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6502 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6505 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6509 final Phylogeny species7 = factory
6510 .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,"
6511 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6512 new NHXParser() )[ 0 ];
6513 final Phylogeny gene7 = factory
6514 .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],"
6515 + "(((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],"
6516 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6517 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6518 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6519 new NHXParser() )[ 0 ];
6520 species7.setRooted( true );
6521 gene7.setRooted( true );
6522 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6523 if ( sdi_unrooted.getCount() != 1 ) {
6526 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6529 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6532 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6535 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6538 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6541 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6544 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6547 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6550 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6553 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6556 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6559 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6563 final Phylogeny species8 = factory
6564 .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,"
6565 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6566 new NHXParser() )[ 0 ];
6567 final Phylogeny gene8 = factory
6568 .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],"
6569 + "(((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],"
6570 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6571 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6572 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6573 new NHXParser() )[ 0 ];
6574 species8.setRooted( true );
6575 gene8.setRooted( true );
6576 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6577 if ( sdi_unrooted.getCount() != 1 ) {
6580 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6583 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6586 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6589 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6592 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6595 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6598 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6601 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6604 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6607 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6610 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6613 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6618 catch ( final Exception e ) {
6619 e.printStackTrace( System.out );
6625 private static boolean testSplit() {
6627 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6628 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6629 //Archaeopteryx.createApplication( p0 );
6630 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6631 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6632 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6633 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6634 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6635 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6636 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6637 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6638 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6639 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6640 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6641 // System.out.println( s0.toString() );
6643 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6646 if ( s0.match( query_nodes ) ) {
6649 query_nodes = new HashSet<PhylogenyNode>();
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6657 if ( !s0.match( query_nodes ) ) {
6661 query_nodes = new HashSet<PhylogenyNode>();
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6665 if ( !s0.match( query_nodes ) ) {
6669 query_nodes = new HashSet<PhylogenyNode>();
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6674 if ( !s0.match( query_nodes ) ) {
6678 query_nodes = new HashSet<PhylogenyNode>();
6679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6683 if ( !s0.match( query_nodes ) ) {
6687 query_nodes = new HashSet<PhylogenyNode>();
6688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6691 if ( !s0.match( query_nodes ) ) {
6695 query_nodes = new HashSet<PhylogenyNode>();
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6698 if ( !s0.match( query_nodes ) ) {
6702 query_nodes = new HashSet<PhylogenyNode>();
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6708 if ( !s0.match( query_nodes ) ) {
6712 query_nodes = new HashSet<PhylogenyNode>();
6713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6714 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6715 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6716 if ( !s0.match( query_nodes ) ) {
6720 query_nodes = new HashSet<PhylogenyNode>();
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6724 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6725 if ( !s0.match( query_nodes ) ) {
6729 query_nodes = new HashSet<PhylogenyNode>();
6730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6732 if ( s0.match( query_nodes ) ) {
6736 query_nodes = new HashSet<PhylogenyNode>();
6737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6741 if ( s0.match( query_nodes ) ) {
6745 query_nodes = new HashSet<PhylogenyNode>();
6746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6751 if ( s0.match( query_nodes ) ) {
6755 query_nodes = new HashSet<PhylogenyNode>();
6756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6758 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6759 if ( s0.match( query_nodes ) ) {
6763 query_nodes = new HashSet<PhylogenyNode>();
6764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6766 if ( s0.match( query_nodes ) ) {
6770 query_nodes = new HashSet<PhylogenyNode>();
6771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6773 if ( s0.match( query_nodes ) ) {
6777 query_nodes = new HashSet<PhylogenyNode>();
6778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6780 if ( s0.match( query_nodes ) ) {
6784 query_nodes = new HashSet<PhylogenyNode>();
6785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6786 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6787 if ( s0.match( query_nodes ) ) {
6791 query_nodes = new HashSet<PhylogenyNode>();
6792 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6793 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6794 if ( s0.match( query_nodes ) ) {
6798 query_nodes = new HashSet<PhylogenyNode>();
6799 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6800 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6801 if ( s0.match( query_nodes ) ) {
6805 query_nodes = new HashSet<PhylogenyNode>();
6806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6807 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6808 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6809 if ( s0.match( query_nodes ) ) {
6813 query_nodes = new HashSet<PhylogenyNode>();
6814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6815 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6817 if ( s0.match( query_nodes ) ) {
