2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
6 // Copyright (C) 2014 Sanford-Burnham Medical Research Institute
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 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.test;
27 import java.io.ByteArrayInputStream;
29 import java.io.FileInputStream;
30 import java.io.IOException;
31 import java.io.StringWriter;
32 import java.io.Writer;
34 import java.util.ArrayList;
35 import java.util.Date;
36 import java.util.HashSet;
37 import java.util.Iterator;
38 import java.util.List;
39 import java.util.Locale;
41 import java.util.SortedSet;
43 import org.forester.application.support_transfer;
44 import org.forester.archaeopteryx.AptxUtil;
45 import org.forester.archaeopteryx.TreePanelUtil;
46 import org.forester.archaeopteryx.webservices.WebserviceUtil;
47 import org.forester.development.DevelopmentTools;
48 import org.forester.evoinference.TestPhylogenyReconstruction;
49 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
50 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
51 import org.forester.go.TestGo;
52 import org.forester.io.parsers.FastaParser;
53 import org.forester.io.parsers.GeneralMsaParser;
54 import org.forester.io.parsers.HmmscanPerDomainTableParser;
55 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
56 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
57 import org.forester.io.parsers.nexus.NexusCharactersParser;
58 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
59 import org.forester.io.parsers.nhx.NHXParser;
60 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
61 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
62 import org.forester.io.parsers.tol.TolParser;
63 import org.forester.io.parsers.util.ParserUtils;
64 import org.forester.io.writers.PhylogenyWriter;
65 import org.forester.io.writers.SequenceWriter;
66 import org.forester.msa.BasicMsa;
67 import org.forester.msa.DeleteableMsa;
68 import org.forester.msa.Mafft;
69 import org.forester.msa.Msa;
70 import org.forester.msa.Msa.MSA_FORMAT;
71 import org.forester.msa.MsaInferrer;
72 import org.forester.msa.MsaMethods;
73 import org.forester.pccx.TestPccx;
74 import org.forester.phylogeny.Phylogeny;
75 import org.forester.phylogeny.PhylogenyBranch;
76 import org.forester.phylogeny.PhylogenyMethods;
77 import org.forester.phylogeny.PhylogenyNode;
78 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
79 import org.forester.phylogeny.data.Accession;
80 import org.forester.phylogeny.data.Accession.Source;
81 import org.forester.phylogeny.data.BinaryCharacters;
82 import org.forester.phylogeny.data.BranchWidth;
83 import org.forester.phylogeny.data.Confidence;
84 import org.forester.phylogeny.data.Distribution;
85 import org.forester.phylogeny.data.DomainArchitecture;
86 import org.forester.phylogeny.data.Event;
87 import org.forester.phylogeny.data.Identifier;
88 import org.forester.phylogeny.data.PhylogenyData;
89 import org.forester.phylogeny.data.PhylogenyDataUtil;
90 import org.forester.phylogeny.data.Polygon;
91 import org.forester.phylogeny.data.PropertiesMap;
92 import org.forester.phylogeny.data.Property;
93 import org.forester.phylogeny.data.Property.AppliesTo;
94 import org.forester.phylogeny.data.ProteinDomain;
95 import org.forester.phylogeny.data.Taxonomy;
96 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
97 import org.forester.phylogeny.factories.PhylogenyFactory;
98 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
99 import org.forester.protein.BasicDomain;
100 import org.forester.protein.BasicProtein;
101 import org.forester.protein.Domain;
102 import org.forester.protein.Protein;
103 import org.forester.protein.ProteinId;
104 import org.forester.rio.TestRIO;
105 import org.forester.sdi.SDI;
106 import org.forester.sdi.SDIR;
107 import org.forester.sdi.TestGSDI;
108 import org.forester.sequence.BasicSequence;
109 import org.forester.sequence.MolecularSequence;
110 import org.forester.species.BasicSpecies;
111 import org.forester.species.Species;
112 import org.forester.surfacing.TestSurfacing;
113 import org.forester.tools.ConfidenceAssessor;
114 import org.forester.tools.SupportCount;
115 import org.forester.tools.TreeSplitMatrix;
116 import org.forester.util.AsciiHistogram;
117 import org.forester.util.BasicDescriptiveStatistics;
118 import org.forester.util.BasicTable;
119 import org.forester.util.BasicTableParser;
120 import org.forester.util.DescriptiveStatistics;
121 import org.forester.util.ForesterConstants;
122 import org.forester.util.ForesterUtil;
123 import org.forester.util.GeneralTable;
124 import org.forester.util.SequenceAccessionTools;
125 import org.forester.ws.seqdb.SequenceDatabaseEntry;
126 import org.forester.ws.seqdb.SequenceDbWsTools;
127 import org.forester.ws.seqdb.UniProtTaxonomy;
128 import org.forester.ws.wabi.TxSearch;
129 import org.forester.ws.wabi.TxSearch.RANKS;
130 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
131 import org.forester.ws.wabi.TxSearch.TAX_RANK;
133 @SuppressWarnings( "unused")
134 public final class Test {
136 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
