2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.BasicMsa;
58 import org.forester.msa.Mafft;
59 import org.forester.msa.Msa;
60 import org.forester.msa.MsaInferrer;
61 import org.forester.msa.MsaMethods;
62 import org.forester.pccx.TestPccx;
63 import org.forester.phylogeny.Phylogeny;
64 import org.forester.phylogeny.PhylogenyBranch;
65 import org.forester.phylogeny.PhylogenyMethods;
66 import org.forester.phylogeny.PhylogenyNode;
67 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
68 import org.forester.phylogeny.data.BinaryCharacters;
69 import org.forester.phylogeny.data.BranchWidth;
70 import org.forester.phylogeny.data.Confidence;
71 import org.forester.phylogeny.data.Distribution;
72 import org.forester.phylogeny.data.DomainArchitecture;
73 import org.forester.phylogeny.data.Event;
74 import org.forester.phylogeny.data.Identifier;
75 import org.forester.phylogeny.data.PhylogenyData;
76 import org.forester.phylogeny.data.PhylogenyDataUtil;
77 import org.forester.phylogeny.data.Polygon;
78 import org.forester.phylogeny.data.PropertiesMap;
79 import org.forester.phylogeny.data.Property;
80 import org.forester.phylogeny.data.Property.AppliesTo;
81 import org.forester.phylogeny.data.ProteinDomain;
82 import org.forester.phylogeny.data.Taxonomy;
83 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
84 import org.forester.phylogeny.factories.PhylogenyFactory;
85 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
86 import org.forester.protein.Protein;
87 import org.forester.sdi.SDI;
88 import org.forester.sdi.SDIR;
89 import org.forester.sdi.SDIse;
90 import org.forester.sdi.TestGSDI;
91 import org.forester.sequence.BasicSequence;
92 import org.forester.sequence.Sequence;
93 import org.forester.surfacing.TestSurfacing;
94 import org.forester.tools.ConfidenceAssessor;
95 import org.forester.tools.SupportCount;
96 import org.forester.tools.TreeSplitMatrix;
97 import org.forester.util.AsciiHistogram;
98 import org.forester.util.BasicDescriptiveStatistics;
99 import org.forester.util.BasicTable;
100 import org.forester.util.BasicTableParser;
101 import org.forester.util.DescriptiveStatistics;
102 import org.forester.util.ForesterConstants;
103 import org.forester.util.ForesterUtil;
104 import org.forester.util.GeneralTable;
105 import org.forester.util.SequenceIdParser;
106 import org.forester.ws.seqdb.SequenceDatabaseEntry;
107 import org.forester.ws.seqdb.SequenceDbWsTools;
108 import org.forester.ws.seqdb.UniProtTaxonomy;
109 import org.forester.ws.wabi.TxSearch;
110 import org.forester.ws.wabi.TxSearch.RANKS;
111 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
112 import org.forester.ws.wabi.TxSearch.TAX_RANK;
114 @SuppressWarnings( "unused")
115 public final class Test {
117 private final static double ZERO_DIFF = 1.0E-9;
118 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
119 + ForesterUtil.getFileSeparator() + "test_data"
120 + ForesterUtil.getFileSeparator();
121 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
122 + ForesterUtil.getFileSeparator() + "resources"
123 + ForesterUtil.getFileSeparator();
124 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
125 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
126 + ForesterConstants.PHYLO_XML_VERSION + "/"
127 + ForesterConstants.PHYLO_XML_XSD;
128 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
129 + ForesterConstants.PHYLO_XML_VERSION + "/"
130 + ForesterConstants.PHYLO_XML_XSD;
132 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
133 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
137 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
138 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
139 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
142 public static boolean isEqual( final double a, final double b ) {
143 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
146 public static void main( final String[] args ) {
147 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
148 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
150 Locale.setDefault( Locale.US );
151 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
154 System.out.print( "[Test if directory with files for testing exists/is readable: " );
155 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
156 System.out.println( "OK.]" );
159 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
160 System.out.println( "Testing aborted." );
163 System.out.print( "[Test if resources directory exists/is readable: " );
164 if ( testDir( PATH_TO_RESOURCES ) ) {
165 System.out.println( "OK.]" );
168 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
169 System.out.println( "Testing aborted." );
172 final long start_time = new Date().getTime();
173 System.out.print( "Sequence id parsing: " );
174 if ( testSequenceIdParsing() ) {
175 System.out.println( "OK." );
179 System.out.println( "failed." );
180 System.exit( -1 ); //TODO FIXME remove me!! ~
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Basic node construction and parsing of NHX (node level): " );
202 if ( Test.testNHXNodeParsing() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "NH parsing: " );
211 if ( Test.testNHParsing() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Conversion to NHX (node level): " );
220 if ( Test.testNHXconversion() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing: " );
229 if ( Test.testNHXParsing() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NHX parsing with quotes: " );
238 if ( Test.testNHXParsingQuotes() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "NHX parsing (MrBayes): " );
247 if ( Test.testNHXParsingMB() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "Nexus characters parsing: " );
256 if ( Test.testNexusCharactersParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "Nexus tree parsing: " );
265 if ( Test.testNexusTreeParsing() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "Nexus tree parsing (translating): " );
274 if ( Test.testNexusTreeParsingTranslating() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus matrix parsing: " );
283 if ( Test.testNexusMatrixParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Basic phyloXML parsing: " );
292 if ( Test.testBasicPhyloXMLparsing() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Basic phyloXML parsing (validating against schema): " );
301 if ( testBasicPhyloXMLparsingValidating() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
310 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "phyloXML Distribution Element: " );
319 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Tol XML parsing: " );
328 if ( Test.testBasicTolXMLparsing() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Copying of node data: " );
337 if ( Test.testCopyOfNodeData() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Basic tree methods: " );
346 if ( Test.testBasicTreeMethods() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "Postorder Iterator: " );
355 if ( Test.testPostOrderIterator() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Preorder Iterator: " );
364 if ( Test.testPreOrderIterator() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Levelorder Iterator: " );
373 if ( Test.testLevelOrderIterator() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Re-id methods: " );
382 if ( Test.testReIdMethods() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Methods on last external nodes: " );
391 if ( Test.testLastExternalNodeMethods() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Methods on external nodes: " );
400 if ( Test.testExternalNodeRelatedMethods() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Deletion of external nodes: " );
409 if ( Test.testDeletionOfExternalNodes() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Subtree deletion: " );
418 if ( Test.testSubtreeDeletion() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Phylogeny branch: " );
427 if ( Test.testPhylogenyBranch() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Rerooting: " );
436 if ( Test.testRerooting() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Mipoint rooting: " );
445 if ( Test.testMidpointrooting() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Support count: " );
454 if ( Test.testSupportCount() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Support transfer: " );
463 if ( Test.testSupportTransfer() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Finding of LCA: " );
472 if ( Test.testGetLCA() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Calculation of distance between nodes: " );
481 if ( Test.testGetDistance() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "SDIse: " );
490 if ( Test.testSDIse() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "SDIunrooted: " );
499 if ( Test.testSDIunrooted() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "GSDI: " );
508 if ( TestGSDI.test() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Descriptive statistics: " );
517 if ( Test.testDescriptiveStatistics() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Data objects and methods: " );
526 if ( Test.testDataObjects() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Properties map: " );
535 if ( Test.testPropertiesMap() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Phylogeny reconstruction:" );
544 System.out.println();
545 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Analysis of domain architectures: " );
554 System.out.println();
555 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "GO: " );
564 System.out.println();
565 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
566 System.out.println( "OK." );
570 System.out.println( "failed." );
573 System.out.print( "Modeling tools: " );
574 if ( TestPccx.test() ) {
575 System.out.println( "OK." );
579 System.out.println( "failed." );
582 System.out.print( "Split Matrix strict: " );
583 if ( Test.testSplitStrict() ) {
584 System.out.println( "OK." );
588 System.out.println( "failed." );
591 System.out.print( "Split Matrix: " );
592 if ( Test.testSplit() ) {
593 System.out.println( "OK." );
597 System.out.println( "failed." );
600 System.out.print( "Confidence Assessor: " );
601 if ( Test.testConfidenceAssessor() ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "Basic table: " );
610 if ( Test.testBasicTable() ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "General table: " );
619 if ( Test.testGeneralTable() ) {
620 System.out.println( "OK." );
624 System.out.println( "failed." );
627 System.out.print( "Amino acid sequence: " );
628 if ( Test.testAminoAcidSequence() ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "General MSA parser: " );
637 if ( Test.testGeneralMsaParser() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Fasta parser for msa: " );
646 if ( Test.testFastaParser() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Creation of balanced phylogeny: " );
655 if ( Test.testCreateBalancedPhylogeny() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "EMBL Entry Retrieval: " );
664 if ( Test.testEmblEntryRetrieval() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Uniprot Entry Retrieval: " );
673 if ( Test.testUniprotEntryRetrieval() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "Uniprot Taxonomy Search: " );
682 if ( Test.testUniprotTaxonomySearch() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
692 final String os = ForesterUtil.OS_NAME.toLowerCase();
693 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
694 path = "/usr/local/bin/mafft";
696 else if ( os.indexOf( "win" ) >= 0 ) {
697 path = "C:\\Program Files\\mafft-win\\mafft.bat";
700 path = "/home/czmasek/bin/mafft";
702 if ( !Mafft.isInstalled( path ) ) {
705 if ( !Mafft.isInstalled( path ) ) {
706 path = "/usr/local/bin/mafft";
708 if ( Mafft.isInstalled( path ) ) {
709 System.out.print( "MAFFT (external program): " );
710 if ( Test.testMafft( path ) ) {
711 System.out.println( "OK." );
715 System.out.println( "failed [will not count towards failed tests]" );
719 System.out.print( "Next nodes with collapsed: " );
720 if ( Test.testNextNodeWithCollapsing() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 System.out.print( "Simple MSA quality: " );
729 if ( Test.testMsaQualityMethod() ) {
730 System.out.println( "OK." );
734 System.out.println( "failed." );
737 // System.out.print( "WABI TxSearch: " );
738 // if ( Test.testWabiTxSearch() ) {
739 // System.out.println( "OK." );
744 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
746 System.out.println();
747 final Runtime rt = java.lang.Runtime.getRuntime();
748 final long free_memory = rt.freeMemory() / 1000000;
749 final long total_memory = rt.totalMemory() / 1000000;
750 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
751 + free_memory + "MB, total memory: " + total_memory + "MB)" );
752 System.out.println();
753 System.out.println( "Successful tests: " + succeeded );
754 System.out.println( "Failed tests: " + failed );
755 System.out.println();
757 System.out.println( "OK." );
760 System.out.println( "Not OK." );
762 // System.out.println();
763 // Development.setTime( true );
765 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
766 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
767 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
768 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
769 // "multifurcations_ex_1.nhx";
770 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
771 // final Phylogeny t1 = factory.create( new File( domains ), new
772 // NHXParser() )[ 0 ];
773 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
775 // catch ( final Exception e ) {
776 // e.printStackTrace();
778 // t1.getRoot().preorderPrint();
779 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
783 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
784 // + "\\AtNBSpos.nhx" ) );
786 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
787 // new NHXParser() );
788 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
789 // + "\\AtNBSpos.nhx" ) );
791 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
792 // new NHXParser() );
795 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
796 // + "\\big_tree.nhx" ) );
797 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
798 // + "\\big_tree.nhx" ) );
800 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
801 // new NHXParser() );
803 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
804 // new NHXParser() );
806 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
807 // + "\\big_tree.nhx" ) );
808 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
809 // + "\\big_tree.nhx" ) );
812 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
813 // new NHXParser() );
815 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
816 // new NHXParser() );
818 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
819 // + "\\AtNBSpos.nhx" ) );
821 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
822 // new NHXParser() );
825 // catch ( IOException e ) {
826 // // TODO Auto-generated catch block
827 // e.printStackTrace();
831 private static boolean testBasicNodeMethods() {
833 if ( PhylogenyNode.getNodeCount() != 0 ) {
836 final PhylogenyNode n1 = new PhylogenyNode();
837 final PhylogenyNode n2 = PhylogenyNode
838 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
839 final PhylogenyNode n3 = PhylogenyNode
840 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
841 final PhylogenyNode n4 = PhylogenyNode
842 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
843 if ( n1.isHasAssignedEvent() ) {
846 if ( PhylogenyNode.getNodeCount() != 4 ) {
849 if ( n3.getIndicator() != 0 ) {
852 if ( n3.getNumberOfExternalNodes() != 1 ) {
855 if ( !n3.isExternal() ) {
858 if ( !n3.isRoot() ) {
861 if ( !n4.getName().equals( "n4" ) ) {
865 catch ( final Exception e ) {
866 e.printStackTrace( System.out );
872 private static boolean testBasicPhyloXMLparsing() {
874 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
875 final PhyloXmlParser xml_parser = new PhyloXmlParser();
876 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
878 if ( xml_parser.getErrorCount() > 0 ) {
879 System.out.println( xml_parser.getErrorMessages().toString() );
882 if ( phylogenies_0.length != 4 ) {
885 final Phylogeny t1 = phylogenies_0[ 0 ];
886 final Phylogeny t2 = phylogenies_0[ 1 ];
887 final Phylogeny t3 = phylogenies_0[ 2 ];
888 final Phylogeny t4 = phylogenies_0[ 3 ];
889 if ( t1.getNumberOfExternalNodes() != 1 ) {
892 if ( !t1.isRooted() ) {
895 if ( t1.isRerootable() ) {
898 if ( !t1.getType().equals( "gene_tree" ) ) {
901 if ( t2.getNumberOfExternalNodes() != 2 ) {
904 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
907 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
910 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
913 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
916 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
919 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
922 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
923 .startsWith( "actgtgggggt" ) ) {
926 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
927 .startsWith( "ctgtgatgcat" ) ) {
930 if ( t3.getNumberOfExternalNodes() != 4 ) {
933 if ( !t1.getName().equals( "t1" ) ) {
936 if ( !t2.getName().equals( "t2" ) ) {
939 if ( !t3.getName().equals( "t3" ) ) {
942 if ( !t4.getName().equals( "t4" ) ) {
945 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
948 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
951 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
954 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
955 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
958 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
961 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
964 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
967 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
968 .equals( "apoptosis" ) ) {
971 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
972 .equals( "GO:0006915" ) ) {
975 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
976 .equals( "UniProtKB" ) ) {
979 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
980 .equals( "experimental" ) ) {
983 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
984 .equals( "function" ) ) {
987 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
991 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
992 .getType().equals( "ml" ) ) {
995 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
996 .equals( "apoptosis" ) ) {
999 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1000 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1003 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1004 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1007 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1008 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1011 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1012 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1015 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1016 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1019 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1020 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1023 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1024 .equals( "GO:0005829" ) ) {
1027 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1028 .equals( "intracellular organelle" ) ) {
1031 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1034 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1035 .equals( "UniProt link" ) ) ) {
1038 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1041 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1044 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1047 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1050 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1053 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1056 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1059 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1062 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1065 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1068 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1069 // .equals( "B" ) ) {
1072 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1075 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1078 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1081 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1082 // .getConfidence() != 2144 ) {
1085 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1086 // .equals( "pfam" ) ) {
1089 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1092 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1095 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1098 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1101 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1102 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1106 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1109 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1112 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1115 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1118 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1121 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1124 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1127 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1129 // if ( xml_parser.getErrorCount() > 0 ) {
1130 // System.out.println( xml_parser.getErrorMessages().toString() );
1133 // if ( phylogenies_1.length != 2 ) {
1136 // final Phylogeny a = phylogenies_1[ 0 ];
1137 // if ( !a.getName().equals( "tree 4" ) ) {
1140 // if ( a.getNumberOfExternalNodes() != 3 ) {
1143 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1146 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1150 catch ( final Exception e ) {
1151 e.printStackTrace( System.out );
1157 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1159 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1160 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1161 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1162 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1165 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1167 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1169 if ( xml_parser.getErrorCount() > 0 ) {
1170 System.out.println( xml_parser.getErrorMessages().toString() );
1173 if ( phylogenies_0.length != 4 ) {
1176 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1177 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1178 if ( phylogenies_t1.length != 1 ) {
1181 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1182 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1185 if ( !t1_rt.isRooted() ) {
1188 if ( t1_rt.isRerootable() ) {
1191 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1194 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1195 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1196 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1197 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1200 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1203 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1206 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1209 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1210 .startsWith( "actgtgggggt" ) ) {
1213 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1214 .startsWith( "ctgtgatgcat" ) ) {
1217 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1218 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1219 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1220 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1221 if ( phylogenies_1.length != 1 ) {
1224 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1225 if ( !t3_rt.getName().equals( "t3" ) ) {
1228 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1231 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1234 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1237 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1240 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1241 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1244 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1247 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1250 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1251 .equals( "UniProtKB" ) ) {
1254 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1255 .equals( "apoptosis" ) ) {
1258 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1259 .equals( "GO:0006915" ) ) {
1262 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1263 .equals( "UniProtKB" ) ) {
1266 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1267 .equals( "experimental" ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1271 .equals( "function" ) ) {
1274 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1275 .getValue() != 1 ) {
1278 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1279 .getType().equals( "ml" ) ) {
1282 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1283 .equals( "apoptosis" ) ) {
1286 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1287 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1290 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1291 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1294 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1295 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1298 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1299 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1302 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1303 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1306 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1307 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1310 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1311 .equals( "GO:0005829" ) ) {
1314 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1315 .equals( "intracellular organelle" ) ) {
1318 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1321 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1322 .equals( "UniProt link" ) ) ) {
1325 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1328 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1331 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1332 .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." ) ) ) {
1335 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1338 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1341 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1344 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1347 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1348 .equals( "ncbi" ) ) {
1351 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1354 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1355 .getName().equals( "B" ) ) {
1358 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1359 .getFrom() != 21 ) {
1362 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1365 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1366 .getLength() != 24 ) {
1369 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1370 .getConfidence() != 2144 ) {
1373 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1374 .equals( "pfam" ) ) {
1377 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1380 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1383 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1386 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1389 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1390 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1393 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1396 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1399 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1402 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1405 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1408 if ( taxbb.getSynonyms().size() != 2 ) {
1411 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1414 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1417 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1420 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1423 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1426 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1427 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1431 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1434 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1437 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1440 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1443 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1446 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1449 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1453 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1456 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1457 .equalsIgnoreCase( "435" ) ) {
1460 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1463 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1464 .equalsIgnoreCase( "443.7" ) ) {
1467 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1470 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1473 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1474 .equalsIgnoreCase( "433" ) ) {
1478 catch ( final Exception e ) {
1479 e.printStackTrace( System.out );
1485 private static boolean testBasicPhyloXMLparsingValidating() {
1487 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1488 PhyloXmlParser xml_parser = null;
1490 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1492 catch ( final Exception e ) {
1493 // Do nothing -- means were not running from jar.
