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.uniprot.DatabaseTools;
108 import org.forester.ws.uniprot.SequenceDatabaseEntry;
109 import org.forester.ws.uniprot.UniProtTaxonomy;
110 import org.forester.ws.uniprot.UniProtWsTools;
111 import org.forester.ws.wabi.TxSearch;
112 import org.forester.ws.wabi.TxSearch.RANKS;
113 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
114 import org.forester.ws.wabi.TxSearch.TAX_RANK;
116 @SuppressWarnings( "unused")
117 public final class Test {
119 private final static double ZERO_DIFF = 1.0E-9;
120 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "test_data"
122 + ForesterUtil.getFileSeparator();
123 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "resources"
125 + ForesterUtil.getFileSeparator();
126 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
127 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
130 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
134 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
135 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
139 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
140 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
141 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
144 public static boolean isEqual( final double a, final double b ) {
145 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
148 public static void main( final String[] args ) {
149 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
150 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
152 Locale.setDefault( Locale.US );
153 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
156 System.out.print( "[Test if directory with files for testing exists/is readable: " );
157 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
158 System.out.println( "OK.]" );
161 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
162 System.out.println( "Testing aborted." );
165 System.out.print( "[Test if resources directory exists/is readable: " );
166 if ( testDir( PATH_TO_RESOURCES ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
171 System.out.println( "Testing aborted." );
174 final long start_time = new Date().getTime();
178 System.out.print( "Sequence id parsing: " );
179 if ( testSequenceIdParsing() ) {
180 System.out.println( "OK." );
184 System.out.println( "failed." );
185 System.exit( -1 ); //TODO FIXME remove me!! ~
188 System.out.print( "Hmmscan output parser: " );
189 if ( testHmmscanOutputParser() ) {
190 System.out.println( "OK." );
194 System.out.println( "failed." );
197 System.out.print( "Basic node methods: " );
198 if ( Test.testBasicNodeMethods() ) {
199 System.out.println( "OK." );
203 System.out.println( "failed." );
206 System.out.print( "Basic node construction and parsing of NHX (node level): " );
207 if ( Test.testNHXNodeParsing() ) {
208 System.out.println( "OK." );
212 System.out.println( "failed." );
215 System.out.print( "NH parsing: " );
216 if ( Test.testNHParsing() ) {
217 System.out.println( "OK." );
221 System.out.println( "failed." );
224 System.out.print( "Conversion to NHX (node level): " );
225 if ( Test.testNHXconversion() ) {
226 System.out.println( "OK." );
230 System.out.println( "failed." );
233 System.out.print( "NHX parsing: " );
234 if ( Test.testNHXParsing() ) {
235 System.out.println( "OK." );
239 System.out.println( "failed." );
242 System.out.print( "NHX parsing with quotes: " );
243 if ( Test.testNHXParsingQuotes() ) {
244 System.out.println( "OK." );
248 System.out.println( "failed." );
251 System.out.print( "NHX parsing (MrBayes): " );
252 if ( Test.testNHXParsingMB() ) {
253 System.out.println( "OK." );
257 System.out.println( "failed." );
260 System.out.print( "Nexus characters parsing: " );
261 if ( Test.testNexusCharactersParsing() ) {
262 System.out.println( "OK." );
266 System.out.println( "failed." );
269 System.out.print( "Nexus tree parsing: " );
270 if ( Test.testNexusTreeParsing() ) {
271 System.out.println( "OK." );
275 System.out.println( "failed." );
278 System.out.print( "Nexus tree parsing (translating): " );
279 if ( Test.testNexusTreeParsingTranslating() ) {
280 System.out.println( "OK." );
284 System.out.println( "failed." );
287 System.out.print( "Nexus matrix parsing: " );
288 if ( Test.testNexusMatrixParsing() ) {
289 System.out.println( "OK." );
293 System.out.println( "failed." );
296 System.out.print( "Basic phyloXML parsing: " );
297 if ( Test.testBasicPhyloXMLparsing() ) {
298 System.out.println( "OK." );
302 System.out.println( "failed." );
305 System.out.print( "Basic phyloXML parsing (validating against schema): " );
306 if ( testBasicPhyloXMLparsingValidating() ) {
307 System.out.println( "OK." );
311 System.out.println( "failed." );
314 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
315 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
316 System.out.println( "OK." );
320 System.out.println( "failed." );
323 System.out.print( "phyloXML Distribution Element: " );
324 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
325 System.out.println( "OK." );
329 System.out.println( "failed." );
332 System.out.print( "Tol XML parsing: " );
333 if ( Test.testBasicTolXMLparsing() ) {
334 System.out.println( "OK." );
338 System.out.println( "failed." );
341 System.out.print( "Copying of node data: " );
342 if ( Test.testCopyOfNodeData() ) {
343 System.out.println( "OK." );
347 System.out.println( "failed." );
350 System.out.print( "Basic tree methods: " );
351 if ( Test.testBasicTreeMethods() ) {
352 System.out.println( "OK." );
356 System.out.println( "failed." );
359 System.out.print( "Postorder Iterator: " );
360 if ( Test.testPostOrderIterator() ) {
361 System.out.println( "OK." );
365 System.out.println( "failed." );
368 System.out.print( "Preorder Iterator: " );
369 if ( Test.testPreOrderIterator() ) {
370 System.out.println( "OK." );
374 System.out.println( "failed." );
377 System.out.print( "Levelorder Iterator: " );
378 if ( Test.testLevelOrderIterator() ) {
379 System.out.println( "OK." );
383 System.out.println( "failed." );
386 System.out.print( "Re-id methods: " );
387 if ( Test.testReIdMethods() ) {
388 System.out.println( "OK." );
392 System.out.println( "failed." );
395 System.out.print( "Methods on last external nodes: " );
396 if ( Test.testLastExternalNodeMethods() ) {
397 System.out.println( "OK." );
401 System.out.println( "failed." );
404 System.out.print( "Methods on external nodes: " );
405 if ( Test.testExternalNodeRelatedMethods() ) {
406 System.out.println( "OK." );
410 System.out.println( "failed." );
413 System.out.print( "Deletion of external nodes: " );
414 if ( Test.testDeletionOfExternalNodes() ) {
415 System.out.println( "OK." );
419 System.out.println( "failed." );
422 System.out.print( "Subtree deletion: " );
423 if ( Test.testSubtreeDeletion() ) {
424 System.out.println( "OK." );
428 System.out.println( "failed." );
431 System.out.print( "Phylogeny branch: " );
432 if ( Test.testPhylogenyBranch() ) {
433 System.out.println( "OK." );
437 System.out.println( "failed." );
440 System.out.print( "Rerooting: " );
441 if ( Test.testRerooting() ) {
442 System.out.println( "OK." );
446 System.out.println( "failed." );
449 System.out.print( "Mipoint rooting: " );
450 if ( Test.testMidpointrooting() ) {
451 System.out.println( "OK." );
455 System.out.println( "failed." );
458 System.out.print( "Support count: " );
459 if ( Test.testSupportCount() ) {
460 System.out.println( "OK." );
464 System.out.println( "failed." );
467 System.out.print( "Support transfer: " );
468 if ( Test.testSupportTransfer() ) {
469 System.out.println( "OK." );
473 System.out.println( "failed." );
476 System.out.print( "Finding of LCA: " );
477 if ( Test.testGetLCA() ) {
478 System.out.println( "OK." );
482 System.out.println( "failed." );
485 System.out.print( "Calculation of distance between nodes: " );
486 if ( Test.testGetDistance() ) {
487 System.out.println( "OK." );
491 System.out.println( "failed." );
494 System.out.print( "SDIse: " );
495 if ( Test.testSDIse() ) {
496 System.out.println( "OK." );
500 System.out.println( "failed." );
503 System.out.print( "Taxonomy assigner: " );
504 if ( Test.testTaxonomyAssigner() ) {
505 System.out.println( "OK." );
509 System.out.println( "failed." );
512 System.out.print( "SDIunrooted: " );
513 if ( Test.testSDIunrooted() ) {
514 System.out.println( "OK." );
518 System.out.println( "failed." );
521 System.out.print( "GSDI: " );
522 if ( TestGSDI.test() ) {
523 System.out.println( "OK." );
527 System.out.println( "failed." );
530 System.out.print( "Descriptive statistics: " );
531 if ( Test.testDescriptiveStatistics() ) {
532 System.out.println( "OK." );
536 System.out.println( "failed." );
539 System.out.print( "Data objects and methods: " );
540 if ( Test.testDataObjects() ) {
541 System.out.println( "OK." );
545 System.out.println( "failed." );
548 System.out.print( "Properties map: " );
549 if ( Test.testPropertiesMap() ) {
550 System.out.println( "OK." );
554 System.out.println( "failed." );
557 System.out.print( "Phylogeny reconstruction:" );
558 System.out.println();
559 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
560 System.out.println( "OK." );
564 System.out.println( "failed." );
567 System.out.print( "Analysis of domain architectures: " );
568 System.out.println();
569 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
570 System.out.println( "OK." );
574 System.out.println( "failed." );
577 System.out.print( "GO: " );
578 System.out.println();
579 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
580 System.out.println( "OK." );
584 System.out.println( "failed." );
587 System.out.print( "Modeling tools: " );
588 if ( TestPccx.test() ) {
589 System.out.println( "OK." );
593 System.out.println( "failed." );
596 System.out.print( "Split Matrix strict: " );
597 if ( Test.testSplitStrict() ) {
598 System.out.println( "OK." );
602 System.out.println( "failed." );
605 System.out.print( "Split Matrix: " );
606 if ( Test.testSplit() ) {
607 System.out.println( "OK." );
611 System.out.println( "failed." );
614 System.out.print( "Confidence Assessor: " );
615 if ( Test.testConfidenceAssessor() ) {
616 System.out.println( "OK." );
620 System.out.println( "failed." );
623 System.out.print( "Basic table: " );
624 if ( Test.testBasicTable() ) {
625 System.out.println( "OK." );
629 System.out.println( "failed." );
632 System.out.print( "General table: " );
633 if ( Test.testGeneralTable() ) {
634 System.out.println( "OK." );
638 System.out.println( "failed." );
641 System.out.print( "Amino acid sequence: " );
642 if ( Test.testAminoAcidSequence() ) {
643 System.out.println( "OK." );
647 System.out.println( "failed." );
650 System.out.print( "General MSA parser: " );
651 if ( Test.testGeneralMsaParser() ) {
652 System.out.println( "OK." );
656 System.out.println( "failed." );
659 System.out.print( "Fasta parser for msa: " );
660 if ( Test.testFastaParser() ) {
661 System.out.println( "OK." );
665 System.out.println( "failed." );
668 System.out.print( "Creation of balanced phylogeny: " );
669 if ( Test.testCreateBalancedPhylogeny() ) {
670 System.out.println( "OK." );
674 System.out.println( "failed." );
677 System.out.print( "EMBL Entry Retrieval: " );
678 if ( Test.testEmblEntryRetrieval() ) {
679 System.out.println( "OK." );
683 System.out.println( "failed." );
686 System.out.print( "Uniprot Entry Retrieval: " );
687 if ( Test.testUniprotEntryRetrieval() ) {
688 System.out.println( "OK." );
692 System.out.println( "failed." );
695 System.out.print( "Uniprot Taxonomy Search: " );
696 if ( Test.testUniprotTaxonomySearch() ) {
697 System.out.println( "OK." );
701 System.out.println( "failed." );
704 if ( Mafft.isInstalled() ) {
705 System.out.print( "MAFFT (external program): " );
706 if ( Test.testMafft() ) {
707 System.out.println( "OK." );
711 System.out.println( "failed [will not count towards failed tests]" );
714 System.out.print( "Next nodes with collapsed: " );
715 if ( Test.testNextNodeWithCollapsing() ) {
716 System.out.println( "OK." );
720 System.out.println( "failed." );
723 System.out.print( "Simple MSA quality: " );
724 if ( Test.testMsaQualityMethod() ) {
725 System.out.println( "OK." );
729 System.out.println( "failed." );
732 // System.out.print( "WABI TxSearch: " );
733 // if ( Test.testWabiTxSearch() ) {
734 // System.out.println( "OK." );
739 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
741 System.out.println();
742 final Runtime rt = java.lang.Runtime.getRuntime();
743 final long free_memory = rt.freeMemory() / 1000000;
744 final long total_memory = rt.totalMemory() / 1000000;
745 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
746 + free_memory + "MB, total memory: " + total_memory + "MB)" );
747 System.out.println();
748 System.out.println( "Successful tests: " + succeeded );
749 System.out.println( "Failed tests: " + failed );
750 System.out.println();
752 System.out.println( "OK." );
755 System.out.println( "Not OK." );
757 // System.out.println();
758 // Development.setTime( true );
760 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
761 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
762 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
763 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
764 // "multifurcations_ex_1.nhx";
765 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
766 // final Phylogeny t1 = factory.create( new File( domains ), new
767 // NHXParser() )[ 0 ];
768 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
770 // catch ( final Exception e ) {
771 // e.printStackTrace();
773 // t1.getRoot().preorderPrint();
774 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
778 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
779 // + "\\AtNBSpos.nhx" ) );
781 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
782 // new NHXParser() );
783 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
784 // + "\\AtNBSpos.nhx" ) );
786 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
787 // new NHXParser() );
790 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
791 // + "\\big_tree.nhx" ) );
792 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
793 // + "\\big_tree.nhx" ) );
795 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
796 // new NHXParser() );
798 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
799 // new NHXParser() );
801 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
802 // + "\\big_tree.nhx" ) );
803 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
804 // + "\\big_tree.nhx" ) );
807 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
808 // new NHXParser() );
810 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
811 // new NHXParser() );
813 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
814 // + "\\AtNBSpos.nhx" ) );
816 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
817 // new NHXParser() );
820 // catch ( IOException e ) {
821 // // TODO Auto-generated catch block
822 // e.printStackTrace();
826 private static boolean testBasicNodeMethods() {
828 if ( PhylogenyNode.getNodeCount() != 0 ) {
831 final PhylogenyNode n1 = new PhylogenyNode();
832 final PhylogenyNode n2 = PhylogenyNode
833 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
834 final PhylogenyNode n3 = PhylogenyNode
835 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
836 final PhylogenyNode n4 = PhylogenyNode
837 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
838 if ( n1.isHasAssignedEvent() ) {
841 if ( PhylogenyNode.getNodeCount() != 4 ) {
844 if ( n3.getIndicator() != 0 ) {
847 if ( n3.getNumberOfExternalNodes() != 1 ) {
850 if ( !n3.isExternal() ) {
853 if ( !n3.isRoot() ) {
856 if ( !n4.getName().equals( "n4" ) ) {
860 catch ( final Exception e ) {
861 e.printStackTrace( System.out );
867 private static boolean testBasicPhyloXMLparsing() {
869 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
870 final PhyloXmlParser xml_parser = new PhyloXmlParser();
871 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
873 if ( xml_parser.getErrorCount() > 0 ) {
874 System.out.println( xml_parser.getErrorMessages().toString() );
877 if ( phylogenies_0.length != 4 ) {
880 final Phylogeny t1 = phylogenies_0[ 0 ];
881 final Phylogeny t2 = phylogenies_0[ 1 ];
882 final Phylogeny t3 = phylogenies_0[ 2 ];
883 final Phylogeny t4 = phylogenies_0[ 3 ];
884 if ( t1.getNumberOfExternalNodes() != 1 ) {
887 if ( !t1.isRooted() ) {
890 if ( t1.isRerootable() ) {
893 if ( !t1.getType().equals( "gene_tree" ) ) {
896 if ( t2.getNumberOfExternalNodes() != 2 ) {
899 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
902 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
905 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
908 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
911 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
914 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
917 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
918 .startsWith( "actgtgggggt" ) ) {
921 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
922 .startsWith( "ctgtgatgcat" ) ) {
925 if ( t3.getNumberOfExternalNodes() != 4 ) {
928 if ( !t1.getName().equals( "t1" ) ) {
931 if ( !t2.getName().equals( "t2" ) ) {
934 if ( !t3.getName().equals( "t3" ) ) {
937 if ( !t4.getName().equals( "t4" ) ) {
940 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
943 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
946 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
949 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
950 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
953 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
956 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
959 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
962 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
963 .equals( "apoptosis" ) ) {
966 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
967 .equals( "GO:0006915" ) ) {
970 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
971 .equals( "UniProtKB" ) ) {
974 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
975 .equals( "experimental" ) ) {
978 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
979 .equals( "function" ) ) {
982 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
986 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
987 .getType().equals( "ml" ) ) {
990 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
991 .equals( "apoptosis" ) ) {
994 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
995 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
998 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
999 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1002 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1003 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1006 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1007 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1010 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1011 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1014 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1015 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1018 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1019 .equals( "GO:0005829" ) ) {
1022 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1023 .equals( "intracellular organelle" ) ) {
1026 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1029 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1030 .equals( "UniProt link" ) ) ) {
1033 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1036 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1039 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1042 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1045 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1048 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1051 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1054 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1057 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1060 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1063 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1064 // .equals( "B" ) ) {
1067 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1070 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1073 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1076 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1077 // .getConfidence() != 2144 ) {
1080 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1081 // .equals( "pfam" ) ) {
1084 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1087 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1090 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1093 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1096 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1097 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1101 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1104 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1107 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1110 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1113 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1116 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1119 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1122 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1124 // if ( xml_parser.getErrorCount() > 0 ) {
1125 // System.out.println( xml_parser.getErrorMessages().toString() );
1128 // if ( phylogenies_1.length != 2 ) {
1131 // final Phylogeny a = phylogenies_1[ 0 ];
1132 // if ( !a.getName().equals( "tree 4" ) ) {
1135 // if ( a.getNumberOfExternalNodes() != 3 ) {
1138 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1141 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1145 catch ( final Exception e ) {
1146 e.printStackTrace( System.out );
1152 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1154 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1155 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1156 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1157 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1160 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1162 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1164 if ( xml_parser.getErrorCount() > 0 ) {
1165 System.out.println( xml_parser.getErrorMessages().toString() );
1168 if ( phylogenies_0.length != 4 ) {
1171 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1172 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1173 if ( phylogenies_t1.length != 1 ) {
1176 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1177 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1180 if ( !t1_rt.isRooted() ) {
1183 if ( t1_rt.isRerootable() ) {
1186 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1189 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1190 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1191 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1192 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1195 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1198 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1201 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1204 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1205 .startsWith( "actgtgggggt" ) ) {
1208 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1209 .startsWith( "ctgtgatgcat" ) ) {
1212 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1213 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1214 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1215 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1216 if ( phylogenies_1.length != 1 ) {
1219 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1220 if ( !t3_rt.getName().equals( "t3" ) ) {
1223 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1226 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1229 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1232 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1235 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1236 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1239 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1242 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1245 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1246 .equals( "UniProtKB" ) ) {
1249 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1250 .equals( "apoptosis" ) ) {
1253 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1254 .equals( "GO:0006915" ) ) {
1257 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1258 .equals( "UniProtKB" ) ) {
1261 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1262 .equals( "experimental" ) ) {
1265 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1266 .equals( "function" ) ) {
1269 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1270 .getValue() != 1 ) {
1273 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1274 .getType().equals( "ml" ) ) {
1277 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1278 .equals( "apoptosis" ) ) {
1281 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1282 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1285 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1286 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1289 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1290 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1293 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1294 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1297 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1298 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1301 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1302 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1305 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1306 .equals( "GO:0005829" ) ) {
1309 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1310 .equals( "intracellular organelle" ) ) {
1313 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1316 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1317 .equals( "UniProt link" ) ) ) {
1320 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1323 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1326 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1327 .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." ) ) ) {
1330 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1333 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1336 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1339 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1342 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1343 .equals( "ncbi" ) ) {
1346 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1349 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1350 .getName().equals( "B" ) ) {
1353 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1354 .getFrom() != 21 ) {
1357 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1360 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1361 .getLength() != 24 ) {
1364 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1365 .getConfidence() != 2144 ) {
1368 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1369 .equals( "pfam" ) ) {
1372 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1375 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1378 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1381 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1384 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1385 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1388 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1391 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1394 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1397 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1400 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1403 if ( taxbb.getSynonyms().size() != 2 ) {
1406 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1409 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1412 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1415 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1418 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1421 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1422 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1426 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1429 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1432 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1435 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1438 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1441 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1444 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1448 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1451 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1452 .equalsIgnoreCase( "435" ) ) {
1455 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1458 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1459 .equalsIgnoreCase( "443.7" ) ) {
1462 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1465 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1468 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1469 .equalsIgnoreCase( "433" ) ) {
1473 catch ( final Exception e ) {
1474 e.printStackTrace( System.out );
1480 private static boolean testBasicPhyloXMLparsingValidating() {
1482 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1483 PhyloXmlParser xml_parser = null;
1485 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1487 catch ( final Exception e ) {
1488 // Do nothing -- means were not running from jar.