137 + ForesterUtil.getFileSeparator() + "resources"
138 + ForesterUtil.getFileSeparator();
139 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
140 + ForesterUtil.getFileSeparator() + "test_data"
141 + ForesterUtil.getFileSeparator();
142 private final static boolean PERFORM_DB_TESTS = false;
143 private static final boolean PERFORM_WEB_TREE_ACCESS = true;
144 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
145 + ForesterConstants.PHYLO_XML_VERSION + "/"
146 + ForesterConstants.PHYLO_XML_XSD;
147 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
148 + ForesterConstants.PHYLO_XML_VERSION + "/"
149 + ForesterConstants.PHYLO_XML_XSD;
150 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
151 private final static double ZERO_DIFF = 1.0E-9;
153 public static boolean isEqual( final double a, final double b ) {
154 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
157 public static void main( final String[] args ) {
158 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
159 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
161 Locale.setDefault( Locale.US );
162 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
165 System.out.print( "[Test if directory with files for testing exists/is readable: " );
166 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
171 System.out.println( "Testing aborted." );
174 System.out.print( "[Test if resources directory exists/is readable: " );
175 if ( testDir( PATH_TO_RESOURCES ) ) {
176 System.out.println( "OK.]" );
179 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
180 System.out.println( "Testing aborted." );
183 final long start_time = new Date().getTime();
187 System.out.print( "MSA entropy: " );
188 if ( Test.testMsaEntropy() ) {
189 System.out.println( "OK." );
193 System.out.println( "failed." );
196 System.out.print( "Basic node methods: " );
197 if ( Test.testBasicNodeMethods() ) {
198 System.out.println( "OK." );
202 System.out.println( "failed." );
205 System.out.print( "Protein id: " );
206 if ( !testProteinId() ) {
207 System.out.println( "failed." );
213 System.out.println( "OK." );
214 System.out.print( "Species: " );
215 if ( !testSpecies() ) {
216 System.out.println( "failed." );
222 System.out.println( "OK." );
223 System.out.print( "Basic domain: " );
224 if ( !testBasicDomain() ) {
225 System.out.println( "failed." );
231 System.out.println( "OK." );
232 System.out.print( "Basic protein: " );
233 if ( !testBasicProtein() ) {
234 System.out.println( "failed." );
240 System.out.println( "OK." );
241 System.out.print( "Sequence writer: " );
242 if ( testSequenceWriter() ) {
243 System.out.println( "OK." );
247 System.out.println( "failed." );
250 System.out.print( "Sequence id parsing: " );
251 if ( testSequenceIdParsing() ) {
252 System.out.println( "OK." );
256 System.out.println( "failed." );
259 System.out.print( "UniProtKB id extraction: " );
260 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
261 System.out.println( "OK." );
265 System.out.println( "failed." );
268 System.out.print( "Sequence DB tools 1: " );
269 if ( testSequenceDbWsTools1() ) {
270 System.out.println( "OK." );
274 System.out.println( "failed." );
277 System.out.print( "Hmmscan output parser: " );
278 if ( testHmmscanOutputParser() ) {
279 System.out.println( "OK." );
283 System.out.println( "failed." );
286 System.out.print( "Overlap removal: " );
287 if ( !org.forester.test.Test.testOverlapRemoval() ) {
288 System.out.println( "failed." );
294 System.out.println( "OK." );
295 System.out.print( "Engulfing overlap removal: " );
296 if ( !Test.testEngulfingOverlapRemoval() ) {
297 System.out.println( "failed." );
303 System.out.println( "OK." );
304 System.out.print( "Taxonomy data extraction: " );
305 if ( Test.testExtractTaxonomyDataFromNodeName() ) {
306 System.out.println( "OK." );
310 System.out.println( "failed." );
313 System.out.print( "Taxonomy code extraction: " );
314 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
315 System.out.println( "OK." );
319 System.out.println( "failed." );
322 System.out.print( "SN extraction: " );
323 if ( Test.testExtractSNFromNodeName() ) {
324 System.out.println( "OK." );
328 System.out.println( "failed." );
331 System.out.print( "Taxonomy extraction (general): " );
332 if ( Test.testTaxonomyExtraction() ) {
333 System.out.println( "OK." );
337 System.out.println( "failed." );
340 System.out.print( "Uri for Aptx web sequence accession: " );
341 if ( Test.testCreateUriForSeqWeb() ) {
342 System.out.println( "OK." );
346 System.out.println( "failed." );
349 System.out.print( "Basic node construction and parsing of NHX (node level): " );
350 if ( Test.testNHXNodeParsing() ) {
351 System.out.println( "OK." );
355 System.out.println( "failed." );
358 System.out.print( "NHX parsing iterating: " );
359 if ( Test.testNHParsingIter() ) {
360 System.out.println( "OK." );
364 System.out.println( "failed." );
367 System.out.print( "NH parsing: " );
368 if ( Test.testNHParsing() ) {
369 System.out.println( "OK." );
373 System.out.println( "failed." );
376 System.out.print( "Conversion to NHX (node level): " );