6821 query_nodes = new HashSet<PhylogenyNode>();
6822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6825 if ( s0.match( query_nodes ) ) {
6829 query_nodes = new HashSet<PhylogenyNode>();
6830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6834 if ( s0.match( query_nodes ) ) {
6838 // query_nodes = new HashSet<PhylogenyNode>();
6839 // query_nodes.add( new PhylogenyNode( "X" ) );
6840 // query_nodes.add( new PhylogenyNode( "Y" ) );
6841 // query_nodes.add( new PhylogenyNode( "A" ) );
6842 // query_nodes.add( new PhylogenyNode( "B" ) );
6843 // query_nodes.add( new PhylogenyNode( "C" ) );
6844 // query_nodes.add( new PhylogenyNode( "D" ) );
6845 // query_nodes.add( new PhylogenyNode( "E" ) );
6846 // query_nodes.add( new PhylogenyNode( "F" ) );
6847 // query_nodes.add( new PhylogenyNode( "G" ) );
6848 // if ( !s0.match( query_nodes ) ) {
6851 // query_nodes = new HashSet<PhylogenyNode>();
6852 // query_nodes.add( new PhylogenyNode( "X" ) );
6853 // query_nodes.add( new PhylogenyNode( "Y" ) );
6854 // query_nodes.add( new PhylogenyNode( "A" ) );
6855 // query_nodes.add( new PhylogenyNode( "B" ) );
6856 // query_nodes.add( new PhylogenyNode( "C" ) );
6857 // if ( !s0.match( query_nodes ) ) {
6861 // query_nodes = new HashSet<PhylogenyNode>();
6862 // query_nodes.add( new PhylogenyNode( "X" ) );
6863 // query_nodes.add( new PhylogenyNode( "Y" ) );
6864 // query_nodes.add( new PhylogenyNode( "D" ) );
6865 // query_nodes.add( new PhylogenyNode( "E" ) );
6866 // query_nodes.add( new PhylogenyNode( "F" ) );
6867 // query_nodes.add( new PhylogenyNode( "G" ) );
6868 // if ( !s0.match( query_nodes ) ) {
6872 // query_nodes = new HashSet<PhylogenyNode>();
6873 // query_nodes.add( new PhylogenyNode( "X" ) );
6874 // query_nodes.add( new PhylogenyNode( "Y" ) );
6875 // query_nodes.add( new PhylogenyNode( "A" ) );
6876 // query_nodes.add( new PhylogenyNode( "B" ) );
6877 // query_nodes.add( new PhylogenyNode( "C" ) );
6878 // query_nodes.add( new PhylogenyNode( "D" ) );
6879 // if ( !s0.match( query_nodes ) ) {
6883 // query_nodes = new HashSet<PhylogenyNode>();
6884 // query_nodes.add( new PhylogenyNode( "X" ) );
6885 // query_nodes.add( new PhylogenyNode( "Y" ) );
6886 // query_nodes.add( new PhylogenyNode( "E" ) );
6887 // query_nodes.add( new PhylogenyNode( "F" ) );
6888 // query_nodes.add( new PhylogenyNode( "G" ) );
6889 // if ( !s0.match( query_nodes ) ) {
6893 // query_nodes = new HashSet<PhylogenyNode>();
6894 // query_nodes.add( new PhylogenyNode( "X" ) );
6895 // query_nodes.add( new PhylogenyNode( "Y" ) );
6896 // query_nodes.add( new PhylogenyNode( "F" ) );
6897 // query_nodes.add( new PhylogenyNode( "G" ) );
6898 // if ( !s0.match( query_nodes ) ) {
6902 query_nodes = new HashSet<PhylogenyNode>();
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
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( "X" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6916 if ( s0.match( query_nodes ) ) {
6919 ///////////////////////////
6921 query_nodes = new HashSet<PhylogenyNode>();
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6926 if ( s0.match( query_nodes ) ) {
6930 query_nodes = new HashSet<PhylogenyNode>();
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6934 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6935 if ( s0.match( query_nodes ) ) {
6939 query_nodes = new HashSet<PhylogenyNode>();
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6943 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6944 if ( s0.match( query_nodes ) ) {
6948 query_nodes = new HashSet<PhylogenyNode>();
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6952 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6953 if ( s0.match( query_nodes ) ) {
6957 query_nodes = new HashSet<PhylogenyNode>();
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6960 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6961 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6962 if ( s0.match( query_nodes ) ) {
6966 query_nodes = new HashSet<PhylogenyNode>();
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6969 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6970 if ( s0.match( query_nodes ) ) {
6974 query_nodes = new HashSet<PhylogenyNode>();
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6978 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6980 if ( s0.match( query_nodes ) ) {
6984 query_nodes = new HashSet<PhylogenyNode>();
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6990 if ( s0.match( query_nodes ) ) {
6994 query_nodes = new HashSet<PhylogenyNode>();
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7000 if ( s0.match( query_nodes ) ) {
7004 query_nodes = new HashSet<PhylogenyNode>();
7005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7011 if ( s0.match( query_nodes ) ) {
7015 catch ( final Exception e ) {
7016 e.printStackTrace();
7022 private static boolean testSplitStrict() {
7024 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7025 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7026 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7027 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7028 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7029 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7030 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7031 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7032 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7033 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7034 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7035 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7036 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7037 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7038 if ( s0.match( query_nodes ) ) {
7041 query_nodes = new HashSet<PhylogenyNode>();
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7049 if ( !s0.match( query_nodes ) ) {
7053 query_nodes = new HashSet<PhylogenyNode>();
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7057 if ( !s0.match( query_nodes ) ) {
7061 query_nodes = new HashSet<PhylogenyNode>();
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7066 if ( !s0.match( query_nodes ) ) {
7070 query_nodes = new HashSet<PhylogenyNode>();
7071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7075 if ( !s0.match( query_nodes ) ) {
7079 query_nodes = new HashSet<PhylogenyNode>();
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7083 if ( !s0.match( query_nodes ) ) {
7087 query_nodes = new HashSet<PhylogenyNode>();
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7090 if ( !s0.match( query_nodes ) ) {
7094 query_nodes = new HashSet<PhylogenyNode>();
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7100 if ( !s0.match( query_nodes ) ) {
7104 query_nodes = new HashSet<PhylogenyNode>();
7105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7108 if ( !s0.match( query_nodes ) ) {
7112 query_nodes = new HashSet<PhylogenyNode>();
7113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7117 if ( !s0.match( query_nodes ) ) {
7121 query_nodes = new HashSet<PhylogenyNode>();
7122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7124 if ( s0.match( query_nodes ) ) {
7128 query_nodes = new HashSet<PhylogenyNode>();
7129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7133 if ( s0.match( query_nodes ) ) {
7137 query_nodes = new HashSet<PhylogenyNode>();
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7143 if ( s0.match( query_nodes ) ) {
7147 query_nodes = new HashSet<PhylogenyNode>();
7148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7151 if ( s0.match( query_nodes ) ) {
7155 query_nodes = new HashSet<PhylogenyNode>();