1490 if ( xml_parser == null ) {
1491 xml_parser = new PhyloXmlParser();
1492 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1493 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1496 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1499 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1501 if ( xml_parser.getErrorCount() > 0 ) {
1502 System.out.println( xml_parser.getErrorMessages().toString() );
1505 if ( phylogenies_0.length != 4 ) {
1508 final Phylogeny t1 = phylogenies_0[ 0 ];
1509 final Phylogeny t2 = phylogenies_0[ 1 ];
1510 final Phylogeny t3 = phylogenies_0[ 2 ];
1511 final Phylogeny t4 = phylogenies_0[ 3 ];
1512 if ( !t1.getName().equals( "t1" ) ) {
1515 if ( !t2.getName().equals( "t2" ) ) {
1518 if ( !t3.getName().equals( "t3" ) ) {
1521 if ( !t4.getName().equals( "t4" ) ) {
1524 if ( t1.getNumberOfExternalNodes() != 1 ) {
1527 if ( t2.getNumberOfExternalNodes() != 2 ) {
1530 if ( t3.getNumberOfExternalNodes() != 4 ) {
1533 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1534 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1535 if ( xml_parser.getErrorCount() > 0 ) {
1536 System.out.println( "errors:" );
1537 System.out.println( xml_parser.getErrorMessages().toString() );
1540 if ( phylogenies_1.length != 4 ) {
1543 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1545 if ( xml_parser.getErrorCount() > 0 ) {
1546 System.out.println( "errors:" );
1547 System.out.println( xml_parser.getErrorMessages().toString() );
1550 if ( phylogenies_2.length != 1 ) {
1553 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1556 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1558 if ( xml_parser.getErrorCount() > 0 ) {
1559 System.out.println( xml_parser.getErrorMessages().toString() );
1562 if ( phylogenies_3.length != 2 ) {
1565 final Phylogeny a = phylogenies_3[ 0 ];
1566 if ( !a.getName().equals( "tree 4" ) ) {
1569 if ( a.getNumberOfExternalNodes() != 3 ) {
1572 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1575 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1578 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1580 if ( xml_parser.getErrorCount() > 0 ) {
1581 System.out.println( xml_parser.getErrorMessages().toString() );
1584 if ( phylogenies_4.length != 1 ) {
1587 final Phylogeny s = phylogenies_4[ 0 ];
1588 if ( s.getNumberOfExternalNodes() != 6 ) {
1591 s.getNode( "first" );
1593 s.getNode( "\"<a'b&c'd\">\"" );
1594 s.getNode( "'''\"" );
1595 s.getNode( "\"\"\"" );
1596 s.getNode( "dick & doof" );
1598 catch ( final Exception e ) {
1599 e.printStackTrace( System.out );
1605 private static boolean testBasicTable() {
1607 final BasicTable<String> t0 = new BasicTable<String>();
1608 if ( t0.getNumberOfColumns() != 0 ) {
1611 if ( t0.getNumberOfRows() != 0 ) {
1614 t0.setValue( 3, 2, "23" );
1615 t0.setValue( 10, 1, "error" );
1616 t0.setValue( 10, 1, "110" );
1617 t0.setValue( 9, 1, "19" );
1618 t0.setValue( 1, 10, "101" );
1619 t0.setValue( 10, 10, "1010" );
1620 t0.setValue( 100, 10, "10100" );
1621 t0.setValue( 0, 0, "00" );
1622 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1625 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1628 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1631 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1634 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1637 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1640 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1643 if ( t0.getNumberOfColumns() != 101 ) {
1646 if ( t0.getNumberOfRows() != 11 ) {
1649 if ( t0.getValueAsString( 49, 4 ) != null ) {
1652 final String l = ForesterUtil.getLineSeparator();
1653 final StringBuffer source = new StringBuffer();
1654 source.append( "" + l );
1655 source.append( "# 1 1 1 1 1 1 1 1" + l );
1656 source.append( " 00 01 02 03" + l );
1657 source.append( " 10 11 12 13 " + l );
1658 source.append( "20 21 22 23 " + l );
1659 source.append( " 30 31 32 33" + l );
1660 source.append( "40 41 42 43" + l );
1661 source.append( " # 1 1 1 1 1 " + l );
1662 source.append( "50 51 52 53 54" + l );
1663 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1664 if ( t1.getNumberOfColumns() != 5 ) {
1667 if ( t1.getNumberOfRows() != 6 ) {
1670 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1673 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1676 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1679 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1682 final StringBuffer source1 = new StringBuffer();
1683 source1.append( "" + l );
1684 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1685 source1.append( " 00; 01 ;02;03" + l );
1686 source1.append( " 10; 11; 12; 13 " + l );
1687 source1.append( "20; 21; 22; 23 " + l );
1688 source1.append( " 30; 31; 32; 33" + l );
1689 source1.append( "40;41;42;43" + l );
1690 source1.append( " # 1 1 1 1 1 " + l );
1691 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1692 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1693 if ( t2.getNumberOfColumns() != 5 ) {
1696 if ( t2.getNumberOfRows() != 6 ) {
1699 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1702 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1705 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1708 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1711 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1714 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1717 final StringBuffer source2 = new StringBuffer();
1718 source2.append( "" + l );
1719 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1720 source2.append( " 00; 01 ;02;03" + l );
1721 source2.append( " 10; 11; 12; 13 " + l );
1722 source2.append( "20; 21; 22; 23 " + l );
1723 source2.append( " " + l );
1724 source2.append( " 30; 31; 32; 33" + l );
1725 source2.append( "40;41;42;43" + l );
1726 source2.append( " comment: 1 1 1 1 1 " + l );
1727 source2.append( ";;;50 ; 52; 53;;54 " + l );
1728 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1733 if ( tl.size() != 2 ) {
1736 final BasicTable<String> t3 = tl.get( 0 );
1737 final BasicTable<String> t4 = tl.get( 1 );
1738 if ( t3.getNumberOfColumns() != 4 ) {
1741 if ( t3.getNumberOfRows() != 3 ) {
1744 if ( t4.getNumberOfColumns() != 4 ) {
1747 if ( t4.getNumberOfRows() != 3 ) {
1750 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1753 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1757 catch ( final Exception e ) {
1758 e.printStackTrace( System.out );
1764 private static boolean testBasicTolXMLparsing() {
1766 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1767 final TolParser parser = new TolParser();
1768 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1769 if ( parser.getErrorCount() > 0 ) {
1770 System.out.println( parser.getErrorMessages().toString() );
1773 if ( phylogenies_0.length != 1 ) {
1776 final Phylogeny t1 = phylogenies_0[ 0 ];
1777 if ( t1.getNumberOfExternalNodes() != 5 ) {
1780 if ( !t1.isRooted() ) {
1783 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1786 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1789 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1792 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1795 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1796 if ( parser.getErrorCount() > 0 ) {
1797 System.out.println( parser.getErrorMessages().toString() );
1800 if ( phylogenies_1.length != 1 ) {
1803 final Phylogeny t2 = phylogenies_1[ 0 ];
1804 if ( t2.getNumberOfExternalNodes() != 664 ) {
1807 if ( !t2.isRooted() ) {
1810 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1813 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1816 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1819 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1822 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1825 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1826 .equals( "Aquifex" ) ) {
1829 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1830 if ( parser.getErrorCount() > 0 ) {
1831 System.out.println( parser.getErrorMessages().toString() );
1834 if ( phylogenies_2.length != 1 ) {
1837 final Phylogeny t3 = phylogenies_2[ 0 ];
1838 if ( t3.getNumberOfExternalNodes() != 184 ) {
1841 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1844 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1847 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1850 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1851 if ( parser.getErrorCount() > 0 ) {
1852 System.out.println( parser.getErrorMessages().toString() );
1855 if ( phylogenies_3.length != 1 ) {
1858 final Phylogeny t4 = phylogenies_3[ 0 ];
1859 if ( t4.getNumberOfExternalNodes() != 1 ) {
1862 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1865 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1868 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1871 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1872 if ( parser.getErrorCount() > 0 ) {
1873 System.out.println( parser.getErrorMessages().toString() );
1876 if ( phylogenies_4.length != 1 ) {
1879 final Phylogeny t5 = phylogenies_4[ 0 ];
1880 if ( t5.getNumberOfExternalNodes() != 13 ) {
1883 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1886 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1889 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1893 catch ( final Exception e ) {
1894 e.printStackTrace( System.out );
1900 private static boolean testBasicTreeMethods() {
1902 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1903 final Phylogeny t1 = factory.create();
1904 if ( !t1.isEmpty() ) {
1907 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1908 if ( t2.getNumberOfExternalNodes() != 4 ) {
1911 if ( t2.getHeight() != 8.5 ) {
1914 if ( !t2.isCompletelyBinary() ) {
1917 if ( t2.isEmpty() ) {
1920 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1921 if ( t3.getNumberOfExternalNodes() != 5 ) {
1924 if ( t3.getHeight() != 11 ) {
1927 if ( t3.isCompletelyBinary() ) {
1930 final PhylogenyNode n = t3.getNode( "ABC" );
1931 PhylogenyNodeIterator it;
1932 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1935 for( it.reset(); it.hasNext(); ) {
1938 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1939 if ( !it2.next().getName().equals( "A" ) ) {
1942 if ( !it2.next().getName().equals( "B" ) ) {
1945 if ( !it2.next().getName().equals( "C" ) ) {
1948 if ( it2.hasNext() ) {
1951 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 ];
1952 if ( t4.getNumberOfExternalNodes() != 9 ) {
1955 if ( t4.getHeight() != 11 ) {
1958 if ( t4.isCompletelyBinary() ) {
1961 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)" );
1962 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1963 if ( t5.getNumberOfExternalNodes() != 8 ) {
1966 if ( t5.getHeight() != 15 ) {
1969 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)" );
1970 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1971 if ( t6.getHeight() != 15 ) {
1974 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)" );
1975 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1976 if ( t7.getHeight() != 15 ) {
1979 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)" );
1980 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1981 if ( t8.getNumberOfExternalNodes() != 10 ) {
1984 if ( t8.getHeight() != 15 ) {
1987 final char[] a9 = new char[] {};
1988 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1989 if ( t9.getHeight() != 0 ) {
1992 final char[] a10 = new char[] { 'a', ':', '6' };
1993 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1994 if ( t10.getHeight() != 6 ) {
1998 catch ( final Exception e ) {
1999 e.printStackTrace( System.out );
2005 private static boolean testConfidenceAssessor() {
2007 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2008 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2009 final Phylogeny[] ev0 = factory
2010 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2012 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2013 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2016 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2019 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2020 final Phylogeny[] ev1 = factory
2021 .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)));",
2023 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2024 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2027 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2030 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2031 final Phylogeny[] ev_b = factory
2032 .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",
2034 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2035 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2036 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2039 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2043 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2044 final Phylogeny[] ev1x = factory
2045 .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)));",
2047 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2048 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2051 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2054 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2055 final Phylogeny[] ev_bx = factory
2056 .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",
2058 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2059 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2062 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2066 final Phylogeny[] t2 = factory
2067 .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);",
2069 final Phylogeny[] ev2 = factory
2070 .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);",
2072 for( final Phylogeny target : t2 ) {
2073 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2076 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2077 new NHXParser() )[ 0 ];
2078 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2079 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2080 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2083 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2086 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2090 catch ( final Exception e ) {
2091 e.printStackTrace();
2097 private static boolean testCopyOfNodeData() {
2099 final PhylogenyNode n1 = PhylogenyNode
2100 .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]" );
2101 final PhylogenyNode n2 = n1.copyNodeData();
2102 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2106 catch ( final Exception e ) {
2107 e.printStackTrace();
2113 private static boolean testDataObjects() {
2115 final Confidence s0 = new Confidence();
2116 final Confidence s1 = new Confidence();
2117 if ( !s0.isEqual( s1 ) ) {
2120 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2121 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2122 if ( s2.isEqual( s1 ) ) {
2125 if ( !s2.isEqual( s3 ) ) {
2128 final Confidence s4 = ( Confidence ) s3.copy();
2129 if ( !s4.isEqual( s3 ) ) {
2136 final Taxonomy t1 = new Taxonomy();
2137 final Taxonomy t2 = new Taxonomy();
2138 final Taxonomy t3 = new Taxonomy();
2139 final Taxonomy t4 = new Taxonomy();
2140 final Taxonomy t5 = new Taxonomy();
2141 t1.setIdentifier( new Identifier( "ecoli" ) );
2142 t1.setTaxonomyCode( "ECOLI" );
2143 t1.setScientificName( "E. coli" );
2144 t1.setCommonName( "coli" );
2145 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2146 if ( !t1.isEqual( t0 ) ) {
2149 t2.setIdentifier( new Identifier( "ecoli" ) );
2150 t2.setTaxonomyCode( "other" );
2151 t2.setScientificName( "what" );
2152 t2.setCommonName( "something" );
2153 if ( !t1.isEqual( t2 ) ) {
2156 t2.setIdentifier( new Identifier( "nemve" ) );
2157 if ( t1.isEqual( t2 ) ) {
2160 t1.setIdentifier( null );
2161 t3.setTaxonomyCode( "ECOLI" );
2162 t3.setScientificName( "what" );
2163 t3.setCommonName( "something" );
2164 if ( !t1.isEqual( t3 ) ) {
2167 t1.setIdentifier( null );
2168 t1.setTaxonomyCode( "" );
2169 t4.setScientificName( "E. ColI" );
2170 t4.setCommonName( "something" );
2171 if ( !t1.isEqual( t4 ) ) {
2174 t4.setScientificName( "B. subtilis" );
2175 t4.setCommonName( "something" );
2176 if ( t1.isEqual( t4 ) ) {
2179 t1.setIdentifier( null );
2180 t1.setTaxonomyCode( "" );
2181 t1.setScientificName( "" );
2182 t5.setCommonName( "COLI" );
2183 if ( !t1.isEqual( t5 ) ) {
2186 t5.setCommonName( "vibrio" );
2187 if ( t1.isEqual( t5 ) ) {
2192 final Identifier id0 = new Identifier( "123", "pfam" );
2193 final Identifier id1 = ( Identifier ) id0.copy();
2194 if ( !id1.isEqual( id1 ) ) {
2197 if ( !id1.isEqual( id0 ) ) {
2200 if ( !id0.isEqual( id1 ) ) {
2207 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2208 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2209 if ( !pd1.isEqual( pd1 ) ) {
2212 if ( !pd1.isEqual( pd0 ) ) {
2217 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2218 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2219 if ( !pd3.isEqual( pd3 ) ) {
2222 if ( !pd2.isEqual( pd3 ) ) {
2225 if ( !pd0.isEqual( pd3 ) ) {
2230 // DomainArchitecture
2231 // ------------------
2232 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2233 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2234 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2235 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2236 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2237 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2242 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2243 if ( ds0.getNumberOfDomains() != 4 ) {
2246 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2247 if ( !ds0.isEqual( ds0 ) ) {
2250 if ( !ds0.isEqual( ds1 ) ) {
2253 if ( ds1.getNumberOfDomains() != 4 ) {
2256 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2261 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2262 if ( ds0.isEqual( ds2 ) ) {
2268 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2269 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2270 System.out.println( ds3.toNHX() );
2273 if ( ds3.getNumberOfDomains() != 3 ) {
2278 final Event e1 = new Event( Event.EventType.fusion );
2279 if ( e1.isDuplication() ) {
2282 if ( !e1.isFusion() ) {
2285 if ( !e1.asText().toString().equals( "fusion" ) ) {
2288 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2291 final Event e11 = new Event( Event.EventType.fusion );
2292 if ( !e11.isEqual( e1 ) ) {
2295 if ( !e11.toNHX().toString().equals( "" ) ) {
2298 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2299 if ( e2.isDuplication() ) {
2302 if ( !e2.isSpeciationOrDuplication() ) {
2305 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2308 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2311 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2314 if ( e11.isEqual( e2 ) ) {
2317 final Event e2c = ( Event ) e2.copy();
2318 if ( !e2c.isEqual( e2 ) ) {
2321 Event e3 = new Event( 1, 2, 3 );
2322 if ( e3.isDuplication() ) {
2325 if ( e3.isSpeciation() ) {
2328 if ( e3.isGeneLoss() ) {
2331 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2334 final Event e3c = ( Event ) e3.copy();
2335 final Event e3cc = ( Event ) e3c.copy();
2336 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2340 if ( !e3c.isEqual( e3cc ) ) {
2343 Event e4 = new Event( 1, 2, 3 );
2344 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2347 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2350 final Event e4c = ( Event ) e4.copy();
2352 final Event e4cc = ( Event ) e4c.copy();
2353 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2356 if ( !e4c.isEqual( e4cc ) ) {
2359 final Event e5 = new Event();
2360 if ( !e5.isUnassigned() ) {
2363 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2366 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2369 final Event e6 = new Event( 1, 0, 0 );
2370 if ( !e6.asText().toString().equals( "duplication" ) ) {
2373 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2376 final Event e7 = new Event( 0, 1, 0 );
2377 if ( !e7.asText().toString().equals( "speciation" ) ) {
2380 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2383 final Event e8 = new Event( 0, 0, 1 );
2384 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2387 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2391 catch ( final Exception e ) {
2392 e.printStackTrace( System.out );
2398 private static boolean testDeletionOfExternalNodes() {
2400 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2401 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2402 final PhylogenyWriter w = new PhylogenyWriter();
2403 if ( t0.isEmpty() ) {
2406 if ( t0.getNumberOfExternalNodes() != 1 ) {
2409 t0.deleteSubtree( t0.getNode( "A" ), false );
2410 if ( t0.getNumberOfExternalNodes() != 0 ) {
2413 if ( !t0.isEmpty() ) {
2416 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2417 if ( t1.getNumberOfExternalNodes() != 2 ) {
2420 t1.deleteSubtree( t1.getNode( "A" ), false );
2421 if ( t1.getNumberOfExternalNodes() != 1 ) {
2424 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2427 t1.deleteSubtree( t1.getNode( "B" ), false );
2428 if ( t1.getNumberOfExternalNodes() != 1 ) {
2431 t1.deleteSubtree( t1.getNode( "r" ), false );
2432 if ( !t1.isEmpty() ) {
2435 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2436 if ( t2.getNumberOfExternalNodes() != 3 ) {
2439 t2.deleteSubtree( t2.getNode( "B" ), false );
2440 if ( t2.getNumberOfExternalNodes() != 2 ) {
2443 t2.toNewHampshireX();
2444 PhylogenyNode n = t2.getNode( "A" );
2445 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2448 t2.deleteSubtree( t2.getNode( "A" ), false );
2449 if ( t2.getNumberOfExternalNodes() != 2 ) {
2452 t2.deleteSubtree( t2.getNode( "C" ), true );
2453 if ( t2.getNumberOfExternalNodes() != 1 ) {
2456 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2457 if ( t3.getNumberOfExternalNodes() != 4 ) {
2460 t3.deleteSubtree( t3.getNode( "B" ), true );
2461 if ( t3.getNumberOfExternalNodes() != 3 ) {
2464 n = t3.getNode( "A" );
2465 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2468 n = n.getNextExternalNode();
2469 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2472 t3.deleteSubtree( t3.getNode( "A" ), true );
2473 if ( t3.getNumberOfExternalNodes() != 2 ) {
2476 n = t3.getNode( "C" );
2477 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2480 t3.deleteSubtree( t3.getNode( "C" ), true );
2481 if ( t3.getNumberOfExternalNodes() != 1 ) {
2484 t3.deleteSubtree( t3.getNode( "D" ), true );
2485 if ( t3.getNumberOfExternalNodes() != 0 ) {
2488 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2489 if ( t4.getNumberOfExternalNodes() != 6 ) {
2492 t4.deleteSubtree( t4.getNode( "B2" ), true );
2493 if ( t4.getNumberOfExternalNodes() != 5 ) {
2496 String s = w.toNewHampshire( t4, false, true ).toString();
2497 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2500 t4.deleteSubtree( t4.getNode( "B11" ), true );
2501 if ( t4.getNumberOfExternalNodes() != 4 ) {
2504 t4.deleteSubtree( t4.getNode( "C" ), true );
2505 if ( t4.getNumberOfExternalNodes() != 3 ) {
2508 n = t4.getNode( "A" );
2509 n = n.getNextExternalNode();
2510 if ( !n.getName().equals( "B12" ) ) {
2513 n = n.getNextExternalNode();
2514 if ( !n.getName().equals( "D" ) ) {
2517 s = w.toNewHampshire( t4, false, true ).toString();
2518 if ( !s.equals( "((A,B12),D);" ) ) {
2521 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2522 t5.deleteSubtree( t5.getNode( "A" ), true );
2523 if ( t5.getNumberOfExternalNodes() != 5 ) {
2526 s = w.toNewHampshire( t5, false, true ).toString();
2527 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2530 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2531 t6.deleteSubtree( t6.getNode( "B11" ), true );
2532 if ( t6.getNumberOfExternalNodes() != 5 ) {
2535 s = w.toNewHampshire( t6, false, false ).toString();
2536 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2539 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2540 t7.deleteSubtree( t7.getNode( "B12" ), true );
2541 if ( t7.getNumberOfExternalNodes() != 5 ) {
2544 s = w.toNewHampshire( t7, false, true ).toString();
2545 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2548 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2549 t8.deleteSubtree( t8.getNode( "B2" ), true );
2550 if ( t8.getNumberOfExternalNodes() != 5 ) {
2553 s = w.toNewHampshire( t8, false, false ).toString();
2554 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2557 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2558 t9.deleteSubtree( t9.getNode( "C" ), true );
2559 if ( t9.getNumberOfExternalNodes() != 5 ) {
2562 s = w.toNewHampshire( t9, false, true ).toString();
2563 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2566 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2567 t10.deleteSubtree( t10.getNode( "D" ), true );
2568 if ( t10.getNumberOfExternalNodes() != 5 ) {
2571 s = w.toNewHampshire( t10, false, true ).toString();
2572 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2575 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2576 t11.deleteSubtree( t11.getNode( "A" ), true );
2577 if ( t11.getNumberOfExternalNodes() != 2 ) {
2580 s = w.toNewHampshire( t11, false, true ).toString();
2581 if ( !s.equals( "(B,C);" ) ) {
2584 t11.deleteSubtree( t11.getNode( "C" ), true );
2585 if ( t11.getNumberOfExternalNodes() != 1 ) {
2588 s = w.toNewHampshire( t11, false, false ).toString();