377 if ( Test.testNHXconversion() ) {
378 System.out.println( "OK." );
382 System.out.println( "failed." );
385 System.out.print( "NHX parsing: " );
386 if ( Test.testNHXParsing() ) {
387 System.out.println( "OK." );
391 System.out.println( "failed." );
394 System.out.print( "NHX parsing with quotes: " );
395 if ( Test.testNHXParsingQuotes() ) {
396 System.out.println( "OK." );
400 System.out.println( "failed." );
403 System.out.print( "NHX parsing (MrBayes): " );
404 if ( Test.testNHXParsingMB() ) {
405 System.out.println( "OK." );
409 System.out.println( "failed." );
412 System.out.print( "Nexus characters parsing: " );
413 if ( Test.testNexusCharactersParsing() ) {
414 System.out.println( "OK." );
418 System.out.println( "failed." );
421 System.out.print( "Nexus tree parsing iterating: " );
422 if ( Test.testNexusTreeParsingIterating() ) {
423 System.out.println( "OK." );
427 System.out.println( "failed." );
430 System.out.print( "Nexus tree parsing: " );
431 if ( Test.testNexusTreeParsing() ) {
432 System.out.println( "OK." );
436 System.out.println( "failed." );
439 System.out.print( "Nexus tree parsing (translating): " );
440 if ( Test.testNexusTreeParsingTranslating() ) {
441 System.out.println( "OK." );
445 System.out.println( "failed." );
448 System.out.print( "Nexus matrix parsing: " );
449 if ( Test.testNexusMatrixParsing() ) {
450 System.out.println( "OK." );
454 System.out.println( "failed." );
457 System.out.print( "Basic phyloXML parsing: " );
458 if ( Test.testBasicPhyloXMLparsing() ) {
459 System.out.println( "OK." );
463 System.out.println( "failed." );
466 System.out.print( "Basic phyloXML parsing (validating against schema): " );
467 if ( testBasicPhyloXMLparsingValidating() ) {
468 System.out.println( "OK." );
472 System.out.println( "failed." );
475 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
476 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
477 System.out.println( "OK." );
481 System.out.println( "failed." );
484 System.out.print( "phyloXML Distribution Element: " );
485 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
486 System.out.println( "OK." );
490 System.out.println( "failed." );
493 System.out.print( "Tol XML parsing: " );
494 if ( Test.testBasicTolXMLparsing() ) {
495 System.out.println( "OK." );
499 System.out.println( "failed." );
502 System.out.print( "Copying of node data: " );
503 if ( Test.testCopyOfNodeData() ) {
504 System.out.println( "OK." );
508 System.out.println( "failed." );
511 System.out.print( "Tree copy: " );
512 if ( Test.testTreeCopy() ) {
513 System.out.println( "OK." );
517 System.out.println( "failed." );
520 System.out.print( "Basic tree methods: " );
521 if ( Test.testBasicTreeMethods() ) {
522 System.out.println( "OK." );
526 System.out.println( "failed." );
529 System.out.print( "Tree methods: " );
530 if ( Test.testTreeMethods() ) {
531 System.out.println( "OK." );
535 System.out.println( "failed." );
538 System.out.print( "Postorder Iterator: " );
539 if ( Test.testPostOrderIterator() ) {
540 System.out.println( "OK." );
544 System.out.println( "failed." );
547 System.out.print( "Preorder Iterator: " );
548 if ( Test.testPreOrderIterator() ) {
549 System.out.println( "OK." );
553 System.out.println( "failed." );
556 System.out.print( "Levelorder Iterator: " );
557 if ( Test.testLevelOrderIterator() ) {
558 System.out.println( "OK." );
562 System.out.println( "failed." );
565 System.out.print( "Re-id methods: " );
566 if ( Test.testReIdMethods() ) {
567 System.out.println( "OK." );
571 System.out.println( "failed." );
574 System.out.print( "Methods on last external nodes: " );
575 if ( Test.testLastExternalNodeMethods() ) {
576 System.out.println( "OK." );
580 System.out.println( "failed." );
583 System.out.print( "Methods on external nodes: " );
584 if ( Test.testExternalNodeRelatedMethods() ) {
585 System.out.println( "OK." );
589 System.out.println( "failed." );
592 System.out.print( "Deletion of external nodes: " );
593 if ( Test.testDeletionOfExternalNodes() ) {
594 System.out.println( "OK." );
598 System.out.println( "failed." );
601 System.out.print( "Subtree deletion: " );
602 if ( Test.testSubtreeDeletion() ) {
603 System.out.println( "OK." );
607 System.out.println( "failed." );
610 System.out.print( "Phylogeny branch: " );
611 if ( Test.testPhylogenyBranch() ) {
612 System.out.println( "OK." );
616 System.out.println( "failed." );
619 System.out.print( "Rerooting: " );
620 if ( Test.testRerooting() ) {
621 System.out.println( "OK." );
625 System.out.println( "failed." );
628 System.out.print( "Mipoint rooting: " );
629 if ( Test.testMidpointrooting() ) {
630 System.out.println( "OK." );
634 System.out.println( "failed." );
637 System.out.print( "Node removal: " );
638 if ( Test.testNodeRemoval() ) {
639 System.out.println( "OK." );
643 System.out.println( "failed." );
646 System.out.print( "Support count: " );
647 if ( Test.testSupportCount() ) {
648 System.out.println( "OK." );
652 System.out.println( "failed." );
655 System.out.print( "Support transfer: " );
656 if ( Test.testSupportTransfer() ) {