1495 if ( xml_parser == null ) {
1496 xml_parser = new PhyloXmlParser();
1497 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1498 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1501 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1504 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1506 if ( xml_parser.getErrorCount() > 0 ) {
1507 System.out.println( xml_parser.getErrorMessages().toString() );
1510 if ( phylogenies_0.length != 4 ) {
1513 final Phylogeny t1 = phylogenies_0[ 0 ];
1514 final Phylogeny t2 = phylogenies_0[ 1 ];
1515 final Phylogeny t3 = phylogenies_0[ 2 ];
1516 final Phylogeny t4 = phylogenies_0[ 3 ];
1517 if ( !t1.getName().equals( "t1" ) ) {
1520 if ( !t2.getName().equals( "t2" ) ) {
1523 if ( !t3.getName().equals( "t3" ) ) {
1526 if ( !t4.getName().equals( "t4" ) ) {
1529 if ( t1.getNumberOfExternalNodes() != 1 ) {
1532 if ( t2.getNumberOfExternalNodes() != 2 ) {
1535 if ( t3.getNumberOfExternalNodes() != 4 ) {
1538 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1539 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1540 if ( xml_parser.getErrorCount() > 0 ) {
1541 System.out.println( "errors:" );
1542 System.out.println( xml_parser.getErrorMessages().toString() );
1545 if ( phylogenies_1.length != 4 ) {
1548 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1550 if ( xml_parser.getErrorCount() > 0 ) {
1551 System.out.println( "errors:" );
1552 System.out.println( xml_parser.getErrorMessages().toString() );
1555 if ( phylogenies_2.length != 1 ) {
1558 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1561 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1563 if ( xml_parser.getErrorCount() > 0 ) {
1564 System.out.println( xml_parser.getErrorMessages().toString() );
1567 if ( phylogenies_3.length != 2 ) {
1570 final Phylogeny a = phylogenies_3[ 0 ];
1571 if ( !a.getName().equals( "tree 4" ) ) {
1574 if ( a.getNumberOfExternalNodes() != 3 ) {
1577 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1580 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1583 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1585 if ( xml_parser.getErrorCount() > 0 ) {
1586 System.out.println( xml_parser.getErrorMessages().toString() );
1589 if ( phylogenies_4.length != 1 ) {
1592 final Phylogeny s = phylogenies_4[ 0 ];
1593 if ( s.getNumberOfExternalNodes() != 6 ) {
1596 s.getNode( "first" );
1598 s.getNode( "\"<a'b&c'd\">\"" );
1599 s.getNode( "'''\"" );
1600 s.getNode( "\"\"\"" );
1601 s.getNode( "dick & doof" );
1603 catch ( final Exception e ) {
1604 e.printStackTrace( System.out );
1610 private static boolean testBasicTable() {
1612 final BasicTable<String> t0 = new BasicTable<String>();
1613 if ( t0.getNumberOfColumns() != 0 ) {
1616 if ( t0.getNumberOfRows() != 0 ) {
1619 t0.setValue( 3, 2, "23" );
1620 t0.setValue( 10, 1, "error" );
1621 t0.setValue( 10, 1, "110" );
1622 t0.setValue( 9, 1, "19" );
1623 t0.setValue( 1, 10, "101" );
1624 t0.setValue( 10, 10, "1010" );
1625 t0.setValue( 100, 10, "10100" );
1626 t0.setValue( 0, 0, "00" );
1627 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1630 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1633 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1636 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1639 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1642 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1645 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1648 if ( t0.getNumberOfColumns() != 101 ) {
1651 if ( t0.getNumberOfRows() != 11 ) {
1654 if ( t0.getValueAsString( 49, 4 ) != null ) {
1657 final String l = ForesterUtil.getLineSeparator();
1658 final StringBuffer source = new StringBuffer();
1659 source.append( "" + l );
1660 source.append( "# 1 1 1 1 1 1 1 1" + l );
1661 source.append( " 00 01 02 03" + l );
1662 source.append( " 10 11 12 13 " + l );
1663 source.append( "20 21 22 23 " + l );
1664 source.append( " 30 31 32 33" + l );
1665 source.append( "40 41 42 43" + l );
1666 source.append( " # 1 1 1 1 1 " + l );
1667 source.append( "50 51 52 53 54" + l );
1668 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1669 if ( t1.getNumberOfColumns() != 5 ) {
1672 if ( t1.getNumberOfRows() != 6 ) {
1675 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1678 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1681 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1684 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1687 final StringBuffer source1 = new StringBuffer();
1688 source1.append( "" + l );
1689 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1690 source1.append( " 00; 01 ;02;03" + l );
1691 source1.append( " 10; 11; 12; 13 " + l );
1692 source1.append( "20; 21; 22; 23 " + l );
1693 source1.append( " 30; 31; 32; 33" + l );
1694 source1.append( "40;41;42;43" + l );
1695 source1.append( " # 1 1 1 1 1 " + l );
1696 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1697 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1698 if ( t2.getNumberOfColumns() != 5 ) {
1701 if ( t2.getNumberOfRows() != 6 ) {
1704 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1707 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1710 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1713 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1716 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1719 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1722 final StringBuffer source2 = new StringBuffer();
1723 source2.append( "" + l );
1724 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1725 source2.append( " 00; 01 ;02;03" + l );
1726 source2.append( " 10; 11; 12; 13 " + l );
1727 source2.append( "20; 21; 22; 23 " + l );
1728 source2.append( " " + l );
1729 source2.append( " 30; 31; 32; 33" + l );
1730 source2.append( "40;41;42;43" + l );
1731 source2.append( " comment: 1 1 1 1 1 " + l );
1732 source2.append( ";;;50 ; 52; 53;;54 " + l );
1733 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1738 if ( tl.size() != 2 ) {
1741 final BasicTable<String> t3 = tl.get( 0 );
1742 final BasicTable<String> t4 = tl.get( 1 );
1743 if ( t3.getNumberOfColumns() != 4 ) {
1746 if ( t3.getNumberOfRows() != 3 ) {
1749 if ( t4.getNumberOfColumns() != 4 ) {
1752 if ( t4.getNumberOfRows() != 3 ) {
1755 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1758 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1762 catch ( final Exception e ) {
1763 e.printStackTrace( System.out );
1769 private static boolean testBasicTolXMLparsing() {
1771 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1772 final TolParser parser = new TolParser();
1773 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1774 if ( parser.getErrorCount() > 0 ) {
1775 System.out.println( parser.getErrorMessages().toString() );
1778 if ( phylogenies_0.length != 1 ) {
1781 final Phylogeny t1 = phylogenies_0[ 0 ];
1782 if ( t1.getNumberOfExternalNodes() != 5 ) {
1785 if ( !t1.isRooted() ) {
1788 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1791 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1794 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1797 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1800 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1801 if ( parser.getErrorCount() > 0 ) {
1802 System.out.println( parser.getErrorMessages().toString() );
1805 if ( phylogenies_1.length != 1 ) {
1808 final Phylogeny t2 = phylogenies_1[ 0 ];
1809 if ( t2.getNumberOfExternalNodes() != 664 ) {
1812 if ( !t2.isRooted() ) {
1815 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1818 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1821 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1824 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1827 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1830 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1831 .equals( "Aquifex" ) ) {
1834 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1835 if ( parser.getErrorCount() > 0 ) {
1836 System.out.println( parser.getErrorMessages().toString() );
1839 if ( phylogenies_2.length != 1 ) {
1842 final Phylogeny t3 = phylogenies_2[ 0 ];
1843 if ( t3.getNumberOfExternalNodes() != 184 ) {
1846 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1849 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1852 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1855 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1856 if ( parser.getErrorCount() > 0 ) {
1857 System.out.println( parser.getErrorMessages().toString() );
1860 if ( phylogenies_3.length != 1 ) {
1863 final Phylogeny t4 = phylogenies_3[ 0 ];
1864 if ( t4.getNumberOfExternalNodes() != 1 ) {
1867 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1870 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1873 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1876 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1877 if ( parser.getErrorCount() > 0 ) {
1878 System.out.println( parser.getErrorMessages().toString() );
1881 if ( phylogenies_4.length != 1 ) {
1884 final Phylogeny t5 = phylogenies_4[ 0 ];
1885 if ( t5.getNumberOfExternalNodes() != 13 ) {
1888 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1891 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1894 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1898 catch ( final Exception e ) {
1899 e.printStackTrace( System.out );
1905 private static boolean testBasicTreeMethods() {
1907 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1908 final Phylogeny t1 = factory.create();
1909 if ( !t1.isEmpty() ) {
1912 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1913 if ( t2.getNumberOfExternalNodes() != 4 ) {
1916 if ( t2.getHeight() != 8.5 ) {
1919 if ( !t2.isCompletelyBinary() ) {
1922 if ( t2.isEmpty() ) {
1925 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1926 if ( t3.getNumberOfExternalNodes() != 5 ) {
1929 if ( t3.getHeight() != 11 ) {
1932 if ( t3.isCompletelyBinary() ) {
1935 final PhylogenyNode n = t3.getNode( "ABC" );
1936 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 ];
1937 if ( t4.getNumberOfExternalNodes() != 9 ) {
1940 if ( t4.getHeight() != 11 ) {
1943 if ( t4.isCompletelyBinary() ) {
1946 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)" );
1947 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1948 if ( t5.getNumberOfExternalNodes() != 8 ) {
1951 if ( t5.getHeight() != 15 ) {
1954 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)" );
1955 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1956 if ( t6.getHeight() != 15 ) {
1959 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)" );
1960 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1961 if ( t7.getHeight() != 15 ) {
1964 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)" );
1965 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1966 if ( t8.getNumberOfExternalNodes() != 10 ) {
1969 if ( t8.getHeight() != 15 ) {
1972 final char[] a9 = new char[] {};
1973 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1974 if ( t9.getHeight() != 0 ) {
1977 final char[] a10 = new char[] { 'a', ':', '6' };
1978 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1979 if ( t10.getHeight() != 6 ) {
1983 catch ( final Exception e ) {
1984 e.printStackTrace( System.out );
1990 private static boolean testConfidenceAssessor() {
1992 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1993 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1994 final Phylogeny[] ev0 = factory
1995 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1997 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1998 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2001 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2004 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2005 final Phylogeny[] ev1 = factory
2006 .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)));",
2008 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2009 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2012 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2015 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2016 final Phylogeny[] ev_b = factory
2017 .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",
2019 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2020 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2021 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2024 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2028 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2029 final Phylogeny[] ev1x = factory
2030 .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)));",
2032 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2033 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2036 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2039 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2040 final Phylogeny[] ev_bx = factory
2041 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2043 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2044 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2047 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2051 final Phylogeny[] t2 = factory
2052 .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);",
2054 final Phylogeny[] ev2 = factory
2055 .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);",
2057 for( final Phylogeny target : t2 ) {
2058 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2061 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2062 new NHXParser() )[ 0 ];
2063 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2064 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2065 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2068 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2071 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2075 catch ( final Exception e ) {
2076 e.printStackTrace();
2082 private static boolean testCopyOfNodeData() {
2084 final PhylogenyNode n1 = PhylogenyNode
2085 .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]" );
2086 final PhylogenyNode n2 = n1.copyNodeData();
2087 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2091 catch ( final Exception e ) {
2092 e.printStackTrace();
2098 private static boolean testDataObjects() {
2100 final Confidence s0 = new Confidence();
2101 final Confidence s1 = new Confidence();
2102 if ( !s0.isEqual( s1 ) ) {
2105 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2106 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2107 if ( s2.isEqual( s1 ) ) {
2110 if ( !s2.isEqual( s3 ) ) {
2113 final Confidence s4 = ( Confidence ) s3.copy();
2114 if ( !s4.isEqual( s3 ) ) {
2121 final Taxonomy t1 = new Taxonomy();
2122 final Taxonomy t2 = new Taxonomy();
2123 final Taxonomy t3 = new Taxonomy();
2124 final Taxonomy t4 = new Taxonomy();
2125 final Taxonomy t5 = new Taxonomy();
2126 t1.setIdentifier( new Identifier( "ecoli" ) );
2127 t1.setTaxonomyCode( "ECOLI" );
2128 t1.setScientificName( "E. coli" );
2129 t1.setCommonName( "coli" );
2130 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2131 if ( !t1.isEqual( t0 ) ) {
2134 t2.setIdentifier( new Identifier( "ecoli" ) );
2135 t2.setTaxonomyCode( "OTHER" );
2136 t2.setScientificName( "what" );
2137 t2.setCommonName( "something" );
2138 if ( !t1.isEqual( t2 ) ) {
2141 t2.setIdentifier( new Identifier( "nemve" ) );
2142 if ( t1.isEqual( t2 ) ) {
2145 t1.setIdentifier( null );
2146 t3.setTaxonomyCode( "ECOLI" );
2147 t3.setScientificName( "what" );
2148 t3.setCommonName( "something" );
2149 if ( !t1.isEqual( t3 ) ) {
2152 t1.setIdentifier( null );
2153 t1.setTaxonomyCode( "" );
2154 t4.setScientificName( "E. ColI" );
2155 t4.setCommonName( "something" );
2156 if ( !t1.isEqual( t4 ) ) {
2159 t4.setScientificName( "B. subtilis" );
2160 t4.setCommonName( "something" );
2161 if ( t1.isEqual( t4 ) ) {
2164 t1.setIdentifier( null );
2165 t1.setTaxonomyCode( "" );
2166 t1.setScientificName( "" );
2167 t5.setCommonName( "COLI" );
2168 if ( !t1.isEqual( t5 ) ) {
2171 t5.setCommonName( "vibrio" );
2172 if ( t1.isEqual( t5 ) ) {
2177 final Identifier id0 = new Identifier( "123", "pfam" );
2178 final Identifier id1 = ( Identifier ) id0.copy();
2179 if ( !id1.isEqual( id1 ) ) {
2182 if ( !id1.isEqual( id0 ) ) {
2185 if ( !id0.isEqual( id1 ) ) {
2192 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2193 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2194 if ( !pd1.isEqual( pd1 ) ) {
2197 if ( !pd1.isEqual( pd0 ) ) {
2202 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2203 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2204 if ( !pd3.isEqual( pd3 ) ) {
2207 if ( !pd2.isEqual( pd3 ) ) {
2210 if ( !pd0.isEqual( pd3 ) ) {
2215 // DomainArchitecture
2216 // ------------------
2217 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2218 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2219 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2220 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2221 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2222 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2227 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2228 if ( ds0.getNumberOfDomains() != 4 ) {
2231 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2232 if ( !ds0.isEqual( ds0 ) ) {
2235 if ( !ds0.isEqual( ds1 ) ) {
2238 if ( ds1.getNumberOfDomains() != 4 ) {
2241 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2246 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2247 if ( ds0.isEqual( ds2 ) ) {
2253 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2254 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2255 System.out.println( ds3.toNHX() );
2258 if ( ds3.getNumberOfDomains() != 3 ) {
2263 final Event e1 = new Event( Event.EventType.fusion );
2264 if ( e1.isDuplication() ) {
2267 if ( !e1.isFusion() ) {
2270 if ( !e1.asText().toString().equals( "fusion" ) ) {
2273 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2276 final Event e11 = new Event( Event.EventType.fusion );
2277 if ( !e11.isEqual( e1 ) ) {
2280 if ( !e11.toNHX().toString().equals( "" ) ) {
2283 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2284 if ( e2.isDuplication() ) {
2287 if ( !e2.isSpeciationOrDuplication() ) {
2290 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2293 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2296 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2299 if ( e11.isEqual( e2 ) ) {
2302 final Event e2c = ( Event ) e2.copy();
2303 if ( !e2c.isEqual( e2 ) ) {
2306 Event e3 = new Event( 1, 2, 3 );
2307 if ( e3.isDuplication() ) {
2310 if ( e3.isSpeciation() ) {
2313 if ( e3.isGeneLoss() ) {
2316 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2319 final Event e3c = ( Event ) e3.copy();
2320 final Event e3cc = ( Event ) e3c.copy();
2321 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2325 if ( !e3c.isEqual( e3cc ) ) {
2328 Event e4 = new Event( 1, 2, 3 );
2329 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2332 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2335 final Event e4c = ( Event ) e4.copy();
2337 final Event e4cc = ( Event ) e4c.copy();
2338 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2341 if ( !e4c.isEqual( e4cc ) ) {
2344 final Event e5 = new Event();
2345 if ( !e5.isUnassigned() ) {
2348 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2351 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2354 final Event e6 = new Event( 1, 0, 0 );
2355 if ( !e6.asText().toString().equals( "duplication" ) ) {
2358 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2361 final Event e7 = new Event( 0, 1, 0 );
2362 if ( !e7.asText().toString().equals( "speciation" ) ) {
2365 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2368 final Event e8 = new Event( 0, 0, 1 );
2369 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2372 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2376 catch ( final Exception e ) {
2377 e.printStackTrace( System.out );
2383 private static boolean testDeletionOfExternalNodes() {
2385 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2386 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2387 final PhylogenyWriter w = new PhylogenyWriter();
2388 if ( t0.isEmpty() ) {
2391 if ( t0.getNumberOfExternalNodes() != 1 ) {
2394 t0.deleteSubtree( t0.getNode( "A" ), false );
2395 if ( t0.getNumberOfExternalNodes() != 0 ) {
2398 if ( !t0.isEmpty() ) {
2401 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2402 if ( t1.getNumberOfExternalNodes() != 2 ) {
2405 t1.deleteSubtree( t1.getNode( "A" ), false );
2406 if ( t1.getNumberOfExternalNodes() != 1 ) {
2409 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2412 t1.deleteSubtree( t1.getNode( "B" ), false );
2413 if ( t1.getNumberOfExternalNodes() != 1 ) {
2416 t1.deleteSubtree( t1.getNode( "r" ), false );
2417 if ( !t1.isEmpty() ) {
2420 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2421 if ( t2.getNumberOfExternalNodes() != 3 ) {
2424 t2.deleteSubtree( t2.getNode( "B" ), false );
2425 if ( t2.getNumberOfExternalNodes() != 2 ) {
2428 t2.toNewHampshireX();
2429 PhylogenyNode n = t2.getNode( "A" );
2430 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2433 t2.deleteSubtree( t2.getNode( "A" ), false );
2434 if ( t2.getNumberOfExternalNodes() != 2 ) {
2437 t2.deleteSubtree( t2.getNode( "C" ), true );
2438 if ( t2.getNumberOfExternalNodes() != 1 ) {
2441 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2442 if ( t3.getNumberOfExternalNodes() != 4 ) {
2445 t3.deleteSubtree( t3.getNode( "B" ), true );
2446 if ( t3.getNumberOfExternalNodes() != 3 ) {
2449 n = t3.getNode( "A" );
2450 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2453 n = n.getNextExternalNode();
2454 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2457 t3.deleteSubtree( t3.getNode( "A" ), true );
2458 if ( t3.getNumberOfExternalNodes() != 2 ) {
2461 n = t3.getNode( "C" );
2462 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2465 t3.deleteSubtree( t3.getNode( "C" ), true );
2466 if ( t3.getNumberOfExternalNodes() != 1 ) {
2469 t3.deleteSubtree( t3.getNode( "D" ), true );
2470 if ( t3.getNumberOfExternalNodes() != 0 ) {
2473 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2474 if ( t4.getNumberOfExternalNodes() != 6 ) {
2477 t4.deleteSubtree( t4.getNode( "B2" ), true );
2478 if ( t4.getNumberOfExternalNodes() != 5 ) {
