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 PhylogenyMethods pm = PhylogenyMethods.getInstance();
3214 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3215 if ( !A.getName().equals( "A" ) ) {
3218 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3219 if ( !gh.getName().equals( "gh" ) ) {
3222 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3223 if ( !ab.getName().equals( "ab" ) ) {
3226 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3227 if ( !ab2.getName().equals( "ab" ) ) {
3230 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3231 if ( !gh2.getName().equals( "gh" ) ) {
3234 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3235 if ( !gh3.getName().equals( "gh" ) ) {
3238 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3239 if ( !abc.getName().equals( "abc" ) ) {
3242 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3243 if ( !abc2.getName().equals( "abc" ) ) {
3246 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3247 if ( !abcd.getName().equals( "abcd" ) ) {
3250 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3251 if ( !abcd2.getName().equals( "abcd" ) ) {
3254 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3255 if ( !abcdef.getName().equals( "abcdef" ) ) {
3258 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3259 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3262 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3263 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3266 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3267 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3270 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3271 if ( !abcde.getName().equals( "abcde" ) ) {
3274 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3275 if ( !abcde2.getName().equals( "abcde" ) ) {
3278 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3279 if ( !r.getName().equals( "abcdefgh" ) ) {
3282 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3283 if ( !r2.getName().equals( "abcdefgh" ) ) {
3286 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3287 if ( !r3.getName().equals( "abcdefgh" ) ) {
3290 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3291 if ( !abcde3.getName().equals( "abcde" ) ) {
3294 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3295 if ( !abcde4.getName().equals( "abcde" ) ) {
3298 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3299 if ( !ab3.getName().equals( "ab" ) ) {
3302 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3303 if ( !ab4.getName().equals( "ab" ) ) {
3306 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3307 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3308 if ( !cd.getName().equals( "cd" ) ) {
3311 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3312 if ( !cd2.getName().equals( "cd" ) ) {
3315 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3316 if ( !cde.getName().equals( "cde" ) ) {
3319 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3320 if ( !cde2.getName().equals( "cde" ) ) {
3323 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3324 if ( !cdef.getName().equals( "cdef" ) ) {
3327 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3328 if ( !cdef2.getName().equals( "cdef" ) ) {
3331 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3332 if ( !cdef3.getName().equals( "cdef" ) ) {
3335 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3336 if ( !rt.getName().equals( "r" ) ) {
3339 final Phylogeny p3 = factory
3340 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3341 new NHXParser() )[ 0 ];
3342 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3343 if ( !bc_3.getName().equals( "bc" ) ) {
3346 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3347 if ( !ac_3.getName().equals( "abc" ) ) {
3350 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3351 if ( !ad_3.getName().equals( "abcde" ) ) {
3354 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3355 if ( !af_3.getName().equals( "abcdef" ) ) {
3358 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3359 if ( !ag_3.getName().equals( "" ) ) {
3362 if ( !ag_3.isRoot() ) {
3365 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3366 if ( !al_3.getName().equals( "" ) ) {
3369 if ( !al_3.isRoot() ) {
3372 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3373 if ( !kl_3.getName().equals( "" ) ) {
3376 if ( !kl_3.isRoot() ) {
3379 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3380 if ( !fl_3.getName().equals( "" ) ) {
3383 if ( !fl_3.isRoot() ) {
3386 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3387 if ( !gk_3.getName().equals( "ghijk" ) ) {
3390 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3391 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3392 if ( !r_4.getName().equals( "r" ) ) {
3395 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3396 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3397 if ( !r_5.getName().equals( "root" ) ) {
3400 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3401 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3402 if ( !r_6.getName().equals( "rot" ) ) {
3405 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3406 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3407 if ( !r_7.getName().equals( "rott" ) ) {
3411 catch ( final Exception e ) {
3412 e.printStackTrace( System.out );
3418 private static boolean testHmmscanOutputParser() {
3419 final String test_dir = Test.PATH_TO_TEST_DATA;
3421 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3422 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3424 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3425 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3426 final List<Protein> proteins = parser2.parse();
3427 if ( parser2.getProteinsEncountered() != 4 ) {
3430 if ( proteins.size() != 4 ) {
3433 if ( parser2.getDomainsEncountered() != 69 ) {
3436 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3439 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3442 final Protein p1 = proteins.get( 0 );
3443 if ( p1.getNumberOfProteinDomains() != 15 ) {
3446 if ( p1.getLength() != 850 ) {
3449 final Protein p2 = proteins.get( 1 );
3450 if ( p2.getNumberOfProteinDomains() != 51 ) {
3453 if ( p2.getLength() != 1291 ) {
3456 final Protein p3 = proteins.get( 2 );
3457 if ( p3.getNumberOfProteinDomains() != 2 ) {
3460 final Protein p4 = proteins.get( 3 );
3461 if ( p4.getNumberOfProteinDomains() != 1 ) {
3464 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3467 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3470 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3473 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3476 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3479 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3482 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3485 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3488 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3492 catch ( final Exception e ) {
3493 e.printStackTrace( System.out );
3499 private static boolean testLastExternalNodeMethods() {
3501 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3502 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3503 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3504 final PhylogenyNode n1 = t0.getNode( "A" );
3505 if ( n1.isLastExternalNode() ) {
3508 final PhylogenyNode n2 = t0.getNode( "B" );
3509 if ( n2.isLastExternalNode() ) {
3512 final PhylogenyNode n3 = t0.getNode( "C" );
3513 if ( n3.isLastExternalNode() ) {
3516 final PhylogenyNode n4 = t0.getNode( "D" );
3517 if ( !n4.isLastExternalNode() ) {
3521 catch ( final Exception e ) {
3522 e.printStackTrace( System.out );
3528 private static boolean testLevelOrderIterator() {
3530 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3531 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3532 PhylogenyNodeIterator it0;
3533 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3536 for( it0.reset(); it0.hasNext(); ) {
3539 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3540 if ( !it.next().getName().equals( "r" ) ) {
3543 if ( !it.next().getName().equals( "ab" ) ) {
3546 if ( !it.next().getName().equals( "cd" ) ) {
3549 if ( !it.next().getName().equals( "A" ) ) {
3552 if ( !it.next().getName().equals( "B" ) ) {
3555 if ( !it.next().getName().equals( "C" ) ) {
3558 if ( !it.next().getName().equals( "D" ) ) {
3561 if ( it.hasNext() ) {
3564 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",
3565 new NHXParser() )[ 0 ];
3566 PhylogenyNodeIterator it2;
3567 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3570 for( it2.reset(); it2.hasNext(); ) {
3573 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3574 if ( !it3.next().getName().equals( "r" ) ) {
3577 if ( !it3.next().getName().equals( "abc" ) ) {
3580 if ( !it3.next().getName().equals( "defg" ) ) {
3583 if ( !it3.next().getName().equals( "A" ) ) {
3586 if ( !it3.next().getName().equals( "B" ) ) {
3589 if ( !it3.next().getName().equals( "C" ) ) {
3592 if ( !it3.next().getName().equals( "D" ) ) {
3595 if ( !it3.next().getName().equals( "E" ) ) {
3598 if ( !it3.next().getName().equals( "F" ) ) {
3601 if ( !it3.next().getName().equals( "G" ) ) {
3604 if ( !it3.next().getName().equals( "1" ) ) {
3607 if ( !it3.next().getName().equals( "2" ) ) {
3610 if ( !it3.next().getName().equals( "3" ) ) {
3613 if ( !it3.next().getName().equals( "4" ) ) {
3616 if ( !it3.next().getName().equals( "5" ) ) {
3619 if ( !it3.next().getName().equals( "6" ) ) {
3622 if ( !it3.next().getName().equals( "f1" ) ) {
3625 if ( !it3.next().getName().equals( "f2" ) ) {
3628 if ( !it3.next().getName().equals( "f3" ) ) {
3631 if ( !it3.next().getName().equals( "a" ) ) {
3634 if ( !it3.next().getName().equals( "b" ) ) {
3637 if ( !it3.next().getName().equals( "f21" ) ) {
3640 if ( !it3.next().getName().equals( "X" ) ) {
3643 if ( !it3.next().getName().equals( "Y" ) ) {
3646 if ( !it3.next().getName().equals( "Z" ) ) {
3649 if ( it3.hasNext() ) {
3652 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3653 PhylogenyNodeIterator it4;
3654 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3657 for( it4.reset(); it4.hasNext(); ) {
3660 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3661 if ( !it5.next().getName().equals( "r" ) ) {
3664 if ( !it5.next().getName().equals( "A" ) ) {
3667 if ( !it5.next().getName().equals( "B" ) ) {
3670 if ( !it5.next().getName().equals( "C" ) ) {
3673 if ( !it5.next().getName().equals( "D" ) ) {
3676 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3677 PhylogenyNodeIterator it6;
3678 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3681 for( it6.reset(); it6.hasNext(); ) {
3684 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3685 if ( !it7.next().getName().equals( "A" ) ) {
3688 if ( it.hasNext() ) {
3692 catch ( final Exception e ) {
3693 e.printStackTrace( System.out );
3699 private static boolean testMidpointrooting() {
3701 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3702 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",
3703 new NHXParser() )[ 0 ];
3704 if ( !t1.isRooted() ) {
3707 PhylogenyMethods.midpointRoot( t1 );
3708 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3711 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3714 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3717 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3720 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3723 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3726 t1.reRoot( t1.getNode( "A" ) );
3727 PhylogenyMethods.midpointRoot( t1 );
3728 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3731 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3734 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3737 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3740 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3743 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3747 catch ( final Exception e ) {
3748 e.printStackTrace( System.out );
3754 private static boolean testNexusCharactersParsing() {
3756 final NexusCharactersParser parser = new NexusCharactersParser();
3757 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3759 String[] labels = parser.getCharStateLabels();
3760 if ( labels.length != 7 ) {
3763 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3766 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3769 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3772 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3775 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3778 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3781 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3784 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3786 labels = parser.getCharStateLabels();
3787 if ( labels.length != 7 ) {
3790 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3793 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3796 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3799 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3802 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3805 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3808 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3812 catch ( final Exception e ) {
3813 e.printStackTrace( System.out );
3819 private static boolean testNexusMatrixParsing() {
3821 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3822 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3824 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3825 if ( m.getNumberOfCharacters() != 9 ) {
3828 if ( m.getNumberOfIdentifiers() != 5 ) {
3831 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3834 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3837 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3840 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3843 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3846 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3849 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3852 // if ( labels.length != 7 ) {
3855 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3858 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3861 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3864 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3867 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3870 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3873 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3876 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3878 // labels = parser.getCharStateLabels();
3879 // if ( labels.length != 7 ) {
3882 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3885 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3888 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3891 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3894 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3897 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3900 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3904 catch ( final Exception e ) {
3905 e.printStackTrace( System.out );
3911 private static boolean testNexusTreeParsing() {
3913 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3914 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3915 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3916 if ( phylogenies.length != 1 ) {
3919 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3922 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3926 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3927 if ( phylogenies.length != 1 ) {
3930 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3933 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3937 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3938 if ( phylogenies.length != 1 ) {
3941 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3944 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3947 if ( phylogenies[ 0 ].isRooted() ) {
3951 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3952 if ( phylogenies.length != 18 ) {
3955 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3958 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3961 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3964 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3967 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3970 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3973 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3976 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3979 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3982 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3985 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3988 if ( phylogenies[ 8 ].isRooted() ) {