2589 if ( !s.equals( "B;" ) ) {
2592 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2593 t12.deleteSubtree( t12.getNode( "B2" ), true );
2594 if ( t12.getNumberOfExternalNodes() != 8 ) {
2597 s = w.toNewHampshire( t12, false, true ).toString();
2598 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2601 t12.deleteSubtree( t12.getNode( "B3" ), true );
2602 if ( t12.getNumberOfExternalNodes() != 7 ) {
2605 s = w.toNewHampshire( t12, false, true ).toString();
2606 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2609 t12.deleteSubtree( t12.getNode( "C3" ), true );
2610 if ( t12.getNumberOfExternalNodes() != 6 ) {
2613 s = w.toNewHampshire( t12, false, true ).toString();
2614 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2617 t12.deleteSubtree( t12.getNode( "A1" ), true );
2618 if ( t12.getNumberOfExternalNodes() != 5 ) {
2621 s = w.toNewHampshire( t12, false, true ).toString();
2622 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2625 t12.deleteSubtree( t12.getNode( "B1" ), true );
2626 if ( t12.getNumberOfExternalNodes() != 4 ) {
2629 s = w.toNewHampshire( t12, false, true ).toString();
2630 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2633 t12.deleteSubtree( t12.getNode( "A3" ), true );
2634 if ( t12.getNumberOfExternalNodes() != 3 ) {
2637 s = w.toNewHampshire( t12, false, true ).toString();
2638 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2641 t12.deleteSubtree( t12.getNode( "A2" ), true );
2642 if ( t12.getNumberOfExternalNodes() != 2 ) {
2645 s = w.toNewHampshire( t12, false, true ).toString();
2646 if ( !s.equals( "(C1,C2);" ) ) {
2649 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2650 t13.deleteSubtree( t13.getNode( "D" ), true );
2651 if ( t13.getNumberOfExternalNodes() != 4 ) {
2654 s = w.toNewHampshire( t13, false, true ).toString();
2655 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2658 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2659 t14.deleteSubtree( t14.getNode( "E" ), true );
2660 if ( t14.getNumberOfExternalNodes() != 5 ) {
2663 s = w.toNewHampshire( t14, false, true ).toString();
2664 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2667 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2668 t15.deleteSubtree( t15.getNode( "B2" ), true );
2669 if ( t15.getNumberOfExternalNodes() != 11 ) {
2672 t15.deleteSubtree( t15.getNode( "B1" ), true );
2673 if ( t15.getNumberOfExternalNodes() != 10 ) {
2676 t15.deleteSubtree( t15.getNode( "B3" ), true );
2677 if ( t15.getNumberOfExternalNodes() != 9 ) {
2680 t15.deleteSubtree( t15.getNode( "B4" ), true );
2681 if ( t15.getNumberOfExternalNodes() != 8 ) {
2684 t15.deleteSubtree( t15.getNode( "A1" ), true );
2685 if ( t15.getNumberOfExternalNodes() != 7 ) {
2688 t15.deleteSubtree( t15.getNode( "C4" ), true );
2689 if ( t15.getNumberOfExternalNodes() != 6 ) {
2693 catch ( final Exception e ) {
2694 e.printStackTrace( System.out );
2700 private static boolean testDescriptiveStatistics() {
2702 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2703 dss1.addValue( 82 );
2704 dss1.addValue( 78 );
2705 dss1.addValue( 70 );
2706 dss1.addValue( 58 );
2707 dss1.addValue( 42 );
2708 if ( dss1.getN() != 5 ) {
2711 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2714 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2717 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2720 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2723 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2726 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2729 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2732 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2735 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2738 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2741 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2744 dss1.addValue( 123 );
2745 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2748 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2751 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2754 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2755 dss2.addValue( -1.85 );
2756 dss2.addValue( 57.5 );
2757 dss2.addValue( 92.78 );
2758 dss2.addValue( 57.78 );
2759 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2762 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2765 final double[] a = dss2.getDataAsDoubleArray();
2766 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2769 dss2.addValue( -100 );
2770 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2773 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2776 final double[] ds = new double[ 14 ];
2791 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2792 if ( bins.length != 4 ) {
2795 if ( bins[ 0 ] != 2 ) {
2798 if ( bins[ 1 ] != 3 ) {
2801 if ( bins[ 2 ] != 4 ) {
2804 if ( bins[ 3 ] != 5 ) {
2807 final double[] ds1 = new double[ 9 ];
2817 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2818 if ( bins1.length != 4 ) {
2821 if ( bins1[ 0 ] != 2 ) {
2824 if ( bins1[ 1 ] != 3 ) {
2827 if ( bins1[ 2 ] != 0 ) {
2830 if ( bins1[ 3 ] != 4 ) {
2833 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2834 if ( bins1_1.length != 3 ) {
2837 if ( bins1_1[ 0 ] != 3 ) {
2840 if ( bins1_1[ 1 ] != 2 ) {
2843 if ( bins1_1[ 2 ] != 4 ) {
2846 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2847 if ( bins1_2.length != 3 ) {
2850 if ( bins1_2[ 0 ] != 2 ) {
2853 if ( bins1_2[ 1 ] != 2 ) {
2856 if ( bins1_2[ 2 ] != 2 ) {
2859 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2873 dss3.addValue( 10 );
2874 dss3.addValue( 10 );
2875 dss3.addValue( 10 );
2876 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2877 histo.toStringBuffer( 10, '=', 40, 5 );
2878 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2880 catch ( final Exception e ) {
2881 e.printStackTrace( System.out );
2887 private static boolean testDir( final String file ) {
2889 final File f = new File( file );
2890 if ( !f.exists() ) {
2893 if ( !f.isDirectory() ) {
2896 if ( !f.canRead() ) {
2900 catch ( final Exception e ) {
2906 private static boolean testExternalNodeRelatedMethods() {
2908 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2909 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2910 PhylogenyNode n = t1.getNode( "A" );
2911 n = n.getNextExternalNode();
2912 if ( !n.getName().equals( "B" ) ) {
2915 n = n.getNextExternalNode();
2916 if ( !n.getName().equals( "C" ) ) {
2919 n = n.getNextExternalNode();
2920 if ( !n.getName().equals( "D" ) ) {
2923 n = t1.getNode( "B" );
2924 while ( !n.isLastExternalNode() ) {
2925 n = n.getNextExternalNode();
2927 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2928 n = t2.getNode( "A" );
2929 n = n.getNextExternalNode();
2930 if ( !n.getName().equals( "B" ) ) {
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "C" ) ) {
2937 n = n.getNextExternalNode();
2938 if ( !n.getName().equals( "D" ) ) {
2941 n = t2.getNode( "B" );
2942 while ( !n.isLastExternalNode() ) {
2943 n = n.getNextExternalNode();
2945 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2946 n = t3.getNode( "A" );
2947 n = n.getNextExternalNode();
2948 if ( !n.getName().equals( "B" ) ) {
2951 n = n.getNextExternalNode();
2952 if ( !n.getName().equals( "C" ) ) {
2955 n = n.getNextExternalNode();
2956 if ( !n.getName().equals( "D" ) ) {
2959 n = n.getNextExternalNode();
2960 if ( !n.getName().equals( "E" ) ) {
2963 n = n.getNextExternalNode();
2964 if ( !n.getName().equals( "F" ) ) {
2967 n = n.getNextExternalNode();
2968 if ( !n.getName().equals( "G" ) ) {
2971 n = n.getNextExternalNode();
2972 if ( !n.getName().equals( "H" ) ) {
2975 n = t3.getNode( "B" );
2976 while ( !n.isLastExternalNode() ) {
2977 n = n.getNextExternalNode();
2979 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2980 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2981 final PhylogenyNode node = iter.next();
2983 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2984 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2985 final PhylogenyNode node = iter.next();
2988 catch ( final Exception e ) {
2989 e.printStackTrace( System.out );
2995 private static boolean testGeneralTable() {
2997 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2998 t0.setValue( 3, 2, "23" );
2999 t0.setValue( 10, 1, "error" );
3000 t0.setValue( 10, 1, "110" );
3001 t0.setValue( 9, 1, "19" );
3002 t0.setValue( 1, 10, "101" );
3003 t0.setValue( 10, 10, "1010" );
3004 t0.setValue( 100, 10, "10100" );
3005 t0.setValue( 0, 0, "00" );
3006 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
3009 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
3012 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
3015 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
3018 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
3021 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
3024 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3027 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3030 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3033 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3034 t1.setValue( "3", "2", "23" );
3035 t1.setValue( "10", "1", "error" );
3036 t1.setValue( "10", "1", "110" );
3037 t1.setValue( "9", "1", "19" );
3038 t1.setValue( "1", "10", "101" );
3039 t1.setValue( "10", "10", "1010" );
3040 t1.setValue( "100", "10", "10100" );
3041 t1.setValue( "0", "0", "00" );
3042 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3043 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3046 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3049 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3052 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3055 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3058 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3061 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3064 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3067 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3070 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3074 catch ( final Exception e ) {
3075 e.printStackTrace( System.out );
3081 private static boolean testGetDistance() {
3083 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3084 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",
3085 new NHXParser() )[ 0 ];
3086 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3087 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3090 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3093 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3096 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3099 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3102 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3105 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3108 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3111 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3114 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3117 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3120 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3123 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3126 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3129 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3132 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3135 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3138 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3141 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3144 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3147 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3150 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3153 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3156 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3159 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3162 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3165 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3168 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3171 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3174 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3177 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3180 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",
3181 new NHXParser() )[ 0 ];
3182 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3185 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3188 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3191 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3194 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3197 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3200 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3203 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3206 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3209 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3212 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3216 catch ( final Exception e ) {
3217 e.printStackTrace( System.out );
3223 private static boolean testGetLCA() {
3225 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3226 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3227 new NHXParser() )[ 0 ];
3228 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3229 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3230 if ( !A.getName().equals( "A" ) ) {
3233 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3234 if ( !gh.getName().equals( "gh" ) ) {
3237 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3238 if ( !ab.getName().equals( "ab" ) ) {
3241 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3242 if ( !ab2.getName().equals( "ab" ) ) {
3245 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3246 if ( !gh2.getName().equals( "gh" ) ) {
3249 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3250 if ( !gh3.getName().equals( "gh" ) ) {
3253 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3254 if ( !abc.getName().equals( "abc" ) ) {
3257 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3258 if ( !abc2.getName().equals( "abc" ) ) {
3261 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3262 if ( !abcd.getName().equals( "abcd" ) ) {
3265 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3266 if ( !abcd2.getName().equals( "abcd" ) ) {
3269 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3270 if ( !abcdef.getName().equals( "abcdef" ) ) {
3273 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3274 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3277 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3278 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3281 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3282 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3285 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3286 if ( !abcde.getName().equals( "abcde" ) ) {
3289 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3290 if ( !abcde2.getName().equals( "abcde" ) ) {
3293 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3294 if ( !r.getName().equals( "abcdefgh" ) ) {
3297 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3298 if ( !r2.getName().equals( "abcdefgh" ) ) {
3301 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3302 if ( !r3.getName().equals( "abcdefgh" ) ) {
3305 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3306 if ( !abcde3.getName().equals( "abcde" ) ) {
3309 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3310 if ( !abcde4.getName().equals( "abcde" ) ) {
3313 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3314 if ( !ab3.getName().equals( "ab" ) ) {
3317 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3318 if ( !ab4.getName().equals( "ab" ) ) {
3321 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3322 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3323 if ( !cd.getName().equals( "cd" ) ) {
3326 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3327 if ( !cd2.getName().equals( "cd" ) ) {
3330 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3331 if ( !cde.getName().equals( "cde" ) ) {
3334 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3335 if ( !cde2.getName().equals( "cde" ) ) {
3338 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3339 if ( !cdef.getName().equals( "cdef" ) ) {
3342 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3343 if ( !cdef2.getName().equals( "cdef" ) ) {
3346 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3347 if ( !cdef3.getName().equals( "cdef" ) ) {
3350 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3351 if ( !rt.getName().equals( "r" ) ) {
3354 final Phylogeny p3 = factory
3355 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3356 new NHXParser() )[ 0 ];
3357 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3358 if ( !bc_3.getName().equals( "bc" ) ) {
3361 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3362 if ( !ac_3.getName().equals( "abc" ) ) {
3365 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3366 if ( !ad_3.getName().equals( "abcde" ) ) {
3369 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3370 if ( !af_3.getName().equals( "abcdef" ) ) {
3373 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3374 if ( !ag_3.getName().equals( "" ) ) {
3377 if ( !ag_3.isRoot() ) {
3380 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3381 if ( !al_3.getName().equals( "" ) ) {
3384 if ( !al_3.isRoot() ) {
3387 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3388 if ( !kl_3.getName().equals( "" ) ) {
3391 if ( !kl_3.isRoot() ) {
3394 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3395 if ( !fl_3.getName().equals( "" ) ) {
3398 if ( !fl_3.isRoot() ) {
3401 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3402 if ( !gk_3.getName().equals( "ghijk" ) ) {
3405 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3406 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3407 if ( !r_4.getName().equals( "r" ) ) {
3410 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3411 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3412 if ( !r_5.getName().equals( "root" ) ) {
3415 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3416 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3417 if ( !r_6.getName().equals( "rot" ) ) {
3420 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3421 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3422 if ( !r_7.getName().equals( "rott" ) ) {
3426 catch ( final Exception e ) {
3427 e.printStackTrace( System.out );
3433 private static boolean testHmmscanOutputParser() {
3434 final String test_dir = Test.PATH_TO_TEST_DATA;
3436 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3437 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3439 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3440 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3441 final List<Protein> proteins = parser2.parse();
3442 if ( parser2.getProteinsEncountered() != 4 ) {
3445 if ( proteins.size() != 4 ) {
3448 if ( parser2.getDomainsEncountered() != 69 ) {
3451 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3454 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3457 final Protein p1 = proteins.get( 0 );
3458 if ( p1.getNumberOfProteinDomains() != 15 ) {
3461 if ( p1.getLength() != 850 ) {
3464 final Protein p2 = proteins.get( 1 );
3465 if ( p2.getNumberOfProteinDomains() != 51 ) {
3468 if ( p2.getLength() != 1291 ) {
3471 final Protein p3 = proteins.get( 2 );
3472 if ( p3.getNumberOfProteinDomains() != 2 ) {
3475 final Protein p4 = proteins.get( 3 );
3476 if ( p4.getNumberOfProteinDomains() != 1 ) {
3479 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3482 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3485 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3488 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3491 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3494 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3497 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3500 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3503 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3507 catch ( final Exception e ) {
3508 e.printStackTrace( System.out );
3514 private static boolean testLastExternalNodeMethods() {
3516 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3517 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3518 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3519 final PhylogenyNode n1 = t0.getNode( "A" );
3520 if ( n1.isLastExternalNode() ) {
3523 final PhylogenyNode n2 = t0.getNode( "B" );
3524 if ( n2.isLastExternalNode() ) {
3527 final PhylogenyNode n3 = t0.getNode( "C" );
3528 if ( n3.isLastExternalNode() ) {
3531 final PhylogenyNode n4 = t0.getNode( "D" );
3532 if ( !n4.isLastExternalNode() ) {
3536 catch ( final Exception e ) {
3537 e.printStackTrace( System.out );
3543 private static boolean testLevelOrderIterator() {
3545 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3546 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3547 PhylogenyNodeIterator it0;
3548 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3551 for( it0.reset(); it0.hasNext(); ) {
3554 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3555 if ( !it.next().getName().equals( "r" ) ) {
3558 if ( !it.next().getName().equals( "ab" ) ) {
3561 if ( !it.next().getName().equals( "cd" ) ) {
3564 if ( !it.next().getName().equals( "A" ) ) {
3567 if ( !it.next().getName().equals( "B" ) ) {
3570 if ( !it.next().getName().equals( "C" ) ) {
3573 if ( !it.next().getName().equals( "D" ) ) {
3576 if ( it.hasNext() ) {
3579 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",
3580 new NHXParser() )[ 0 ];
3581 PhylogenyNodeIterator it2;
3582 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3585 for( it2.reset(); it2.hasNext(); ) {
3588 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3589 if ( !it3.next().getName().equals( "r" ) ) {
3592 if ( !it3.next().getName().equals( "abc" ) ) {
3595 if ( !it3.next().getName().equals( "defg" ) ) {
3598 if ( !it3.next().getName().equals( "A" ) ) {
3601 if ( !it3.next().getName().equals( "B" ) ) {
3604 if ( !it3.next().getName().equals( "C" ) ) {
3607 if ( !it3.next().getName().equals( "D" ) ) {
3610 if ( !it3.next().getName().equals( "E" ) ) {
3613 if ( !it3.next().getName().equals( "F" ) ) {
3616 if ( !it3.next().getName().equals( "G" ) ) {
3619 if ( !it3.next().getName().equals( "1" ) ) {
3622 if ( !it3.next().getName().equals( "2" ) ) {
3625 if ( !it3.next().getName().equals( "3" ) ) {
3628 if ( !it3.next().getName().equals( "4" ) ) {
3631 if ( !it3.next().getName().equals( "5" ) ) {
3634 if ( !it3.next().getName().equals( "6" ) ) {
3637 if ( !it3.next().getName().equals( "f1" ) ) {
3640 if ( !it3.next().getName().equals( "f2" ) ) {
3643 if ( !it3.next().getName().equals( "f3" ) ) {
3646 if ( !it3.next().getName().equals( "a" ) ) {
3649 if ( !it3.next().getName().equals( "b" ) ) {
3652 if ( !it3.next().getName().equals( "f21" ) ) {
3655 if ( !it3.next().getName().equals( "X" ) ) {
3658 if ( !it3.next().getName().equals( "Y" ) ) {
3661 if ( !it3.next().getName().equals( "Z" ) ) {
3664 if ( it3.hasNext() ) {
3667 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3668 PhylogenyNodeIterator it4;
3669 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3672 for( it4.reset(); it4.hasNext(); ) {
3675 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3676 if ( !it5.next().getName().equals( "r" ) ) {
3679 if ( !it5.next().getName().equals( "A" ) ) {
3682 if ( !it5.next().getName().equals( "B" ) ) {
3685 if ( !it5.next().getName().equals( "C" ) ) {
3688 if ( !it5.next().getName().equals( "D" ) ) {
3691 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3692 PhylogenyNodeIterator it6;
3693 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3696 for( it6.reset(); it6.hasNext(); ) {
3699 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3700 if ( !it7.next().getName().equals( "A" ) ) {
3703 if ( it.hasNext() ) {
3707 catch ( final Exception e ) {
3708 e.printStackTrace( System.out );
3714 private static boolean testMidpointrooting() {
3716 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3717 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",
3718 new NHXParser() )[ 0 ];
3719 if ( !t1.isRooted() ) {
3722 PhylogenyMethods.midpointRoot( t1 );
3723 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3726 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3729 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3732 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3735 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3738 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3741 t1.reRoot( t1.getNode( "A" ) );
3742 PhylogenyMethods.midpointRoot( t1 );
3743 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3746 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3749 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3752 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3755 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3758 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3762 catch ( final Exception e ) {
3763 e.printStackTrace( System.out );
3769 private static boolean testNexusCharactersParsing() {
3771 final NexusCharactersParser parser = new NexusCharactersParser();
3772 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3774 String[] labels = parser.getCharStateLabels();
3775 if ( labels.length != 7 ) {