657 System.out.println( "OK." );
661 System.out.println( "failed." );
664 System.out.print( "Finding of LCA: " );
665 if ( Test.testGetLCA() ) {
666 System.out.println( "OK." );
670 System.out.println( "failed." );
673 System.out.print( "Finding of LCA 2: " );
674 if ( Test.testGetLCA2() ) {
675 System.out.println( "OK." );
679 System.out.println( "failed." );
682 System.out.print( "Calculation of distance between nodes: " );
683 if ( Test.testGetDistance() ) {
684 System.out.println( "OK." );
688 System.out.println( "failed." );
691 System.out.print( "Descriptive statistics: " );
692 if ( Test.testDescriptiveStatistics() ) {
693 System.out.println( "OK." );
697 System.out.println( "failed." );
700 System.out.print( "Data objects and methods: " );
701 if ( Test.testDataObjects() ) {
702 System.out.println( "OK." );
706 System.out.println( "failed." );
709 System.out.print( "Properties map: " );
710 if ( Test.testPropertiesMap() ) {
711 System.out.println( "OK." );
715 System.out.println( "failed." );
718 System.out.print( "SDIse: " );
719 if ( Test.testSDIse() ) {
720 System.out.println( "OK." );
724 System.out.println( "failed." );
727 System.out.print( "SDIunrooted: " );
728 if ( Test.testSDIunrooted() ) {
729 System.out.println( "OK." );
733 System.out.println( "failed." );
736 System.out.print( "GSDI: " );
737 if ( TestGSDI.test() ) {
738 System.out.println( "OK." );
742 System.out.println( "failed." );
745 System.out.print( "RIO: " );
746 if ( TestRIO.test() ) {
747 System.out.println( "OK." );
751 System.out.println( "failed." );
754 System.out.print( "Phylogeny reconstruction:" );
755 System.out.println();
756 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
757 System.out.println( "OK." );
761 System.out.println( "failed." );
764 System.out.print( "Analysis of domain architectures: " );
765 System.out.println();
766 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
767 System.out.println( "OK." );
771 System.out.println( "failed." );
774 System.out.print( "GO: " );
775 System.out.println();
776 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
777 System.out.println( "OK." );
781 System.out.println( "failed." );
784 System.out.print( "Modeling tools: " );
785 if ( TestPccx.test() ) {
786 System.out.println( "OK." );
790 System.out.println( "failed." );
793 System.out.print( "Split Matrix strict: " );
794 if ( Test.testSplitStrict() ) {
795 System.out.println( "OK." );
799 System.out.println( "failed." );
802 System.out.print( "Split Matrix: " );
803 if ( Test.testSplit() ) {
804 System.out.println( "OK." );
808 System.out.println( "failed." );
811 System.out.print( "Confidence Assessor: " );
812 if ( Test.testConfidenceAssessor() ) {
813 System.out.println( "OK." );
817 System.out.println( "failed." );
820 System.out.print( "Basic table: " );
821 if ( Test.testBasicTable() ) {
822 System.out.println( "OK." );
826 System.out.println( "failed." );
829 System.out.print( "General table: " );
830 if ( Test.testGeneralTable() ) {
831 System.out.println( "OK." );
835 System.out.println( "failed." );
838 System.out.print( "Amino acid sequence: " );
839 if ( Test.testAminoAcidSequence() ) {
840 System.out.println( "OK." );
844 System.out.println( "failed." );
847 System.out.print( "General MSA parser: " );
848 if ( Test.testGeneralMsaParser() ) {
849 System.out.println( "OK." );
853 System.out.println( "failed." );
856 System.out.print( "Fasta parser for msa: " );
857 if ( Test.testFastaParser() ) {
858 System.out.println( "OK." );
862 System.out.println( "failed." );
865 System.out.print( "Creation of balanced phylogeny: " );
866 if ( Test.testCreateBalancedPhylogeny() ) {
867 System.out.println( "OK." );
871 System.out.println( "failed." );
874 System.out.print( "Genbank accessor parsing: " );
875 if ( Test.testGenbankAccessorParsing() ) {
876 System.out.println( "OK." );
880 System.out.println( "failed." );
884 final String os = ForesterUtil.OS_NAME.toLowerCase();
885 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
886 path = "/usr/local/bin/mafft";
888 else if ( os.indexOf( "win" ) >= 0 ) {
889 path = "C:\\Program Files\\mafft-win\\mafft.bat";
893 if ( !MsaInferrer.isInstalled( path ) ) {
894 path = "/usr/bin/mafft";
896 if ( !MsaInferrer.isInstalled( path ) ) {
897 path = "/usr/local/bin/mafft";
900 if ( MsaInferrer.isInstalled( path ) ) {
901 System.out.print( "MAFFT (external program): " );
902 if ( Test.testMafft( path ) ) {
903 System.out.println( "OK." );
907 System.out.println( "failed [will not count towards failed tests]" );
910 System.out.print( "Next nodes with collapsed: " );
911 if ( Test.testNextNodeWithCollapsing() ) {
912 System.out.println( "OK." );
916 System.out.println( "failed." );
919 System.out.print( "Simple MSA quality: " );
920 if ( Test.testMsaQualityMethod() ) {
921 System.out.println( "OK." );
925 System.out.println( "failed." );
928 System.out.print( "Deleteable MSA: " );
929 if ( Test.testDeleteableMsa() ) {
930 System.out.println( "OK." );
934 System.out.println( "failed." );
937 if ( PERFORM_DB_TESTS ) {
938 System.out.print( "Uniprot Entry Retrieval: " );