3991 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3994 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3997 if ( !phylogenies[ 9 ].isRooted() ) {
4000 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4003 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4006 if ( !phylogenies[ 10 ].isRooted() ) {
4009 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4012 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4015 if ( phylogenies[ 11 ].isRooted() ) {
4018 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4021 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4024 if ( !phylogenies[ 12 ].isRooted() ) {
4027 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4030 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4033 if ( !phylogenies[ 13 ].isRooted() ) {
4036 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4039 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4042 if ( !phylogenies[ 14 ].isRooted() ) {
4045 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4048 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4051 if ( phylogenies[ 15 ].isRooted() ) {
4054 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4057 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4060 if ( !phylogenies[ 16 ].isRooted() ) {
4063 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4066 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4069 if ( phylogenies[ 17 ].isRooted() ) {
4072 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4076 catch ( final Exception e ) {
4077 e.printStackTrace( System.out );
4083 private static boolean testNexusTreeParsingTranslating() {
4085 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4086 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4087 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4088 if ( phylogenies.length != 1 ) {
4091 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4094 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4097 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4100 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4103 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4104 .equals( "Aranaeus" ) ) {
4108 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4109 if ( phylogenies.length != 3 ) {
4112 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4115 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4118 if ( phylogenies[ 0 ].isRooted() ) {
4121 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4124 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4127 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4128 .equals( "Aranaeus" ) ) {
4131 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4134 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4137 if ( phylogenies[ 1 ].isRooted() ) {
4140 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4143 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4146 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4147 .equals( "Aranaeus" ) ) {
4150 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4153 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4156 if ( !phylogenies[ 2 ].isRooted() ) {
4159 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4162 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4165 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4166 .equals( "Aranaeus" ) ) {
4170 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4171 if ( phylogenies.length != 3 ) {
4174 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4177 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4180 if ( phylogenies[ 0 ].isRooted() ) {
4183 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4186 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4189 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4190 .equals( "Aranaeus" ) ) {
4193 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4196 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4199 if ( phylogenies[ 1 ].isRooted() ) {
4202 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4205 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4208 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4209 .equals( "Aranaeus" ) ) {
4212 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4215 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4218 if ( !phylogenies[ 2 ].isRooted() ) {
4221 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4224 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4227 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4228 .equals( "Aranaeus" ) ) {
4232 catch ( final Exception e ) {
4233 e.printStackTrace( System.out );
4239 private static boolean testNHParsing() {
4241 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4242 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4243 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4246 final NHXParser nhxp = new NHXParser();
4247 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4248 nhxp.setReplaceUnderscores( true );
4249 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4250 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4253 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4256 final Phylogeny p1b = factory
4257 .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 ",
4258 new NHXParser() )[ 0 ];
4259 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4262 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4265 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4266 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4267 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4268 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4269 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4270 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4271 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4272 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4273 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4274 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4275 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4276 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4277 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4279 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4282 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4285 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4288 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4291 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4292 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4293 final String p16_S = "((A,B),C)";
4294 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4295 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4298 final String p17_S = "(C,(A,B))";
4299 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4300 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4303 final String p18_S = "((A,B),(C,D))";
4304 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4305 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4308 final String p19_S = "(((A,B),C),D)";
4309 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4310 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4313 final String p20_S = "(A,(B,(C,D)))";
4314 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4315 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4318 final String p21_S = "(A,(B,(C,(D,E))))";
4319 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4320 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4323 final String p22_S = "((((A,B),C),D),E)";
4324 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4325 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4328 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4329 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4330 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4333 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4334 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4335 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4338 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4339 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4340 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4341 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4344 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4347 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4348 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4349 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4350 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4351 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4352 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4353 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4354 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4355 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4356 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4359 final String p26_S = "(A,B)ab";
4360 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4361 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4364 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4365 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4367 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4370 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4371 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4372 final String p28_S3 = "(A,B)ab";
4373 final String p28_S4 = "((((A,B),C),D),;E;)";
4374 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4376 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4379 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4382 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4385 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4388 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";
4389 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4390 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4393 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";
4394 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4395 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4398 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4399 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4400 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4403 final String p33_S = "A";
4404 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4405 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4408 final String p34_S = "B;";
4409 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4410 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4413 final String p35_S = "B:0.2";
4414 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4415 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4418 final String p36_S = "(A)";
4419 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4420 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4423 final String p37_S = "((A))";
4424 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4425 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4428 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4429 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4430 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4433 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4434 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4435 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4438 final String p40_S = "(A,B,C)";
4439 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4440 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4443 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4444 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4445 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4448 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4449 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4450 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4453 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)";
4454 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4455 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4458 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)))";
4459 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4460 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4463 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4464 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4465 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4468 final String p46_S = "";
4469 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4470 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4473 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4474 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4477 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4478 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4481 final Phylogeny p49 = factory
4482 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4483 new NHXParser() )[ 0 ];
4484 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4487 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4488 if ( p50.getNode( "A" ) == null ) {
4491 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4492 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4495 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4498 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4499 .equals( "((A,B)88:2.0,C);" ) ) {
4502 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4503 if ( p51.getNode( "A(A" ) == null ) {
4506 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4507 if ( p52.getNode( "A(A" ) == null ) {
4510 final Phylogeny p53 = factory
4511 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4512 new NHXParser() )[ 0 ];
4513 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4517 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4518 if ( p54.getNode( "A" ) == null ) {
4521 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4522 .equals( "((A,B)[88],C);" ) ) {
4526 catch ( final Exception e ) {
4527 e.printStackTrace( System.out );
4533 private static boolean testNHXconversion() {
4535 final PhylogenyNode n1 = new PhylogenyNode();
4536 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4537 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4538 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4539 final PhylogenyNode n5 = PhylogenyNode
4540 .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]" );
4541 final PhylogenyNode n6 = PhylogenyNode
4542 .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]" );
4543 if ( !n1.toNewHampshireX().equals( "" ) ) {
4546 if ( !n2.toNewHampshireX().equals( "" ) ) {
4549 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4552 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4555 if ( !n5.toNewHampshireX()
4556 .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]" ) ) {
4559 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]" ) ) {
4563 catch ( final Exception e ) {
4564 e.printStackTrace( System.out );
4570 private static boolean testNHXNodeParsing() {
4572 final PhylogenyNode n1 = new PhylogenyNode();
4573 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4574 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4575 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4576 final PhylogenyNode n5 = PhylogenyNode
4577 .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]" );
4578 if ( !n3.getName().equals( "n3" ) ) {
4581 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4584 if ( n3.isDuplication() ) {
4587 if ( n3.isHasAssignedEvent() ) {
4590 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4593 if ( !n4.getName().equals( "n4" ) ) {
4596 if ( n4.getDistanceToParent() != 0.01 ) {
4599 if ( !n5.getName().equals( "n5" ) ) {
4602 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4605 if ( n5.getDistanceToParent() != 0.1 ) {
4608 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4611 if ( !n5.isDuplication() ) {
4614 if ( !n5.isHasAssignedEvent() ) {
4617 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4620 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4623 final PhylogenyNode n8 = PhylogenyNode
4624 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4625 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4626 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4629 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4632 final PhylogenyNode n9 = PhylogenyNode
4633 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4634 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4635 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4638 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4641 final PhylogenyNode n10 = PhylogenyNode