3778 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3781 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3784 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3787 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3790 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3793 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3796 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3799 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3801 labels = parser.getCharStateLabels();
3802 if ( labels.length != 7 ) {
3805 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3808 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3811 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3814 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3817 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3820 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3823 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3827 catch ( final Exception e ) {
3828 e.printStackTrace( System.out );
3834 private static boolean testNexusMatrixParsing() {
3836 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3837 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3839 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3840 if ( m.getNumberOfCharacters() != 9 ) {
3843 if ( m.getNumberOfIdentifiers() != 5 ) {
3846 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3849 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3852 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3855 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3858 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3861 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3864 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3867 // if ( labels.length != 7 ) {
3870 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3873 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3876 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3879 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3882 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3885 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3888 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3891 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3893 // labels = parser.getCharStateLabels();
3894 // if ( labels.length != 7 ) {
3897 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3900 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3903 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3906 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3909 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3912 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3915 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3919 catch ( final Exception e ) {
3920 e.printStackTrace( System.out );
3926 private static boolean testNexusTreeParsing() {
3928 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3929 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3930 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3931 if ( phylogenies.length != 1 ) {
3934 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3937 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3941 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3942 if ( phylogenies.length != 1 ) {
3945 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3948 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3952 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3953 if ( phylogenies.length != 1 ) {
3956 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3959 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3962 if ( phylogenies[ 0 ].isRooted() ) {
3966 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3967 if ( phylogenies.length != 18 ) {
3970 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3973 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3976 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3979 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3982 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3985 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3988 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3991 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3994 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3997 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4000 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4003 if ( phylogenies[ 8 ].isRooted() ) {
4006 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4009 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4012 if ( !phylogenies[ 9 ].isRooted() ) {
4015 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4018 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4021 if ( !phylogenies[ 10 ].isRooted() ) {
4024 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4027 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4030 if ( phylogenies[ 11 ].isRooted() ) {
4033 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4036 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4039 if ( !phylogenies[ 12 ].isRooted() ) {
4042 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4045 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4048 if ( !phylogenies[ 13 ].isRooted() ) {
4051 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4054 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4057 if ( !phylogenies[ 14 ].isRooted() ) {
4060 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4063 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4066 if ( phylogenies[ 15 ].isRooted() ) {
4069 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4072 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4075 if ( !phylogenies[ 16 ].isRooted() ) {
4078 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4081 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4084 if ( phylogenies[ 17 ].isRooted() ) {
4087 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4091 catch ( final Exception e ) {
4092 e.printStackTrace( System.out );
4098 private static boolean testNexusTreeParsingTranslating() {
4100 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4101 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4102 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4103 if ( phylogenies.length != 1 ) {
4106 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4109 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4112 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4115 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4118 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4119 .equals( "Aranaeus" ) ) {
4123 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4124 if ( phylogenies.length != 3 ) {
4127 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4130 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4133 if ( phylogenies[ 0 ].isRooted() ) {
4136 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4139 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4142 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4143 .equals( "Aranaeus" ) ) {
4146 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4149 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4152 if ( phylogenies[ 1 ].isRooted() ) {
4155 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4158 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4161 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4162 .equals( "Aranaeus" ) ) {
4165 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4168 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4171 if ( !phylogenies[ 2 ].isRooted() ) {
4174 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4177 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4180 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4181 .equals( "Aranaeus" ) ) {
4185 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4186 if ( phylogenies.length != 3 ) {
4189 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4192 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4195 if ( phylogenies[ 0 ].isRooted() ) {
4198 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4201 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4204 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4205 .equals( "Aranaeus" ) ) {
4208 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4211 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4214 if ( phylogenies[ 1 ].isRooted() ) {
4217 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4220 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4223 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4224 .equals( "Aranaeus" ) ) {
4227 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4230 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4233 if ( !phylogenies[ 2 ].isRooted() ) {
4236 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4239 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4242 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4243 .equals( "Aranaeus" ) ) {
4247 catch ( final Exception e ) {
4248 e.printStackTrace( System.out );
4254 private static boolean testNHParsing() {
4256 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4257 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4258 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4261 final NHXParser nhxp = new NHXParser();
4262 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4263 nhxp.setReplaceUnderscores( true );
4264 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4265 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4268 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4271 final Phylogeny p1b = factory
4272 .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 ",
4273 new NHXParser() )[ 0 ];
4274 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4277 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4280 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4281 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4282 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4283 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4284 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4285 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4286 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4287 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4288 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4289 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4290 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4291 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4292 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4294 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4297 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4300 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4303 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4306 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4307 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4308 final String p16_S = "((A,B),C)";
4309 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4310 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4313 final String p17_S = "(C,(A,B))";
4314 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4315 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4318 final String p18_S = "((A,B),(C,D))";
4319 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4320 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4323 final String p19_S = "(((A,B),C),D)";
4324 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4325 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4328 final String p20_S = "(A,(B,(C,D)))";
4329 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4330 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4333 final String p21_S = "(A,(B,(C,(D,E))))";
4334 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4335 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4338 final String p22_S = "((((A,B),C),D),E)";
4339 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4340 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4343 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4344 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4345 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4348 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4349 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4350 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4353 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4354 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4355 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4356 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4359 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4362 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4363 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4364 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4365 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4366 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4367 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4368 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4369 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4370 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4371 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4374 final String p26_S = "(A,B)ab";
4375 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4376 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4379 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4380 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4382 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4385 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4386 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4387 final String p28_S3 = "(A,B)ab";
4388 final String p28_S4 = "((((A,B),C),D),;E;)";
4389 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4391 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4394 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4397 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4400 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4403 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";
4404 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4405 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4408 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";
4409 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4410 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4413 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4414 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4415 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4418 final String p33_S = "A";
4419 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4420 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4423 final String p34_S = "B;";
4424 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4425 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4428 final String p35_S = "B:0.2";
4429 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4430 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4433 final String p36_S = "(A)";
4434 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4435 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4438 final String p37_S = "((A))";
4439 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4440 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4443 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4444 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4445 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4448 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4449 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4450 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4453 final String p40_S = "(A,B,C)";
4454 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4455 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4458 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4459 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4460 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4463 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4464 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4465 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4468 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)";
4469 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4470 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4473 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)))";
4474 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4475 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4478 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4479 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4480 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4483 final String p46_S = "";
4484 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4485 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4488 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4489 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4492 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4493 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4496 final Phylogeny p49 = factory
4497 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4498 new NHXParser() )[ 0 ];
4499 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4502 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4503 if ( p50.getNode( "A" ) == null ) {
4506 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4507 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4510 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4513 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4514 .equals( "((A,B)88:2.0,C);" ) ) {
4517 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4518 if ( p51.getNode( "A(A" ) == null ) {
4521 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4522 if ( p52.getNode( "A(A" ) == null ) {
4525 final Phylogeny p53 = factory
4526 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4527 new NHXParser() )[ 0 ];
4528 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4532 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4533 if ( p54.getNode( "A" ) == null ) {
4536 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4537 .equals( "((A,B)[88],C);" ) ) {
4541 catch ( final Exception e ) {
4542 e.printStackTrace( System.out );
4548 private static boolean testNHXconversion() {
4550 final PhylogenyNode n1 = new PhylogenyNode();
4551 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4552 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4553 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4554 final PhylogenyNode n5 = PhylogenyNode
4555 .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]" );
4556 final PhylogenyNode n6 = PhylogenyNode
4557 .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]" );
4558 if ( !n1.toNewHampshireX().equals( "" ) ) {
4561 if ( !n2.toNewHampshireX().equals( "" ) ) {
4564 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4567 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4570 if ( !n5.toNewHampshireX()
4571 .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]" ) ) {
4574 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]" ) ) {
4578 catch ( final Exception e ) {
4579 e.printStackTrace( System.out );
4585 private static boolean testNHXNodeParsing() {
4587 final PhylogenyNode n1 = new PhylogenyNode();
4588 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4589 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4590 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4591 final PhylogenyNode n5 = PhylogenyNode
4592 .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]" );
4593 if ( !n3.getName().equals( "n3" ) ) {
4596 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4599 if ( n3.isDuplication() ) {
4602 if ( n3.isHasAssignedEvent() ) {
4605 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4608 if ( !n4.getName().equals( "n4" ) ) {
4611 if ( n4.getDistanceToParent() != 0.01 ) {
4614 if ( !n5.getName().equals( "n5" ) ) {
4617 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4620 if ( n5.getDistanceToParent() != 0.1 ) {
4623 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4626 if ( !n5.isDuplication() ) {
4629 if ( !n5.isHasAssignedEvent() ) {
4632 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4635 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4638 final PhylogenyNode n8 = PhylogenyNode
4639 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4640 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4641 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4644 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4647 final PhylogenyNode n9 = PhylogenyNode
4648 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4649 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4650 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4653 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4656 final PhylogenyNode n10 = PhylogenyNode
4657 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4658 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4661 final PhylogenyNode n20 = PhylogenyNode
4662 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4663 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4666 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4669 final PhylogenyNode n20x = PhylogenyNode
4670 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4671 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4674 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4677 final PhylogenyNode n20xx = PhylogenyNode
4678 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4679 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4682 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4685 final PhylogenyNode n20xxx = PhylogenyNode
4686 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4687 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4690 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4693 final PhylogenyNode n20xxxx = PhylogenyNode
4694 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4695 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4698 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4701 final PhylogenyNode n21 = PhylogenyNode
4702 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4703 if ( !n21.getName().equals( "n21_PIG" ) ) {
4706 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4709 final PhylogenyNode n21x = PhylogenyNode
4710 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4711 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4714 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4717 final PhylogenyNode n22 = PhylogenyNode
4718 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4719 if ( !n22.getName().equals( "n22/PIG" ) ) {
4722 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4725 final PhylogenyNode n23 = PhylogenyNode
4726 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4727 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4730 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4733 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4734 final PhylogenyNode a = PhylogenyNode
4735 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4736 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4737 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4740 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4743 final PhylogenyNode b = PhylogenyNode
4744 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4745 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4746 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4749 if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
4752 final PhylogenyNode c = PhylogenyNode
4753 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4754 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4755 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4758 if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
4761 final PhylogenyNode c1 = PhylogenyNode
4762 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4763 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4764 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4767 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4770 final PhylogenyNode c2 = PhylogenyNode
4771 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4772 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4773 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4776 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4779 final PhylogenyNode d = PhylogenyNode
4780 .createInstanceFromNhxString( "n10_RAT1/1-2",
4781 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4782 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4785 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4788 final PhylogenyNode e = PhylogenyNode
4789 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4790 if ( !e.getName().equals( "n10_RAT1" ) ) {
4793 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4797 final PhylogenyNode n11 = PhylogenyNode
4798 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4799 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4800 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4803 if ( n11.getDistanceToParent() != 0.4 ) {
4806 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4809 final PhylogenyNode n12 = PhylogenyNode