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7158 if ( s0.match( query_nodes ) ) {
7162 query_nodes = new HashSet<PhylogenyNode>();
7163 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7165 if ( s0.match( query_nodes ) ) {
7169 query_nodes = new HashSet<PhylogenyNode>();
7170 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7171 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7172 if ( s0.match( query_nodes ) ) {
7176 query_nodes = new HashSet<PhylogenyNode>();
7177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7178 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7179 if ( s0.match( query_nodes ) ) {
7183 query_nodes = new HashSet<PhylogenyNode>();
7184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7186 if ( s0.match( query_nodes ) ) {
7190 query_nodes = new HashSet<PhylogenyNode>();
7191 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7192 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7193 if ( s0.match( query_nodes ) ) {
7197 query_nodes = new HashSet<PhylogenyNode>();
7198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7199 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7201 if ( s0.match( query_nodes ) ) {
7205 query_nodes = new HashSet<PhylogenyNode>();
7206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7209 if ( s0.match( query_nodes ) ) {
7213 query_nodes = new HashSet<PhylogenyNode>();
7214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7217 if ( s0.match( query_nodes ) ) {
7221 query_nodes = new HashSet<PhylogenyNode>();
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7224 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7225 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7226 if ( s0.match( query_nodes ) ) {
7230 catch ( final Exception e ) {
7231 e.printStackTrace();
7237 private static boolean testSubtreeDeletion() {
7239 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7240 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7241 t1.deleteSubtree( t1.getNode( "A" ), false );
7242 if ( t1.getNumberOfExternalNodes() != 5 ) {
7245 t1.toNewHampshireX();
7246 t1.deleteSubtree( t1.getNode( "E" ), false );
7247 if ( t1.getNumberOfExternalNodes() != 4 ) {
7250 t1.toNewHampshireX();
7251 t1.deleteSubtree( t1.getNode( "F" ), false );
7252 if ( t1.getNumberOfExternalNodes() != 3 ) {
7255 t1.toNewHampshireX();
7256 t1.deleteSubtree( t1.getNode( "D" ), false );
7257 t1.toNewHampshireX();
7258 if ( t1.getNumberOfExternalNodes() != 3 ) {
7261 t1.deleteSubtree( t1.getNode( "def" ), false );
7262 t1.toNewHampshireX();
7263 if ( t1.getNumberOfExternalNodes() != 2 ) {
7266 t1.deleteSubtree( t1.getNode( "B" ), false );
7267 t1.toNewHampshireX();
7268 if ( t1.getNumberOfExternalNodes() != 1 ) {
7271 t1.deleteSubtree( t1.getNode( "C" ), false );
7272 t1.toNewHampshireX();
7273 if ( t1.getNumberOfExternalNodes() != 1 ) {
7276 t1.deleteSubtree( t1.getNode( "abc" ), false );
7277 t1.toNewHampshireX();
7278 if ( t1.getNumberOfExternalNodes() != 1 ) {
7281 t1.deleteSubtree( t1.getNode( "r" ), false );
7282 if ( t1.getNumberOfExternalNodes() != 0 ) {
7285 if ( !t1.isEmpty() ) {
7288 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7289 t2.deleteSubtree( t2.getNode( "A" ), false );
7290 t2.toNewHampshireX();
7291 if ( t2.getNumberOfExternalNodes() != 5 ) {
7294 t2.deleteSubtree( t2.getNode( "abc" ), false );
7295 t2.toNewHampshireX();
7296 if ( t2.getNumberOfExternalNodes() != 3 ) {
7299 t2.deleteSubtree( t2.getNode( "def" ), false );
7300 t2.toNewHampshireX();
7301 if ( t2.getNumberOfExternalNodes() != 1 ) {
7305 catch ( final Exception e ) {
7306 e.printStackTrace( System.out );
7312 private static boolean testSupportCount() {
7314 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7315 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7316 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7317 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7318 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7319 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7320 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7322 SupportCount.count( t0_1, phylogenies_1, true, false );
7323 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7324 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7325 + "(((((A,B),C),D),E),((F,G),X))"
7326 + "(((((A,Y),B),C),D),((F,G),E))"
7327 + "(((((A,B),C),D),E),(F,G))"
7328 + "(((((A,B),C),D),E),(F,G))"
7329 + "(((((A,B),C),D),E),(F,G))"
7330 + "(((((A,B),C),D),E),(F,G),Z)"
7331 + "(((((A,B),C),D),E),(F,G))"
7332 + "((((((A,B),C),D),E),F),G)"
7333 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7335 SupportCount.count( t0_2, phylogenies_2, true, false );
7336 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7337 while ( it.hasNext() ) {
7338 final PhylogenyNode n = it.next();
7339 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7343 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7344 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7345 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7346 SupportCount.count( t0_3, phylogenies_3, true, false );
7347 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7348 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7351 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7354 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7357 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7360 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7363 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7366 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7369 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7372 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7375 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7378 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7379 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7380 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7381 SupportCount.count( t0_4, phylogenies_4, true, false );
7382 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7383 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7386 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7389 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7392 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7395 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7398 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7401 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7404 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7407 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7410 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7413 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7414 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7415 double d = SupportCount.compare( b1, a, true, true, true );
7416 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7419 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7420 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7421 d = SupportCount.compare( b2, a, true, true, true );
7422 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7425 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7426 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7427 d = SupportCount.compare( b3, a, true, true, true );
7428 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7431 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7432 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7433 d = SupportCount.compare( b4, a, true, true, false );
7434 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7438 catch ( final Exception e ) {
7439 e.printStackTrace( System.out );
7445 private static boolean testSupportTransfer() {