4642 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4643 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4646 final PhylogenyNode n20 = PhylogenyNode
4647 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4648 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4651 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4654 final PhylogenyNode n20x = PhylogenyNode
4655 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4656 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4659 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4662 final PhylogenyNode n20xx = PhylogenyNode
4663 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4664 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4667 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4670 final PhylogenyNode n20xxx = PhylogenyNode
4671 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4672 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4675 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4678 final PhylogenyNode n20xxxx = PhylogenyNode
4679 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4680 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4683 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4686 final PhylogenyNode n21 = PhylogenyNode
4687 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4688 if ( !n21.getName().equals( "n21_PIG" ) ) {
4691 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4694 final PhylogenyNode n21x = PhylogenyNode
4695 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4696 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4699 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4702 final PhylogenyNode n22 = PhylogenyNode
4703 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4704 if ( !n22.getName().equals( "n22/PIG" ) ) {
4707 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4710 final PhylogenyNode n23 = PhylogenyNode
4711 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4712 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4715 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4718 final PhylogenyNode a = PhylogenyNode
4719 .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4720 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4723 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4726 final PhylogenyNode b = PhylogenyNode
4727 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4728 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4729 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4732 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4735 final PhylogenyNode c = PhylogenyNode
4736 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4737 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4738 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4741 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4744 final PhylogenyNode c1 = PhylogenyNode
4745 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4746 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4747 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4750 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4753 final PhylogenyNode c2 = PhylogenyNode
4754 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4755 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4756 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4759 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4762 final PhylogenyNode d = PhylogenyNode
4763 .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4764 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4767 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4770 final PhylogenyNode e = PhylogenyNode
4771 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4772 if ( !e.getName().equals( "n10_RAT1" ) ) {
4775 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4778 final PhylogenyNode e2 = PhylogenyNode
4779 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4780 if ( !e2.getName().equals( "n10_RAT1" ) ) {
4783 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
4786 final PhylogenyNode e3 = PhylogenyNode
4787 .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4788 if ( !e3.getName().equals( "n10_RAT~" ) ) {
4791 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
4794 final PhylogenyNode n11 = PhylogenyNode
4795 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4796 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4797 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4800 if ( n11.getDistanceToParent() != 0.4 ) {
4803 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4806 final PhylogenyNode n12 = PhylogenyNode
4807 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4808 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4809 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4812 if ( n12.getDistanceToParent() != 0.4 ) {
4815 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4818 final PhylogenyNode m = PhylogenyNode
4819 .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4820 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
4823 if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
4826 final PhylogenyNode o = PhylogenyNode
4827 .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4828 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
4831 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
4834 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4835 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4836 if ( !tvu1.getRef().equals( "tag1" ) ) {
4839 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4842 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4845 if ( !tvu1.getValue().equals( "value1" ) ) {
4848 if ( !tvu3.getRef().equals( "tag3" ) ) {
4851 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4854 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4857 if ( !tvu3.getValue().equals( "value3" ) ) {
4860 if ( n1.getName().compareTo( "" ) != 0 ) {
4863 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4866 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4869 if ( n2.getName().compareTo( "" ) != 0 ) {
4872 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4875 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4878 final PhylogenyNode n00 = PhylogenyNode
4879 .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]" );
4880 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4883 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4886 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4889 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4892 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4895 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4898 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4901 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4904 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4905 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4908 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4909 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4912 final PhylogenyNode n13 = PhylogenyNode
4913 .createInstanceFromNhxString( "blah_12345/1-2",
4914 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4915 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4918 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
4921 final PhylogenyNode n14 = PhylogenyNode
4922 .createInstanceFromNhxString( "blah_12X45/1-2",
4923 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4924 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4927 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4930 final PhylogenyNode n15 = PhylogenyNode
4931 .createInstanceFromNhxString( "something_wicked[123]",
4932 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4933 if ( !n15.getName().equals( "something_wicked" ) ) {
4936 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4939 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4942 final PhylogenyNode n16 = PhylogenyNode
4943 .createInstanceFromNhxString( "something_wicked2[9]",
4944 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4945 if ( !n16.getName().equals( "something_wicked2" ) ) {
4948 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4951 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4954 final PhylogenyNode n17 = PhylogenyNode
4955 .createInstanceFromNhxString( "something_wicked3[a]",
4956 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4957 if ( !n17.getName().equals( "something_wicked3" ) ) {
4960 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4963 final PhylogenyNode n18 = PhylogenyNode
4964 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4965 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4968 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4971 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4975 catch ( final Exception e ) {
4976 e.printStackTrace( System.out );
4982 private static boolean testNHXParsing() {
4984 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4985 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4986 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4989 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]";
4990 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4991 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4994 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]";
4995 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4996 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4999 final Phylogeny[] p3 = factory
5000 .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]",
5002 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5005 final Phylogeny[] p4 = factory
5006 .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(]",
5008 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5011 final Phylogeny[] p5 = factory
5012 .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(((]",
5014 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5017 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)";
5018 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)";
5019 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5020 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5023 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)))";
5024 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)))";
5025 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5026 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5029 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]) ))[,,, ])))))))";
5030 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5031 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5032 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5035 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5036 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5039 final Phylogeny p10 = factory
5040 .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]",
5041 new NHXParser() )[ 0 ];
5042 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5046 catch ( final Exception e ) {
5047 e.printStackTrace( System.out );
5053 private static boolean testNHXParsingQuotes() {
5055 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5056 final NHXParser p = new NHXParser();
5057 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5058 if ( phylogenies_0.length != 5 ) {
5061 final Phylogeny phy = phylogenies_0[ 4 ];
5062 if ( phy.getNumberOfExternalNodes() != 7 ) {
5065 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5068 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5071 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5072 .getScientificName().equals( "hsapiens" ) ) {
5075 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5078 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5081 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5084 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5087 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5090 final NHXParser p1p = new NHXParser();
5091 p1p.setIgnoreQuotes( true );
5092 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5093 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5096 final NHXParser p2p = new NHXParser();
5097 p1p.setIgnoreQuotes( false );
5098 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5099 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5102 final NHXParser p3p = new NHXParser();
5103 p3p.setIgnoreQuotes( false );
5104 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5105 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5108 final NHXParser p4p = new NHXParser();
5109 p4p.setIgnoreQuotes( false );
5110 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5111 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5114 final Phylogeny p10 = factory
5115 .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]",
5116 new NHXParser() )[ 0 ];
5117 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]";
5118 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5121 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5122 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5126 final Phylogeny p12 = factory
5127 .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]",
5128 new NHXParser() )[ 0 ];
5129 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]";
5130 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5133 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5134 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5137 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;";
5138 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5141 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5142 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5146 catch ( final Exception e ) {
5147 e.printStackTrace( System.out );
5153 private static boolean testNHXParsingMB() {
5155 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5156 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5157 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5158 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5159 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5160 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5161 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5162 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5163 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5164 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5165 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5168 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5171 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5172 0.1100000000000000e+00 ) ) {
5175 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5178 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5181 final Phylogeny p2 = factory
5182 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5183 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5184 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5185 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5186 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5187 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5188 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5189 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5190 + "7.369400000000000e-02}])",
5191 new NHXParser() )[ 0 ];
5192 if ( p2.getNode( "1" ) == null ) {
5195 if ( p2.getNode( "2" ) == null ) {
5199 catch ( final Exception e ) {
5200 e.printStackTrace( System.out );
5207 private static boolean testPhylogenyBranch() {
5209 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5210 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5211 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5212 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5213 if ( !a1b1.equals( a1b1 ) ) {
5216 if ( !a1b1.equals( b1a1 ) ) {
5219 if ( !b1a1.equals( a1b1 ) ) {
5222 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5223 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5224 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5225 if ( a1_b1.equals( b1_a1 ) ) {
5228 if ( a1_b1.equals( a1_b1_ ) ) {
5231 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5232 if ( !a1_b1.equals( b1_a1_ ) ) {
5235 if ( a1_b1_.equals( b1_a1_ ) ) {
5238 if ( !a1_b1_.equals( b1_a1 ) ) {
5242 catch ( final Exception e ) {
5243 e.printStackTrace( System.out );
5249 private static boolean testPhyloXMLparsingOfDistributionElement() {
5251 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5252 PhyloXmlParser xml_parser = null;
5254 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5256 catch ( final Exception e ) {
5257 // Do nothing -- means were not running from jar.