939 if ( Test.testUniprotEntryRetrieval() ) {
940 System.out.println( "OK." );
944 System.out.println( "failed." );
947 System.out.print( "Ebi Entry Retrieval: " );
948 if ( Test.testEbiEntryRetrieval() ) {
949 System.out.println( "OK." );
953 System.out.println( "failed." );
956 System.out.print( "Sequence DB tools 2: " );
957 if ( testSequenceDbWsTools2() ) {
958 System.out.println( "OK." );
962 System.out.println( "failed." );
966 System.out.print( "Uniprot Taxonomy Search: " );
967 if ( Test.testUniprotTaxonomySearch() ) {
968 System.out.println( "OK." );
972 System.out.println( "failed." );
976 if ( PERFORM_WEB_TREE_ACCESS ) {
977 System.out.print( "NHX parsing from URL: " );
978 if ( Test.testNHXparsingFromURL() ) {
979 System.out.println( "OK." );
983 System.out.println( "failed." );
986 System.out.print( "NHX parsing from URL 2: " );
987 if ( Test.testNHXparsingFromURL2() ) {
988 System.out.println( "OK." );
992 System.out.println( "failed." );
995 System.out.print( "phyloXML parsing from URL: " );
996 if ( Test.testPhyloXMLparsingFromURL() ) {
997 System.out.println( "OK." );
1001 System.out.println( "failed." );
1004 System.out.print( "TreeBase acccess: " );
1005 if ( Test.testTreeBaseReading() ) {
1006 System.out.println( "OK." );
1010 System.out.println( "failed." );
1014 System.out.print( "ToL access: " );
1015 if ( Test.testToLReading() ) {
1016 System.out.println( "OK." );
1020 System.out.println( "failed." );
1024 System.out.print( "TreeFam access: " );
1025 if ( Test.testTreeFamReading() ) {
1026 System.out.println( "OK." );
1030 System.out.println( "failed." );
1035 System.out.print( "Pfam tree access: " );
1036 if ( Test.testPfamTreeReading() ) {
1037 System.out.println( "OK." );
1041 System.out.println( "failed." );
1045 System.out.println();
1046 final Runtime rt = java.lang.Runtime.getRuntime();
1047 final long free_memory = rt.freeMemory() / 1000000;
1048 final long total_memory = rt.totalMemory() / 1000000;
1049 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1050 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1051 System.out.println();
1052 System.out.println( "Successful tests: " + succeeded );
1053 System.out.println( "Failed tests: " + failed );
1054 System.out.println();
1056 System.out.println( "OK." );
1059 System.out.println( "Not OK." );
1063 public static boolean testEngulfingOverlapRemoval() {
1065 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1066 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
1067 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
1068 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1069 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1070 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1071 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1072 final List<Boolean> covered = new ArrayList<Boolean>();
1073 covered.add( true ); // 0
1074 covered.add( false ); // 1
1075 covered.add( true ); // 2
1076 covered.add( false ); // 3
1077 covered.add( true ); // 4
1078 covered.add( true ); // 5
1079 covered.add( false ); // 6
1080 covered.add( true ); // 7
1081 covered.add( true ); // 8
1082 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
1085 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
1088 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
1091 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
1094 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
1097 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
1100 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
1103 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1104 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
1105 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
1106 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
1107 abc.addProteinDomain( a );
1108 abc.addProteinDomain( b );
1109 abc.addProteinDomain( c );
1110 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
1111 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
1112 if ( abc.getNumberOfProteinDomains() != 3 ) {
1115 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
1118 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
1121 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
1124 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
1127 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1128 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
1129 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
1130 final Protein def = new BasicProtein( "def", "nemve", 0 );
1131 def.addProteinDomain( d );
1132 def.addProteinDomain( e );
1133 def.addProteinDomain( f );
1134 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
1135 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
1136 if ( def.getNumberOfProteinDomains() != 3 ) {
1139 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
1142 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
1145 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
1148 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
1151 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