7447 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7448 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)",
7449 new NHXParser() )[ 0 ];
7450 final Phylogeny p2 = factory
7451 .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 ];
7452 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7455 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7458 support_transfer.moveBranchLengthsToBootstrap( p1 );
7459 support_transfer.transferSupportValues( p1, p2 );
7460 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7463 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7466 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7469 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7472 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7475 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7478 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7481 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7485 catch ( final Exception e ) {
7486 e.printStackTrace( System.out );
7492 private static boolean testTaxonomyAssigner() {
7494 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]";
7495 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7496 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7497 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7498 s0.setRooted( true );
7499 g0.setRooted( true );
7500 TaxonomyAssigner.execute( g0, s0 );
7501 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7504 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7507 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7510 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7511 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7512 g0.setRooted( true );
7513 TaxonomyAssigner.execute( g0, s0 );
7514 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7517 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7520 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7523 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7524 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7525 g0.setRooted( true );
7526 TaxonomyAssigner.execute( g0, s0 );
7527 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7530 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7533 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7536 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7537 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7538 g0.setRooted( true );
7539 TaxonomyAssigner.execute( g0, s0 );
7540 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7543 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7546 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7549 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7550 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7551 g0.setRooted( true );
7552 TaxonomyAssigner.execute( g0, s0 );
7553 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7556 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7559 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7562 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7563 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7564 g0.setRooted( true );
7565 TaxonomyAssigner.execute( g0, s0 );
7566 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7569 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7572 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7575 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7576 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7577 g0.setRooted( true );
7578 TaxonomyAssigner.execute( g0, s0 );
7579 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7582 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7585 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7588 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7589 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7590 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7591 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7592 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7593 s0.setRooted( true );
7594 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7595 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7596 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7597 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7598 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7599 g0.setRooted( true );
7600 TaxonomyAssigner.execute( g0, s0 );
7601 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7604 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7607 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7610 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7613 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7616 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7617 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7618 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7619 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7620 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7621 g0.setRooted( true );
7622 TaxonomyAssigner.execute( g0, s0 );
7623 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7626 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7629 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7632 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7635 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7638 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7639 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7640 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7641 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7642 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7643 g0.setRooted( true );
7644 TaxonomyAssigner.execute( g0, s0 );
7645 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7648 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7651 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7654 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7657 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7660 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7661 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7662 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7663 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7664 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7665 g0.setRooted( true );
7666 TaxonomyAssigner.execute( g0, s0 );
7667 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7670 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7673 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7676 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7679 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7682 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7683 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7684 g0.setRooted( true );
7685 TaxonomyAssigner.execute( g0, s0 );
7686 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7689 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7692 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7695 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7696 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7697 g0.setRooted( true );
7698 TaxonomyAssigner.execute( g0, s0 );
7699 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7702 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7705 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7708 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7709 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7710 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7711 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7712 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7713 g0.setRooted( true );