5259 if ( xml_parser == null ) {
5260 xml_parser = new PhyloXmlParser();
5261 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5262 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5265 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5268 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5270 if ( xml_parser.getErrorCount() > 0 ) {
5271 System.out.println( xml_parser.getErrorMessages().toString() );
5274 if ( phylogenies_0.length != 1 ) {
5277 final Phylogeny t1 = phylogenies_0[ 0 ];
5278 PhylogenyNode n = null;
5279 Distribution d = null;
5280 n = t1.getNode( "root node" );
5281 if ( !n.getNodeData().isHasDistribution() ) {
5284 if ( n.getNodeData().getDistributions().size() != 1 ) {
5287 d = n.getNodeData().getDistribution();
5288 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5291 if ( d.getPoints().size() != 1 ) {
5294 if ( d.getPolygons() != null ) {
5297 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5300 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5303 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5306 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5309 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5312 n = t1.getNode( "node a" );
5313 if ( !n.getNodeData().isHasDistribution() ) {
5316 if ( n.getNodeData().getDistributions().size() != 2 ) {
5319 d = n.getNodeData().getDistribution( 1 );
5320 if ( !d.getDesc().equals( "San Diego" ) ) {
5323 if ( d.getPoints().size() != 1 ) {
5326 if ( d.getPolygons() != null ) {
5329 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5332 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5335 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5338 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5341 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5344 n = t1.getNode( "node bb" );
5345 if ( !n.getNodeData().isHasDistribution() ) {
5348 if ( n.getNodeData().getDistributions().size() != 1 ) {
5351 d = n.getNodeData().getDistribution( 0 );
5352 if ( d.getPoints().size() != 3 ) {
5355 if ( d.getPolygons().size() != 2 ) {
5358 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5361 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5364 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5367 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5370 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5373 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5376 Polygon p = d.getPolygons().get( 0 );
5377 if ( p.getPoints().size() != 3 ) {
5380 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5383 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5386 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5389 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5392 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5395 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5398 p = d.getPolygons().get( 1 );
5399 if ( p.getPoints().size() != 3 ) {
5402 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5405 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5408 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5412 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5413 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5414 if ( rt.length != 1 ) {
5417 final Phylogeny t1_rt = rt[ 0 ];
5418 n = t1_rt.getNode( "root node" );
5419 if ( !n.getNodeData().isHasDistribution() ) {
5422 if ( n.getNodeData().getDistributions().size() != 1 ) {
5425 d = n.getNodeData().getDistribution();
5426 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5429 if ( d.getPoints().size() != 1 ) {
5432 if ( d.getPolygons() != null ) {
5435 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5438 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5441 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5444 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5447 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5450 n = t1_rt.getNode( "node a" );
5451 if ( !n.getNodeData().isHasDistribution() ) {
5454 if ( n.getNodeData().getDistributions().size() != 2 ) {
5457 d = n.getNodeData().getDistribution( 1 );
5458 if ( !d.getDesc().equals( "San Diego" ) ) {
5461 if ( d.getPoints().size() != 1 ) {
5464 if ( d.getPolygons() != null ) {
5467 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5470 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5473 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5476 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5479 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5482 n = t1_rt.getNode( "node bb" );
5483 if ( !n.getNodeData().isHasDistribution() ) {
5486 if ( n.getNodeData().getDistributions().size() != 1 ) {
5489 d = n.getNodeData().getDistribution( 0 );
5490 if ( d.getPoints().size() != 3 ) {
5493 if ( d.getPolygons().size() != 2 ) {
5496 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5499 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5502 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5505 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5508 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5511 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5514 p = d.getPolygons().get( 0 );
5515 if ( p.getPoints().size() != 3 ) {
5518 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5521 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5524 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5527 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5530 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5533 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5536 p = d.getPolygons().get( 1 );
5537 if ( p.getPoints().size() != 3 ) {
5540 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5543 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5546 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5550 catch ( final Exception e ) {
5551 e.printStackTrace( System.out );
5557 private static boolean testPostOrderIterator() {
5559 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5560 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5561 PhylogenyNodeIterator it0;
5562 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5565 for( it0.reset(); it0.hasNext(); ) {
5568 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5569 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5570 if ( !it.next().getName().equals( "A" ) ) {
5573 if ( !it.next().getName().equals( "B" ) ) {
5576 if ( !it.next().getName().equals( "ab" ) ) {
5579 if ( !it.next().getName().equals( "C" ) ) {
5582 if ( !it.next().getName().equals( "D" ) ) {
5585 if ( !it.next().getName().equals( "cd" ) ) {
5588 if ( !it.next().getName().equals( "abcd" ) ) {
5591 if ( !it.next().getName().equals( "E" ) ) {
5594 if ( !it.next().getName().equals( "F" ) ) {
5597 if ( !it.next().getName().equals( "ef" ) ) {
5600 if ( !it.next().getName().equals( "G" ) ) {
5603 if ( !it.next().getName().equals( "H" ) ) {
5606 if ( !it.next().getName().equals( "gh" ) ) {
5609 if ( !it.next().getName().equals( "efgh" ) ) {
5612 if ( !it.next().getName().equals( "r" ) ) {
5615 if ( it.hasNext() ) {
5619 catch ( final Exception e ) {
5620 e.printStackTrace( System.out );
5626 private static boolean testPreOrderIterator() {
5628 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5629 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5630 PhylogenyNodeIterator it0;
5631 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5634 for( it0.reset(); it0.hasNext(); ) {
5637 PhylogenyNodeIterator it = t0.iteratorPreorder();
5638 if ( !it.next().getName().equals( "r" ) ) {
5641 if ( !it.next().getName().equals( "ab" ) ) {
5644 if ( !it.next().getName().equals( "A" ) ) {
5647 if ( !it.next().getName().equals( "B" ) ) {
5650 if ( !it.next().getName().equals( "cd" ) ) {
5653 if ( !it.next().getName().equals( "C" ) ) {
5656 if ( !it.next().getName().equals( "D" ) ) {
5659 if ( it.hasNext() ) {
5662 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5663 it = t1.iteratorPreorder();
5664 if ( !it.next().getName().equals( "r" ) ) {
5667 if ( !it.next().getName().equals( "abcd" ) ) {
5670 if ( !it.next().getName().equals( "ab" ) ) {
5673 if ( !it.next().getName().equals( "A" ) ) {
5676 if ( !it.next().getName().equals( "B" ) ) {
5679 if ( !it.next().getName().equals( "cd" ) ) {
5682 if ( !it.next().getName().equals( "C" ) ) {
5685 if ( !it.next().getName().equals( "D" ) ) {
5688 if ( !it.next().getName().equals( "efgh" ) ) {
5691 if ( !it.next().getName().equals( "ef" ) ) {
5694 if ( !it.next().getName().equals( "E" ) ) {
5697 if ( !it.next().getName().equals( "F" ) ) {
5700 if ( !it.next().getName().equals( "gh" ) ) {
5703 if ( !it.next().getName().equals( "G" ) ) {
5706 if ( !it.next().getName().equals( "H" ) ) {
5709 if ( it.hasNext() ) {
5713 catch ( final Exception e ) {
5714 e.printStackTrace( System.out );
5720 private static boolean testPropertiesMap() {
5722 final PropertiesMap pm = new PropertiesMap();
5723 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5724 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5725 final Property p2 = new Property( "something:else",
5727 "improbable:research",
5730 pm.addProperty( p0 );
5731 pm.addProperty( p1 );
5732 pm.addProperty( p2 );
5733 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5736 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5739 if ( pm.getProperties().size() != 3 ) {
5742 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5745 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5748 if ( pm.getProperties().size() != 3 ) {
5751 pm.removeProperty( "dimensions:diameter" );
5752 if ( pm.getProperties().size() != 2 ) {
5755 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5758 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5762 catch ( final Exception e ) {
5763 e.printStackTrace( System.out );
5769 private static boolean testReIdMethods() {
5771 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5772 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5773 final int count = PhylogenyNode.getNodeCount();
5775 if ( p.getNode( "r" ).getId() != count ) {
5778 if ( p.getNode( "A" ).getId() != count + 1 ) {
5781 if ( p.getNode( "B" ).getId() != count + 1 ) {
5784 if ( p.getNode( "C" ).getId() != count + 1 ) {
5787 if ( p.getNode( "1" ).getId() != count + 2 ) {
5790 if ( p.getNode( "2" ).getId() != count + 2 ) {
5793 if ( p.getNode( "3" ).getId() != count + 2 ) {
5796 if ( p.getNode( "4" ).getId() != count + 2 ) {
5799 if ( p.getNode( "5" ).getId() != count + 2 ) {
5802 if ( p.getNode( "6" ).getId() != count + 2 ) {
5805 if ( p.getNode( "a" ).getId() != count + 3 ) {
5808 if ( p.getNode( "b" ).getId() != count + 3 ) {
5811 if ( p.getNode( "X" ).getId() != count + 4 ) {
5814 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5817 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5821 catch ( final Exception e ) {
5822 e.printStackTrace( System.out );
5828 private static boolean testRerooting() {
5830 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5831 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",
5832 new NHXParser() )[ 0 ];
5833 if ( !t1.isRooted() ) {
5836 t1.reRoot( t1.getNode( "D" ) );
5837 t1.reRoot( t1.getNode( "CD" ) );
5838 t1.reRoot( t1.getNode( "A" ) );
5839 t1.reRoot( t1.getNode( "B" ) );
5840 t1.reRoot( t1.getNode( "AB" ) );
5841 t1.reRoot( t1.getNode( "D" ) );
5842 t1.reRoot( t1.getNode( "C" ) );
5843 t1.reRoot( t1.getNode( "CD" ) );
5844 t1.reRoot( t1.getNode( "A" ) );
5845 t1.reRoot( t1.getNode( "B" ) );
5846 t1.reRoot( t1.getNode( "AB" ) );
5847 t1.reRoot( t1.getNode( "D" ) );
5848 t1.reRoot( t1.getNode( "D" ) );
5849 t1.reRoot( t1.getNode( "C" ) );
5850 t1.reRoot( t1.getNode( "A" ) );
5851 t1.reRoot( t1.getNode( "B" ) );
5852 t1.reRoot( t1.getNode( "AB" ) );
5853 t1.reRoot( t1.getNode( "C" ) );
5854 t1.reRoot( t1.getNode( "D" ) );
5855 t1.reRoot( t1.getNode( "CD" ) );
5856 t1.reRoot( t1.getNode( "D" ) );
5857 t1.reRoot( t1.getNode( "A" ) );
5858 t1.reRoot( t1.getNode( "B" ) );
5859 t1.reRoot( t1.getNode( "AB" ) );
5860 t1.reRoot( t1.getNode( "C" ) );
5861 t1.reRoot( t1.getNode( "D" ) );
5862 t1.reRoot( t1.getNode( "CD" ) );
5863 t1.reRoot( t1.getNode( "D" ) );
5864 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5867 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5870 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5873 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5876 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5879 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5882 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",
5883 new NHXParser() )[ 0 ];
5884 t2.reRoot( t2.getNode( "A" ) );
5885 t2.reRoot( t2.getNode( "D" ) );
5886 t2.reRoot( t2.getNode( "ABC" ) );
5887 t2.reRoot( t2.getNode( "A" ) );
5888 t2.reRoot( t2.getNode( "B" ) );
5889 t2.reRoot( t2.getNode( "D" ) );
5890 t2.reRoot( t2.getNode( "C" ) );
5891 t2.reRoot( t2.getNode( "ABC" ) );
5892 t2.reRoot( t2.getNode( "A" ) );
5893 t2.reRoot( t2.getNode( "B" ) );
5894 t2.reRoot( t2.getNode( "AB" ) );
5895 t2.reRoot( t2.getNode( "AB" ) );
5896 t2.reRoot( t2.getNode( "D" ) );
5897 t2.reRoot( t2.getNode( "C" ) );
5898 t2.reRoot( t2.getNode( "B" ) );
5899 t2.reRoot( t2.getNode( "AB" ) );
5900 t2.reRoot( t2.getNode( "D" ) );
5901 t2.reRoot( t2.getNode( "D" ) );
5902 t2.reRoot( t2.getNode( "ABC" ) );
5903 t2.reRoot( t2.getNode( "A" ) );
5904 t2.reRoot( t2.getNode( "B" ) );
5905 t2.reRoot( t2.getNode( "AB" ) );
5906 t2.reRoot( t2.getNode( "D" ) );
5907 t2.reRoot( t2.getNode( "C" ) );
5908 t2.reRoot( t2.getNode( "ABC" ) );
5909 t2.reRoot( t2.getNode( "A" ) );
5910 t2.reRoot( t2.getNode( "B" ) );
5911 t2.reRoot( t2.getNode( "AB" ) );
5912 t2.reRoot( t2.getNode( "D" ) );
5913 t2.reRoot( t2.getNode( "D" ) );
5914 t2.reRoot( t2.getNode( "C" ) );
5915 t2.reRoot( t2.getNode( "A" ) );
5916 t2.reRoot( t2.getNode( "B" ) );
5917 t2.reRoot( t2.getNode( "AB" ) );
5918 t2.reRoot( t2.getNode( "C" ) );
5919 t2.reRoot( t2.getNode( "D" ) );
5920 t2.reRoot( t2.getNode( "ABC" ) );
5921 t2.reRoot( t2.getNode( "D" ) );
5922 t2.reRoot( t2.getNode( "A" ) );
5923 t2.reRoot( t2.getNode( "B" ) );
5924 t2.reRoot( t2.getNode( "AB" ) );
5925 t2.reRoot( t2.getNode( "C" ) );
5926 t2.reRoot( t2.getNode( "D" ) );
5927 t2.reRoot( t2.getNode( "ABC" ) );
5928 t2.reRoot( t2.getNode( "D" ) );
5929 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5932 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5935 t2.reRoot( t2.getNode( "ABC" ) );
5936 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5939 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5942 t2.reRoot( t2.getNode( "AB" ) );
5943 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5946 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5949 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5952 t2.reRoot( t2.getNode( "AB" ) );
5953 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5956 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5959 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5962 t2.reRoot( t2.getNode( "D" ) );
5963 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5966 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5969 t2.reRoot( t2.getNode( "ABC" ) );
5970 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5973 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5976 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5977 new NHXParser() )[ 0 ];
5978 t3.reRoot( t3.getNode( "B" ) );
5979 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5982 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5985 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5988 t3.reRoot( t3.getNode( "B" ) );
5989 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5992 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5995 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5998 t3.reRoot( t3.getRoot() );