2481 String s = w.toNewHampshire( t4, false, true ).toString();
2482 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2485 t4.deleteSubtree( t4.getNode( "B11" ), true );
2486 if ( t4.getNumberOfExternalNodes() != 4 ) {
2489 t4.deleteSubtree( t4.getNode( "C" ), true );
2490 if ( t4.getNumberOfExternalNodes() != 3 ) {
2493 n = t4.getNode( "A" );
2494 n = n.getNextExternalNode();
2495 if ( !n.getName().equals( "B12" ) ) {
2498 n = n.getNextExternalNode();
2499 if ( !n.getName().equals( "D" ) ) {
2502 s = w.toNewHampshire( t4, false, true ).toString();
2503 if ( !s.equals( "((A,B12),D);" ) ) {
2506 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2507 t5.deleteSubtree( t5.getNode( "A" ), true );
2508 if ( t5.getNumberOfExternalNodes() != 5 ) {
2511 s = w.toNewHampshire( t5, false, true ).toString();
2512 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2515 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2516 t6.deleteSubtree( t6.getNode( "B11" ), true );
2517 if ( t6.getNumberOfExternalNodes() != 5 ) {
2520 s = w.toNewHampshire( t6, false, false ).toString();
2521 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2524 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2525 t7.deleteSubtree( t7.getNode( "B12" ), true );
2526 if ( t7.getNumberOfExternalNodes() != 5 ) {
2529 s = w.toNewHampshire( t7, false, true ).toString();
2530 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2533 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2534 t8.deleteSubtree( t8.getNode( "B2" ), true );
2535 if ( t8.getNumberOfExternalNodes() != 5 ) {
2538 s = w.toNewHampshire( t8, false, false ).toString();
2539 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2542 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2543 t9.deleteSubtree( t9.getNode( "C" ), true );
2544 if ( t9.getNumberOfExternalNodes() != 5 ) {
2547 s = w.toNewHampshire( t9, false, true ).toString();
2548 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2551 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2552 t10.deleteSubtree( t10.getNode( "D" ), true );
2553 if ( t10.getNumberOfExternalNodes() != 5 ) {
2556 s = w.toNewHampshire( t10, false, true ).toString();
2557 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2560 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2561 t11.deleteSubtree( t11.getNode( "A" ), true );
2562 if ( t11.getNumberOfExternalNodes() != 2 ) {
2565 s = w.toNewHampshire( t11, false, true ).toString();
2566 if ( !s.equals( "(B,C);" ) ) {
2569 t11.deleteSubtree( t11.getNode( "C" ), true );
2570 if ( t11.getNumberOfExternalNodes() != 1 ) {
2573 s = w.toNewHampshire( t11, false, false ).toString();
2574 if ( !s.equals( "B;" ) ) {
2577 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2578 t12.deleteSubtree( t12.getNode( "B2" ), true );
2579 if ( t12.getNumberOfExternalNodes() != 8 ) {
2582 s = w.toNewHampshire( t12, false, true ).toString();
2583 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2586 t12.deleteSubtree( t12.getNode( "B3" ), true );
2587 if ( t12.getNumberOfExternalNodes() != 7 ) {
2590 s = w.toNewHampshire( t12, false, true ).toString();
2591 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2594 t12.deleteSubtree( t12.getNode( "C3" ), true );
2595 if ( t12.getNumberOfExternalNodes() != 6 ) {
2598 s = w.toNewHampshire( t12, false, true ).toString();
2599 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2602 t12.deleteSubtree( t12.getNode( "A1" ), true );
2603 if ( t12.getNumberOfExternalNodes() != 5 ) {
2606 s = w.toNewHampshire( t12, false, true ).toString();
2607 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2610 t12.deleteSubtree( t12.getNode( "B1" ), true );
2611 if ( t12.getNumberOfExternalNodes() != 4 ) {
2614 s = w.toNewHampshire( t12, false, true ).toString();
2615 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2618 t12.deleteSubtree( t12.getNode( "A3" ), true );
2619 if ( t12.getNumberOfExternalNodes() != 3 ) {
2622 s = w.toNewHampshire( t12, false, true ).toString();
2623 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2626 t12.deleteSubtree( t12.getNode( "A2" ), true );
2627 if ( t12.getNumberOfExternalNodes() != 2 ) {
2630 s = w.toNewHampshire( t12, false, true ).toString();
2631 if ( !s.equals( "(C1,C2);" ) ) {
2634 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2635 t13.deleteSubtree( t13.getNode( "D" ), true );
2636 if ( t13.getNumberOfExternalNodes() != 4 ) {
2639 s = w.toNewHampshire( t13, false, true ).toString();
2640 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2643 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2644 t14.deleteSubtree( t14.getNode( "E" ), true );
2645 if ( t14.getNumberOfExternalNodes() != 5 ) {
2648 s = w.toNewHampshire( t14, false, true ).toString();
2649 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2652 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2653 t15.deleteSubtree( t15.getNode( "B2" ), true );
2654 if ( t15.getNumberOfExternalNodes() != 11 ) {
2657 t15.deleteSubtree( t15.getNode( "B1" ), true );
2658 if ( t15.getNumberOfExternalNodes() != 10 ) {
2661 t15.deleteSubtree( t15.getNode( "B3" ), true );
2662 if ( t15.getNumberOfExternalNodes() != 9 ) {
2665 t15.deleteSubtree( t15.getNode( "B4" ), true );
2666 if ( t15.getNumberOfExternalNodes() != 8 ) {
2669 t15.deleteSubtree( t15.getNode( "A1" ), true );
2670 if ( t15.getNumberOfExternalNodes() != 7 ) {
2673 t15.deleteSubtree( t15.getNode( "C4" ), true );
2674 if ( t15.getNumberOfExternalNodes() != 6 ) {
2678 catch ( final Exception e ) {
2679 e.printStackTrace( System.out );
2685 private static boolean testDescriptiveStatistics() {
2687 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2688 dss1.addValue( 82 );
2689 dss1.addValue( 78 );
2690 dss1.addValue( 70 );
2691 dss1.addValue( 58 );
2692 dss1.addValue( 42 );
2693 if ( dss1.getN() != 5 ) {
2696 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2699 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2702 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2705 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2708 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2711 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2714 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2717 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2720 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2723 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2726 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2729 dss1.addValue( 123 );
2730 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2733 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2736 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2739 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2740 dss2.addValue( -1.85 );
2741 dss2.addValue( 57.5 );
2742 dss2.addValue( 92.78 );
2743 dss2.addValue( 57.78 );
2744 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2747 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2750 final double[] a = dss2.getDataAsDoubleArray();
2751 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2754 dss2.addValue( -100 );
2755 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2758 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2761 final double[] ds = new double[ 14 ];
2776 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2777 if ( bins.length != 4 ) {
2780 if ( bins[ 0 ] != 2 ) {
2783 if ( bins[ 1 ] != 3 ) {
2786 if ( bins[ 2 ] != 4 ) {
2789 if ( bins[ 3 ] != 5 ) {
2792 final double[] ds1 = new double[ 9 ];
2802 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2803 if ( bins1.length != 4 ) {
2806 if ( bins1[ 0 ] != 2 ) {
2809 if ( bins1[ 1 ] != 3 ) {
2812 if ( bins1[ 2 ] != 0 ) {
2815 if ( bins1[ 3 ] != 4 ) {
2818 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2819 if ( bins1_1.length != 3 ) {
2822 if ( bins1_1[ 0 ] != 3 ) {
2825 if ( bins1_1[ 1 ] != 2 ) {
2828 if ( bins1_1[ 2 ] != 4 ) {
2831 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2832 if ( bins1_2.length != 3 ) {
2835 if ( bins1_2[ 0 ] != 2 ) {
2838 if ( bins1_2[ 1 ] != 2 ) {
2841 if ( bins1_2[ 2 ] != 2 ) {
2844 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2858 dss3.addValue( 10 );
2859 dss3.addValue( 10 );
2860 dss3.addValue( 10 );
2861 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2862 histo.toStringBuffer( 10, '=', 40, 5 );
2863 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2865 catch ( final Exception e ) {
2866 e.printStackTrace( System.out );
2872 private static boolean testDir( final String file ) {
2874 final File f = new File( file );
2875 if ( !f.exists() ) {
2878 if ( !f.isDirectory() ) {
2881 if ( !f.canRead() ) {
2885 catch ( final Exception e ) {
2891 private static boolean testExternalNodeRelatedMethods() {
2893 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2894 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2895 PhylogenyNode n = t1.getNode( "A" );
2896 n = n.getNextExternalNode();
2897 if ( !n.getName().equals( "B" ) ) {
2900 n = n.getNextExternalNode();
2901 if ( !n.getName().equals( "C" ) ) {
2904 n = n.getNextExternalNode();
2905 if ( !n.getName().equals( "D" ) ) {
2908 n = t1.getNode( "B" );
2909 while ( !n.isLastExternalNode() ) {
2910 n = n.getNextExternalNode();
2912 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2913 n = t2.getNode( "A" );
2914 n = n.getNextExternalNode();
2915 if ( !n.getName().equals( "B" ) ) {
2918 n = n.getNextExternalNode();
2919 if ( !n.getName().equals( "C" ) ) {
2922 n = n.getNextExternalNode();
2923 if ( !n.getName().equals( "D" ) ) {
2926 n = t2.getNode( "B" );
2927 while ( !n.isLastExternalNode() ) {
2928 n = n.getNextExternalNode();
2930 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2931 n = t3.getNode( "A" );
2932 n = n.getNextExternalNode();
2933 if ( !n.getName().equals( "B" ) ) {
2936 n = n.getNextExternalNode();
2937 if ( !n.getName().equals( "C" ) ) {
2940 n = n.getNextExternalNode();
2941 if ( !n.getName().equals( "D" ) ) {
2944 n = n.getNextExternalNode();
2945 if ( !n.getName().equals( "E" ) ) {
2948 n = n.getNextExternalNode();
2949 if ( !n.getName().equals( "F" ) ) {
2952 n = n.getNextExternalNode();
2953 if ( !n.getName().equals( "G" ) ) {
2956 n = n.getNextExternalNode();
2957 if ( !n.getName().equals( "H" ) ) {
2960 n = t3.getNode( "B" );
2961 while ( !n.isLastExternalNode() ) {
2962 n = n.getNextExternalNode();
2964 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2965 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2966 final PhylogenyNode node = iter.next();
2968 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2969 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2970 final PhylogenyNode node = iter.next();
2973 catch ( final Exception e ) {
2974 e.printStackTrace( System.out );
2980 private static boolean testGeneralTable() {
2982 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2983 t0.setValue( 3, 2, "23" );
2984 t0.setValue( 10, 1, "error" );
2985 t0.setValue( 10, 1, "110" );
2986 t0.setValue( 9, 1, "19" );
2987 t0.setValue( 1, 10, "101" );
2988 t0.setValue( 10, 10, "1010" );
2989 t0.setValue( 100, 10, "10100" );
2990 t0.setValue( 0, 0, "00" );
2991 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2994 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2997 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
3000 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
3003 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
3006 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
3009 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3012 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3015 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3018 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3019 t1.setValue( "3", "2", "23" );
3020 t1.setValue( "10", "1", "error" );
3021 t1.setValue( "10", "1", "110" );
3022 t1.setValue( "9", "1", "19" );
3023 t1.setValue( "1", "10", "101" );
3024 t1.setValue( "10", "10", "1010" );
3025 t1.setValue( "100", "10", "10100" );
3026 t1.setValue( "0", "0", "00" );
3027 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3028 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3031 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3034 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3037 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3040 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3043 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3046 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3049 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3052 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3055 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3059 catch ( final Exception e ) {
3060 e.printStackTrace( System.out );
3066 private static boolean testGetDistance() {
3068 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3069 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",
3070 new NHXParser() )[ 0 ];
3071 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3072 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3075 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3078 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3081 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3084 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3087 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3090 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3093 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3096 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3099 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3102 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3105 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3108 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3111 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3114 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3117 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3120 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3123 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3126 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3129 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3132 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3135 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3138 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3141 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3144 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3147 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3150 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3153 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3156 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3159 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3162 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3165 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",
3166 new NHXParser() )[ 0 ];
3167 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3170 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3173 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3176 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3179 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3182 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3185 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3188 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3191 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3194 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3197 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3201 catch ( final Exception e ) {
3202 e.printStackTrace( System.out );
3208 private static boolean testGetLCA() {
3210 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3211 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3212 new NHXParser() )[ 0 ];
3213 final PhylogenyNode A = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3214 if ( !A.getName().equals( "A" ) ) {
3217 final PhylogenyNode gh = PhylogenyMethods.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3218 if ( !gh.getName().equals( "gh" ) ) {
3221 final PhylogenyNode ab = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3222 if ( !ab.getName().equals( "ab" ) ) {
3225 final PhylogenyNode ab2 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3226 if ( !ab2.getName().equals( "ab" ) ) {
3229 final PhylogenyNode gh2 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3230 if ( !gh2.getName().equals( "gh" ) ) {
3233 final PhylogenyNode gh3 = PhylogenyMethods.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3234 if ( !gh3.getName().equals( "gh" ) ) {
3237 final PhylogenyNode abc = PhylogenyMethods.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3238 if ( !abc.getName().equals( "abc" ) ) {
3241 final PhylogenyNode abc2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3242 if ( !abc2.getName().equals( "abc" ) ) {
3245 final PhylogenyNode abcd = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3246 if ( !abcd.getName().equals( "abcd" ) ) {
3249 final PhylogenyNode abcd2 = PhylogenyMethods.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3250 if ( !abcd2.getName().equals( "abcd" ) ) {
3253 final PhylogenyNode abcdef = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3254 if ( !abcdef.getName().equals( "abcdef" ) ) {
3257 final PhylogenyNode abcdef2 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3258 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3261 final PhylogenyNode abcdef3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3262 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3265 final PhylogenyNode abcdef4 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3266 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3269 final PhylogenyNode abcde = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3270 if ( !abcde.getName().equals( "abcde" ) ) {
3273 final PhylogenyNode abcde2 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3274 if ( !abcde2.getName().equals( "abcde" ) ) {
3277 final PhylogenyNode r = PhylogenyMethods.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3278 if ( !r.getName().equals( "abcdefgh" ) ) {
3281 final PhylogenyNode r2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3282 if ( !r2.getName().equals( "abcdefgh" ) ) {
3285 final PhylogenyNode r3 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3286 if ( !r3.getName().equals( "abcdefgh" ) ) {
3289 final PhylogenyNode abcde3 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3290 if ( !abcde3.getName().equals( "abcde" ) ) {
3293 final PhylogenyNode abcde4 = PhylogenyMethods.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3294 if ( !abcde4.getName().equals( "abcde" ) ) {
3297 final PhylogenyNode ab3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3298 if ( !ab3.getName().equals( "ab" ) ) {
3301 final PhylogenyNode ab4 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3302 if ( !ab4.getName().equals( "ab" ) ) {
3305 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3306 final PhylogenyNode cd = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3307 if ( !cd.getName().equals( "cd" ) ) {
3310 final PhylogenyNode cd2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3311 if ( !cd2.getName().equals( "cd" ) ) {
3314 final PhylogenyNode cde = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3315 if ( !cde.getName().equals( "cde" ) ) {
3318 final PhylogenyNode cde2 = PhylogenyMethods.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3319 if ( !cde2.getName().equals( "cde" ) ) {
3322 final PhylogenyNode cdef = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3323 if ( !cdef.getName().equals( "cdef" ) ) {
3326 final PhylogenyNode cdef2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3327 if ( !cdef2.getName().equals( "cdef" ) ) {
3330 final PhylogenyNode cdef3 = PhylogenyMethods.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3331 if ( !cdef3.getName().equals( "cdef" ) ) {
3334 final PhylogenyNode rt = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3335 if ( !rt.getName().equals( "r" ) ) {
3338 final Phylogeny p3 = factory
3339 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3340 new NHXParser() )[ 0 ];
3341 final PhylogenyNode bc_3 = PhylogenyMethods.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3342 if ( !bc_3.getName().equals( "bc" ) ) {
3345 final PhylogenyNode ac_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3346 if ( !ac_3.getName().equals( "abc" ) ) {
3349 final PhylogenyNode ad_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3350 if ( !ad_3.getName().equals( "abcde" ) ) {
3353 final PhylogenyNode af_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3354 if ( !af_3.getName().equals( "abcdef" ) ) {
3357 final PhylogenyNode ag_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3358 if ( !ag_3.getName().equals( "" ) ) {
3361 if ( !ag_3.isRoot() ) {
3364 final PhylogenyNode al_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3365 if ( !al_3.getName().equals( "" ) ) {
3368 if ( !al_3.isRoot() ) {
3371 final PhylogenyNode kl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3372 if ( !kl_3.getName().equals( "" ) ) {
3375 if ( !kl_3.isRoot() ) {
3378 final PhylogenyNode fl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3379 if ( !fl_3.getName().equals( "" ) ) {
3382 if ( !fl_3.isRoot() ) {
3385 final PhylogenyNode gk_3 = PhylogenyMethods.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3386 if ( !gk_3.getName().equals( "ghijk" ) ) {
3389 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3390 final PhylogenyNode r_4 = PhylogenyMethods.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3391 if ( !r_4.getName().equals( "r" ) ) {
3394 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3395 final PhylogenyNode r_5 = PhylogenyMethods.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3396 if ( !r_5.getName().equals( "root" ) ) {
3399 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3400 final PhylogenyNode r_6 = PhylogenyMethods.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3401 if ( !r_6.getName().equals( "rot" ) ) {
3404 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3405 final PhylogenyNode r_7 = PhylogenyMethods.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3406 if ( !r_7.getName().equals( "rott" ) ) {