7714 TaxonomyAssigner.execute( g0, s0 );
7715 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7718 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7721 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7724 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7727 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7730 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7733 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7736 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7737 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7738 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7739 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7740 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7741 g0.setRooted( true );
7742 TaxonomyAssigner.execute( g0, s0 );
7743 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7746 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7749 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7752 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7755 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7758 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7761 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7764 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7765 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7766 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7767 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7768 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7769 g0.setRooted( true );
7770 TaxonomyAssigner.execute( g0, s0 );
7771 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7774 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7777 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7780 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7783 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7786 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7789 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7792 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7793 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7794 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7795 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7796 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7797 g0.setRooted( true );
7798 TaxonomyAssigner.execute( g0, s0 );
7799 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7802 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7805 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7808 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7811 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7814 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7817 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7820 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7821 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7822 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7823 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7824 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7825 s0.setRooted( true );
7826 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7827 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7828 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7829 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7830 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7831 g0.setRooted( true );
7832 TaxonomyAssigner.execute( g0, s0 );
7833 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7836 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7840 catch ( final Exception e ) {
7841 e.printStackTrace( System.out );
7847 private static boolean testUniprotTaxonomySearch() {
7849 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7851 if ( results.size() != 1 ) {
7854 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7857 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7860 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7863 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7866 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7870 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7871 if ( results.size() != 1 ) {
7874 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7877 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7880 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7883 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7886 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7890 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7891 if ( results.size() != 1 ) {
7894 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7897 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7900 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7903 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7906 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7910 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7911 if ( results.size() != 1 ) {
7914 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7917 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7920 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7923 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7926 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7929 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7932 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7935 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7936 .equals( "Nematostella vectensis" ) ) {
7937 System.out.println( results.get( 0 ).getLineage() );
7941 catch ( final IOException e ) {
7942 System.out.println();
7943 System.out.println( "the following might be due to absence internet connection:" );
7944 e.printStackTrace( System.out );
7947 catch ( final Exception e ) {
7953 private static boolean testEmblEntryRetrieval() {
7954 //The format for GenBank Accession numbers are:
7955 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7956 //Protein: 3 letters + 5 numerals
7957 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7958 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7961 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7964 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7967 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7970 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7973 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7976 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7979 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7982 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7985 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7988 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7991 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7994 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8000 private static boolean testUniprotEntryRetrieval() {
8001 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8004 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8007 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8010 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8013 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8016 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8019 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8022 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8025 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8028 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8031 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8034 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8037 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8041 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8042 if ( !entry.getAccession().equals( "P12345" ) ) {