5999 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6002 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6005 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6009 catch ( final Exception e ) {
6010 e.printStackTrace( System.out );
6016 private static boolean testSDIse() {
6018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6019 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6020 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6021 gene1.setRooted( true );
6022 species1.setRooted( true );
6023 final SDI sdi = new SDIse( gene1, species1 );
6024 if ( !gene1.getRoot().isDuplication() ) {
6027 final Phylogeny species2 = factory
6028 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6029 new NHXParser() )[ 0 ];
6030 final Phylogeny gene2 = factory
6031 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6032 new NHXParser() )[ 0 ];
6033 species2.setRooted( true );
6034 gene2.setRooted( true );
6035 final SDI sdi2 = new SDIse( gene2, species2 );
6036 if ( sdi2.getDuplicationsSum() != 0 ) {
6039 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6042 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6045 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6048 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6051 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6054 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6057 final Phylogeny species3 = factory
6058 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6059 new NHXParser() )[ 0 ];
6060 final Phylogeny gene3 = factory
6061 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6062 new NHXParser() )[ 0 ];
6063 species3.setRooted( true );
6064 gene3.setRooted( true );
6065 final SDI sdi3 = new SDIse( gene3, species3 );
6066 if ( sdi3.getDuplicationsSum() != 1 ) {
6069 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6072 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6075 final Phylogeny species4 = factory
6076 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6077 new NHXParser() )[ 0 ];
6078 final Phylogeny gene4 = factory
6079 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6080 new NHXParser() )[ 0 ];
6081 species4.setRooted( true );
6082 gene4.setRooted( true );
6083 final SDI sdi4 = new SDIse( gene4, species4 );
6084 if ( sdi4.getDuplicationsSum() != 1 ) {
6087 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6090 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6093 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6096 if ( species4.getNumberOfExternalNodes() != 6 ) {
6099 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6102 final Phylogeny species5 = factory
6103 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6104 new NHXParser() )[ 0 ];
6105 final Phylogeny gene5 = factory
6106 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6107 new NHXParser() )[ 0 ];
6108 species5.setRooted( true );
6109 gene5.setRooted( true );
6110 final SDI sdi5 = new SDIse( gene5, species5 );
6111 if ( sdi5.getDuplicationsSum() != 2 ) {
6114 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6117 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6120 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6123 if ( species5.getNumberOfExternalNodes() != 6 ) {
6126 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6129 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6130 // Conjecture for Comparing Molecular Phylogenies"
6131 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6132 final Phylogeny species6 = factory
6133 .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,"
6134 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6135 new NHXParser() )[ 0 ];
6136 final Phylogeny gene6 = factory
6137 .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,"
6138 + "((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,"
6139 + "(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;",
6140 new NHXParser() )[ 0 ];
6141 species6.setRooted( true );
6142 gene6.setRooted( true );
6143 final SDI sdi6 = new SDIse( gene6, species6 );
6144 if ( sdi6.getDuplicationsSum() != 3 ) {
6147 if ( !gene6.getNode( "r" ).isDuplication() ) {
6150 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6153 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6156 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6159 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6162 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6165 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6168 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6171 sdi6.computeMappingCostL();
6172 if ( sdi6.computeMappingCostL() != 17 ) {
6175 if ( species6.getNumberOfExternalNodes() != 9 ) {
6178 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6181 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6182 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6183 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6184 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6185 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6186 species7.setRooted( true );
6187 final Phylogeny gene7_1 = Test
6188 .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])" );
6189 gene7_1.setRooted( true );
6190 final SDI sdi7 = new SDIse( gene7_1, species7 );
6191 if ( sdi7.getDuplicationsSum() != 0 ) {
6194 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6197 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6200 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6203 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6206 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6209 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6212 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6215 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6218 final Phylogeny gene7_2 = Test
6219 .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])" );
6220 gene7_2.setRooted( true );
6221 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6222 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6225 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6228 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6231 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6234 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6237 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6240 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6243 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6246 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6249 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6253 catch ( final Exception e ) {
6259 private static boolean testSDIunrooted() {
6261 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6262 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6263 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6264 final Iterator<PhylogenyBranch> iter = l.iterator();
6265 PhylogenyBranch br = iter.next();
6266 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6269 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6273 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6276 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6280 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6283 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6287 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6290 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6294 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6297 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6301 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6304 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6308 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6311 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6315 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6318 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6322 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6325 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6329 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6332 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6336 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6339 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6343 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6346 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6350 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6353 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6357 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6360 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6364 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6367 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6370 if ( iter.hasNext() ) {
6373 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6374 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6375 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6377 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6380 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6384 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6387 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6391 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6394 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6397 if ( iter1.hasNext() ) {
6400 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6401 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6402 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6404 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6407 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6411 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6414 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6418 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6421 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6424 if ( iter2.hasNext() ) {
6427 final Phylogeny species0 = factory
6428 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6429 new NHXParser() )[ 0 ];
6430 final Phylogeny gene1 = factory
6431 .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])",
6432 new NHXParser() )[ 0 ];
6433 species0.setRooted( true );
6434 gene1.setRooted( true );
6435 final SDIR sdi_unrooted = new SDIR();
6436 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6437 if ( sdi_unrooted.getCount() != 1 ) {
6440 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6443 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6446 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6449 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6452 final Phylogeny gene2 = factory
6453 .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])",
6454 new NHXParser() )[ 0 ];
6455 gene2.setRooted( true );
6456 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6457 if ( sdi_unrooted.getCount() != 1 ) {
6460 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6463 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6466 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6469 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6472 final Phylogeny species6 = factory
6473 .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,"
6474 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6475 new NHXParser() )[ 0 ];
6476 final Phylogeny gene6 = factory
6477 .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],"
6478 + "(((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],"
6479 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6480 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6481 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6482 new NHXParser() )[ 0 ];
6483 species6.setRooted( true );
6484 gene6.setRooted( true );
6485 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6486 if ( sdi_unrooted.getCount() != 1 ) {
6489 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6492 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6495 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6498 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6501 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6504 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6507 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6510 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6513 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6516 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6519 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6522 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6526 final Phylogeny species7 = factory
6527 .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,"
6528 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6529 new NHXParser() )[ 0 ];
6530 final Phylogeny gene7 = factory
6531 .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],"
6532 + "(((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],"
6533 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6534 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6535 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6536 new NHXParser() )[ 0 ];
6537 species7.setRooted( true );
6538 gene7.setRooted( true );
6539 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6540 if ( sdi_unrooted.getCount() != 1 ) {
6543 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6546 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6549 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6552 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6555 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6558 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6561 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6564 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6567 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6570 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6573 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6576 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6580 final Phylogeny species8 = factory
6581 .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,"
6582 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6583 new NHXParser() )[ 0 ];
6584 final Phylogeny gene8 = factory
6585 .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],"
6586 + "(((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],"
6587 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6588 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6589 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6590 new NHXParser() )[ 0 ];
6591 species8.setRooted( true );
6592 gene8.setRooted( true );
6593 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6594 if ( sdi_unrooted.getCount() != 1 ) {
6597 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6600 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6603 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6606 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6609 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6612 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6615 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6618 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6621 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6624 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6627 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6630 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6635 catch ( final Exception e ) {
6636 e.printStackTrace( System.out );
6642 private static boolean testSplit() {
6644 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6645 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6646 //Archaeopteryx.createApplication( p0 );