3410 catch ( final Exception e ) {
3411 e.printStackTrace( System.out );
3417 private static boolean testHmmscanOutputParser() {
3418 final String test_dir = Test.PATH_TO_TEST_DATA;
3420 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3421 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3423 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3424 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3425 final List<Protein> proteins = parser2.parse();
3426 if ( parser2.getProteinsEncountered() != 4 ) {
3429 if ( proteins.size() != 4 ) {
3432 if ( parser2.getDomainsEncountered() != 69 ) {
3435 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3438 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3441 final Protein p1 = proteins.get( 0 );
3442 if ( p1.getNumberOfProteinDomains() != 15 ) {
3445 if ( p1.getLength() != 850 ) {
3448 final Protein p2 = proteins.get( 1 );
3449 if ( p2.getNumberOfProteinDomains() != 51 ) {
3452 if ( p2.getLength() != 1291 ) {
3455 final Protein p3 = proteins.get( 2 );
3456 if ( p3.getNumberOfProteinDomains() != 2 ) {
3459 final Protein p4 = proteins.get( 3 );
3460 if ( p4.getNumberOfProteinDomains() != 1 ) {
3463 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3466 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3469 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3472 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3475 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3478 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3481 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3484 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3487 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3491 catch ( final Exception e ) {
3492 e.printStackTrace( System.out );
3498 private static boolean testLastExternalNodeMethods() {
3500 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3501 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3502 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3503 final PhylogenyNode n1 = t0.getNode( "A" );
3504 if ( n1.isLastExternalNode() ) {
3507 final PhylogenyNode n2 = t0.getNode( "B" );
3508 if ( n2.isLastExternalNode() ) {
3511 final PhylogenyNode n3 = t0.getNode( "C" );
3512 if ( n3.isLastExternalNode() ) {
3515 final PhylogenyNode n4 = t0.getNode( "D" );
3516 if ( !n4.isLastExternalNode() ) {
3520 catch ( final Exception e ) {
3521 e.printStackTrace( System.out );
3527 private static boolean testLevelOrderIterator() {
3529 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3530 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3531 PhylogenyNodeIterator it0;
3532 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3535 for( it0.reset(); it0.hasNext(); ) {
3538 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3539 if ( !it.next().getName().equals( "r" ) ) {
3542 if ( !it.next().getName().equals( "ab" ) ) {
3545 if ( !it.next().getName().equals( "cd" ) ) {
3548 if ( !it.next().getName().equals( "A" ) ) {
3551 if ( !it.next().getName().equals( "B" ) ) {
3554 if ( !it.next().getName().equals( "C" ) ) {
3557 if ( !it.next().getName().equals( "D" ) ) {
3560 if ( it.hasNext() ) {
3563 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",
3564 new NHXParser() )[ 0 ];
3565 PhylogenyNodeIterator it2;
3566 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3569 for( it2.reset(); it2.hasNext(); ) {
3572 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3573 if ( !it3.next().getName().equals( "r" ) ) {
3576 if ( !it3.next().getName().equals( "abc" ) ) {
3579 if ( !it3.next().getName().equals( "defg" ) ) {
3582 if ( !it3.next().getName().equals( "A" ) ) {
3585 if ( !it3.next().getName().equals( "B" ) ) {
3588 if ( !it3.next().getName().equals( "C" ) ) {
3591 if ( !it3.next().getName().equals( "D" ) ) {
3594 if ( !it3.next().getName().equals( "E" ) ) {
3597 if ( !it3.next().getName().equals( "F" ) ) {
3600 if ( !it3.next().getName().equals( "G" ) ) {
3603 if ( !it3.next().getName().equals( "1" ) ) {
3606 if ( !it3.next().getName().equals( "2" ) ) {
3609 if ( !it3.next().getName().equals( "3" ) ) {
3612 if ( !it3.next().getName().equals( "4" ) ) {
3615 if ( !it3.next().getName().equals( "5" ) ) {
3618 if ( !it3.next().getName().equals( "6" ) ) {
3621 if ( !it3.next().getName().equals( "f1" ) ) {
3624 if ( !it3.next().getName().equals( "f2" ) ) {
3627 if ( !it3.next().getName().equals( "f3" ) ) {
3630 if ( !it3.next().getName().equals( "a" ) ) {
3633 if ( !it3.next().getName().equals( "b" ) ) {
3636 if ( !it3.next().getName().equals( "f21" ) ) {
3639 if ( !it3.next().getName().equals( "X" ) ) {
3642 if ( !it3.next().getName().equals( "Y" ) ) {
3645 if ( !it3.next().getName().equals( "Z" ) ) {
3648 if ( it3.hasNext() ) {
3651 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3652 PhylogenyNodeIterator it4;
3653 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3656 for( it4.reset(); it4.hasNext(); ) {
3659 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3660 if ( !it5.next().getName().equals( "r" ) ) {
3663 if ( !it5.next().getName().equals( "A" ) ) {
3666 if ( !it5.next().getName().equals( "B" ) ) {
3669 if ( !it5.next().getName().equals( "C" ) ) {
3672 if ( !it5.next().getName().equals( "D" ) ) {
3675 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3676 PhylogenyNodeIterator it6;
3677 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3680 for( it6.reset(); it6.hasNext(); ) {
3683 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3684 if ( !it7.next().getName().equals( "A" ) ) {
3687 if ( it.hasNext() ) {
3691 catch ( final Exception e ) {
3692 e.printStackTrace( System.out );
3698 private static boolean testMidpointrooting() {
3700 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3701 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",
3702 new NHXParser() )[ 0 ];
3703 if ( !t1.isRooted() ) {
3706 PhylogenyMethods.midpointRoot( t1 );
3707 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3710 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3713 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3716 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3719 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3722 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3725 t1.reRoot( t1.getNode( "A" ) );
3726 PhylogenyMethods.midpointRoot( t1 );
3727 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3730 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3733 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3736 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3739 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3742 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3746 catch ( final Exception e ) {
3747 e.printStackTrace( System.out );
3753 private static boolean testNexusCharactersParsing() {
3755 final NexusCharactersParser parser = new NexusCharactersParser();
3756 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3758 String[] labels = parser.getCharStateLabels();
3759 if ( labels.length != 7 ) {
3762 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3765 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3768 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3771 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3774 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3777 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3780 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3783 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3785 labels = parser.getCharStateLabels();
3786 if ( labels.length != 7 ) {
3789 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3792 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3795 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3798 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3801 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3804 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3807 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3811 catch ( final Exception e ) {
3812 e.printStackTrace( System.out );
3818 private static boolean testNexusMatrixParsing() {
3820 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3821 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3823 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3824 if ( m.getNumberOfCharacters() != 9 ) {
3827 if ( m.getNumberOfIdentifiers() != 5 ) {
3830 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3833 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3836 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3839 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3842 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3845 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3848 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3851 // if ( labels.length != 7 ) {
3854 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3857 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3860 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3863 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3866 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3869 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3872 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3875 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3877 // labels = parser.getCharStateLabels();
3878 // if ( labels.length != 7 ) {
3881 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3884 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3887 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3890 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3893 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3896 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3899 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3903 catch ( final Exception e ) {
3904 e.printStackTrace( System.out );
3910 private static boolean testNexusTreeParsing() {
3912 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3913 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3914 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3915 if ( phylogenies.length != 1 ) {
3918 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3921 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3925 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3926 if ( phylogenies.length != 1 ) {
3929 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3932 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3936 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3937 if ( phylogenies.length != 1 ) {
3940 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3943 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3946 if ( phylogenies[ 0 ].isRooted() ) {
3950 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3951 if ( phylogenies.length != 18 ) {
3954 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3957 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3960 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3963 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3966 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3969 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3972 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3975 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3978 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3981 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3984 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3987 if ( phylogenies[ 8 ].isRooted() ) {
3990 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3993 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3996 if ( !phylogenies[ 9 ].isRooted() ) {
3999 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4002 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4005 if ( !phylogenies[ 10 ].isRooted() ) {
4008 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4011 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4014 if ( phylogenies[ 11 ].isRooted() ) {
4017 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4020 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4023 if ( !phylogenies[ 12 ].isRooted() ) {
4026 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4029 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4032 if ( !phylogenies[ 13 ].isRooted() ) {
4035 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4038 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4041 if ( !phylogenies[ 14 ].isRooted() ) {
4044 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4047 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4050 if ( phylogenies[ 15 ].isRooted() ) {
4053 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4056 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4059 if ( !phylogenies[ 16 ].isRooted() ) {
4062 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4065 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4068 if ( phylogenies[ 17 ].isRooted() ) {
4071 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4075 catch ( final Exception e ) {
4076 e.printStackTrace( System.out );
4082 private static boolean testNexusTreeParsingTranslating() {
4084 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4085 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4086 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4087 if ( phylogenies.length != 1 ) {
4090 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4093 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4096 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4099 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4102 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4103 .equals( "Aranaeus" ) ) {
4107 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4108 if ( phylogenies.length != 3 ) {
4111 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4114 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4117 if ( phylogenies[ 0 ].isRooted() ) {
4120 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4123 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4126 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4127 .equals( "Aranaeus" ) ) {
4130 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4133 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4136 if ( phylogenies[ 1 ].isRooted() ) {
4139 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4142 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4145 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4146 .equals( "Aranaeus" ) ) {
4149 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4152 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4155 if ( !phylogenies[ 2 ].isRooted() ) {
4158 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4161 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4164 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4165 .equals( "Aranaeus" ) ) {
4169 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4170 if ( phylogenies.length != 3 ) {
4173 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4176 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4179 if ( phylogenies[ 0 ].isRooted() ) {
4182 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4185 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4188 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4189 .equals( "Aranaeus" ) ) {
4192 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4195 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4198 if ( phylogenies[ 1 ].isRooted() ) {
4201 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4204 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4207 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4208 .equals( "Aranaeus" ) ) {
4211 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4214 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4217 if ( !phylogenies[ 2 ].isRooted() ) {
4220 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4223 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4226 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4227 .equals( "Aranaeus" ) ) {
4231 catch ( final Exception e ) {
4232 e.printStackTrace( System.out );
4238 private static boolean testNHParsing() {
4240 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4241 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4242 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4245 final NHXParser nhxp = new NHXParser();
4246 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4247 nhxp.setReplaceUnderscores( true );
4248 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4249 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4252 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4255 final Phylogeny p1b = factory
4256 .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 ",
4257 new NHXParser() )[ 0 ];
4258 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4261 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4264 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4265 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4266 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4267 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4268 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4269 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4270 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4271 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4272 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4273 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4274 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4275 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4276 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4278 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4281 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4284 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4287 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4290 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4291 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4292 final String p16_S = "((A,B),C)";
4293 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4294 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4297 final String p17_S = "(C,(A,B))";
4298 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4299 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4302 final String p18_S = "((A,B),(C,D))";
4303 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4304 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4307 final String p19_S = "(((A,B),C),D)";
4308 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4309 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4312 final String p20_S = "(A,(B,(C,D)))";
4313 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4314 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4317 final String p21_S = "(A,(B,(C,(D,E))))";
4318 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4319 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4322 final String p22_S = "((((A,B),C),D),E)";
4323 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4324 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4327 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4328 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4329 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4332 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4333 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4334 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4337 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4338 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4339 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4340 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4343 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4346 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4347 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4348 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4349 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4350 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4351 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4352 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4353 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4354 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4355 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4358 final String p26_S = "(A,B)ab";
4359 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4360 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4363 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4364 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4366 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4369 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4370 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4371 final String p28_S3 = "(A,B)ab";
4372 final String p28_S4 = "((((A,B),C),D),;E;)";
4373 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4375 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4378 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4381 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4384 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4387 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";
4388 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4389 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4392 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";
4393 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4394 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4397 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4398 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4399 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4402 final String p33_S = "A";
4403 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4404 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4407 final String p34_S = "B;";
4408 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4409 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4412 final String p35_S = "B:0.2";
4413 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4414 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4417 final String p36_S = "(A)";
4418 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4419 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4422 final String p37_S = "((A))";