4810 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4811 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4812 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4815 if ( n12.getDistanceToParent() != 0.4 ) {
4818 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4821 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4822 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4823 if ( !tvu1.getRef().equals( "tag1" ) ) {
4826 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4829 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4832 if ( !tvu1.getValue().equals( "value1" ) ) {
4835 if ( !tvu3.getRef().equals( "tag3" ) ) {
4838 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4841 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4844 if ( !tvu3.getValue().equals( "value3" ) ) {
4847 if ( n1.getName().compareTo( "" ) != 0 ) {
4850 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4853 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4856 if ( n2.getName().compareTo( "" ) != 0 ) {
4859 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4862 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4865 final PhylogenyNode n00 = PhylogenyNode
4866 .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]" );
4867 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4870 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4873 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4876 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4879 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4882 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4885 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4888 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4891 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4892 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4895 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4896 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4899 final PhylogenyNode n13 = PhylogenyNode
4900 .createInstanceFromNhxString( "blah_12345/1-2",
4901 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4902 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4905 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4908 final PhylogenyNode n14 = PhylogenyNode
4909 .createInstanceFromNhxString( "blah_12X45/1-2",
4910 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4911 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4914 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4917 final PhylogenyNode n15 = PhylogenyNode
4918 .createInstanceFromNhxString( "something_wicked[123]",
4919 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4920 if ( !n15.getName().equals( "something_wicked" ) ) {
4923 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4926 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4929 final PhylogenyNode n16 = PhylogenyNode
4930 .createInstanceFromNhxString( "something_wicked2[9]",
4931 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4932 if ( !n16.getName().equals( "something_wicked2" ) ) {
4935 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4938 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4941 final PhylogenyNode n17 = PhylogenyNode
4942 .createInstanceFromNhxString( "something_wicked3[a]",
4943 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4944 if ( !n17.getName().equals( "something_wicked3" ) ) {
4947 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4950 final PhylogenyNode n18 = PhylogenyNode
4951 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4952 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4955 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4958 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4962 catch ( final Exception e ) {
4963 e.printStackTrace( System.out );
4969 private static boolean testNHXParsing() {
4971 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4972 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4973 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4976 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]";
4977 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4978 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4981 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]";
4982 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4983 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4986 final Phylogeny[] p3 = factory
4987 .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]",
4989 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4992 final Phylogeny[] p4 = factory
4993 .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(]",
4995 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4998 final Phylogeny[] p5 = factory
4999 .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(((]",
5001 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5004 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)";
5005 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)";
5006 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5007 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5010 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)))";
5011 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)))";
5012 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5013 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5016 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]) ))[,,, ])))))))";
5017 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5018 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5019 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5022 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5023 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5026 final Phylogeny p10 = factory
5027 .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]",
5028 new NHXParser() )[ 0 ];
5029 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5033 catch ( final Exception e ) {
5034 e.printStackTrace( System.out );
5040 private static boolean testNHXParsingQuotes() {
5042 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5043 final NHXParser p = new NHXParser();
5044 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5045 if ( phylogenies_0.length != 5 ) {
5048 final Phylogeny phy = phylogenies_0[ 4 ];
5049 if ( phy.getNumberOfExternalNodes() != 7 ) {
5052 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5055 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5058 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5059 .getScientificName().equals( "hsapiens" ) ) {
5062 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5065 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5068 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5071 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5074 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5077 final NHXParser p1p = new NHXParser();
5078 p1p.setIgnoreQuotes( true );
5079 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5080 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5083 final NHXParser p2p = new NHXParser();
5084 p1p.setIgnoreQuotes( false );
5085 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5086 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5089 final NHXParser p3p = new NHXParser();
5090 p3p.setIgnoreQuotes( false );
5091 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5092 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5095 final NHXParser p4p = new NHXParser();
5096 p4p.setIgnoreQuotes( false );
5097 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5098 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5101 final Phylogeny p10 = factory
5102 .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]",
5103 new NHXParser() )[ 0 ];
5104 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]";
5105 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5108 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5109 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5113 final Phylogeny p12 = factory
5114 .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]",
5115 new NHXParser() )[ 0 ];
5116 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]";
5117 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5120 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5121 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5124 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;";
5125 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5128 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5129 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5133 catch ( final Exception e ) {
5134 e.printStackTrace( System.out );
5140 private static boolean testNHXParsingMB() {
5142 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5143 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5144 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5145 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5146 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5147 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5148 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5149 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5150 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5151 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5152 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5155 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5158 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5159 0.1100000000000000e+00 ) ) {
5162 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5165 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5168 final Phylogeny p2 = factory
5169 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5170 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5171 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5172 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5173 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5174 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5175 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5176 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5177 + "7.369400000000000e-02}])",
5178 new NHXParser() )[ 0 ];
5179 if ( p2.getNode( "1" ) == null ) {
5182 if ( p2.getNode( "2" ) == null ) {
5186 catch ( final Exception e ) {
5187 e.printStackTrace( System.out );
5194 private static boolean testPhylogenyBranch() {
5196 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5197 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5198 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5199 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5200 if ( !a1b1.equals( a1b1 ) ) {
5203 if ( !a1b1.equals( b1a1 ) ) {
5206 if ( !b1a1.equals( a1b1 ) ) {
5209 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5210 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5211 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5212 if ( a1_b1.equals( b1_a1 ) ) {
5215 if ( a1_b1.equals( a1_b1_ ) ) {
5218 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5219 if ( !a1_b1.equals( b1_a1_ ) ) {
5222 if ( a1_b1_.equals( b1_a1_ ) ) {
5225 if ( !a1_b1_.equals( b1_a1 ) ) {
5229 catch ( final Exception e ) {
5230 e.printStackTrace( System.out );
5236 private static boolean testPhyloXMLparsingOfDistributionElement() {
5238 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5239 PhyloXmlParser xml_parser = null;
5241 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5243 catch ( final Exception e ) {
5244 // Do nothing -- means were not running from jar.
5246 if ( xml_parser == null ) {
5247 xml_parser = new PhyloXmlParser();
5248 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5249 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5252 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5255 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5257 if ( xml_parser.getErrorCount() > 0 ) {
5258 System.out.println( xml_parser.getErrorMessages().toString() );
5261 if ( phylogenies_0.length != 1 ) {
5264 final Phylogeny t1 = phylogenies_0[ 0 ];
5265 PhylogenyNode n = null;
5266 Distribution d = null;
5267 n = t1.getNode( "root node" );
5268 if ( !n.getNodeData().isHasDistribution() ) {
5271 if ( n.getNodeData().getDistributions().size() != 1 ) {
5274 d = n.getNodeData().getDistribution();
5275 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5278 if ( d.getPoints().size() != 1 ) {
5281 if ( d.getPolygons() != null ) {
5284 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5287 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5290 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5293 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5296 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5299 n = t1.getNode( "node a" );
5300 if ( !n.getNodeData().isHasDistribution() ) {
5303 if ( n.getNodeData().getDistributions().size() != 2 ) {
5306 d = n.getNodeData().getDistribution( 1 );
5307 if ( !d.getDesc().equals( "San Diego" ) ) {
5310 if ( d.getPoints().size() != 1 ) {
5313 if ( d.getPolygons() != null ) {
5316 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5319 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5322 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5325 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5328 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5331 n = t1.getNode( "node bb" );
5332 if ( !n.getNodeData().isHasDistribution() ) {
5335 if ( n.getNodeData().getDistributions().size() != 1 ) {
5338 d = n.getNodeData().getDistribution( 0 );
5339 if ( d.getPoints().size() != 3 ) {
5342 if ( d.getPolygons().size() != 2 ) {
5345 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5348 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5351 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5354 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5357 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5360 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5363 Polygon p = d.getPolygons().get( 0 );
5364 if ( p.getPoints().size() != 3 ) {
5367 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5370 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5373 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5376 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5379 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5382 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5385 p = d.getPolygons().get( 1 );
5386 if ( p.getPoints().size() != 3 ) {
5389 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5392 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5395 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5399 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5400 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5401 if ( rt.length != 1 ) {
5404 final Phylogeny t1_rt = rt[ 0 ];
5405 n = t1_rt.getNode( "root node" );
5406 if ( !n.getNodeData().isHasDistribution() ) {
5409 if ( n.getNodeData().getDistributions().size() != 1 ) {
5412 d = n.getNodeData().getDistribution();
5413 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5416 if ( d.getPoints().size() != 1 ) {
5419 if ( d.getPolygons() != null ) {
5422 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5425 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5428 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5431 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5434 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5437 n = t1_rt.getNode( "node a" );
5438 if ( !n.getNodeData().isHasDistribution() ) {
5441 if ( n.getNodeData().getDistributions().size() != 2 ) {
5444 d = n.getNodeData().getDistribution( 1 );
5445 if ( !d.getDesc().equals( "San Diego" ) ) {
5448 if ( d.getPoints().size() != 1 ) {
5451 if ( d.getPolygons() != null ) {
5454 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5457 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5460 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5463 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5466 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5469 n = t1_rt.getNode( "node bb" );
5470 if ( !n.getNodeData().isHasDistribution() ) {
5473 if ( n.getNodeData().getDistributions().size() != 1 ) {
5476 d = n.getNodeData().getDistribution( 0 );
5477 if ( d.getPoints().size() != 3 ) {
5480 if ( d.getPolygons().size() != 2 ) {
5483 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5486 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5489 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5492 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5495 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5498 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5501 p = d.getPolygons().get( 0 );
5502 if ( p.getPoints().size() != 3 ) {
5505 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5508 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5511 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5514 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5517 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5520 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5523 p = d.getPolygons().get( 1 );
5524 if ( p.getPoints().size() != 3 ) {
5527 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5530 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5533 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5537 catch ( final Exception e ) {
5538 e.printStackTrace( System.out );
5544 private static boolean testPostOrderIterator() {
5546 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5547 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5548 PhylogenyNodeIterator it0;
5549 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5552 for( it0.reset(); it0.hasNext(); ) {
5555 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5556 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5557 if ( !it.next().getName().equals( "A" ) ) {
5560 if ( !it.next().getName().equals( "B" ) ) {
5563 if ( !it.next().getName().equals( "ab" ) ) {
5566 if ( !it.next().getName().equals( "C" ) ) {
5569 if ( !it.next().getName().equals( "D" ) ) {
5572 if ( !it.next().getName().equals( "cd" ) ) {
5575 if ( !it.next().getName().equals( "abcd" ) ) {
5578 if ( !it.next().getName().equals( "E" ) ) {
5581 if ( !it.next().getName().equals( "F" ) ) {
5584 if ( !it.next().getName().equals( "ef" ) ) {
5587 if ( !it.next().getName().equals( "G" ) ) {
5590 if ( !it.next().getName().equals( "H" ) ) {
5593 if ( !it.next().getName().equals( "gh" ) ) {
5596 if ( !it.next().getName().equals( "efgh" ) ) {
5599 if ( !it.next().getName().equals( "r" ) ) {
5602 if ( it.hasNext() ) {
5606 catch ( final Exception e ) {
5607 e.printStackTrace( System.out );
5613 private static boolean testPreOrderIterator() {
5615 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5616 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5617 PhylogenyNodeIterator it0;
5618 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5621 for( it0.reset(); it0.hasNext(); ) {
5624 PhylogenyNodeIterator it = t0.iteratorPreorder();
5625 if ( !it.next().getName().equals( "r" ) ) {
5628 if ( !it.next().getName().equals( "ab" ) ) {
5631 if ( !it.next().getName().equals( "A" ) ) {
5634 if ( !it.next().getName().equals( "B" ) ) {
5637 if ( !it.next().getName().equals( "cd" ) ) {
5640 if ( !it.next().getName().equals( "C" ) ) {
5643 if ( !it.next().getName().equals( "D" ) ) {
5646 if ( it.hasNext() ) {
5649 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5650 it = t1.iteratorPreorder();
5651 if ( !it.next().getName().equals( "r" ) ) {
5654 if ( !it.next().getName().equals( "abcd" ) ) {
5657 if ( !it.next().getName().equals( "ab" ) ) {
5660 if ( !it.next().getName().equals( "A" ) ) {
5663 if ( !it.next().getName().equals( "B" ) ) {
5666 if ( !it.next().getName().equals( "cd" ) ) {
5669 if ( !it.next().getName().equals( "C" ) ) {
5672 if ( !it.next().getName().equals( "D" ) ) {
5675 if ( !it.next().getName().equals( "efgh" ) ) {
5678 if ( !it.next().getName().equals( "ef" ) ) {
5681 if ( !it.next().getName().equals( "E" ) ) {
5684 if ( !it.next().getName().equals( "F" ) ) {
5687 if ( !it.next().getName().equals( "gh" ) ) {
5690 if ( !it.next().getName().equals( "G" ) ) {
5693 if ( !it.next().getName().equals( "H" ) ) {
5696 if ( it.hasNext() ) {
5700 catch ( final Exception e ) {
5701 e.printStackTrace( System.out );
5707 private static boolean testPropertiesMap() {
5709 final PropertiesMap pm = new PropertiesMap();
5710 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5711 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5712 final Property p2 = new Property( "something:else",
5714 "improbable:research",
5717 pm.addProperty( p0 );
5718 pm.addProperty( p1 );
5719 pm.addProperty( p2 );
5720 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5723 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5726 if ( pm.getProperties().size() != 3 ) {
5729 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5732 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5735 if ( pm.getProperties().size() != 3 ) {
5738 pm.removeProperty( "dimensions:diameter" );
5739 if ( pm.getProperties().size() != 2 ) {
5742 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5745 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5749 catch ( final Exception e ) {
5750 e.printStackTrace( System.out );
5756 private static boolean testReIdMethods() {
5758 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5759 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5760 final int count = PhylogenyNode.getNodeCount();
5762 if ( p.getNode( "r" ).getId() != count ) {
5765 if ( p.getNode( "A" ).getId() != count + 1 ) {
5768 if ( p.getNode( "B" ).getId() != count + 1 ) {
5771 if ( p.getNode( "C" ).getId() != count + 1 ) {
5774 if ( p.getNode( "1" ).getId() != count + 2 ) {
5777 if ( p.getNode( "2" ).getId() != count + 2 ) {
5780 if ( p.getNode( "3" ).getId() != count + 2 ) {
5783 if ( p.getNode( "4" ).getId() != count + 2 ) {
5786 if ( p.getNode( "5" ).getId() != count + 2 ) {
5789 if ( p.getNode( "6" ).getId() != count + 2 ) {
5792 if ( p.getNode( "a" ).getId() != count + 3 ) {
5795 if ( p.getNode( "b" ).getId() != count + 3 ) {
5798 if ( p.getNode( "X" ).getId() != count + 4 ) {
5801 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5804 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5808 catch ( final Exception e ) {
5809 e.printStackTrace( System.out );
5815 private static boolean testRerooting() {
5817 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5818 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",
5819 new NHXParser() )[ 0 ];
5820 if ( !t1.isRooted() ) {
5823 t1.reRoot( t1.getNode( "D" ) );
5824 t1.reRoot( t1.getNode( "CD" ) );
5825 t1.reRoot( t1.getNode( "A" ) );
5826 t1.reRoot( t1.getNode( "B" ) );
5827 t1.reRoot( t1.getNode( "AB" ) );
5828 t1.reRoot( t1.getNode( "D" ) );
5829 t1.reRoot( t1.getNode( "C" ) );
5830 t1.reRoot( t1.getNode( "CD" ) );
5831 t1.reRoot( t1.getNode( "A" ) );
5832 t1.reRoot( t1.getNode( "B" ) );
5833 t1.reRoot( t1.getNode( "AB" ) );
5834 t1.reRoot( t1.getNode( "D" ) );
5835 t1.reRoot( t1.getNode( "D" ) );
5836 t1.reRoot( t1.getNode( "C" ) );
5837 t1.reRoot( t1.getNode( "A" ) );
5838 t1.reRoot( t1.getNode( "B" ) );
5839 t1.reRoot( t1.getNode( "AB" ) );
5840 t1.reRoot( t1.getNode( "C" ) );
5841 t1.reRoot( t1.getNode( "D" ) );
5842 t1.reRoot( t1.getNode( "CD" ) );
5843 t1.reRoot( t1.getNode( "D" ) );
5844 t1.reRoot( t1.getNode( "A" ) );
5845 t1.reRoot( t1.getNode( "B" ) );
5846 t1.reRoot( t1.getNode( "AB" ) );
5847 t1.reRoot( t1.getNode( "C" ) );
5848 t1.reRoot( t1.getNode( "D" ) );
5849 t1.reRoot( t1.getNode( "CD" ) );
5850 t1.reRoot( t1.getNode( "D" ) );
5851 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5854 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5857 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5860 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5863 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5866 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5869 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",
5870 new NHXParser() )[ 0 ];
5871 t2.reRoot( t2.getNode( "A" ) );
5872 t2.reRoot( t2.getNode( "D" ) );
5873 t2.reRoot( t2.getNode( "ABC" ) );
5874 t2.reRoot( t2.getNode( "A" ) );
5875 t2.reRoot( t2.getNode( "B" ) );
5876 t2.reRoot( t2.getNode( "D" ) );
5877 t2.reRoot( t2.getNode( "C" ) );
5878 t2.reRoot( t2.getNode( "ABC" ) );
5879 t2.reRoot( t2.getNode( "A" ) );
5880 t2.reRoot( t2.getNode( "B" ) );
5881 t2.reRoot( t2.getNode( "AB" ) );
5882 t2.reRoot( t2.getNode( "AB" ) );
5883 t2.reRoot( t2.getNode( "D" ) );
5884 t2.reRoot( t2.getNode( "C" ) );
5885 t2.reRoot( t2.getNode( "B" ) );
5886 t2.reRoot( t2.getNode( "AB" ) );
5887 t2.reRoot( t2.getNode( "D" ) );
5888 t2.reRoot( t2.getNode( "D" ) );
5889 t2.reRoot( t2.getNode( "ABC" ) );
5890 t2.reRoot( t2.getNode( "A" ) );
5891 t2.reRoot( t2.getNode( "B" ) );
5892 t2.reRoot( t2.getNode( "AB" ) );
5893 t2.reRoot( t2.getNode( "D" ) );
5894 t2.reRoot( t2.getNode( "C" ) );
5895 t2.reRoot( t2.getNode( "ABC" ) );
5896 t2.reRoot( t2.getNode( "A" ) );
5897 t2.reRoot( t2.getNode( "B" ) );
5898 t2.reRoot( t2.getNode( "AB" ) );
5899 t2.reRoot( t2.getNode( "D" ) );
5900 t2.reRoot( t2.getNode( "D" ) );
5901 t2.reRoot( t2.getNode( "C" ) );
5902 t2.reRoot( t2.getNode( "A" ) );
5903 t2.reRoot( t2.getNode( "B" ) );