6647 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6648 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6649 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6650 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6651 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6652 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6653 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6654 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6655 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6656 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6657 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6658 // System.out.println( s0.toString() );
6660 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6663 if ( s0.match( query_nodes ) ) {
6666 query_nodes = new HashSet<PhylogenyNode>();
6667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6674 if ( !s0.match( query_nodes ) ) {
6678 query_nodes = new HashSet<PhylogenyNode>();
6679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6682 if ( !s0.match( query_nodes ) ) {
6686 query_nodes = new HashSet<PhylogenyNode>();
6687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6691 if ( !s0.match( query_nodes ) ) {
6695 query_nodes = new HashSet<PhylogenyNode>();
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6700 if ( !s0.match( query_nodes ) ) {
6704 query_nodes = new HashSet<PhylogenyNode>();
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6708 if ( !s0.match( query_nodes ) ) {
6712 query_nodes = new HashSet<PhylogenyNode>();
6713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6714 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6715 if ( !s0.match( query_nodes ) ) {
6719 query_nodes = new HashSet<PhylogenyNode>();
6720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6724 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6725 if ( !s0.match( query_nodes ) ) {
6729 query_nodes = new HashSet<PhylogenyNode>();
6730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6733 if ( !s0.match( query_nodes ) ) {
6737 query_nodes = new HashSet<PhylogenyNode>();
6738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6742 if ( !s0.match( query_nodes ) ) {
6746 query_nodes = new HashSet<PhylogenyNode>();
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6749 if ( s0.match( query_nodes ) ) {
6753 query_nodes = new HashSet<PhylogenyNode>();
6754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6758 if ( s0.match( query_nodes ) ) {
6762 query_nodes = new HashSet<PhylogenyNode>();
6763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6767 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6768 if ( s0.match( query_nodes ) ) {
6772 query_nodes = new HashSet<PhylogenyNode>();
6773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6774 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6776 if ( s0.match( query_nodes ) ) {
6780 query_nodes = new HashSet<PhylogenyNode>();
6781 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6782 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6783 if ( s0.match( query_nodes ) ) {
6787 query_nodes = new HashSet<PhylogenyNode>();
6788 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6790 if ( s0.match( query_nodes ) ) {
6794 query_nodes = new HashSet<PhylogenyNode>();
6795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6797 if ( s0.match( query_nodes ) ) {
6801 query_nodes = new HashSet<PhylogenyNode>();
6802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6804 if ( s0.match( query_nodes ) ) {
6808 query_nodes = new HashSet<PhylogenyNode>();
6809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6810 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6811 if ( s0.match( query_nodes ) ) {
6815 query_nodes = new HashSet<PhylogenyNode>();
6816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6817 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6818 if ( s0.match( query_nodes ) ) {
6822 query_nodes = new HashSet<PhylogenyNode>();
6823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6826 if ( s0.match( query_nodes ) ) {
6830 query_nodes = new HashSet<PhylogenyNode>();
6831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6834 if ( s0.match( query_nodes ) ) {
6838 query_nodes = new HashSet<PhylogenyNode>();
6839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6842 if ( s0.match( query_nodes ) ) {
6846 query_nodes = new HashSet<PhylogenyNode>();
6847 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6851 if ( s0.match( query_nodes ) ) {
6855 // query_nodes = new HashSet<PhylogenyNode>();
6856 // query_nodes.add( new PhylogenyNode( "X" ) );
6857 // query_nodes.add( new PhylogenyNode( "Y" ) );
6858 // query_nodes.add( new PhylogenyNode( "A" ) );
6859 // query_nodes.add( new PhylogenyNode( "B" ) );
6860 // query_nodes.add( new PhylogenyNode( "C" ) );
6861 // query_nodes.add( new PhylogenyNode( "D" ) );
6862 // query_nodes.add( new PhylogenyNode( "E" ) );
6863 // query_nodes.add( new PhylogenyNode( "F" ) );
6864 // query_nodes.add( new PhylogenyNode( "G" ) );
6865 // if ( !s0.match( query_nodes ) ) {
6868 // query_nodes = new HashSet<PhylogenyNode>();
6869 // query_nodes.add( new PhylogenyNode( "X" ) );
6870 // query_nodes.add( new PhylogenyNode( "Y" ) );
6871 // query_nodes.add( new PhylogenyNode( "A" ) );
6872 // query_nodes.add( new PhylogenyNode( "B" ) );
6873 // query_nodes.add( new PhylogenyNode( "C" ) );
6874 // if ( !s0.match( query_nodes ) ) {
6878 // query_nodes = new HashSet<PhylogenyNode>();
6879 // query_nodes.add( new PhylogenyNode( "X" ) );
6880 // query_nodes.add( new PhylogenyNode( "Y" ) );
6881 // query_nodes.add( new PhylogenyNode( "D" ) );
6882 // query_nodes.add( new PhylogenyNode( "E" ) );
6883 // query_nodes.add( new PhylogenyNode( "F" ) );
6884 // query_nodes.add( new PhylogenyNode( "G" ) );
6885 // if ( !s0.match( query_nodes ) ) {
6889 // query_nodes = new HashSet<PhylogenyNode>();
6890 // query_nodes.add( new PhylogenyNode( "X" ) );
6891 // query_nodes.add( new PhylogenyNode( "Y" ) );
6892 // query_nodes.add( new PhylogenyNode( "A" ) );
6893 // query_nodes.add( new PhylogenyNode( "B" ) );
6894 // query_nodes.add( new PhylogenyNode( "C" ) );
6895 // query_nodes.add( new PhylogenyNode( "D" ) );
6896 // if ( !s0.match( query_nodes ) ) {
6900 // query_nodes = new HashSet<PhylogenyNode>();
6901 // query_nodes.add( new PhylogenyNode( "X" ) );
6902 // query_nodes.add( new PhylogenyNode( "Y" ) );
6903 // query_nodes.add( new PhylogenyNode( "E" ) );
6904 // query_nodes.add( new PhylogenyNode( "F" ) );
6905 // query_nodes.add( new PhylogenyNode( "G" ) );
6906 // if ( !s0.match( query_nodes ) ) {
6910 // query_nodes = new HashSet<PhylogenyNode>();
6911 // query_nodes.add( new PhylogenyNode( "X" ) );
6912 // query_nodes.add( new PhylogenyNode( "Y" ) );
6913 // query_nodes.add( new PhylogenyNode( "F" ) );
6914 // query_nodes.add( new PhylogenyNode( "G" ) );
6915 // if ( !s0.match( query_nodes ) ) {
6919 query_nodes = new HashSet<PhylogenyNode>();
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6924 if ( s0.match( query_nodes ) ) {
6928 query_nodes = new HashSet<PhylogenyNode>();
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6933 if ( s0.match( query_nodes ) ) {
6936 ///////////////////////////
6938 query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6943 if ( s0.match( query_nodes ) ) {
6947 query_nodes = new HashSet<PhylogenyNode>();
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6952 if ( s0.match( query_nodes ) ) {
6956 query_nodes = new HashSet<PhylogenyNode>();
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6960 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6961 if ( s0.match( query_nodes ) ) {
6965 query_nodes = new HashSet<PhylogenyNode>();
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6969 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6970 if ( s0.match( query_nodes ) ) {
6974 query_nodes = new HashSet<PhylogenyNode>();
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6978 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6979 if ( s0.match( query_nodes ) ) {
6983 query_nodes = new HashSet<PhylogenyNode>();
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6987 if ( s0.match( query_nodes ) ) {
6991 query_nodes = new HashSet<PhylogenyNode>();
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6997 if ( s0.match( query_nodes ) ) {
7001 query_nodes = new HashSet<PhylogenyNode>();
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7007 if ( s0.match( query_nodes ) ) {
7011 query_nodes = new HashSet<PhylogenyNode>();
7012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7017 if ( s0.match( query_nodes ) ) {
7021 query_nodes = new HashSet<PhylogenyNode>();
7022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7028 if ( s0.match( query_nodes ) ) {
7032 catch ( final Exception e ) {
7033 e.printStackTrace();
7039 private static boolean testSplitStrict() {
7041 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7042 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7043 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7044 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7045 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7046 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7047 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7048 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7049 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7050 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7051 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7052 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7055 if ( s0.match( query_nodes ) ) {
7058 query_nodes = new HashSet<PhylogenyNode>();
7059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7066 if ( !s0.match( query_nodes ) ) {
7070 query_nodes = new HashSet<PhylogenyNode>();
7071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7074 if ( !s0.match( query_nodes ) ) {
7078 query_nodes = new HashSet<PhylogenyNode>();
7079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7083 if ( !s0.match( query_nodes ) ) {
7087 query_nodes = new HashSet<PhylogenyNode>();
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7092 if ( !s0.match( query_nodes ) ) {
7096 query_nodes = new HashSet<PhylogenyNode>();
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7100 if ( !s0.match( query_nodes ) ) {
7104 query_nodes = new HashSet<PhylogenyNode>();
7105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7107 if ( !s0.match( query_nodes ) ) {
7111 query_nodes = new HashSet<PhylogenyNode>();
7112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7117 if ( !s0.match( query_nodes ) ) {
7121 query_nodes = new HashSet<PhylogenyNode>();
7122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7124 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7125 if ( !s0.match( query_nodes ) ) {
7129 query_nodes = new HashSet<PhylogenyNode>();
7130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7134 if ( !s0.match( query_nodes ) ) {
7138 query_nodes = new HashSet<PhylogenyNode>();
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7141 if ( s0.match( query_nodes ) ) {
7145 query_nodes = new HashSet<PhylogenyNode>();
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7150 if ( s0.match( query_nodes ) ) {
7154 query_nodes = new HashSet<PhylogenyNode>();
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7159 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7160 if ( s0.match( query_nodes ) ) {
7164 query_nodes = new HashSet<PhylogenyNode>();
7165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7168 if ( s0.match( query_nodes ) ) {
7172 query_nodes = new HashSet<PhylogenyNode>();
7173 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7175 if ( s0.match( query_nodes ) ) {
7179 query_nodes = new HashSet<PhylogenyNode>();
7180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7182 if ( s0.match( query_nodes ) ) {
7186 query_nodes = new HashSet<PhylogenyNode>();
7187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7189 if ( s0.match( query_nodes ) ) {
7193 query_nodes = new HashSet<PhylogenyNode>();
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7196 if ( s0.match( query_nodes ) ) {
7200 query_nodes = new HashSet<PhylogenyNode>();
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7203 if ( s0.match( query_nodes ) ) {
7207 query_nodes = new HashSet<PhylogenyNode>();
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7209 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7210 if ( s0.match( query_nodes ) ) {
7214 query_nodes = new HashSet<PhylogenyNode>();
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7217 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7218 if ( s0.match( query_nodes ) ) {
7222 query_nodes = new HashSet<PhylogenyNode>();
7223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7224 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7225 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7226 if ( s0.match( query_nodes ) ) {
7230 query_nodes = new HashSet<PhylogenyNode>();
7231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7232 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7233 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7234 if ( s0.match( query_nodes ) ) {
7238 query_nodes = new HashSet<PhylogenyNode>();
7239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7242 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7243 if ( s0.match( query_nodes ) ) {
7247 catch ( final Exception e ) {
7248 e.printStackTrace();
7254 private static boolean testSubtreeDeletion() {
7256 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7257 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7258 t1.deleteSubtree( t1.getNode( "A" ), false );
7259 if ( t1.getNumberOfExternalNodes() != 5 ) {
7262 t1.toNewHampshireX();
7263 t1.deleteSubtree( t1.getNode( "E" ), false );
7264 if ( t1.getNumberOfExternalNodes() != 4 ) {
7267 t1.toNewHampshireX();
7268 t1.deleteSubtree( t1.getNode( "F" ), false );
7269 if ( t1.getNumberOfExternalNodes() != 3 ) {
7272 t1.toNewHampshireX();
7273 t1.deleteSubtree( t1.getNode( "D" ), false );
7274 t1.toNewHampshireX();
7275 if ( t1.getNumberOfExternalNodes() != 3 ) {
7278 t1.deleteSubtree( t1.getNode( "def" ), false );
7279 t1.toNewHampshireX();
7280 if ( t1.getNumberOfExternalNodes() != 2 ) {
7283 t1.deleteSubtree( t1.getNode( "B" ), false );
7284 t1.toNewHampshireX();
7285 if ( t1.getNumberOfExternalNodes() != 1 ) {
7288 t1.deleteSubtree( t1.getNode( "C" ), false );
7289 t1.toNewHampshireX();
7290 if ( t1.getNumberOfExternalNodes() != 1 ) {
7293 t1.deleteSubtree( t1.getNode( "abc" ), false );
7294 t1.toNewHampshireX();
7295 if ( t1.getNumberOfExternalNodes() != 1 ) {
7298 t1.deleteSubtree( t1.getNode( "r" ), false );
7299 if ( t1.getNumberOfExternalNodes() != 0 ) {
7302 if ( !t1.isEmpty() ) {
7305 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7306 t2.deleteSubtree( t2.getNode( "A" ), false );
7307 t2.toNewHampshireX();
7308 if ( t2.getNumberOfExternalNodes() != 5 ) {
7311 t2.deleteSubtree( t2.getNode( "abc" ), false );
7312 t2.toNewHampshireX();
7313 if ( t2.getNumberOfExternalNodes() != 3 ) {
7316 t2.deleteSubtree( t2.getNode( "def" ), false );
7317 t2.toNewHampshireX();
7318 if ( t2.getNumberOfExternalNodes() != 1 ) {
7322 catch ( final Exception e ) {
7323 e.printStackTrace( System.out );
7329 private static boolean testSupportCount() {
7331 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7332 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7333 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7334 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7335 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7336 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7337 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7339 SupportCount.count( t0_1, phylogenies_1, true, false );