8045 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8048 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8051 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8054 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8058 catch ( final IOException e ) {
8059 System.out.println();
8060 System.out.println( "the following might be due to absence internet connection:" );
8061 e.printStackTrace( System.out );
8064 catch ( final Exception e ) {
8070 private static boolean testWabiTxSearch() {
8073 result = TxSearch.searchSimple( "nematostella" );
8074 result = TxSearch.getTxId( "nematostella" );
8075 if ( !result.equals( "45350" ) ) {
8078 result = TxSearch.getTxName( "45350" );
8079 if ( !result.equals( "Nematostella" ) ) {
8082 result = TxSearch.getTxId( "nematostella vectensis" );
8083 if ( !result.equals( "45351" ) ) {
8086 result = TxSearch.getTxName( "45351" );
8087 if ( !result.equals( "Nematostella vectensis" ) ) {
8090 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8091 if ( !result.equals( "536089" ) ) {
8094 result = TxSearch.getTxName( "536089" );
8095 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8098 final List<String> queries = new ArrayList<String>();
8099 queries.add( "Campylobacter coli" );
8100 queries.add( "Escherichia coli" );
8101 queries.add( "Arabidopsis" );
8102 queries.add( "Trichoplax" );
8103 queries.add( "Samanea saman" );
8104 queries.add( "Kluyveromyces marxianus" );
8105 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8106 queries.add( "Bornavirus parrot/PDD/2008" );
8107 final List<RANKS> ranks = new ArrayList<RANKS>();
8108 ranks.add( RANKS.SUPERKINGDOM );
8109 ranks.add( RANKS.KINGDOM );
8110 ranks.add( RANKS.FAMILY );
8111 ranks.add( RANKS.GENUS );
8112 ranks.add( RANKS.TRIBE );
8113 result = TxSearch.searchLineage( queries, ranks );
8114 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8115 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8117 catch ( final Exception e ) {
8118 System.out.println();
8119 System.out.println( "the following might be due to absence internet connection:" );
8120 e.printStackTrace( System.out );
8126 private static boolean testAminoAcidSequence() {
8128 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8129 if ( aa1.getLength() != 13 ) {
8132 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8135 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8138 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8141 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8142 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8145 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8146 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8149 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8150 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8154 catch ( final Exception e ) {
8155 e.printStackTrace();
8161 private static boolean testCreateBalancedPhylogeny() {
8163 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8164 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8167 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8170 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8171 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8174 if ( p1.getNumberOfExternalNodes() != 100 ) {
8178 catch ( final Exception e ) {
8179 e.printStackTrace();
8185 private static boolean testFastaParser() {
8187 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8190 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8193 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8194 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8197 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8200 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8203 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8206 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8209 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8213 catch ( final Exception e ) {
8214 e.printStackTrace();
8220 private static boolean testGeneralMsaParser() {
8222 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8223 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8224 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8225 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8226 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8227 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8228 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8229 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8230 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8233 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8236 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8239 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8242 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8245 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8248 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8251 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8254 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8257 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8260 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8263 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8266 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8267 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8270 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8273 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8276 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8277 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8280 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8283 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8286 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8287 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8290 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8293 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8297 catch ( final Exception e ) {
8298 e.printStackTrace();
8304 private static boolean testMafft() {
8306 final List<String> opts = new ArrayList<String>();
8307 opts.add( "--maxiterate" );
8309 opts.add( "--localpair" );
8310 opts.add( "--quiet" );
8312 final MsaInferrer mafft = Mafft.createInstance();
8313 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8314 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8317 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8321 catch ( final Exception e ) {
8322 e.printStackTrace( System.out );
8328 private static boolean testNextNodeWithCollapsing() {
8330 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8332 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8333 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8334 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8335 t0.getNode( "cd" ).setCollapse( true );
8336 t0.getNode( "cde" ).setCollapse( true );
8337 n = t0.getFirstExternalNode();
8338 while ( n != null ) {
8340 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8342 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8345 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8348 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8351 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8354 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8357 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8361 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8362 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8363 t1.getNode( "ab" ).setCollapse( true );
8364 t1.getNode( "cd" ).setCollapse( true );
8365 t1.getNode( "cde" ).setCollapse( true );
8366 n = t1.getNode( "ab" );
8367 ext = new ArrayList<PhylogenyNode>();
8368 while ( n != null ) {