5904 t2.reRoot( t2.getNode( "AB" ) );
5905 t2.reRoot( t2.getNode( "C" ) );
5906 t2.reRoot( t2.getNode( "D" ) );
5907 t2.reRoot( t2.getNode( "ABC" ) );
5908 t2.reRoot( t2.getNode( "D" ) );
5909 t2.reRoot( t2.getNode( "A" ) );
5910 t2.reRoot( t2.getNode( "B" ) );
5911 t2.reRoot( t2.getNode( "AB" ) );
5912 t2.reRoot( t2.getNode( "C" ) );
5913 t2.reRoot( t2.getNode( "D" ) );
5914 t2.reRoot( t2.getNode( "ABC" ) );
5915 t2.reRoot( t2.getNode( "D" ) );
5916 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5919 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5922 t2.reRoot( t2.getNode( "ABC" ) );
5923 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5926 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5929 t2.reRoot( t2.getNode( "AB" ) );
5930 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5933 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5936 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5939 t2.reRoot( t2.getNode( "AB" ) );
5940 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5943 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5946 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5949 t2.reRoot( t2.getNode( "D" ) );
5950 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5953 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5956 t2.reRoot( t2.getNode( "ABC" ) );
5957 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5960 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5963 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5964 new NHXParser() )[ 0 ];
5965 t3.reRoot( t3.getNode( "B" ) );
5966 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5969 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5972 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5975 t3.reRoot( t3.getNode( "B" ) );
5976 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5979 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5982 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5985 t3.reRoot( t3.getRoot() );
5986 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5989 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5992 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5996 catch ( final Exception e ) {
5997 e.printStackTrace( System.out );
6003 private static boolean testSDIse() {
6005 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6006 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6007 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6008 gene1.setRooted( true );
6009 species1.setRooted( true );
6010 final SDI sdi = new SDIse( gene1, species1 );
6011 if ( !gene1.getRoot().isDuplication() ) {
6014 final Phylogeny species2 = factory
6015 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6016 new NHXParser() )[ 0 ];
6017 final Phylogeny gene2 = factory
6018 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6019 new NHXParser() )[ 0 ];
6020 species2.setRooted( true );
6021 gene2.setRooted( true );
6022 final SDI sdi2 = new SDIse( gene2, species2 );
6023 if ( sdi2.getDuplicationsSum() != 0 ) {
6026 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6029 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6032 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6035 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6038 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6041 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6044 final Phylogeny species3 = factory
6045 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6046 new NHXParser() )[ 0 ];
6047 final Phylogeny gene3 = factory
6048 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6049 new NHXParser() )[ 0 ];
6050 species3.setRooted( true );
6051 gene3.setRooted( true );
6052 final SDI sdi3 = new SDIse( gene3, species3 );
6053 if ( sdi3.getDuplicationsSum() != 1 ) {
6056 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6059 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6062 final Phylogeny species4 = factory
6063 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6064 new NHXParser() )[ 0 ];
6065 final Phylogeny gene4 = factory
6066 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6067 new NHXParser() )[ 0 ];
6068 species4.setRooted( true );
6069 gene4.setRooted( true );
6070 final SDI sdi4 = new SDIse( gene4, species4 );
6071 if ( sdi4.getDuplicationsSum() != 1 ) {
6074 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6077 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6080 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6083 if ( species4.getNumberOfExternalNodes() != 6 ) {
6086 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6089 final Phylogeny species5 = factory
6090 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6091 new NHXParser() )[ 0 ];
6092 final Phylogeny gene5 = factory
6093 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6094 new NHXParser() )[ 0 ];
6095 species5.setRooted( true );
6096 gene5.setRooted( true );
6097 final SDI sdi5 = new SDIse( gene5, species5 );
6098 if ( sdi5.getDuplicationsSum() != 2 ) {
6101 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6104 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6107 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6110 if ( species5.getNumberOfExternalNodes() != 6 ) {
6113 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6116 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6117 // Conjecture for Comparing Molecular Phylogenies"
6118 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6119 final Phylogeny species6 = factory
6120 .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,"
6121 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6122 new NHXParser() )[ 0 ];
6123 final Phylogeny gene6 = factory
6124 .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,"
6125 + "((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,"
6126 + "(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;",
6127 new NHXParser() )[ 0 ];
6128 species6.setRooted( true );
6129 gene6.setRooted( true );
6130 final SDI sdi6 = new SDIse( gene6, species6 );
6131 if ( sdi6.getDuplicationsSum() != 3 ) {
6134 if ( !gene6.getNode( "r" ).isDuplication() ) {
6137 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6140 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6143 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6146 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6149 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6152 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6155 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6158 sdi6.computeMappingCostL();
6159 if ( sdi6.computeMappingCostL() != 17 ) {
6162 if ( species6.getNumberOfExternalNodes() != 9 ) {
6165 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6168 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6169 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6170 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6171 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6172 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6173 species7.setRooted( true );
6174 final Phylogeny gene7_1 = Test
6175 .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])" );
6176 gene7_1.setRooted( true );
6177 final SDI sdi7 = new SDIse( gene7_1, species7 );
6178 if ( sdi7.getDuplicationsSum() != 0 ) {
6181 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6184 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6187 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6190 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6193 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6196 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6199 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6202 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6205 final Phylogeny gene7_2 = Test
6206 .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])" );
6207 gene7_2.setRooted( true );
6208 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6209 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6212 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6215 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6218 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6221 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6224 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6227 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6230 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6233 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6236 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6240 catch ( final Exception e ) {
6246 private static boolean testSDIunrooted() {
6248 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6249 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6250 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6251 final Iterator<PhylogenyBranch> iter = l.iterator();
6252 PhylogenyBranch br = iter.next();
6253 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6256 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6260 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6263 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6267 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6270 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6274 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6277 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6281 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6284 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6288 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6291 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6295 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6298 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6302 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6305 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6309 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6312 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6316 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6319 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6323 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6326 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6330 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6333 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6337 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6340 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6344 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6347 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6351 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6354 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6357 if ( iter.hasNext() ) {
6360 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6361 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6362 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6364 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6367 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6371 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6374 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6378 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6381 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6384 if ( iter1.hasNext() ) {
6387 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6388 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6389 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6391 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6394 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6398 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6401 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6405 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6408 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6411 if ( iter2.hasNext() ) {
6414 final Phylogeny species0 = factory
6415 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6416 new NHXParser() )[ 0 ];
6417 final Phylogeny gene1 = factory
6418 .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])",
6419 new NHXParser() )[ 0 ];
6420 species0.setRooted( true );
6421 gene1.setRooted( true );
6422 final SDIR sdi_unrooted = new SDIR();
6423 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6424 if ( sdi_unrooted.getCount() != 1 ) {
6427 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6430 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6433 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6436 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6439 final Phylogeny gene2 = factory
6440 .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])",
6441 new NHXParser() )[ 0 ];
6442 gene2.setRooted( true );
6443 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6444 if ( sdi_unrooted.getCount() != 1 ) {
6447 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6450 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6453 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6456 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6459 final Phylogeny species6 = factory
6460 .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,"
6461 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6462 new NHXParser() )[ 0 ];
6463 final Phylogeny gene6 = factory
6464 .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],"
6465 + "(((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],"
6466 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6467 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6468 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6469 new NHXParser() )[ 0 ];
6470 species6.setRooted( true );
6471 gene6.setRooted( true );
6472 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6473 if ( sdi_unrooted.getCount() != 1 ) {
6476 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6479 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6482 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6485 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6488 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6491 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6494 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6497 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6500 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6503 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6506 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6509 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6513 final Phylogeny species7 = factory
6514 .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,"
6515 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6516 new NHXParser() )[ 0 ];
6517 final Phylogeny gene7 = factory
6518 .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],"
6519 + "(((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],"
6520 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6521 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6522 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6523 new NHXParser() )[ 0 ];
6524 species7.setRooted( true );
6525 gene7.setRooted( true );
6526 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6527 if ( sdi_unrooted.getCount() != 1 ) {
6530 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6533 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6536 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6539 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6542 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6545 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6548 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6551 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6554 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6557 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6560 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6563 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6567 final Phylogeny species8 = factory
6568 .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,"
6569 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6570 new NHXParser() )[ 0 ];
6571 final Phylogeny gene8 = factory
6572 .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],"
6573 + "(((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],"
6574 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6575 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6576 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6577 new NHXParser() )[ 0 ];
6578 species8.setRooted( true );
6579 gene8.setRooted( true );
6580 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6581 if ( sdi_unrooted.getCount() != 1 ) {
6584 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6587 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6590 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6593 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6596 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6599 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6602 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6605 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6608 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6611 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6614 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6617 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6622 catch ( final Exception e ) {
6623 e.printStackTrace( System.out );
6629 private static boolean testSplit() {
6631 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6632 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6633 //Archaeopteryx.createApplication( p0 );
6634 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6635 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6636 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6637 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6638 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6639 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6640 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6641 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6642 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6643 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6644 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6645 // System.out.println( s0.toString() );
6647 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6650 if ( s0.match( query_nodes ) ) {
6653 query_nodes = new HashSet<PhylogenyNode>();
6654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6661 if ( !s0.match( query_nodes ) ) {
6665 query_nodes = new HashSet<PhylogenyNode>();
6666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6669 if ( !s0.match( query_nodes ) ) {
6673 query_nodes = new HashSet<PhylogenyNode>();
6674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6678 if ( !s0.match( query_nodes ) ) {
6682 query_nodes = new HashSet<PhylogenyNode>();
6683 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6687 if ( !s0.match( query_nodes ) ) {
6691 query_nodes = new HashSet<PhylogenyNode>();
6692 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6695 if ( !s0.match( query_nodes ) ) {
6699 query_nodes = new HashSet<PhylogenyNode>();
6700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6702 if ( !s0.match( query_nodes ) ) {
6706 query_nodes = new HashSet<PhylogenyNode>();
6707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6708 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6712 if ( !s0.match( query_nodes ) ) {
6716 query_nodes = new HashSet<PhylogenyNode>();
6717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6718 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6720 if ( !s0.match( query_nodes ) ) {
6724 query_nodes = new HashSet<PhylogenyNode>();
6725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6729 if ( !s0.match( query_nodes ) ) {
6733 query_nodes = new HashSet<PhylogenyNode>();
6734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6736 if ( s0.match( query_nodes ) ) {
6740 query_nodes = new HashSet<PhylogenyNode>();
6741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6742 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6743 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6745 if ( s0.match( query_nodes ) ) {
6749 query_nodes = new HashSet<PhylogenyNode>();
6750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6755 if ( s0.match( query_nodes ) ) {
6759 query_nodes = new HashSet<PhylogenyNode>();
6760 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6761 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6763 if ( s0.match( query_nodes ) ) {
6767 query_nodes = new HashSet<PhylogenyNode>();
6768 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6770 if ( s0.match( query_nodes ) ) {
6774 query_nodes = new HashSet<PhylogenyNode>();
6775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6777 if ( s0.match( query_nodes ) ) {
6781 query_nodes = new HashSet<PhylogenyNode>();
6782 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6784 if ( s0.match( query_nodes ) ) {
6788 query_nodes = new HashSet<PhylogenyNode>();
6789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6791 if ( s0.match( query_nodes ) ) {
6795 query_nodes = new HashSet<PhylogenyNode>();
6796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6798 if ( s0.match( query_nodes ) ) {
6802 query_nodes = new HashSet<PhylogenyNode>();
6803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6805 if ( s0.match( query_nodes ) ) {
6809 query_nodes = new HashSet<PhylogenyNode>();
6810 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6813 if ( s0.match( query_nodes ) ) {
6817 query_nodes = new HashSet<PhylogenyNode>();
6818 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6819 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6821 if ( s0.match( query_nodes ) ) {
6825 query_nodes = new HashSet<PhylogenyNode>();
6826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6827 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6828 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6829 if ( s0.match( query_nodes ) ) {
6833 query_nodes = new HashSet<PhylogenyNode>();
6834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6835 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6836 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6837 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6838 if ( s0.match( query_nodes ) ) {
6842 // query_nodes = new HashSet<PhylogenyNode>();
6843 // query_nodes.add( new PhylogenyNode( "X" ) );
6844 // query_nodes.add( new PhylogenyNode( "Y" ) );
6845 // query_nodes.add( new PhylogenyNode( "A" ) );
6846 // query_nodes.add( new PhylogenyNode( "B" ) );
6847 // query_nodes.add( new PhylogenyNode( "C" ) );
6848 // query_nodes.add( new PhylogenyNode( "D" ) );
6849 // query_nodes.add( new PhylogenyNode( "E" ) );
6850 // query_nodes.add( new PhylogenyNode( "F" ) );
6851 // query_nodes.add( new PhylogenyNode( "G" ) );
6852 // if ( !s0.match( query_nodes ) ) {
6855 // query_nodes = new HashSet<PhylogenyNode>();
6856 // query_nodes.add( new PhylogenyNode( "X" ) );
6857 // query_nodes.add( new PhylogenyNode( "Y" ) );
6858 // query_nodes.add( new PhylogenyNode( "A" ) );
6859 // query_nodes.add( new PhylogenyNode( "B" ) );
6860 // query_nodes.add( new PhylogenyNode( "C" ) );
6861 // if ( !s0.match( query_nodes ) ) {
6865 // query_nodes = new HashSet<PhylogenyNode>();
6866 // query_nodes.add( new PhylogenyNode( "X" ) );
6867 // query_nodes.add( new PhylogenyNode( "Y" ) );
6868 // query_nodes.add( new PhylogenyNode( "D" ) );
6869 // query_nodes.add( new PhylogenyNode( "E" ) );
6870 // query_nodes.add( new PhylogenyNode( "F" ) );
6871 // query_nodes.add( new PhylogenyNode( "G" ) );
6872 // if ( !s0.match( query_nodes ) ) {
6876 // query_nodes = new HashSet<PhylogenyNode>();
6877 // query_nodes.add( new PhylogenyNode( "X" ) );
6878 // query_nodes.add( new PhylogenyNode( "Y" ) );
6879 // query_nodes.add( new PhylogenyNode( "A" ) );
6880 // query_nodes.add( new PhylogenyNode( "B" ) );
6881 // query_nodes.add( new PhylogenyNode( "C" ) );
6882 // query_nodes.add( new PhylogenyNode( "D" ) );
6883 // if ( !s0.match( query_nodes ) ) {
6887 // query_nodes = new HashSet<PhylogenyNode>();
6888 // query_nodes.add( new PhylogenyNode( "X" ) );
6889 // query_nodes.add( new PhylogenyNode( "Y" ) );
6890 // query_nodes.add( new PhylogenyNode( "E" ) );
6891 // query_nodes.add( new PhylogenyNode( "F" ) );
6892 // query_nodes.add( new PhylogenyNode( "G" ) );
6893 // if ( !s0.match( query_nodes ) ) {
6897 // query_nodes = new HashSet<PhylogenyNode>();
6898 // query_nodes.add( new PhylogenyNode( "X" ) );
6899 // query_nodes.add( new PhylogenyNode( "Y" ) );
6900 // query_nodes.add( new PhylogenyNode( "F" ) );
6901 // query_nodes.add( new PhylogenyNode( "G" ) );
6902 // if ( !s0.match( query_nodes ) ) {
6906 query_nodes = new HashSet<PhylogenyNode>();
6907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6909 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6910 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6911 if ( s0.match( query_nodes ) ) {
6915 query_nodes = new HashSet<PhylogenyNode>();
6916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6920 if ( s0.match( query_nodes ) ) {
6923 ///////////////////////////
6925 query_nodes = new HashSet<PhylogenyNode>();
6926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6930 if ( s0.match( query_nodes ) ) {
6934 query_nodes = new HashSet<PhylogenyNode>();