4423 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4424 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4427 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4428 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4429 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4432 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4433 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4434 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4437 final String p40_S = "(A,B,C)";
4438 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4439 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4442 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4443 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4444 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4447 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4448 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4449 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4452 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)";
4453 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4454 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4457 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)))";
4458 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4459 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4462 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4463 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4464 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4467 final String p46_S = "";
4468 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4469 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4472 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4473 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4476 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4477 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4480 final Phylogeny p49 = factory
4481 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4482 new NHXParser() )[ 0 ];
4483 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4486 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4487 if ( p50.getNode( "A" ) == null ) {
4490 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4491 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4494 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4497 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4498 .equals( "((A,B)88:2.0,C);" ) ) {
4501 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4502 if ( p51.getNode( "A(A" ) == null ) {
4505 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4506 if ( p52.getNode( "A(A" ) == null ) {
4509 final Phylogeny p53 = factory
4510 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4511 new NHXParser() )[ 0 ];
4512 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4516 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4517 if ( p54.getNode( "A" ) == null ) {
4520 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4521 .equals( "((A,B)[88],C);" ) ) {
4525 catch ( final Exception e ) {
4526 e.printStackTrace( System.out );
4532 private static boolean testNHXconversion() {
4534 final PhylogenyNode n1 = new PhylogenyNode();
4535 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4536 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4537 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4538 final PhylogenyNode n5 = PhylogenyNode
4539 .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]" );
4540 final PhylogenyNode n6 = PhylogenyNode
4541 .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]" );
4542 if ( !n1.toNewHampshireX().equals( "" ) ) {
4545 if ( !n2.toNewHampshireX().equals( "" ) ) {
4548 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4551 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4554 if ( !n5.toNewHampshireX()
4555 .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]" ) ) {
4558 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]" ) ) {
4562 catch ( final Exception e ) {
4563 e.printStackTrace( System.out );
4569 private static boolean testNHXNodeParsing() {
4571 final PhylogenyNode n1 = new PhylogenyNode();
4572 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4573 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4574 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4575 final PhylogenyNode n5 = PhylogenyNode
4576 .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]" );
4577 if ( !n3.getName().equals( "n3" ) ) {
4580 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4583 if ( n3.isDuplication() ) {
4586 if ( n3.isHasAssignedEvent() ) {
4589 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4592 if ( !n4.getName().equals( "n4" ) ) {
4595 if ( n4.getDistanceToParent() != 0.01 ) {
4598 if ( !n5.getName().equals( "n5" ) ) {
4601 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4604 if ( n5.getDistanceToParent() != 0.1 ) {
4607 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4610 if ( !n5.isDuplication() ) {
4613 if ( !n5.isHasAssignedEvent() ) {
4616 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4619 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4622 final PhylogenyNode n8 = PhylogenyNode
4623 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4624 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4625 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4628 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4631 final PhylogenyNode n9 = PhylogenyNode
4632 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4633 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4634 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4637 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4640 final PhylogenyNode n10 = PhylogenyNode
4641 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4642 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4645 final PhylogenyNode n20 = PhylogenyNode
4646 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4647 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4650 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4653 final PhylogenyNode n20x = PhylogenyNode
4654 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4655 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4658 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4661 final PhylogenyNode n20xx = PhylogenyNode
4662 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4663 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4666 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4669 final PhylogenyNode n20xxx = PhylogenyNode
4670 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4671 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4674 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4677 final PhylogenyNode n20xxxx = PhylogenyNode
4678 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4679 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4682 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4685 final PhylogenyNode n21 = PhylogenyNode
4686 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4687 if ( !n21.getName().equals( "n21_PIG" ) ) {
4690 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4693 final PhylogenyNode n21x = PhylogenyNode
4694 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4695 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4698 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4701 final PhylogenyNode n22 = PhylogenyNode
4702 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4703 if ( !n22.getName().equals( "n22/PIG" ) ) {
4706 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4709 final PhylogenyNode n23 = PhylogenyNode
4710 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4711 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4714 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4717 final PhylogenyNode a = PhylogenyNode
4718 .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4719 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4722 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4725 final PhylogenyNode b = PhylogenyNode
4726 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4727 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4728 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4731 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4734 final PhylogenyNode c = PhylogenyNode
4735 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4736 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4737 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4740 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4743 final PhylogenyNode c1 = PhylogenyNode
4744 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4745 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4746 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4749 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4752 final PhylogenyNode c2 = PhylogenyNode
4753 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4754 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4755 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4758 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4761 final PhylogenyNode d = PhylogenyNode
4762 .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4763 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4766 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4769 final PhylogenyNode e = PhylogenyNode
4770 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4771 if ( !e.getName().equals( "n10_RAT1" ) ) {
4774 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4777 final PhylogenyNode e2 = PhylogenyNode
4778 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4779 if ( !e2.getName().equals( "n10_RAT1" ) ) {
4782 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
4785 final PhylogenyNode e3 = PhylogenyNode
4786 .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4787 if ( !e3.getName().equals( "n10_RAT~" ) ) {
4790 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
4793 final PhylogenyNode n11 = PhylogenyNode
4794 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4795 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4796 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4799 if ( n11.getDistanceToParent() != 0.4 ) {
4802 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4805 final PhylogenyNode n12 = PhylogenyNode
4806 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4807 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4808 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4811 if ( n12.getDistanceToParent() != 0.4 ) {
4814 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4817 final PhylogenyNode m = PhylogenyNode
4818 .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4819 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
4822 if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
4825 final PhylogenyNode o = PhylogenyNode
4826 .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4827 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
4830 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
4833 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4834 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4835 if ( !tvu1.getRef().equals( "tag1" ) ) {
4838 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4841 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4844 if ( !tvu1.getValue().equals( "value1" ) ) {
4847 if ( !tvu3.getRef().equals( "tag3" ) ) {
4850 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4853 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4856 if ( !tvu3.getValue().equals( "value3" ) ) {
4859 if ( n1.getName().compareTo( "" ) != 0 ) {
4862 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4865 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4868 if ( n2.getName().compareTo( "" ) != 0 ) {
4871 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4874 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4877 final PhylogenyNode n00 = PhylogenyNode
4878 .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]" );
4879 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4882 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4885 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4888 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4891 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4894 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4897 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4900 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4903 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4904 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4907 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4908 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4911 final PhylogenyNode n13 = PhylogenyNode
4912 .createInstanceFromNhxString( "blah_12345/1-2",
4913 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4914 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4917 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
4920 final PhylogenyNode n14 = PhylogenyNode
4921 .createInstanceFromNhxString( "blah_12X45/1-2",
4922 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4923 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4926 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4929 final PhylogenyNode n15 = PhylogenyNode
4930 .createInstanceFromNhxString( "something_wicked[123]",
4931 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4932 if ( !n15.getName().equals( "something_wicked" ) ) {
4935 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4938 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4941 final PhylogenyNode n16 = PhylogenyNode
4942 .createInstanceFromNhxString( "something_wicked2[9]",
4943 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4944 if ( !n16.getName().equals( "something_wicked2" ) ) {
4947 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4950 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4953 final PhylogenyNode n17 = PhylogenyNode
4954 .createInstanceFromNhxString( "something_wicked3[a]",
4955 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4956 if ( !n17.getName().equals( "something_wicked3" ) ) {
4959 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4962 final PhylogenyNode n18 = PhylogenyNode
4963 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4964 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4967 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4970 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4974 catch ( final Exception e ) {
4975 e.printStackTrace( System.out );
4981 private static boolean testNHXParsing() {
4983 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4984 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4985 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4988 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]";
4989 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4990 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4993 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]";
4994 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4995 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4998 final Phylogeny[] p3 = factory
4999 .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]",
5001 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5004 final Phylogeny[] p4 = factory
5005 .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(]",
5007 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5010 final Phylogeny[] p5 = factory
5011 .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(((]",
5013 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5016 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)";
5017 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)";
5018 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5019 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5022 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)))";
5023 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)))";
5024 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5025 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5028 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]) ))[,,, ])))))))";
5029 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5030 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5031 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5034 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5035 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5038 final Phylogeny p10 = factory
5039 .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]",
5040 new NHXParser() )[ 0 ];
5041 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5045 catch ( final Exception e ) {
5046 e.printStackTrace( System.out );
5052 private static boolean testNHXParsingQuotes() {
5054 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5055 final NHXParser p = new NHXParser();
5056 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5057 if ( phylogenies_0.length != 5 ) {
5060 final Phylogeny phy = phylogenies_0[ 4 ];
5061 if ( phy.getNumberOfExternalNodes() != 7 ) {
5064 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5067 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5070 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5071 .getScientificName().equals( "hsapiens" ) ) {
5074 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5077 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5080 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5083 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5086 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5089 final NHXParser p1p = new NHXParser();
5090 p1p.setIgnoreQuotes( true );
5091 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5092 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5095 final NHXParser p2p = new NHXParser();
5096 p1p.setIgnoreQuotes( false );
5097 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5098 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5101 final NHXParser p3p = new NHXParser();
5102 p3p.setIgnoreQuotes( false );
5103 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5104 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5107 final NHXParser p4p = new NHXParser();
5108 p4p.setIgnoreQuotes( false );
5109 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5110 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5113 final Phylogeny p10 = factory
5114 .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]",
5115 new NHXParser() )[ 0 ];
5116 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]";
5117 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5120 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5121 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5125 final Phylogeny p12 = factory
5126 .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]",
5127 new NHXParser() )[ 0 ];
5128 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]";
5129 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5132 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5133 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5136 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;";
5137 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5140 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5141 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5145 catch ( final Exception e ) {
5146 e.printStackTrace( System.out );
5152 private static boolean testNHXParsingMB() {
5154 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5155 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5156 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5157 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5158 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5159 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5160 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5161 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5162 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5163 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5164 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5167 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5170 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5171 0.1100000000000000e+00 ) ) {
5174 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5177 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5180 final Phylogeny p2 = factory
5181 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5182 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5183 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5184 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5185 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5186 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5187 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5188 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5189 + "7.369400000000000e-02}])",
5190 new NHXParser() )[ 0 ];
5191 if ( p2.getNode( "1" ) == null ) {
5194 if ( p2.getNode( "2" ) == null ) {
5198 catch ( final Exception e ) {
5199 e.printStackTrace( System.out );
5206 private static boolean testPhylogenyBranch() {
5208 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5209 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5210 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5211 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5212 if ( !a1b1.equals( a1b1 ) ) {
5215 if ( !a1b1.equals( b1a1 ) ) {
5218 if ( !b1a1.equals( a1b1 ) ) {
5221 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5222 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5223 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5224 if ( a1_b1.equals( b1_a1 ) ) {
5227 if ( a1_b1.equals( a1_b1_ ) ) {
5230 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5231 if ( !a1_b1.equals( b1_a1_ ) ) {
5234 if ( a1_b1_.equals( b1_a1_ ) ) {
5237 if ( !a1_b1_.equals( b1_a1 ) ) {
5241 catch ( final Exception e ) {
5242 e.printStackTrace( System.out );
5248 private static boolean testPhyloXMLparsingOfDistributionElement() {
5250 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5251 PhyloXmlParser xml_parser = null;
5253 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5255 catch ( final Exception e ) {
5256 // Do nothing -- means were not running from jar.