7340 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7341 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7342 + "(((((A,B),C),D),E),((F,G),X))"
7343 + "(((((A,Y),B),C),D),((F,G),E))"
7344 + "(((((A,B),C),D),E),(F,G))"
7345 + "(((((A,B),C),D),E),(F,G))"
7346 + "(((((A,B),C),D),E),(F,G))"
7347 + "(((((A,B),C),D),E),(F,G),Z)"
7348 + "(((((A,B),C),D),E),(F,G))"
7349 + "((((((A,B),C),D),E),F),G)"
7350 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7352 SupportCount.count( t0_2, phylogenies_2, true, false );
7353 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7354 while ( it.hasNext() ) {
7355 final PhylogenyNode n = it.next();
7356 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7360 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7361 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7362 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7363 SupportCount.count( t0_3, phylogenies_3, true, false );
7364 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7365 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7368 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7371 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7374 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7377 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7380 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7383 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7386 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7389 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7392 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7395 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7396 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7397 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7398 SupportCount.count( t0_4, phylogenies_4, true, false );
7399 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7400 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7403 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7406 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7409 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7412 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7415 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7418 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7421 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7424 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7427 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7430 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7431 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7432 double d = SupportCount.compare( b1, a, true, true, true );
7433 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7436 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7437 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7438 d = SupportCount.compare( b2, a, true, true, true );
7439 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7442 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7443 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7444 d = SupportCount.compare( b3, a, true, true, true );
7445 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7448 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7449 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7450 d = SupportCount.compare( b4, a, true, true, false );
7451 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7455 catch ( final Exception e ) {
7456 e.printStackTrace( System.out );
7462 private static boolean testSupportTransfer() {
7464 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7465 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)",
7466 new NHXParser() )[ 0 ];
7467 final Phylogeny p2 = factory
7468 .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 ];
7469 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7472 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7475 support_transfer.moveBranchLengthsToBootstrap( p1 );
7476 support_transfer.transferSupportValues( p1, p2 );
7477 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7480 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7483 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7486 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7489 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7492 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7495 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7498 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7502 catch ( final Exception e ) {
7503 e.printStackTrace( System.out );
7509 private static boolean testUniprotTaxonomySearch() {
7511 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7513 if ( results.size() != 1 ) {
7516 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7519 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7522 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7525 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7528 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7532 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7533 if ( results.size() != 1 ) {
7536 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7539 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7542 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7545 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7548 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7552 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7553 if ( results.size() != 1 ) {
7556 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7559 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7562 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7565 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7568 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7572 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7573 if ( results.size() != 1 ) {
7576 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7579 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7582 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7585 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7588 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7591 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7594 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7597 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7598 .equals( "Nematostella vectensis" ) ) {
7599 System.out.println( results.get( 0 ).getLineage() );
7603 catch ( final IOException e ) {
7604 System.out.println();
7605 System.out.println( "the following might be due to absence internet connection:" );
7606 e.printStackTrace( System.out );
7609 catch ( final Exception e ) {
7615 private static boolean testEmblEntryRetrieval() {
7616 //The format for GenBank Accession numbers are:
7617 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7618 //Protein: 3 letters + 5 numerals
7619 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7620 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7623 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7626 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7629 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7632 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7635 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7638 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7641 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7644 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7647 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7650 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7653 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7656 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7662 private static boolean testUniprotEntryRetrieval() {
7663 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7666 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7669 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7672 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7675 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7678 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7681 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7684 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7687 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7690 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7693 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7696 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7699 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7703 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7704 if ( !entry.getAccession().equals( "P12345" ) ) {
7707 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7710 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7713 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7716 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7720 catch ( final IOException e ) {
7721 System.out.println();
7722 System.out.println( "the following might be due to absence internet connection:" );
7723 e.printStackTrace( System.out );
7726 catch ( final Exception e ) {
7732 private static boolean testWabiTxSearch() {
7735 result = TxSearch.searchSimple( "nematostella" );
7736 result = TxSearch.getTxId( "nematostella" );
7737 if ( !result.equals( "45350" ) ) {
7740 result = TxSearch.getTxName( "45350" );
7741 if ( !result.equals( "Nematostella" ) ) {
7744 result = TxSearch.getTxId( "nematostella vectensis" );
7745 if ( !result.equals( "45351" ) ) {
7748 result = TxSearch.getTxName( "45351" );
7749 if ( !result.equals( "Nematostella vectensis" ) ) {
7752 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7753 if ( !result.equals( "536089" ) ) {
7756 result = TxSearch.getTxName( "536089" );
7757 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7760 final List<String> queries = new ArrayList<String>();
7761 queries.add( "Campylobacter coli" );
7762 queries.add( "Escherichia coli" );
7763 queries.add( "Arabidopsis" );
7764 queries.add( "Trichoplax" );
7765 queries.add( "Samanea saman" );
7766 queries.add( "Kluyveromyces marxianus" );
7767 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7768 queries.add( "Bornavirus parrot/PDD/2008" );
7769 final List<RANKS> ranks = new ArrayList<RANKS>();
7770 ranks.add( RANKS.SUPERKINGDOM );
7771 ranks.add( RANKS.KINGDOM );
7772 ranks.add( RANKS.FAMILY );
7773 ranks.add( RANKS.GENUS );
7774 ranks.add( RANKS.TRIBE );
7775 result = TxSearch.searchLineage( queries, ranks );
7776 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7777 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7779 catch ( final Exception e ) {
7780 System.out.println();
7781 System.out.println( "the following might be due to absence internet connection:" );
7782 e.printStackTrace( System.out );
7788 private static boolean testAminoAcidSequence() {
7790 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7791 if ( aa1.getLength() != 13 ) {
7794 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7797 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7800 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7803 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7804 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7807 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7808 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7811 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7812 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7816 catch ( final Exception e ) {
7817 e.printStackTrace();
7823 private static boolean testCreateBalancedPhylogeny() {
7825 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7826 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7829 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7832 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7833 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7836 if ( p1.getNumberOfExternalNodes() != 100 ) {
7840 catch ( final Exception e ) {
7841 e.printStackTrace();
7847 private static boolean testFastaParser() {
7849 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7852 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7855 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7856 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7859 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7862 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7865 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7868 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7871 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7875 catch ( final Exception e ) {
7876 e.printStackTrace();
7882 private static boolean testGeneralMsaParser() {
7884 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7885 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7886 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
7887 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7888 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7889 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7890 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7891 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7892 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7895 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7898 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7901 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7904 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7907 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7910 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7913 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7916 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
7919 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
7922 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
7925 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
7928 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7929 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7932 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7935 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7938 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7939 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7942 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7945 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7948 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7949 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7952 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7955 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7959 catch ( final Exception e ) {
7960 e.printStackTrace();
7966 private static boolean testMafft( final String path ) {
7968 final List<String> opts = new ArrayList<String>();
7969 opts.add( "--maxiterate" );
7971 opts.add( "--localpair" );
7972 opts.add( "--quiet" );
7974 final MsaInferrer mafft = Mafft.createInstance( path );
7975 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
7976 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
7979 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
7983 catch ( final Exception e ) {
7984 e.printStackTrace( System.out );
7990 private static boolean testNextNodeWithCollapsing() {
7992 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7994 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
7995 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
7996 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
7997 t0.getNode( "cd" ).setCollapse( true );
7998 t0.getNode( "cde" ).setCollapse( true );
7999 n = t0.getFirstExternalNode();
8000 while ( n != null ) {
8002 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8004 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8007 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8010 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8013 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8016 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8019 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8023 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8024 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8025 t1.getNode( "ab" ).setCollapse( true );