6935 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6936 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6937 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6939 if ( s0.match( query_nodes ) ) {
6943 query_nodes = new HashSet<PhylogenyNode>();
6944 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6948 if ( s0.match( query_nodes ) ) {
6952 query_nodes = new HashSet<PhylogenyNode>();
6953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6957 if ( s0.match( query_nodes ) ) {
6961 query_nodes = new HashSet<PhylogenyNode>();
6962 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6966 if ( s0.match( query_nodes ) ) {
6970 query_nodes = new HashSet<PhylogenyNode>();
6971 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6974 if ( s0.match( query_nodes ) ) {
6978 query_nodes = new HashSet<PhylogenyNode>();
6979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6984 if ( s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6994 if ( s0.match( query_nodes ) ) {
6998 query_nodes = new HashSet<PhylogenyNode>();
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7004 if ( s0.match( query_nodes ) ) {
7008 query_nodes = new HashSet<PhylogenyNode>();
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7011 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7015 if ( s0.match( query_nodes ) ) {
7019 catch ( final Exception e ) {
7020 e.printStackTrace();
7026 private static boolean testSplitStrict() {
7028 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7029 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7030 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7031 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7032 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7033 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7034 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7035 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7036 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7037 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7038 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7039 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7042 if ( s0.match( query_nodes ) ) {
7045 query_nodes = new HashSet<PhylogenyNode>();
7046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7053 if ( !s0.match( query_nodes ) ) {
7057 query_nodes = new HashSet<PhylogenyNode>();
7058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7061 if ( !s0.match( query_nodes ) ) {
7065 query_nodes = new HashSet<PhylogenyNode>();
7066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7070 if ( !s0.match( query_nodes ) ) {
7074 query_nodes = new HashSet<PhylogenyNode>();
7075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7079 if ( !s0.match( query_nodes ) ) {
7083 query_nodes = new HashSet<PhylogenyNode>();
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7087 if ( !s0.match( query_nodes ) ) {
7091 query_nodes = new HashSet<PhylogenyNode>();
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7094 if ( !s0.match( query_nodes ) ) {
7098 query_nodes = new HashSet<PhylogenyNode>();
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7104 if ( !s0.match( query_nodes ) ) {
7108 query_nodes = new HashSet<PhylogenyNode>();
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7112 if ( !s0.match( query_nodes ) ) {
7116 query_nodes = new HashSet<PhylogenyNode>();
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7121 if ( !s0.match( query_nodes ) ) {
7125 query_nodes = new HashSet<PhylogenyNode>();
7126 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7128 if ( s0.match( query_nodes ) ) {
7132 query_nodes = new HashSet<PhylogenyNode>();
7133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7134 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7135 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7137 if ( s0.match( query_nodes ) ) {
7141 query_nodes = new HashSet<PhylogenyNode>();
7142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7144 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7147 if ( s0.match( query_nodes ) ) {
7151 query_nodes = new HashSet<PhylogenyNode>();
7152 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7153 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7155 if ( s0.match( query_nodes ) ) {
7159 query_nodes = new HashSet<PhylogenyNode>();
7160 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7162 if ( s0.match( query_nodes ) ) {
7166 query_nodes = new HashSet<PhylogenyNode>();
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7169 if ( s0.match( query_nodes ) ) {
7173 query_nodes = new HashSet<PhylogenyNode>();
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7176 if ( s0.match( query_nodes ) ) {
7180 query_nodes = new HashSet<PhylogenyNode>();
7181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7183 if ( s0.match( query_nodes ) ) {
7187 query_nodes = new HashSet<PhylogenyNode>();
7188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7190 if ( s0.match( query_nodes ) ) {
7194 query_nodes = new HashSet<PhylogenyNode>();
7195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7197 if ( s0.match( query_nodes ) ) {
7201 query_nodes = new HashSet<PhylogenyNode>();
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7203 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7205 if ( s0.match( query_nodes ) ) {
7209 query_nodes = new HashSet<PhylogenyNode>();
7210 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7211 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7213 if ( s0.match( query_nodes ) ) {
7217 query_nodes = new HashSet<PhylogenyNode>();
7218 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7221 if ( s0.match( query_nodes ) ) {
7225 query_nodes = new HashSet<PhylogenyNode>();
7226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7230 if ( s0.match( query_nodes ) ) {
7234 catch ( final Exception e ) {
7235 e.printStackTrace();
7241 private static boolean testSubtreeDeletion() {
7243 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7244 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7245 t1.deleteSubtree( t1.getNode( "A" ), false );
7246 if ( t1.getNumberOfExternalNodes() != 5 ) {
7249 t1.toNewHampshireX();
7250 t1.deleteSubtree( t1.getNode( "E" ), false );
7251 if ( t1.getNumberOfExternalNodes() != 4 ) {
7254 t1.toNewHampshireX();
7255 t1.deleteSubtree( t1.getNode( "F" ), false );
7256 if ( t1.getNumberOfExternalNodes() != 3 ) {
7259 t1.toNewHampshireX();
7260 t1.deleteSubtree( t1.getNode( "D" ), false );
7261 t1.toNewHampshireX();
7262 if ( t1.getNumberOfExternalNodes() != 3 ) {
7265 t1.deleteSubtree( t1.getNode( "def" ), false );
7266 t1.toNewHampshireX();
7267 if ( t1.getNumberOfExternalNodes() != 2 ) {
7270 t1.deleteSubtree( t1.getNode( "B" ), false );
7271 t1.toNewHampshireX();
7272 if ( t1.getNumberOfExternalNodes() != 1 ) {
7275 t1.deleteSubtree( t1.getNode( "C" ), false );
7276 t1.toNewHampshireX();
7277 if ( t1.getNumberOfExternalNodes() != 1 ) {
7280 t1.deleteSubtree( t1.getNode( "abc" ), false );
7281 t1.toNewHampshireX();
7282 if ( t1.getNumberOfExternalNodes() != 1 ) {
7285 t1.deleteSubtree( t1.getNode( "r" ), false );
7286 if ( t1.getNumberOfExternalNodes() != 0 ) {
7289 if ( !t1.isEmpty() ) {
7292 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7293 t2.deleteSubtree( t2.getNode( "A" ), false );
7294 t2.toNewHampshireX();
7295 if ( t2.getNumberOfExternalNodes() != 5 ) {
7298 t2.deleteSubtree( t2.getNode( "abc" ), false );
7299 t2.toNewHampshireX();
7300 if ( t2.getNumberOfExternalNodes() != 3 ) {
7303 t2.deleteSubtree( t2.getNode( "def" ), false );
7304 t2.toNewHampshireX();
7305 if ( t2.getNumberOfExternalNodes() != 1 ) {
7309 catch ( final Exception e ) {
7310 e.printStackTrace( System.out );
7316 private static boolean testSupportCount() {
7318 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7319 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7320 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7321 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7322 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7323 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7324 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7326 SupportCount.count( t0_1, phylogenies_1, true, false );
7327 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7328 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7329 + "(((((A,B),C),D),E),((F,G),X))"
7330 + "(((((A,Y),B),C),D),((F,G),E))"
7331 + "(((((A,B),C),D),E),(F,G))"
7332 + "(((((A,B),C),D),E),(F,G))"
7333 + "(((((A,B),C),D),E),(F,G))"
7334 + "(((((A,B),C),D),E),(F,G),Z)"
7335 + "(((((A,B),C),D),E),(F,G))"
7336 + "((((((A,B),C),D),E),F),G)"
7337 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7339 SupportCount.count( t0_2, phylogenies_2, true, false );
7340 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7341 while ( it.hasNext() ) {
7342 final PhylogenyNode n = it.next();
7343 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7347 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7348 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7349 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7350 SupportCount.count( t0_3, phylogenies_3, true, false );
7351 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7352 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7355 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7358 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7361 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7364 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7367 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7370 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7373 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7376 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7379 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7382 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7383 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7384 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7385 SupportCount.count( t0_4, phylogenies_4, true, false );
7386 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7387 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7390 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7393 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7396 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7399 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7402 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7405 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7408 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7411 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7414 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7417 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7418 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7419 double d = SupportCount.compare( b1, a, true, true, true );
7420 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7423 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7424 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7425 d = SupportCount.compare( b2, a, true, true, true );
7426 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7429 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7430 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7431 d = SupportCount.compare( b3, a, true, true, true );
7432 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7435 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7436 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7437 d = SupportCount.compare( b4, a, true, true, false );
7438 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7442 catch ( final Exception e ) {
7443 e.printStackTrace( System.out );
7449 private static boolean testSupportTransfer() {
7451 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7452 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)",
7453 new NHXParser() )[ 0 ];
7454 final Phylogeny p2 = factory
7455 .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 ];
7456 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7459 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7462 support_transfer.moveBranchLengthsToBootstrap( p1 );
7463 support_transfer.transferSupportValues( p1, p2 );
7464 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7467 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7470 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7473 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7476 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7479 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7482 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7485 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7489 catch ( final Exception e ) {
7490 e.printStackTrace( System.out );
7496 private static boolean testTaxonomyAssigner() {
7498 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]";
7499 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7500 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7501 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7502 s0.setRooted( true );
7503 g0.setRooted( true );
7504 TaxonomyAssigner.execute( g0, s0 );
7505 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7508 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7511 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7514 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7515 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7516 g0.setRooted( true );
7517 TaxonomyAssigner.execute( g0, s0 );
7518 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7521 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7524 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7527 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7528 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7529 g0.setRooted( true );
7530 TaxonomyAssigner.execute( g0, s0 );
7531 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7534 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7537 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7540 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7541 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7542 g0.setRooted( true );
7543 TaxonomyAssigner.execute( g0, s0 );
7544 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7547 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7550 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7553 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7554 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7555 g0.setRooted( true );
7556 TaxonomyAssigner.execute( g0, s0 );
7557 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7560 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7563 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7566 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7567 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7568 g0.setRooted( true );
7569 TaxonomyAssigner.execute( g0, s0 );
7570 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7573 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7576 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7579 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7580 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7581 g0.setRooted( true );
7582 TaxonomyAssigner.execute( g0, s0 );
7583 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7586 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7589 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7592 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7593 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7594 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7595 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7596 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7597 s0.setRooted( true );
7598 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7599 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7600 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7601 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7602 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7603 g0.setRooted( true );
7604 TaxonomyAssigner.execute( g0, s0 );
7605 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7608 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7611 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7614 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7617 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7620 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7621 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7622 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7623 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7624 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7625 g0.setRooted( true );
7626 TaxonomyAssigner.execute( g0, s0 );
7627 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7630 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7633 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7636 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7639 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7642 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7643 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7644 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7645 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7646 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7647 g0.setRooted( true );
7648 TaxonomyAssigner.execute( g0, s0 );
7649 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7652 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7655 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7658 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7661 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7664 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7665 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7666 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7667 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7668 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7669 g0.setRooted( true );
7670 TaxonomyAssigner.execute( g0, s0 );
7671 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7674 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7677 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7680 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7683 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7686 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7687 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7688 g0.setRooted( true );
7689 TaxonomyAssigner.execute( g0, s0 );
7690 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7693 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7696 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7699 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7700 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7701 g0.setRooted( true );
7702 TaxonomyAssigner.execute( g0, s0 );
7703 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7706 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7709 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7712 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7713 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7714 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7715 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7716 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7717 g0.setRooted( true );
7718 TaxonomyAssigner.execute( g0, s0 );
7719 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7722 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7725 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7728 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7731 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7734 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7737 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7740 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7741 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7742 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7743 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7744 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7745 g0.setRooted( true );
7746 TaxonomyAssigner.execute( g0, s0 );
7747 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7750 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7753 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7756 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7759 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7762 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7765 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7768 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7769 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7770 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7771 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7772 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7773 g0.setRooted( true );
7774 TaxonomyAssigner.execute( g0, s0 );
7775 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7778 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7781 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7784 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7787 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7790 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7793 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7796 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7797 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7798 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7799 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7800 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7801 g0.setRooted( true );
7802 TaxonomyAssigner.execute( g0, s0 );
7803 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7806 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7809 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7812 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7815 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7818 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7821 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7824 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7825 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7826 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7827 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7828 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7829 s0.setRooted( true );
7830 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7831 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7832 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7833 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7834 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7835 g0.setRooted( true );
7836 TaxonomyAssigner.execute( g0, s0 );
7837 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7840 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7844 catch ( final Exception e ) {
7845 e.printStackTrace( System.out );
7851 private static boolean testUniprotTaxonomySearch() {
7853 List<UniProtTaxonomy> results = UniProtWsTools
7854 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7855 if ( results.size() != 1 ) {
7858 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7861 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7864 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7867 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7870 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7874 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7875 if ( results.size() != 1 ) {
7878 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7881 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7884 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7887 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7890 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7894 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7895 if ( results.size() != 1 ) {
7898 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7901 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7904 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7907 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7910 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7914 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7915 if ( results.size() != 1 ) {
7918 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7921 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7924 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7927 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7930 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7933 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7936 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7939 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7940 .equals( "Nematostella vectensis" ) ) {
7941 System.out.println( results.get( 0 ).getLineage() );
7945 catch ( final IOException e ) {
7946 System.out.println();
7947 System.out.println( "the following might be due to absence internet connection:" );
7948 e.printStackTrace( System.out );
7951 catch ( final Exception e ) {
7957 private static boolean testEmblEntryRetrieval() {
7958 //The format for GenBank Accession numbers are:
7959 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7960 //Protein: 3 letters + 5 numerals