5258 if ( xml_parser == null ) {
5259 xml_parser = new PhyloXmlParser();
5260 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5261 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5264 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5267 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5269 if ( xml_parser.getErrorCount() > 0 ) {
5270 System.out.println( xml_parser.getErrorMessages().toString() );
5273 if ( phylogenies_0.length != 1 ) {
5276 final Phylogeny t1 = phylogenies_0[ 0 ];
5277 PhylogenyNode n = null;
5278 Distribution d = null;
5279 n = t1.getNode( "root node" );
5280 if ( !n.getNodeData().isHasDistribution() ) {
5283 if ( n.getNodeData().getDistributions().size() != 1 ) {
5286 d = n.getNodeData().getDistribution();
5287 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5290 if ( d.getPoints().size() != 1 ) {
5293 if ( d.getPolygons() != null ) {
5296 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5299 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5302 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5305 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5308 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5311 n = t1.getNode( "node a" );
5312 if ( !n.getNodeData().isHasDistribution() ) {
5315 if ( n.getNodeData().getDistributions().size() != 2 ) {
5318 d = n.getNodeData().getDistribution( 1 );
5319 if ( !d.getDesc().equals( "San Diego" ) ) {
5322 if ( d.getPoints().size() != 1 ) {
5325 if ( d.getPolygons() != null ) {
5328 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5331 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5334 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5337 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5340 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5343 n = t1.getNode( "node bb" );
5344 if ( !n.getNodeData().isHasDistribution() ) {
5347 if ( n.getNodeData().getDistributions().size() != 1 ) {
5350 d = n.getNodeData().getDistribution( 0 );
5351 if ( d.getPoints().size() != 3 ) {
5354 if ( d.getPolygons().size() != 2 ) {
5357 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5360 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5363 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5366 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5369 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5372 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5375 Polygon p = d.getPolygons().get( 0 );
5376 if ( p.getPoints().size() != 3 ) {
5379 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5382 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5385 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5388 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5391 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5394 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5397 p = d.getPolygons().get( 1 );
5398 if ( p.getPoints().size() != 3 ) {
5401 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5404 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5407 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5411 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5412 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5413 if ( rt.length != 1 ) {
5416 final Phylogeny t1_rt = rt[ 0 ];
5417 n = t1_rt.getNode( "root node" );
5418 if ( !n.getNodeData().isHasDistribution() ) {
5421 if ( n.getNodeData().getDistributions().size() != 1 ) {
5424 d = n.getNodeData().getDistribution();
5425 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5428 if ( d.getPoints().size() != 1 ) {
5431 if ( d.getPolygons() != null ) {
5434 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5437 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5440 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5443 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5446 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5449 n = t1_rt.getNode( "node a" );
5450 if ( !n.getNodeData().isHasDistribution() ) {
5453 if ( n.getNodeData().getDistributions().size() != 2 ) {
5456 d = n.getNodeData().getDistribution( 1 );
5457 if ( !d.getDesc().equals( "San Diego" ) ) {
5460 if ( d.getPoints().size() != 1 ) {
5463 if ( d.getPolygons() != null ) {
5466 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5469 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5472 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5475 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5478 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5481 n = t1_rt.getNode( "node bb" );
5482 if ( !n.getNodeData().isHasDistribution() ) {
5485 if ( n.getNodeData().getDistributions().size() != 1 ) {
5488 d = n.getNodeData().getDistribution( 0 );
5489 if ( d.getPoints().size() != 3 ) {
5492 if ( d.getPolygons().size() != 2 ) {
5495 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5498 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5501 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5504 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5507 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5510 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5513 p = d.getPolygons().get( 0 );
5514 if ( p.getPoints().size() != 3 ) {
5517 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5520 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5523 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5526 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5529 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5532 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5535 p = d.getPolygons().get( 1 );
5536 if ( p.getPoints().size() != 3 ) {
5539 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5542 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5545 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5549 catch ( final Exception e ) {
5550 e.printStackTrace( System.out );
5556 private static boolean testPostOrderIterator() {
5558 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5559 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5560 PhylogenyNodeIterator it0;
5561 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5564 for( it0.reset(); it0.hasNext(); ) {
5567 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5568 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5569 if ( !it.next().getName().equals( "A" ) ) {
5572 if ( !it.next().getName().equals( "B" ) ) {
5575 if ( !it.next().getName().equals( "ab" ) ) {
5578 if ( !it.next().getName().equals( "C" ) ) {
5581 if ( !it.next().getName().equals( "D" ) ) {
5584 if ( !it.next().getName().equals( "cd" ) ) {
5587 if ( !it.next().getName().equals( "abcd" ) ) {
5590 if ( !it.next().getName().equals( "E" ) ) {
5593 if ( !it.next().getName().equals( "F" ) ) {
5596 if ( !it.next().getName().equals( "ef" ) ) {
5599 if ( !it.next().getName().equals( "G" ) ) {
5602 if ( !it.next().getName().equals( "H" ) ) {
5605 if ( !it.next().getName().equals( "gh" ) ) {
5608 if ( !it.next().getName().equals( "efgh" ) ) {
5611 if ( !it.next().getName().equals( "r" ) ) {
5614 if ( it.hasNext() ) {
5618 catch ( final Exception e ) {
5619 e.printStackTrace( System.out );
5625 private static boolean testPreOrderIterator() {
5627 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5628 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5629 PhylogenyNodeIterator it0;
5630 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5633 for( it0.reset(); it0.hasNext(); ) {
5636 PhylogenyNodeIterator it = t0.iteratorPreorder();
5637 if ( !it.next().getName().equals( "r" ) ) {
5640 if ( !it.next().getName().equals( "ab" ) ) {
5643 if ( !it.next().getName().equals( "A" ) ) {
5646 if ( !it.next().getName().equals( "B" ) ) {
5649 if ( !it.next().getName().equals( "cd" ) ) {
5652 if ( !it.next().getName().equals( "C" ) ) {
5655 if ( !it.next().getName().equals( "D" ) ) {
5658 if ( it.hasNext() ) {
5661 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5662 it = t1.iteratorPreorder();
5663 if ( !it.next().getName().equals( "r" ) ) {
5666 if ( !it.next().getName().equals( "abcd" ) ) {
5669 if ( !it.next().getName().equals( "ab" ) ) {
5672 if ( !it.next().getName().equals( "A" ) ) {
5675 if ( !it.next().getName().equals( "B" ) ) {
5678 if ( !it.next().getName().equals( "cd" ) ) {
5681 if ( !it.next().getName().equals( "C" ) ) {
5684 if ( !it.next().getName().equals( "D" ) ) {
5687 if ( !it.next().getName().equals( "efgh" ) ) {
5690 if ( !it.next().getName().equals( "ef" ) ) {
5693 if ( !it.next().getName().equals( "E" ) ) {
5696 if ( !it.next().getName().equals( "F" ) ) {
5699 if ( !it.next().getName().equals( "gh" ) ) {
5702 if ( !it.next().getName().equals( "G" ) ) {
5705 if ( !it.next().getName().equals( "H" ) ) {
5708 if ( it.hasNext() ) {
5712 catch ( final Exception e ) {
5713 e.printStackTrace( System.out );
5719 private static boolean testPropertiesMap() {
5721 final PropertiesMap pm = new PropertiesMap();
5722 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5723 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5724 final Property p2 = new Property( "something:else",
5726 "improbable:research",
5729 pm.addProperty( p0 );
5730 pm.addProperty( p1 );
5731 pm.addProperty( p2 );
5732 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5735 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5738 if ( pm.getProperties().size() != 3 ) {
5741 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5744 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5747 if ( pm.getProperties().size() != 3 ) {
5750 pm.removeProperty( "dimensions:diameter" );
5751 if ( pm.getProperties().size() != 2 ) {
5754 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5757 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5761 catch ( final Exception e ) {
5762 e.printStackTrace( System.out );
5768 private static boolean testReIdMethods() {
5770 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5771 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5772 final int count = PhylogenyNode.getNodeCount();
5774 if ( p.getNode( "r" ).getId() != count ) {
5777 if ( p.getNode( "A" ).getId() != count + 1 ) {
5780 if ( p.getNode( "B" ).getId() != count + 1 ) {
5783 if ( p.getNode( "C" ).getId() != count + 1 ) {
5786 if ( p.getNode( "1" ).getId() != count + 2 ) {
5789 if ( p.getNode( "2" ).getId() != count + 2 ) {
5792 if ( p.getNode( "3" ).getId() != count + 2 ) {
5795 if ( p.getNode( "4" ).getId() != count + 2 ) {
5798 if ( p.getNode( "5" ).getId() != count + 2 ) {
5801 if ( p.getNode( "6" ).getId() != count + 2 ) {
5804 if ( p.getNode( "a" ).getId() != count + 3 ) {
5807 if ( p.getNode( "b" ).getId() != count + 3 ) {
5810 if ( p.getNode( "X" ).getId() != count + 4 ) {
5813 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5816 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5820 catch ( final Exception e ) {
5821 e.printStackTrace( System.out );
5827 private static boolean testRerooting() {
5829 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5830 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",
5831 new NHXParser() )[ 0 ];
5832 if ( !t1.isRooted() ) {
5835 t1.reRoot( t1.getNode( "D" ) );
5836 t1.reRoot( t1.getNode( "CD" ) );
5837 t1.reRoot( t1.getNode( "A" ) );
5838 t1.reRoot( t1.getNode( "B" ) );
5839 t1.reRoot( t1.getNode( "AB" ) );
5840 t1.reRoot( t1.getNode( "D" ) );
5841 t1.reRoot( t1.getNode( "C" ) );
5842 t1.reRoot( t1.getNode( "CD" ) );
5843 t1.reRoot( t1.getNode( "A" ) );
5844 t1.reRoot( t1.getNode( "B" ) );
5845 t1.reRoot( t1.getNode( "AB" ) );
5846 t1.reRoot( t1.getNode( "D" ) );
5847 t1.reRoot( t1.getNode( "D" ) );
5848 t1.reRoot( t1.getNode( "C" ) );
5849 t1.reRoot( t1.getNode( "A" ) );
5850 t1.reRoot( t1.getNode( "B" ) );
5851 t1.reRoot( t1.getNode( "AB" ) );
5852 t1.reRoot( t1.getNode( "C" ) );
5853 t1.reRoot( t1.getNode( "D" ) );
5854 t1.reRoot( t1.getNode( "CD" ) );
5855 t1.reRoot( t1.getNode( "D" ) );
5856 t1.reRoot( t1.getNode( "A" ) );
5857 t1.reRoot( t1.getNode( "B" ) );
5858 t1.reRoot( t1.getNode( "AB" ) );
5859 t1.reRoot( t1.getNode( "C" ) );
5860 t1.reRoot( t1.getNode( "D" ) );
5861 t1.reRoot( t1.getNode( "CD" ) );
5862 t1.reRoot( t1.getNode( "D" ) );
5863 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5866 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5869 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5872 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5875 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5878 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5881 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",
5882 new NHXParser() )[ 0 ];
5883 t2.reRoot( t2.getNode( "A" ) );
5884 t2.reRoot( t2.getNode( "D" ) );
5885 t2.reRoot( t2.getNode( "ABC" ) );
5886 t2.reRoot( t2.getNode( "A" ) );
5887 t2.reRoot( t2.getNode( "B" ) );
5888 t2.reRoot( t2.getNode( "D" ) );
5889 t2.reRoot( t2.getNode( "C" ) );
5890 t2.reRoot( t2.getNode( "ABC" ) );
5891 t2.reRoot( t2.getNode( "A" ) );
5892 t2.reRoot( t2.getNode( "B" ) );
5893 t2.reRoot( t2.getNode( "AB" ) );
5894 t2.reRoot( t2.getNode( "AB" ) );
5895 t2.reRoot( t2.getNode( "D" ) );
5896 t2.reRoot( t2.getNode( "C" ) );
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( "ABC" ) );
5902 t2.reRoot( t2.getNode( "A" ) );
5903 t2.reRoot( t2.getNode( "B" ) );
5904 t2.reRoot( t2.getNode( "AB" ) );
5905 t2.reRoot( t2.getNode( "D" ) );
5906 t2.reRoot( t2.getNode( "C" ) );
5907 t2.reRoot( t2.getNode( "ABC" ) );
5908 t2.reRoot( t2.getNode( "A" ) );
5909 t2.reRoot( t2.getNode( "B" ) );
5910 t2.reRoot( t2.getNode( "AB" ) );
5911 t2.reRoot( t2.getNode( "D" ) );
5912 t2.reRoot( t2.getNode( "D" ) );
5913 t2.reRoot( t2.getNode( "C" ) );
5914 t2.reRoot( t2.getNode( "A" ) );
5915 t2.reRoot( t2.getNode( "B" ) );
5916 t2.reRoot( t2.getNode( "AB" ) );
5917 t2.reRoot( t2.getNode( "C" ) );
5918 t2.reRoot( t2.getNode( "D" ) );
5919 t2.reRoot( t2.getNode( "ABC" ) );
5920 t2.reRoot( t2.getNode( "D" ) );
5921 t2.reRoot( t2.getNode( "A" ) );
5922 t2.reRoot( t2.getNode( "B" ) );
5923 t2.reRoot( t2.getNode( "AB" ) );
5924 t2.reRoot( t2.getNode( "C" ) );
5925 t2.reRoot( t2.getNode( "D" ) );
5926 t2.reRoot( t2.getNode( "ABC" ) );
5927 t2.reRoot( t2.getNode( "D" ) );
5928 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5931 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5934 t2.reRoot( t2.getNode( "ABC" ) );
5935 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5938 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5941 t2.reRoot( t2.getNode( "AB" ) );
5942 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5945 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5948 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5951 t2.reRoot( t2.getNode( "AB" ) );
5952 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5955 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5958 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5961 t2.reRoot( t2.getNode( "D" ) );
5962 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5965 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5968 t2.reRoot( t2.getNode( "ABC" ) );
5969 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5972 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5975 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5976 new NHXParser() )[ 0 ];
5977 t3.reRoot( t3.getNode( "B" ) );
5978 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5981 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5984 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5987 t3.reRoot( t3.getNode( "B" ) );
5988 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5991 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5994 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5997 t3.reRoot( t3.getRoot() );
5998 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6001 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6004 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6008 catch ( final Exception e ) {
6009 e.printStackTrace( System.out );
6015 private static boolean testSDIse() {
6017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6018 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6019 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6020 gene1.setRooted( true );
6021 species1.setRooted( true );
6022 final SDI sdi = new SDIse( gene1, species1 );
6023 if ( !gene1.getRoot().isDuplication() ) {
6026 final Phylogeny species2 = factory
6027 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6028 new NHXParser() )[ 0 ];
6029 final Phylogeny gene2 = factory
6030 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6031 new NHXParser() )[ 0 ];
6032 species2.setRooted( true );
6033 gene2.setRooted( true );
6034 final SDI sdi2 = new SDIse( gene2, species2 );
6035 if ( sdi2.getDuplicationsSum() != 0 ) {
6038 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6041 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6044 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6047 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6050 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6053 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6056 final Phylogeny species3 = factory
6057 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6058 new NHXParser() )[ 0 ];
6059 final Phylogeny gene3 = factory
6060 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6061 new NHXParser() )[ 0 ];
6062 species3.setRooted( true );
6063 gene3.setRooted( true );
6064 final SDI sdi3 = new SDIse( gene3, species3 );
6065 if ( sdi3.getDuplicationsSum() != 1 ) {
6068 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6071 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6074 final Phylogeny species4 = factory
6075 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6076 new NHXParser() )[ 0 ];
6077 final Phylogeny gene4 = factory
6078 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6079 new NHXParser() )[ 0 ];
6080 species4.setRooted( true );
6081 gene4.setRooted( true );
6082 final SDI sdi4 = new SDIse( gene4, species4 );
6083 if ( sdi4.getDuplicationsSum() != 1 ) {
6086 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6089 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6092 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6095 if ( species4.getNumberOfExternalNodes() != 6 ) {
6098 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6101 final Phylogeny species5 = factory
6102 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6103 new NHXParser() )[ 0 ];
6104 final Phylogeny gene5 = factory
6105 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6106 new NHXParser() )[ 0 ];
6107 species5.setRooted( true );
6108 gene5.setRooted( true );
6109 final SDI sdi5 = new SDIse( gene5, species5 );
6110 if ( sdi5.getDuplicationsSum() != 2 ) {
6113 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6116 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6119 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6122 if ( species5.getNumberOfExternalNodes() != 6 ) {
6125 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6128 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6129 // Conjecture for Comparing Molecular Phylogenies"
6130 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6131 final Phylogeny species6 = factory
6132 .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,"
6133 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6134 new NHXParser() )[ 0 ];
6135 final Phylogeny gene6 = factory
6136 .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,"
6137 + "((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,"
6138 + "(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;",
6139 new NHXParser() )[ 0 ];
6140 species6.setRooted( true );
6141 gene6.setRooted( true );
6142 final SDI sdi6 = new SDIse( gene6, species6 );
6143 if ( sdi6.getDuplicationsSum() != 3 ) {
6146 if ( !gene6.getNode( "r" ).isDuplication() ) {
6149 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6152 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6155 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6158 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6161 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6164 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6167 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6170 sdi6.computeMappingCostL();
6171 if ( sdi6.computeMappingCostL() != 17 ) {
6174 if ( species6.getNumberOfExternalNodes() != 9 ) {
6177 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6180 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6181 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6182 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6183 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6184 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6185 species7.setRooted( true );
6186 final Phylogeny gene7_1 = Test
6187 .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])" );
6188 gene7_1.setRooted( true );
6189 final SDI sdi7 = new SDIse( gene7_1, species7 );
6190 if ( sdi7.getDuplicationsSum() != 0 ) {
6193 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6196 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6199 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6202 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6205 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6208 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6211 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6214 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6217 final Phylogeny gene7_2 = Test
6218 .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])" );
6219 gene7_2.setRooted( true );
6220 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6221 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6224 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6227 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6230 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6233 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6236 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6239 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6242 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6245 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6248 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6252 catch ( final Exception e ) {
6258 private static boolean testSDIunrooted() {
6260 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6261 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6262 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6263 final Iterator<PhylogenyBranch> iter = l.iterator();
6264 PhylogenyBranch br = iter.next();
6265 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6268 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6272 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6275 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6279 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6282 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6286 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6289 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6293 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6296 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6300 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6303 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6307 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6310 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6314 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6317 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6321 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6324 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6328 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6331 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6335 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6338 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6342 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6345 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6349 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6352 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6356 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6359 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6363 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6366 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6369 if ( iter.hasNext() ) {
6372 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6373 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6374 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6376 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6379 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6383 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6386 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6390 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6393 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6396 if ( iter1.hasNext() ) {
6399 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6400 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6401 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6403 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6406 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6410 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6413 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6417 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6420 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6423 if ( iter2.hasNext() ) {
6426 final Phylogeny species0 = factory
6427 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6428 new NHXParser() )[ 0 ];
6429 final Phylogeny gene1 = factory
6430 .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])",
6431 new NHXParser() )[ 0 ];
6432 species0.setRooted( true );
6433 gene1.setRooted( true );
6434 final SDIR sdi_unrooted = new SDIR();
6435 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6436 if ( sdi_unrooted.getCount() != 1 ) {