8370 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8372 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8375 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8378 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8381 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8384 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8390 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8391 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8392 t2.getNode( "ab" ).setCollapse( true );
8393 t2.getNode( "cd" ).setCollapse( true );
8394 t2.getNode( "cde" ).setCollapse( true );
8395 t2.getNode( "c" ).setCollapse( true );
8396 t2.getNode( "d" ).setCollapse( true );
8397 t2.getNode( "e" ).setCollapse( true );
8398 t2.getNode( "gh" ).setCollapse( true );
8399 n = t2.getNode( "ab" );
8400 ext = new ArrayList<PhylogenyNode>();
8401 while ( n != null ) {
8403 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8405 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8408 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8411 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8414 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8420 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8421 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8422 t3.getNode( "ab" ).setCollapse( true );
8423 t3.getNode( "cd" ).setCollapse( true );
8424 t3.getNode( "cde" ).setCollapse( true );
8425 t3.getNode( "c" ).setCollapse( true );
8426 t3.getNode( "d" ).setCollapse( true );
8427 t3.getNode( "e" ).setCollapse( true );
8428 t3.getNode( "gh" ).setCollapse( true );
8429 t3.getNode( "fgh" ).setCollapse( true );
8430 n = t3.getNode( "ab" );
8431 ext = new ArrayList<PhylogenyNode>();
8432 while ( n != null ) {
8434 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8436 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8439 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8442 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8448 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8449 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8450 t4.getNode( "ab" ).setCollapse( true );
8451 t4.getNode( "cd" ).setCollapse( true );
8452 t4.getNode( "cde" ).setCollapse( true );
8453 t4.getNode( "c" ).setCollapse( true );
8454 t4.getNode( "d" ).setCollapse( true );
8455 t4.getNode( "e" ).setCollapse( true );
8456 t4.getNode( "gh" ).setCollapse( true );
8457 t4.getNode( "fgh" ).setCollapse( true );
8458 t4.getNode( "abcdefgh" ).setCollapse( true );
8459 n = t4.getNode( "abcdefgh" );
8460 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8465 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8466 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8468 n = t5.getFirstExternalNode();
8469 while ( n != null ) {
8471 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8473 if ( ext.size() != 8 ) {
8476 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8479 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8482 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8485 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8488 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8491 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8494 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8497 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8502 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8503 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8505 t6.getNode( "ab" ).setCollapse( true );
8506 n = t6.getNode( "ab" );
8507 while ( n != null ) {
8509 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8511 if ( ext.size() != 7 ) {
8514 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8517 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8520 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8523 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8526 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8529 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8532 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8537 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8538 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8540 t7.getNode( "cd" ).setCollapse( true );
8541 n = t7.getNode( "a" );
8542 while ( n != null ) {
8544 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8546 if ( ext.size() != 7 ) {
8549 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8552 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8555 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8558 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8561 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8564 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8567 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8572 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8573 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8575 t8.getNode( "cd" ).setCollapse( true );
8576 t8.getNode( "c" ).setCollapse( true );
8577 t8.getNode( "d" ).setCollapse( true );
8578 n = t8.getNode( "a" );
8579 while ( n != null ) {
8581 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8583 if ( ext.size() != 7 ) {
8586 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8589 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8592 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8593 System.out.println( "2 fail" );
8596 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8599 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8602 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8605 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8610 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8611 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8613 t9.getNode( "gh" ).setCollapse( true );
8614 n = t9.getNode( "a" );
8615 while ( n != null ) {
8617 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8619 if ( ext.size() != 7 ) {
8622 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8625 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8628 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8631 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8634 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8637 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8640 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8645 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8646 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8648 t10.getNode( "gh" ).setCollapse( true );
8649 t10.getNode( "g" ).setCollapse( true );
8650 t10.getNode( "h" ).setCollapse( true );
8651 n = t10.getNode( "a" );
8652 while ( n != null ) {
8654 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8656 if ( ext.size() != 7 ) {
8659 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8662 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8665 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8668 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8671 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8674 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8677 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8682 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8683 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8685 t11.getNode( "gh" ).setCollapse( true );
8686 t11.getNode( "fgh" ).setCollapse( true );
8687 n = t11.getNode( "a" );
8688 while ( n != null ) {
8690 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8692 if ( ext.size() != 6 ) {