7961 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7962 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7965 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7968 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7971 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7974 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7977 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7980 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7983 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7986 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7989 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7992 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7995 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7998 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8004 private static boolean testUniprotEntryRetrieval() {
8005 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8008 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8011 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8014 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8017 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8020 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8023 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8026 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8029 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8032 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8035 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8038 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8041 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8045 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
8046 if ( !entry.getAccession().equals( "P12345" ) ) {
8049 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8052 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8055 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8058 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8062 catch ( final IOException e ) {
8063 System.out.println();
8064 System.out.println( "the following might be due to absence internet connection:" );
8065 e.printStackTrace( System.out );
8068 catch ( final Exception e ) {
8074 private static boolean testWabiTxSearch() {
8077 result = TxSearch.searchSimple( "nematostella" );
8078 result = TxSearch.getTxId( "nematostella" );
8079 if ( !result.equals( "45350" ) ) {
8082 result = TxSearch.getTxName( "45350" );
8083 if ( !result.equals( "Nematostella" ) ) {
8086 result = TxSearch.getTxId( "nematostella vectensis" );
8087 if ( !result.equals( "45351" ) ) {
8090 result = TxSearch.getTxName( "45351" );
8091 if ( !result.equals( "Nematostella vectensis" ) ) {
8094 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8095 if ( !result.equals( "536089" ) ) {
8098 result = TxSearch.getTxName( "536089" );
8099 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8102 final List<String> queries = new ArrayList<String>();
8103 queries.add( "Campylobacter coli" );
8104 queries.add( "Escherichia coli" );
8105 queries.add( "Arabidopsis" );
8106 queries.add( "Trichoplax" );
8107 queries.add( "Samanea saman" );
8108 queries.add( "Kluyveromyces marxianus" );
8109 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8110 queries.add( "Bornavirus parrot/PDD/2008" );
8111 final List<RANKS> ranks = new ArrayList<RANKS>();
8112 ranks.add( RANKS.SUPERKINGDOM );
8113 ranks.add( RANKS.KINGDOM );
8114 ranks.add( RANKS.FAMILY );
8115 ranks.add( RANKS.GENUS );
8116 ranks.add( RANKS.TRIBE );
8117 result = TxSearch.searchLineage( queries, ranks );
8118 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8119 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8121 catch ( final Exception e ) {
8122 System.out.println();
8123 System.out.println( "the following might be due to absence internet connection:" );
8124 e.printStackTrace( System.out );
8130 private static boolean testAminoAcidSequence() {
8132 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8133 if ( aa1.getLength() != 13 ) {
8136 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8139 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8142 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8145 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8146 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8149 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8150 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8153 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8154 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8158 catch ( final Exception e ) {
8159 e.printStackTrace();
8165 private static boolean testCreateBalancedPhylogeny() {
8167 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8168 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8171 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8174 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8175 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8178 if ( p1.getNumberOfExternalNodes() != 100 ) {
8182 catch ( final Exception e ) {
8183 e.printStackTrace();
8189 private static boolean testFastaParser() {
8191 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8194 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8197 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8198 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8201 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8204 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8207 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8210 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8213 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8217 catch ( final Exception e ) {
8218 e.printStackTrace();
8224 private static boolean testGeneralMsaParser() {
8226 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8227 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8228 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8229 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8230 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8231 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8232 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8233 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8234 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8237 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8240 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8243 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8246 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8249 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8252 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8255 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8258 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8261 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8264 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8267 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8270 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8271 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8274 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8277 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8280 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8281 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8284 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8287 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8290 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8291 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8294 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8297 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8301 catch ( final Exception e ) {
8302 e.printStackTrace();
8308 private static boolean testMafft() {
8310 final List<String> opts = new ArrayList<String>();
8311 opts.add( "--maxiterate" );
8313 opts.add( "--localpair" );
8314 opts.add( "--quiet" );
8316 final MsaInferrer mafft = Mafft.createInstance();
8317 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8318 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8321 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8325 catch ( final Exception e ) {
8326 e.printStackTrace( System.out );
8332 private static boolean testNextNodeWithCollapsing() {
8334 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8336 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8337 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8338 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8339 t0.getNode( "cd" ).setCollapse( true );
8340 t0.getNode( "cde" ).setCollapse( true );
8341 n = t0.getFirstExternalNode();
8342 while ( n != null ) {
8344 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8346 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8349 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8352 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8355 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8358 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8361 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8365 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8366 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8367 t1.getNode( "ab" ).setCollapse( true );
8368 t1.getNode( "cd" ).setCollapse( true );
8369 t1.getNode( "cde" ).setCollapse( true );
8370 n = t1.getNode( "ab" );
8371 ext = new ArrayList<PhylogenyNode>();
8372 while ( n != null ) {
8374 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8376 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8379 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8382 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8385 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8388 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8394 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8395 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8396 t2.getNode( "ab" ).setCollapse( true );
8397 t2.getNode( "cd" ).setCollapse( true );
8398 t2.getNode( "cde" ).setCollapse( true );
8399 t2.getNode( "c" ).setCollapse( true );
8400 t2.getNode( "d" ).setCollapse( true );
8401 t2.getNode( "e" ).setCollapse( true );
8402 t2.getNode( "gh" ).setCollapse( true );
8403 n = t2.getNode( "ab" );
8404 ext = new ArrayList<PhylogenyNode>();
8405 while ( n != null ) {
8407 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8409 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8412 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8415 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8418 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8424 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8425 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8426 t3.getNode( "ab" ).setCollapse( true );
8427 t3.getNode( "cd" ).setCollapse( true );
8428 t3.getNode( "cde" ).setCollapse( true );
8429 t3.getNode( "c" ).setCollapse( true );
8430 t3.getNode( "d" ).setCollapse( true );
8431 t3.getNode( "e" ).setCollapse( true );
8432 t3.getNode( "gh" ).setCollapse( true );
8433 t3.getNode( "fgh" ).setCollapse( true );
8434 n = t3.getNode( "ab" );
8435 ext = new ArrayList<PhylogenyNode>();
8436 while ( n != null ) {
8438 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8440 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8443 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8446 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8452 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8453 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8454 t4.getNode( "ab" ).setCollapse( true );
8455 t4.getNode( "cd" ).setCollapse( true );
8456 t4.getNode( "cde" ).setCollapse( true );
8457 t4.getNode( "c" ).setCollapse( true );
8458 t4.getNode( "d" ).setCollapse( true );
8459 t4.getNode( "e" ).setCollapse( true );
8460 t4.getNode( "gh" ).setCollapse( true );
8461 t4.getNode( "fgh" ).setCollapse( true );
8462 t4.getNode( "abcdefgh" ).setCollapse( true );
8463 n = t4.getNode( "abcdefgh" );
8464 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8469 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8470 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8472 n = t5.getFirstExternalNode();
8473 while ( n != null ) {
8475 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8477 if ( ext.size() != 8 ) {
8480 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8483 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8486 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8489 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8492 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8495 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8498 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8501 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8506 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8507 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8509 t6.getNode( "ab" ).setCollapse( true );
8510 n = t6.getNode( "ab" );
8511 while ( n != null ) {
8513 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8515 if ( ext.size() != 7 ) {
8518 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8521 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8524 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8527 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8530 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8533 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8536 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8541 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8542 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8544 t7.getNode( "cd" ).setCollapse( true );
8545 n = t7.getNode( "a" );
8546 while ( n != null ) {
8548 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8550 if ( ext.size() != 7 ) {
8553 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8556 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8559 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8562 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8565 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8568 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8571 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8576 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8577 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8579 t8.getNode( "cd" ).setCollapse( true );
8580 t8.getNode( "c" ).setCollapse( true );
8581 t8.getNode( "d" ).setCollapse( true );
8582 n = t8.getNode( "a" );
8583 while ( n != null ) {
8585 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8587 if ( ext.size() != 7 ) {
8590 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8593 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8596 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8597 System.out.println( "2 fail" );
8600 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8603 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8606 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8609 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8614 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8615 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8617 t9.getNode( "gh" ).setCollapse( true );
8618 n = t9.getNode( "a" );
8619 while ( n != null ) {
8621 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8623 if ( ext.size() != 7 ) {
8626 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8629 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8632 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8635 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8638 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8641 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8644 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8649 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8650 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8652 t10.getNode( "gh" ).setCollapse( true );
8653 t10.getNode( "g" ).setCollapse( true );
8654 t10.getNode( "h" ).setCollapse( true );
8655 n = t10.getNode( "a" );
8656 while ( n != null ) {
8658 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8660 if ( ext.size() != 7 ) {
8663 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8666 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8669 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8672 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8675 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8678 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8681 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8686 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8687 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8689 t11.getNode( "gh" ).setCollapse( true );
8690 t11.getNode( "fgh" ).setCollapse( true );
8691 n = t11.getNode( "a" );
8692 while ( n != null ) {
8694 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8696 if ( ext.size() != 6 ) {
8699 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8702 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8705 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8708 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8711 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8714 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8719 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8720 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8722 t12.getNode( "gh" ).setCollapse( true );
8723 t12.getNode( "fgh" ).setCollapse( true );
8724 t12.getNode( "g" ).setCollapse( true );
8725 t12.getNode( "h" ).setCollapse( true );
8726 t12.getNode( "f" ).setCollapse( true );
8727 n = t12.getNode( "a" );
8728 while ( n != null ) {
8730 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8732 if ( ext.size() != 6 ) {
8735 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8738 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8741 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8744 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8747 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8750 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8755 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8756 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8758 t13.getNode( "ab" ).setCollapse( true );
8759 t13.getNode( "b" ).setCollapse( true );
8760 t13.getNode( "fgh" ).setCollapse( true );
8761 t13.getNode( "gh" ).setCollapse( true );
8762 n = t13.getNode( "ab" );
8763 while ( n != null ) {
8765 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8767 if ( ext.size() != 5 ) {
8770 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8773 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8776 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8779 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8782 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8787 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8788 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8790 t14.getNode( "ab" ).setCollapse( true );
8791 t14.getNode( "a" ).setCollapse( true );
8792 t14.getNode( "fgh" ).setCollapse( true );
8793 t14.getNode( "gh" ).setCollapse( true );
8794 n = t14.getNode( "ab" );
8795 while ( n != null ) {
8797 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8799 if ( ext.size() != 5 ) {
8802 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8805 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8808 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8811 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8814 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8819 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" );
8820 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8822 t15.getNode( "ab" ).setCollapse( true );
8823 t15.getNode( "a" ).setCollapse( true );
8824 t15.getNode( "fgh" ).setCollapse( true );
8825 t15.getNode( "gh" ).setCollapse( true );
8826 n = t15.getNode( "ab" );
8827 while ( n != null ) {
8829 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8831 if ( ext.size() != 6 ) {
8834 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8837 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8840 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8843 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8846 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8849 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8854 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" );
8855 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8857 t16.getNode( "ab" ).setCollapse( true );
8858 t16.getNode( "a" ).setCollapse( true );
8859 t16.getNode( "fgh" ).setCollapse( true );
8860 t16.getNode( "gh" ).setCollapse( true );
8861 t16.getNode( "cd" ).setCollapse( true );
8862 t16.getNode( "cde" ).setCollapse( true );
8863 t16.getNode( "d" ).setCollapse( true );
8864 t16.getNode( "x" ).setCollapse( true );
8865 n = t16.getNode( "ab" );
8866 while ( n != null ) {
8868 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8870 if ( ext.size() != 4 ) {
8873 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8876 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8879 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8882 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8886 catch ( final Exception e ) {
8887 e.printStackTrace( System.out );
8893 private static boolean testMsaQualityMethod() {
8895 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8896 final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
8897 final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
8898 final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
8899 final List<Sequence> l = new ArrayList<Sequence>();
8904 final Msa msa = BasicMsa.createInstance( l );
8905 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8908 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8911 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8914 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8918 catch ( final Exception e ) {
8919 e.printStackTrace( System.out );
8925 private static boolean testSequenceIdParsing() {
8927 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8929 || ForesterUtil.isEmpty( id.getValue() )
8930 || ForesterUtil.isEmpty( id.getProvider() )
8931 || !id.getValue().equals( "ADF31344" )
8932 || !id.getProvider().equals( "ncbi" ) ) {
8934 System.out.println( "value =" + id.getValue() );
8935 System.out.println( "provider=" + id.getProvider() );
8940 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8942 || ForesterUtil.isEmpty( id.getValue() )
8943 || ForesterUtil.isEmpty( id.getProvider() )
8944 || !id.getValue().equals( "ADF31344" )
8945 || !id.getProvider().equals( "ncbi" ) ) {
8947 System.out.println( "value =" + id.getValue() );
8948 System.out.println( "provider=" + id.getProvider() );
8953 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8955 || ForesterUtil.isEmpty( id.getValue() )
8956 || ForesterUtil.isEmpty( id.getProvider() )
8957 || !id.getValue().equals( "ADF31344" )
8958 || !id.getProvider().equals( "ncbi" ) ) {
8960 System.out.println( "value =" + id.getValue() );
8961 System.out.println( "provider=" + id.getProvider() );
8967 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8969 || ForesterUtil.isEmpty( id.getValue() )
8970 || ForesterUtil.isEmpty( id.getProvider() )
8971 || !id.getValue().equals( "AAA96518" )
8972 || !id.getProvider().equals( "ncbi" ) ) {
8974 System.out.println( "value =" + id.getValue() );
8975 System.out.println( "provider=" + id.getProvider() );
8980 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8982 || ForesterUtil.isEmpty( id.getValue() )
8983 || ForesterUtil.isEmpty( id.getProvider() )
8984 || !id.getValue().equals( "EHB07727" )
8985 || !id.getProvider().equals( "ncbi" ) ) {
8987 System.out.println( "value =" + id.getValue() );
8988 System.out.println( "provider=" + id.getProvider() );
8993 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8995 || ForesterUtil.isEmpty( id.getValue() )
8996 || ForesterUtil.isEmpty( id.getProvider() )
8997 || !id.getValue().equals( "BAF37827" )
8998 || !id.getProvider().equals( "ncbi" ) ) {
9000 System.out.println( "value =" + id.getValue() );
9001 System.out.println( "provider=" + id.getProvider() );
9006 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9008 || ForesterUtil.isEmpty( id.getValue() )
9009 || ForesterUtil.isEmpty( id.getProvider() )
9010 || !id.getValue().equals( "CAA73223" )
9011 || !id.getProvider().equals( "ncbi" ) ) {
9013 System.out.println( "value =" + id.getValue() );
9014 System.out.println( "provider=" + id.getProvider() );
9019 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9021 || ForesterUtil.isEmpty( id.getValue() )
9022 || ForesterUtil.isEmpty( id.getProvider() )
9023 || !id.getValue().equals( "XP_002434188" )
9024 || !id.getProvider().equals( "refseq" ) ) {
9026 System.out.println( "value =" + id.getValue() );
9027 System.out.println( "provider=" + id.getProvider() );
9032 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9034 || ForesterUtil.isEmpty( id.getValue() )
9035 || ForesterUtil.isEmpty( id.getProvider() )
9036 || !id.getValue().equals( "XP_002434188" )
9037 || !id.getProvider().equals( "refseq" ) ) {
9039 System.out.println( "value =" + id.getValue() );
9040 System.out.println( "provider=" + id.getProvider() );
9045 id = SequenceIdParser.parse( "XP_12345" );
9050 // lcl_91970_unknown_
9052 catch ( final Exception e ) {
9053 e.printStackTrace( System.out );