1155 catch ( final Exception e ) {
1156 e.printStackTrace( System.out );
1162 public static final boolean testNHXparsingFromURL2() {
1164 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1165 final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1169 TAXONOMY_EXTRACTION.NO,
1171 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1174 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1175 System.out.println( phys[ 0 ].toNewHampshire() );
1178 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1179 System.out.println( phys[ 1 ].toNewHampshire() );
1182 final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1186 TAXONOMY_EXTRACTION.NO,
1188 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1191 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1192 System.out.println( phys2[ 0 ].toNewHampshire() );
1195 if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1196 System.out.println( phys2[ 1 ].toNewHampshire() );
1199 final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1200 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1201 if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
1206 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1207 System.out.println( phys3[ 0 ].toNewHampshire() );
1210 final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1211 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1212 if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
1217 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1218 System.out.println( phys4[ 0 ].toNewHampshire() );
1222 catch ( final Exception e ) {
1223 e.printStackTrace();
1229 public static final boolean testNHXparsingFromURL() {
1231 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1232 final URL u = new URL( s );
1233 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1234 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1235 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1238 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1239 System.out.println( phys[ 0 ].toNewHampshire() );
1242 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1243 System.out.println( phys[ 1 ].toNewHampshire() );
1247 final URL u2 = new URL( s );
1249 final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
1250 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1253 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1254 System.out.println( phys2[ 0 ].toNewHampshire() );
1257 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1258 final NHXParser p = new NHXParser();
1259 final URL u3 = new URL( s );
1261 if ( !p.hasNext() ) {
1264 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1267 if ( !p.hasNext() ) {
1271 if ( !p.hasNext() ) {
1274 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1277 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1281 if ( !p.hasNext() ) {
1284 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1287 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1291 catch ( final Exception e ) {
1292 System.out.println( e.toString());
1293 e.printStackTrace();
1299 public static boolean testOverlapRemoval() {
1301 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1302 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1303 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1304 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1305 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1306 final List<Boolean> covered = new ArrayList<Boolean>();
1307 covered.add( true ); // 0
1308 covered.add( false ); // 1
1309 covered.add( true ); // 2
1310 covered.add( false ); // 3
1311 covered.add( true ); // 4
1312 covered.add( true ); // 5
1313 covered.add( false ); // 6
1314 covered.add( true ); // 7
1315 covered.add( true ); // 8
1316 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1319 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1322 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1325 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1328 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1331 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1332 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1333 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1334 ab.addProteinDomain( a );
1335 ab.addProteinDomain( b );
1336 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1337 if ( ab.getNumberOfProteinDomains() != 2 ) {
1340 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1343 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1346 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1347 if ( ab.getNumberOfProteinDomains() != 2 ) {
1350 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1353 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1354 final Domain d = new BasicDomain( "d",
1361 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1362 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1363 cde.addProteinDomain( c );
1364 cde.addProteinDomain( d );
1365 cde.addProteinDomain( e );
1366 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1367 if ( cde.getNumberOfProteinDomains() != 3 ) {