6439 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6442 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6445 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6448 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6451 final Phylogeny gene2 = factory
6452 .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])",
6453 new NHXParser() )[ 0 ];
6454 gene2.setRooted( true );
6455 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6456 if ( sdi_unrooted.getCount() != 1 ) {
6459 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6462 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6465 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6468 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6471 final Phylogeny species6 = factory
6472 .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,"
6473 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6474 new NHXParser() )[ 0 ];
6475 final Phylogeny gene6 = factory
6476 .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],"
6477 + "(((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],"
6478 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6479 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6480 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6481 new NHXParser() )[ 0 ];
6482 species6.setRooted( true );
6483 gene6.setRooted( true );
6484 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6485 if ( sdi_unrooted.getCount() != 1 ) {
6488 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6491 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6494 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6497 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6500 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6503 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6506 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6509 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6512 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6515 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6518 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6521 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6525 final Phylogeny species7 = factory
6526 .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,"
6527 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6528 new NHXParser() )[ 0 ];
6529 final Phylogeny gene7 = factory
6530 .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],"
6531 + "(((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],"
6532 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6533 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6534 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6535 new NHXParser() )[ 0 ];
6536 species7.setRooted( true );
6537 gene7.setRooted( true );
6538 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6539 if ( sdi_unrooted.getCount() != 1 ) {
6542 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6545 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6548 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6551 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6554 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6557 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6560 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6563 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6566 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6569 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6572 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6575 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6579 final Phylogeny species8 = factory
6580 .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,"
6581 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6582 new NHXParser() )[ 0 ];
6583 final Phylogeny gene8 = factory
6584 .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],"
6585 + "(((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],"
6586 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6587 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6588 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6589 new NHXParser() )[ 0 ];
6590 species8.setRooted( true );
6591 gene8.setRooted( true );
6592 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6593 if ( sdi_unrooted.getCount() != 1 ) {
6596 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6599 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6602 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6605 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6608 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6611 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6614 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6617 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6620 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6623 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6626 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6629 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6634 catch ( final Exception e ) {
6635 e.printStackTrace( System.out );
6641 private static boolean testSplit() {
6643 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6644 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6645 //Archaeopteryx.createApplication( p0 );
6646 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6647 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6648 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6649 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6650 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6651 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6652 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6653 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6654 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6655 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6656 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6657 // System.out.println( s0.toString() );
6659 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6662 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 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6673 if ( !s0.match( query_nodes ) ) {
6677 query_nodes = new HashSet<PhylogenyNode>();
6678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6681 if ( !s0.match( query_nodes ) ) {
6685 query_nodes = new HashSet<PhylogenyNode>();
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6690 if ( !s0.match( query_nodes ) ) {
6694 query_nodes = new HashSet<PhylogenyNode>();
6695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6699 if ( !s0.match( query_nodes ) ) {
6703 query_nodes = new HashSet<PhylogenyNode>();
6704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6707 if ( !s0.match( query_nodes ) ) {
6711 query_nodes = new HashSet<PhylogenyNode>();
6712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6714 if ( !s0.match( query_nodes ) ) {
6718 query_nodes = new HashSet<PhylogenyNode>();
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6724 if ( !s0.match( query_nodes ) ) {
6728 query_nodes = new HashSet<PhylogenyNode>();
6729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6732 if ( !s0.match( query_nodes ) ) {
6736 query_nodes = new HashSet<PhylogenyNode>();
6737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6741 if ( !s0.match( query_nodes ) ) {
6745 query_nodes = new HashSet<PhylogenyNode>();
6746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6748 if ( s0.match( query_nodes ) ) {
6752 query_nodes = new HashSet<PhylogenyNode>();
6753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6757 if ( s0.match( query_nodes ) ) {
6761 query_nodes = new HashSet<PhylogenyNode>();
6762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6767 if ( s0.match( query_nodes ) ) {
6771 query_nodes = new HashSet<PhylogenyNode>();
6772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6774 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6775 if ( s0.match( query_nodes ) ) {
6779 query_nodes = new HashSet<PhylogenyNode>();
6780 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6781 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6782 if ( s0.match( query_nodes ) ) {
6786 query_nodes = new HashSet<PhylogenyNode>();
6787 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6788 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6789 if ( s0.match( query_nodes ) ) {
6793 query_nodes = new HashSet<PhylogenyNode>();
6794 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6796 if ( s0.match( query_nodes ) ) {
6800 query_nodes = new HashSet<PhylogenyNode>();
6801 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6803 if ( s0.match( query_nodes ) ) {
6807 query_nodes = new HashSet<PhylogenyNode>();
6808 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6810 if ( s0.match( query_nodes ) ) {
6814 query_nodes = new HashSet<PhylogenyNode>();
6815 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6817 if ( s0.match( query_nodes ) ) {
6821 query_nodes = new HashSet<PhylogenyNode>();
6822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6825 if ( s0.match( query_nodes ) ) {
6829 query_nodes = new HashSet<PhylogenyNode>();
6830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6833 if ( s0.match( query_nodes ) ) {
6837 query_nodes = new HashSet<PhylogenyNode>();
6838 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6841 if ( s0.match( query_nodes ) ) {
6845 query_nodes = new HashSet<PhylogenyNode>();
6846 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6847 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6850 if ( s0.match( query_nodes ) ) {
6854 // query_nodes = new HashSet<PhylogenyNode>();
6855 // query_nodes.add( new PhylogenyNode( "X" ) );
6856 // query_nodes.add( new PhylogenyNode( "Y" ) );
6857 // query_nodes.add( new PhylogenyNode( "A" ) );
6858 // query_nodes.add( new PhylogenyNode( "B" ) );
6859 // query_nodes.add( new PhylogenyNode( "C" ) );
6860 // query_nodes.add( new PhylogenyNode( "D" ) );
6861 // query_nodes.add( new PhylogenyNode( "E" ) );
6862 // query_nodes.add( new PhylogenyNode( "F" ) );
6863 // query_nodes.add( new PhylogenyNode( "G" ) );
6864 // if ( !s0.match( query_nodes ) ) {
6867 // query_nodes = new HashSet<PhylogenyNode>();
6868 // query_nodes.add( new PhylogenyNode( "X" ) );
6869 // query_nodes.add( new PhylogenyNode( "Y" ) );
6870 // query_nodes.add( new PhylogenyNode( "A" ) );
6871 // query_nodes.add( new PhylogenyNode( "B" ) );
6872 // query_nodes.add( new PhylogenyNode( "C" ) );
6873 // if ( !s0.match( query_nodes ) ) {
6877 // query_nodes = new HashSet<PhylogenyNode>();
6878 // query_nodes.add( new PhylogenyNode( "X" ) );
6879 // query_nodes.add( new PhylogenyNode( "Y" ) );
6880 // query_nodes.add( new PhylogenyNode( "D" ) );
6881 // query_nodes.add( new PhylogenyNode( "E" ) );
6882 // query_nodes.add( new PhylogenyNode( "F" ) );
6883 // query_nodes.add( new PhylogenyNode( "G" ) );
6884 // if ( !s0.match( query_nodes ) ) {
6888 // query_nodes = new HashSet<PhylogenyNode>();
6889 // query_nodes.add( new PhylogenyNode( "X" ) );
6890 // query_nodes.add( new PhylogenyNode( "Y" ) );
6891 // query_nodes.add( new PhylogenyNode( "A" ) );
6892 // query_nodes.add( new PhylogenyNode( "B" ) );
6893 // query_nodes.add( new PhylogenyNode( "C" ) );
6894 // query_nodes.add( new PhylogenyNode( "D" ) );
6895 // if ( !s0.match( query_nodes ) ) {
6899 // query_nodes = new HashSet<PhylogenyNode>();
6900 // query_nodes.add( new PhylogenyNode( "X" ) );
6901 // query_nodes.add( new PhylogenyNode( "Y" ) );
6902 // query_nodes.add( new PhylogenyNode( "E" ) );
6903 // query_nodes.add( new PhylogenyNode( "F" ) );
6904 // query_nodes.add( new PhylogenyNode( "G" ) );
6905 // if ( !s0.match( query_nodes ) ) {
6909 // query_nodes = new HashSet<PhylogenyNode>();
6910 // query_nodes.add( new PhylogenyNode( "X" ) );
6911 // query_nodes.add( new PhylogenyNode( "Y" ) );
6912 // query_nodes.add( new PhylogenyNode( "F" ) );
6913 // query_nodes.add( new PhylogenyNode( "G" ) );
6914 // if ( !s0.match( query_nodes ) ) {
6918 query_nodes = new HashSet<PhylogenyNode>();
6919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6923 if ( s0.match( query_nodes ) ) {
6927 query_nodes = new HashSet<PhylogenyNode>();
6928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6932 if ( s0.match( query_nodes ) ) {
6935 ///////////////////////////
6937 query_nodes = new HashSet<PhylogenyNode>();
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6942 if ( s0.match( query_nodes ) ) {
6946 query_nodes = new HashSet<PhylogenyNode>();
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6951 if ( s0.match( query_nodes ) ) {
6955 query_nodes = new HashSet<PhylogenyNode>();
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6960 if ( s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6969 if ( s0.match( query_nodes ) ) {
6973 query_nodes = new HashSet<PhylogenyNode>();
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6978 if ( s0.match( query_nodes ) ) {
6982 query_nodes = new HashSet<PhylogenyNode>();
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6986 if ( s0.match( query_nodes ) ) {
6990 query_nodes = new HashSet<PhylogenyNode>();
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6996 if ( s0.match( query_nodes ) ) {
7000 query_nodes = new HashSet<PhylogenyNode>();
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7006 if ( s0.match( query_nodes ) ) {
7010 query_nodes = new HashSet<PhylogenyNode>();
7011 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7016 if ( s0.match( query_nodes ) ) {
7020 query_nodes = new HashSet<PhylogenyNode>();
7021 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7027 if ( s0.match( query_nodes ) ) {
7031 catch ( final Exception e ) {
7032 e.printStackTrace();
7038 private static boolean testSplitStrict() {
7040 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7041 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7042 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7043 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7044 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7045 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7046 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7047 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7048 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7049 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7050 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7051 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7054 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 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7065 if ( !s0.match( query_nodes ) ) {
7069 query_nodes = new HashSet<PhylogenyNode>();
7070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7073 if ( !s0.match( query_nodes ) ) {
7077 query_nodes = new HashSet<PhylogenyNode>();
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7082 if ( !s0.match( query_nodes ) ) {
7086 query_nodes = new HashSet<PhylogenyNode>();
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7091 if ( !s0.match( query_nodes ) ) {
7095 query_nodes = new HashSet<PhylogenyNode>();
7096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7099 if ( !s0.match( query_nodes ) ) {
7103 query_nodes = new HashSet<PhylogenyNode>();
7104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7106 if ( !s0.match( query_nodes ) ) {
7110 query_nodes = new HashSet<PhylogenyNode>();
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7116 if ( !s0.match( query_nodes ) ) {
7120 query_nodes = new HashSet<PhylogenyNode>();
7121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7124 if ( !s0.match( query_nodes ) ) {
7128 query_nodes = new HashSet<PhylogenyNode>();
7129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7133 if ( !s0.match( query_nodes ) ) {
7137 query_nodes = new HashSet<PhylogenyNode>();
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7140 if ( s0.match( query_nodes ) ) {
7144 query_nodes = new HashSet<PhylogenyNode>();
7145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7149 if ( s0.match( query_nodes ) ) {
7153 query_nodes = new HashSet<PhylogenyNode>();
7154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7159 if ( s0.match( query_nodes ) ) {
7163 query_nodes = new HashSet<PhylogenyNode>();
7164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7167 if ( s0.match( query_nodes ) ) {
7171 query_nodes = new HashSet<PhylogenyNode>();
7172 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7173 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7174 if ( s0.match( query_nodes ) ) {
7178 query_nodes = new HashSet<PhylogenyNode>();
7179 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7181 if ( s0.match( query_nodes ) ) {
7185 query_nodes = new HashSet<PhylogenyNode>();
7186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7188 if ( s0.match( query_nodes ) ) {
7192 query_nodes = new HashSet<PhylogenyNode>();
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7195 if ( s0.match( query_nodes ) ) {
7199 query_nodes = new HashSet<PhylogenyNode>();
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7202 if ( s0.match( query_nodes ) ) {
7206 query_nodes = new HashSet<PhylogenyNode>();
7207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7209 if ( s0.match( query_nodes ) ) {
7213 query_nodes = new HashSet<PhylogenyNode>();
7214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7217 if ( s0.match( query_nodes ) ) {
7221 query_nodes = new HashSet<PhylogenyNode>();
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7224 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7225 if ( s0.match( query_nodes ) ) {
7229 query_nodes = new HashSet<PhylogenyNode>();
7230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7232 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7233 if ( s0.match( query_nodes ) ) {
7237 query_nodes = new HashSet<PhylogenyNode>();
7238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7242 if ( s0.match( query_nodes ) ) {
7246 catch ( final Exception e ) {
7247 e.printStackTrace();
7253 private static boolean testSubtreeDeletion() {
7255 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7256 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7257 t1.deleteSubtree( t1.getNode( "A" ), false );
7258 if ( t1.getNumberOfExternalNodes() != 5 ) {
7261 t1.toNewHampshireX();
7262 t1.deleteSubtree( t1.getNode( "E" ), false );
7263 if ( t1.getNumberOfExternalNodes() != 4 ) {
7266 t1.toNewHampshireX();
7267 t1.deleteSubtree( t1.getNode( "F" ), false );
7268 if ( t1.getNumberOfExternalNodes() != 3 ) {
7271 t1.toNewHampshireX();
7272 t1.deleteSubtree( t1.getNode( "D" ), false );
7273 t1.toNewHampshireX();
7274 if ( t1.getNumberOfExternalNodes() != 3 ) {
7277 t1.deleteSubtree( t1.getNode( "def" ), false );
7278 t1.toNewHampshireX();
7279 if ( t1.getNumberOfExternalNodes() != 2 ) {
7282 t1.deleteSubtree( t1.getNode( "B" ), false );
7283 t1.toNewHampshireX();
7284 if ( t1.getNumberOfExternalNodes() != 1 ) {
7287 t1.deleteSubtree( t1.getNode( "C" ), false );
7288 t1.toNewHampshireX();
7289 if ( t1.getNumberOfExternalNodes() != 1 ) {
7292 t1.deleteSubtree( t1.getNode( "abc" ), false );
7293 t1.toNewHampshireX();
7294 if ( t1.getNumberOfExternalNodes() != 1 ) {
7297 t1.deleteSubtree( t1.getNode( "r" ), false );
7298 if ( t1.getNumberOfExternalNodes() != 0 ) {
7301 if ( !t1.isEmpty() ) {
7304 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7305 t2.deleteSubtree( t2.getNode( "A" ), false );
7306 t2.toNewHampshireX();
7307 if ( t2.getNumberOfExternalNodes() != 5 ) {
7310 t2.deleteSubtree( t2.getNode( "abc" ), false );
7311 t2.toNewHampshireX();
7312 if ( t2.getNumberOfExternalNodes() != 3 ) {
7315 t2.deleteSubtree( t2.getNode( "def" ), false );
7316 t2.toNewHampshireX();
7317 if ( t2.getNumberOfExternalNodes() != 1 ) {
7321 catch ( final Exception e ) {
7322 e.printStackTrace( System.out );
7328 private static boolean testSupportCount() {
7330 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7331 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7332 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7333 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7334 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7335 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7336 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7338 SupportCount.count( t0_1, phylogenies_1, true, false );
7339 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7340 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7341 + "(((((A,B),C),D),E),((F,G),X))"
7342 + "(((((A,Y),B),C),D),((F,G),E))"
7343 + "(((((A,B),C),D),E),(F,G))"
7344 + "(((((A,B),C),D),E),(F,G))"
7345 + "(((((A,B),C),D),E),(F,G))"
7346 + "(((((A,B),C),D),E),(F,G),Z)"
7347 + "(((((A,B),C),D),E),(F,G))"
7348 + "((((((A,B),C),D),E),F),G)"
7349 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7351 SupportCount.count( t0_2, phylogenies_2, true, false );
7352 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7353 while ( it.hasNext() ) {
7354 final PhylogenyNode n = it.next();
7355 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7359 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7360 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7361 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7362 SupportCount.count( t0_3, phylogenies_3, true, false );
7363 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7364 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7367 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7370 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7373 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7376 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7379 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7382 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7385 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7388 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7391 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7394 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7395 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7396 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7397 SupportCount.count( t0_4, phylogenies_4, true, false );
7398 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7399 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7402 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7405 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7408 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7411 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7414 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7417 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7420 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7423 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7426 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7429 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7430 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7431 double d = SupportCount.compare( b1, a, true, true, true );
7432 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7435 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7436 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7437 d = SupportCount.compare( b2, a, true, true, true );
7438 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7441 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7442 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7443 d = SupportCount.compare( b3, a, true, true, true );
7444 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7447 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7448 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7449 d = SupportCount.compare( b4, a, true, true, false );
7450 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7454 catch ( final Exception e ) {
7455 e.printStackTrace( System.out );
7461 private static boolean testSupportTransfer() {
7463 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7464 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)",
7465 new NHXParser() )[ 0 ];
7466 final Phylogeny p2 = factory
7467 .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 ];
7468 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7471 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7474 support_transfer.moveBranchLengthsToBootstrap( p1 );
7475 support_transfer.transferSupportValues( p1, p2 );
7476 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7479 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7482 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7485 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7488 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7491 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7494 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7497 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7501 catch ( final Exception e ) {
7502 e.printStackTrace( System.out );
7508 private static boolean testUniprotTaxonomySearch() {
7510 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7512 if ( results.size() != 1 ) {
7515 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7518 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7521 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7524 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7527 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7531 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7532 if ( results.size() != 1 ) {
7535 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7538 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7541 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7544 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7547 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7551 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7552 if ( results.size() != 1 ) {