8695 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8698 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8701 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8704 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8707 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8710 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8715 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8716 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8718 t12.getNode( "gh" ).setCollapse( true );
8719 t12.getNode( "fgh" ).setCollapse( true );
8720 t12.getNode( "g" ).setCollapse( true );
8721 t12.getNode( "h" ).setCollapse( true );
8722 t12.getNode( "f" ).setCollapse( true );
8723 n = t12.getNode( "a" );
8724 while ( n != null ) {
8726 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8728 if ( ext.size() != 6 ) {
8731 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8734 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8737 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8740 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8743 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8746 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8751 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8752 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8754 t13.getNode( "ab" ).setCollapse( true );
8755 t13.getNode( "b" ).setCollapse( true );
8756 t13.getNode( "fgh" ).setCollapse( true );
8757 t13.getNode( "gh" ).setCollapse( true );
8758 n = t13.getNode( "ab" );
8759 while ( n != null ) {
8761 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8763 if ( ext.size() != 5 ) {
8766 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8769 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8772 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8775 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8778 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8783 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8784 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8786 t14.getNode( "ab" ).setCollapse( true );
8787 t14.getNode( "a" ).setCollapse( true );
8788 t14.getNode( "fgh" ).setCollapse( true );
8789 t14.getNode( "gh" ).setCollapse( true );
8790 n = t14.getNode( "ab" );
8791 while ( n != null ) {
8793 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8795 if ( ext.size() != 5 ) {
8798 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8801 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8804 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8807 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8810 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8815 final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8816 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8818 t15.getNode( "ab" ).setCollapse( true );
8819 t15.getNode( "a" ).setCollapse( true );
8820 t15.getNode( "fgh" ).setCollapse( true );
8821 t15.getNode( "gh" ).setCollapse( true );
8822 n = t15.getNode( "ab" );
8823 while ( n != null ) {
8825 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8827 if ( ext.size() != 6 ) {
8830 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8833 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8836 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8839 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8842 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8845 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8850 final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8851 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8853 t16.getNode( "ab" ).setCollapse( true );
8854 t16.getNode( "a" ).setCollapse( true );
8855 t16.getNode( "fgh" ).setCollapse( true );
8856 t16.getNode( "gh" ).setCollapse( true );
8857 t16.getNode( "cd" ).setCollapse( true );
8858 t16.getNode( "cde" ).setCollapse( true );
8859 t16.getNode( "d" ).setCollapse( true );
8860 t16.getNode( "x" ).setCollapse( true );
8861 n = t16.getNode( "ab" );
8862 while ( n != null ) {
8864 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8866 if ( ext.size() != 4 ) {
8869 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8872 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8875 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8878 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8882 catch ( final Exception e ) {
8883 e.printStackTrace( System.out );
8889 private static boolean testMsaQualityMethod() {
8891 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8892 final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
8893 final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
8894 final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
8895 final List<Sequence> l = new ArrayList<Sequence>();
8900 final Msa msa = BasicMsa.createInstance( l );
8901 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8904 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8907 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8910 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8914 catch ( final Exception e ) {
8915 e.printStackTrace( System.out );
8921 private static boolean testSequenceIdParsing() {
8923 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8924 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8925 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8927 System.out.println( "value =" + id.getValue() );
8928 System.out.println( "provider=" + id.getProvider() );
8933 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8934 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8935 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8937 System.out.println( "value =" + id.getValue() );
8938 System.out.println( "provider=" + id.getProvider() );
8943 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8944 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8945 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8947 System.out.println( "value =" + id.getValue() );
8948 System.out.println( "provider=" + id.getProvider() );
8953 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8954 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8955 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8957 System.out.println( "value =" + id.getValue() );
8958 System.out.println( "provider=" + id.getProvider() );
8963 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8964 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8965 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8967 System.out.println( "value =" + id.getValue() );
8968 System.out.println( "provider=" + id.getProvider() );
8973 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8974 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8975 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8977 System.out.println( "value =" + id.getValue() );
8978 System.out.println( "provider=" + id.getProvider() );
8983 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8984 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8985 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8987 System.out.println( "value =" + id.getValue() );
8988 System.out.println( "provider=" + id.getProvider() );
8993 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8994 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8995 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8997 System.out.println( "value =" + id.getValue() );
8998 System.out.println( "provider=" + id.getProvider() );
9003 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9004 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9005 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9007 System.out.println( "value =" + id.getValue() );
9008 System.out.println( "provider=" + id.getProvider() );
9013 id = SequenceIdParser.parse( "XP_12345" );
9017 // lcl_91970_unknown_
9019 catch ( final Exception e ) {
9020 e.printStackTrace( System.out );