8026 t1.getNode( "cd" ).setCollapse( true );
8027 t1.getNode( "cde" ).setCollapse( true );
8028 n = t1.getNode( "ab" );
8029 ext = new ArrayList<PhylogenyNode>();
8030 while ( n != null ) {
8032 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8034 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8037 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8040 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8043 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8046 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8052 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8053 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8054 t2.getNode( "ab" ).setCollapse( true );
8055 t2.getNode( "cd" ).setCollapse( true );
8056 t2.getNode( "cde" ).setCollapse( true );
8057 t2.getNode( "c" ).setCollapse( true );
8058 t2.getNode( "d" ).setCollapse( true );
8059 t2.getNode( "e" ).setCollapse( true );
8060 t2.getNode( "gh" ).setCollapse( true );
8061 n = t2.getNode( "ab" );
8062 ext = new ArrayList<PhylogenyNode>();
8063 while ( n != null ) {
8065 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8067 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8070 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8073 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8076 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8082 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8083 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8084 t3.getNode( "ab" ).setCollapse( true );
8085 t3.getNode( "cd" ).setCollapse( true );
8086 t3.getNode( "cde" ).setCollapse( true );
8087 t3.getNode( "c" ).setCollapse( true );
8088 t3.getNode( "d" ).setCollapse( true );
8089 t3.getNode( "e" ).setCollapse( true );
8090 t3.getNode( "gh" ).setCollapse( true );
8091 t3.getNode( "fgh" ).setCollapse( true );
8092 n = t3.getNode( "ab" );
8093 ext = new ArrayList<PhylogenyNode>();
8094 while ( n != null ) {
8096 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8098 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8101 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8104 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8110 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8111 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8112 t4.getNode( "ab" ).setCollapse( true );
8113 t4.getNode( "cd" ).setCollapse( true );
8114 t4.getNode( "cde" ).setCollapse( true );
8115 t4.getNode( "c" ).setCollapse( true );
8116 t4.getNode( "d" ).setCollapse( true );
8117 t4.getNode( "e" ).setCollapse( true );
8118 t4.getNode( "gh" ).setCollapse( true );
8119 t4.getNode( "fgh" ).setCollapse( true );
8120 t4.getNode( "abcdefgh" ).setCollapse( true );
8121 n = t4.getNode( "abcdefgh" );
8122 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8127 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8128 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8130 n = t5.getFirstExternalNode();
8131 while ( n != null ) {
8133 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8135 if ( ext.size() != 8 ) {
8138 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8141 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8144 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8147 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8150 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8153 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8156 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8159 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8164 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8165 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8167 t6.getNode( "ab" ).setCollapse( true );
8168 n = t6.getNode( "ab" );
8169 while ( n != null ) {
8171 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8173 if ( ext.size() != 7 ) {
8176 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8179 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8182 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8185 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8188 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8191 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8194 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8199 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8200 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8202 t7.getNode( "cd" ).setCollapse( true );
8203 n = t7.getNode( "a" );
8204 while ( n != null ) {
8206 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8208 if ( ext.size() != 7 ) {
8211 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8214 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8217 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8220 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8223 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8226 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8229 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8234 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8235 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8237 t8.getNode( "cd" ).setCollapse( true );
8238 t8.getNode( "c" ).setCollapse( true );
8239 t8.getNode( "d" ).setCollapse( true );
8240 n = t8.getNode( "a" );
8241 while ( n != null ) {
8243 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8245 if ( ext.size() != 7 ) {
8248 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8251 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8254 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8255 System.out.println( "2 fail" );
8258 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8261 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8264 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8267 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8272 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8273 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8275 t9.getNode( "gh" ).setCollapse( true );
8276 n = t9.getNode( "a" );
8277 while ( n != null ) {
8279 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8281 if ( ext.size() != 7 ) {
8284 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8287 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8290 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8293 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8296 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8299 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8302 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8307 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8308 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8310 t10.getNode( "gh" ).setCollapse( true );
8311 t10.getNode( "g" ).setCollapse( true );
8312 t10.getNode( "h" ).setCollapse( true );
8313 n = t10.getNode( "a" );
8314 while ( n != null ) {
8316 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8318 if ( ext.size() != 7 ) {
8321 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8324 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8327 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8330 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8333 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8336 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8339 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8344 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8345 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8347 t11.getNode( "gh" ).setCollapse( true );
8348 t11.getNode( "fgh" ).setCollapse( true );
8349 n = t11.getNode( "a" );
8350 while ( n != null ) {
8352 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8354 if ( ext.size() != 6 ) {
8357 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8360 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8363 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8366 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8369 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8372 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8377 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8378 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8380 t12.getNode( "gh" ).setCollapse( true );
8381 t12.getNode( "fgh" ).setCollapse( true );
8382 t12.getNode( "g" ).setCollapse( true );
8383 t12.getNode( "h" ).setCollapse( true );
8384 t12.getNode( "f" ).setCollapse( true );
8385 n = t12.getNode( "a" );
8386 while ( n != null ) {
8388 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8390 if ( ext.size() != 6 ) {
8393 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8396 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8399 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8402 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8405 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8408 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8413 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8414 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8416 t13.getNode( "ab" ).setCollapse( true );
8417 t13.getNode( "b" ).setCollapse( true );
8418 t13.getNode( "fgh" ).setCollapse( true );
8419 t13.getNode( "gh" ).setCollapse( true );
8420 n = t13.getNode( "ab" );
8421 while ( n != null ) {
8423 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8425 if ( ext.size() != 5 ) {
8428 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8431 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8434 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8437 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8440 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8445 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8446 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8448 t14.getNode( "ab" ).setCollapse( true );
8449 t14.getNode( "a" ).setCollapse( true );
8450 t14.getNode( "fgh" ).setCollapse( true );
8451 t14.getNode( "gh" ).setCollapse( true );
8452 n = t14.getNode( "ab" );
8453 while ( n != null ) {
8455 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8457 if ( ext.size() != 5 ) {
8460 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8463 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8466 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8469 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8472 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8477 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" );
8478 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8480 t15.getNode( "ab" ).setCollapse( true );
8481 t15.getNode( "a" ).setCollapse( true );
8482 t15.getNode( "fgh" ).setCollapse( true );
8483 t15.getNode( "gh" ).setCollapse( true );
8484 n = t15.getNode( "ab" );
8485 while ( n != null ) {
8487 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8489 if ( ext.size() != 6 ) {
8492 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8495 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8498 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8501 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8504 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8507 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8512 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" );
8513 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8515 t16.getNode( "ab" ).setCollapse( true );
8516 t16.getNode( "a" ).setCollapse( true );
8517 t16.getNode( "fgh" ).setCollapse( true );
8518 t16.getNode( "gh" ).setCollapse( true );
8519 t16.getNode( "cd" ).setCollapse( true );
8520 t16.getNode( "cde" ).setCollapse( true );
8521 t16.getNode( "d" ).setCollapse( true );
8522 t16.getNode( "x" ).setCollapse( true );
8523 n = t16.getNode( "ab" );
8524 while ( n != null ) {
8526 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8528 if ( ext.size() != 4 ) {
8531 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8534 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8537 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8540 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8544 catch ( final Exception e ) {
8545 e.printStackTrace( System.out );
8551 private static boolean testMsaQualityMethod() {
8553 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8554 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8555 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8556 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8557 final List<Sequence> l = new ArrayList<Sequence>();
8562 final Msa msa = BasicMsa.createInstance( l );
8563 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8566 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8569 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8572 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8576 catch ( final Exception e ) {
8577 e.printStackTrace( System.out );
8583 private static boolean testSequenceIdParsing() {
8585 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8586 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8587 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8589 System.out.println( "value =" + id.getValue() );
8590 System.out.println( "provider=" + id.getProvider() );
8595 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8596 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8597 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8599 System.out.println( "value =" + id.getValue() );
8600 System.out.println( "provider=" + id.getProvider() );
8605 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8606 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8607 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8609 System.out.println( "value =" + id.getValue() );
8610 System.out.println( "provider=" + id.getProvider() );
8615 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8616 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8617 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8619 System.out.println( "value =" + id.getValue() );
8620 System.out.println( "provider=" + id.getProvider() );
8625 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8626 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8627 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8629 System.out.println( "value =" + id.getValue() );
8630 System.out.println( "provider=" + id.getProvider() );
8635 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8636 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8637 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8639 System.out.println( "value =" + id.getValue() );
8640 System.out.println( "provider=" + id.getProvider() );
8645 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8646 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8647 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8649 System.out.println( "value =" + id.getValue() );
8650 System.out.println( "provider=" + id.getProvider() );
8655 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8656 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8657 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8659 System.out.println( "value =" + id.getValue() );
8660 System.out.println( "provider=" + id.getProvider() );
8665 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8666 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8667 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8669 System.out.println( "value =" + id.getValue() );
8670 System.out.println( "provider=" + id.getProvider() );
8675 id = SequenceIdParser.parse( "XP_12345" );
8679 // lcl_91970_unknown_
8681 catch ( final Exception e ) {
8682 e.printStackTrace( System.out );