7555 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7558 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7561 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7564 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7567 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7571 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7572 if ( results.size() != 1 ) {
7575 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7578 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7581 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7584 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7587 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7590 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7593 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7596 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7597 .equals( "Nematostella vectensis" ) ) {
7598 System.out.println( results.get( 0 ).getLineage() );
7602 catch ( final IOException e ) {
7603 System.out.println();
7604 System.out.println( "the following might be due to absence internet connection:" );
7605 e.printStackTrace( System.out );
7608 catch ( final Exception e ) {
7614 private static boolean testEmblEntryRetrieval() {
7615 //The format for GenBank Accession numbers are:
7616 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7617 //Protein: 3 letters + 5 numerals
7618 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7619 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7622 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7625 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7628 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7631 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7634 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7637 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7640 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7643 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7646 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7649 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7652 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7655 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7661 private static boolean testUniprotEntryRetrieval() {
7662 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7665 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7668 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7671 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7674 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7677 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7680 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7683 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7686 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7689 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7692 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7695 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7698 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7702 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7703 if ( !entry.getAccession().equals( "P12345" ) ) {
7706 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7709 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7712 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7715 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7719 catch ( final IOException e ) {
7720 System.out.println();
7721 System.out.println( "the following might be due to absence internet connection:" );
7722 e.printStackTrace( System.out );
7725 catch ( final Exception e ) {
7731 private static boolean testWabiTxSearch() {
7734 result = TxSearch.searchSimple( "nematostella" );
7735 result = TxSearch.getTxId( "nematostella" );
7736 if ( !result.equals( "45350" ) ) {
7739 result = TxSearch.getTxName( "45350" );
7740 if ( !result.equals( "Nematostella" ) ) {
7743 result = TxSearch.getTxId( "nematostella vectensis" );
7744 if ( !result.equals( "45351" ) ) {
7747 result = TxSearch.getTxName( "45351" );
7748 if ( !result.equals( "Nematostella vectensis" ) ) {
7751 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7752 if ( !result.equals( "536089" ) ) {
7755 result = TxSearch.getTxName( "536089" );
7756 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7759 final List<String> queries = new ArrayList<String>();
7760 queries.add( "Campylobacter coli" );
7761 queries.add( "Escherichia coli" );
7762 queries.add( "Arabidopsis" );
7763 queries.add( "Trichoplax" );
7764 queries.add( "Samanea saman" );
7765 queries.add( "Kluyveromyces marxianus" );
7766 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7767 queries.add( "Bornavirus parrot/PDD/2008" );
7768 final List<RANKS> ranks = new ArrayList<RANKS>();
7769 ranks.add( RANKS.SUPERKINGDOM );
7770 ranks.add( RANKS.KINGDOM );
7771 ranks.add( RANKS.FAMILY );
7772 ranks.add( RANKS.GENUS );
7773 ranks.add( RANKS.TRIBE );
7774 result = TxSearch.searchLineage( queries, ranks );
7775 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7776 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7778 catch ( final Exception e ) {
7779 System.out.println();
7780 System.out.println( "the following might be due to absence internet connection:" );
7781 e.printStackTrace( System.out );
7787 private static boolean testAminoAcidSequence() {
7789 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7790 if ( aa1.getLength() != 13 ) {
7793 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7796 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7799 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7802 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7803 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7806 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7807 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7810 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7811 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7815 catch ( final Exception e ) {
7816 e.printStackTrace();
7822 private static boolean testCreateBalancedPhylogeny() {
7824 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7825 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7828 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7831 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7832 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7835 if ( p1.getNumberOfExternalNodes() != 100 ) {
7839 catch ( final Exception e ) {
7840 e.printStackTrace();
7846 private static boolean testFastaParser() {
7848 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7851 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7854 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7855 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7858 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7861 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7864 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7867 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7870 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7874 catch ( final Exception e ) {
7875 e.printStackTrace();
7881 private static boolean testGeneralMsaParser() {
7883 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7884 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7885 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
7886 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7887 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7888 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7889 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7890 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7891 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7894 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7897 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7900 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7903 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7906 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7909 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7912 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7915 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7918 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7921 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7924 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7927 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7928 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7931 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7934 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7937 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7938 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7941 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7944 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7947 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7948 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7951 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7954 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7958 catch ( final Exception e ) {
7959 e.printStackTrace();
7965 private static boolean testMafft( final String path ) {
7967 final List<String> opts = new ArrayList<String>();
7968 opts.add( "--maxiterate" );
7970 opts.add( "--localpair" );
7971 opts.add( "--quiet" );
7973 final MsaInferrer mafft = Mafft.createInstance( path );
7974 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
7975 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
7978 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
7982 catch ( final Exception e ) {
7983 e.printStackTrace( System.out );
7989 private static boolean testNextNodeWithCollapsing() {
7991 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7993 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
7994 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
7995 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
7996 t0.getNode( "cd" ).setCollapse( true );
7997 t0.getNode( "cde" ).setCollapse( true );
7998 n = t0.getFirstExternalNode();
7999 while ( n != null ) {
8001 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8003 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8006 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8009 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8012 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8015 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8018 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8022 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8023 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8024 t1.getNode( "ab" ).setCollapse( true );
8025 t1.getNode( "cd" ).setCollapse( true );
8026 t1.getNode( "cde" ).setCollapse( true );
8027 n = t1.getNode( "ab" );
8028 ext = new ArrayList<PhylogenyNode>();
8029 while ( n != null ) {
8031 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8033 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8036 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8039 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8042 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8045 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8051 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8052 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8053 t2.getNode( "ab" ).setCollapse( true );
8054 t2.getNode( "cd" ).setCollapse( true );
8055 t2.getNode( "cde" ).setCollapse( true );
8056 t2.getNode( "c" ).setCollapse( true );
8057 t2.getNode( "d" ).setCollapse( true );
8058 t2.getNode( "e" ).setCollapse( true );
8059 t2.getNode( "gh" ).setCollapse( true );
8060 n = t2.getNode( "ab" );
8061 ext = new ArrayList<PhylogenyNode>();
8062 while ( n != null ) {
8064 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8066 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8069 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8072 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8075 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8081 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8082 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8083 t3.getNode( "ab" ).setCollapse( true );
8084 t3.getNode( "cd" ).setCollapse( true );
8085 t3.getNode( "cde" ).setCollapse( true );
8086 t3.getNode( "c" ).setCollapse( true );
8087 t3.getNode( "d" ).setCollapse( true );
8088 t3.getNode( "e" ).setCollapse( true );
8089 t3.getNode( "gh" ).setCollapse( true );
8090 t3.getNode( "fgh" ).setCollapse( true );
8091 n = t3.getNode( "ab" );
8092 ext = new ArrayList<PhylogenyNode>();
8093 while ( n != null ) {
8095 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8097 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8100 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8103 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8109 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8110 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8111 t4.getNode( "ab" ).setCollapse( true );
8112 t4.getNode( "cd" ).setCollapse( true );
8113 t4.getNode( "cde" ).setCollapse( true );
8114 t4.getNode( "c" ).setCollapse( true );
8115 t4.getNode( "d" ).setCollapse( true );
8116 t4.getNode( "e" ).setCollapse( true );
8117 t4.getNode( "gh" ).setCollapse( true );
8118 t4.getNode( "fgh" ).setCollapse( true );
8119 t4.getNode( "abcdefgh" ).setCollapse( true );
8120 n = t4.getNode( "abcdefgh" );
8121 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8126 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8127 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8129 n = t5.getFirstExternalNode();
8130 while ( n != null ) {
8132 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8134 if ( ext.size() != 8 ) {
8137 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8140 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8143 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8146 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8149 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8152 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8155 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8158 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8163 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8164 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8166 t6.getNode( "ab" ).setCollapse( true );
8167 n = t6.getNode( "ab" );
8168 while ( n != null ) {
8170 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8172 if ( ext.size() != 7 ) {
8175 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8178 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8181 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8184 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8187 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8190 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8193 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8198 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8199 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8201 t7.getNode( "cd" ).setCollapse( true );
8202 n = t7.getNode( "a" );
8203 while ( n != null ) {
8205 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8207 if ( ext.size() != 7 ) {
8210 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8213 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8216 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8219 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8222 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8225 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8228 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8233 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8234 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8236 t8.getNode( "cd" ).setCollapse( true );
8237 t8.getNode( "c" ).setCollapse( true );
8238 t8.getNode( "d" ).setCollapse( true );
8239 n = t8.getNode( "a" );
8240 while ( n != null ) {
8242 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8244 if ( ext.size() != 7 ) {
8247 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8250 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8253 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8254 System.out.println( "2 fail" );
8257 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8260 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8263 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8266 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8271 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8272 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8274 t9.getNode( "gh" ).setCollapse( true );
8275 n = t9.getNode( "a" );
8276 while ( n != null ) {
8278 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8280 if ( ext.size() != 7 ) {
8283 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8286 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8289 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8292 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8295 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8298 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8301 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8306 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8307 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8309 t10.getNode( "gh" ).setCollapse( true );
8310 t10.getNode( "g" ).setCollapse( true );
8311 t10.getNode( "h" ).setCollapse( true );
8312 n = t10.getNode( "a" );
8313 while ( n != null ) {
8315 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8317 if ( ext.size() != 7 ) {
8320 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8323 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8326 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8329 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8332 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8335 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8338 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8343 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8344 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8346 t11.getNode( "gh" ).setCollapse( true );
8347 t11.getNode( "fgh" ).setCollapse( true );
8348 n = t11.getNode( "a" );
8349 while ( n != null ) {
8351 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8353 if ( ext.size() != 6 ) {
8356 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8359 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8362 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8365 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8368 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8371 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8376 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8377 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8379 t12.getNode( "gh" ).setCollapse( true );
8380 t12.getNode( "fgh" ).setCollapse( true );
8381 t12.getNode( "g" ).setCollapse( true );
8382 t12.getNode( "h" ).setCollapse( true );
8383 t12.getNode( "f" ).setCollapse( true );
8384 n = t12.getNode( "a" );
8385 while ( n != null ) {
8387 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8389 if ( ext.size() != 6 ) {
8392 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8395 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8398 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8401 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8404 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8407 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8412 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8413 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8415 t13.getNode( "ab" ).setCollapse( true );
8416 t13.getNode( "b" ).setCollapse( true );
8417 t13.getNode( "fgh" ).setCollapse( true );
8418 t13.getNode( "gh" ).setCollapse( true );
8419 n = t13.getNode( "ab" );
8420 while ( n != null ) {
8422 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8424 if ( ext.size() != 5 ) {
8427 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8430 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8433 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8436 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8439 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8444 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8445 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8447 t14.getNode( "ab" ).setCollapse( true );
8448 t14.getNode( "a" ).setCollapse( true );
8449 t14.getNode( "fgh" ).setCollapse( true );
8450 t14.getNode( "gh" ).setCollapse( true );
8451 n = t14.getNode( "ab" );
8452 while ( n != null ) {
8454 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8456 if ( ext.size() != 5 ) {
8459 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8462 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8465 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8468 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8471 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8476 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" );
8477 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8479 t15.getNode( "ab" ).setCollapse( true );
8480 t15.getNode( "a" ).setCollapse( true );
8481 t15.getNode( "fgh" ).setCollapse( true );
8482 t15.getNode( "gh" ).setCollapse( true );
8483 n = t15.getNode( "ab" );
8484 while ( n != null ) {
8486 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8488 if ( ext.size() != 6 ) {
8491 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8494 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8497 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8500 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8503 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8506 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8511 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" );
8512 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8514 t16.getNode( "ab" ).setCollapse( true );
8515 t16.getNode( "a" ).setCollapse( true );
8516 t16.getNode( "fgh" ).setCollapse( true );
8517 t16.getNode( "gh" ).setCollapse( true );
8518 t16.getNode( "cd" ).setCollapse( true );
8519 t16.getNode( "cde" ).setCollapse( true );
8520 t16.getNode( "d" ).setCollapse( true );
8521 t16.getNode( "x" ).setCollapse( true );
8522 n = t16.getNode( "ab" );
8523 while ( n != null ) {
8525 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8527 if ( ext.size() != 4 ) {
8530 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8533 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8536 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8539 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8543 catch ( final Exception e ) {
8544 e.printStackTrace( System.out );
8550 private static boolean testMsaQualityMethod() {
8552 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8553 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8554 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8555 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8556 final List<Sequence> l = new ArrayList<Sequence>();
8561 final Msa msa = BasicMsa.createInstance( l );
8562 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8565 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8568 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8571 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8575 catch ( final Exception e ) {
8576 e.printStackTrace( System.out );
8582 private static boolean testSequenceIdParsing() {
8584 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8585 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8586 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8588 System.out.println( "value =" + id.getValue() );
8589 System.out.println( "provider=" + id.getProvider() );
8594 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8595 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8596 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8598 System.out.println( "value =" + id.getValue() );
8599 System.out.println( "provider=" + id.getProvider() );
8604 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8605 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8606 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8608 System.out.println( "value =" + id.getValue() );
8609 System.out.println( "provider=" + id.getProvider() );
8614 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8615 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8616 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8618 System.out.println( "value =" + id.getValue() );
8619 System.out.println( "provider=" + id.getProvider() );
8624 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8625 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8626 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8628 System.out.println( "value =" + id.getValue() );
8629 System.out.println( "provider=" + id.getProvider() );
8634 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8635 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8636 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8638 System.out.println( "value =" + id.getValue() );
8639 System.out.println( "provider=" + id.getProvider() );
8644 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8645 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8646 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8648 System.out.println( "value =" + id.getValue() );
8649 System.out.println( "provider=" + id.getProvider() );
8654 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8655 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8656 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8658 System.out.println( "value =" + id.getValue() );
8659 System.out.println( "provider=" + id.getProvider() );
8664 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8665 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8666 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8668 System.out.println( "value =" + id.getValue() );
8669 System.out.println( "provider=" + id.getProvider() );
8674 id = SequenceIdParser.parse( "XP_12345" );
8678 // lcl_91970_unknown_
8680 catch ( final Exception e ) {
8681 e.printStackTrace( System.out );