1370 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1373 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1374 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1375 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1376 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1377 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1378 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1379 fghi.addProteinDomain( f );
1380 fghi.addProteinDomain( g );
1381 fghi.addProteinDomain( h );
1382 fghi.addProteinDomain( i );
1383 fghi.addProteinDomain( i );
1384 fghi.addProteinDomain( i );
1385 fghi.addProteinDomain( i2 );
1386 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1387 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1390 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1393 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1396 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1397 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1400 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1403 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1404 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1405 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1406 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1407 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1408 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1409 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1410 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1411 jklm.addProteinDomain( j );
1412 jklm.addProteinDomain( k );
1413 jklm.addProteinDomain( l );
1414 jklm.addProteinDomain( m );
1415 jklm.addProteinDomain( m0 );
1416 jklm.addProteinDomain( m1 );
1417 jklm.addProteinDomain( m2 );
1418 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1419 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1422 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1425 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1428 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1429 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1432 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1435 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1436 final Protein od = new BasicProtein( "od", "varanus", 0 );
1437 od.addProteinDomain( only );
1438 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1439 if ( od.getNumberOfProteinDomains() != 1 ) {
1442 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1446 catch ( final Exception e ) {
1447 e.printStackTrace( System.out );
1453 public static final boolean testPfamTreeReading() {
1455 final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
1456 final NHXParser parser = new NHXParser();
1457 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1458 parser.setReplaceUnderscores( false );
1459 parser.setGuessRootedness( true );
1460 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1461 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1462 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1465 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1469 catch ( final Exception e ) {
1470 e.printStackTrace();
1475 public static final boolean testPhyloXMLparsingFromURL() {
1477 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1478 final URL u = new URL( s );
1479 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1480 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1481 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1485 catch ( final Exception e ) {
1486 e.printStackTrace();
1491 public static final boolean testToLReading() {
1493 final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
1494 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1495 final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
1496 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1499 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
1502 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
1505 if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
1509 catch ( final Exception e ) {
1510 e.printStackTrace();
1515 public static final boolean testTreeBaseReading() {
1517 final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
1518 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1519 parser.setReplaceUnderscores( true );
1520 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1521 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1522 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1525 final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
1526 final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
1527 parser2.setReplaceUnderscores( true );
1528 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1529 final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
1530 if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
1534 catch ( final Exception e ) {
1535 e.printStackTrace();
1540 public static final boolean testTreeFamReading() {
1542 final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
1543 final NHXParser parser = new NHXParser();
1544 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
1545 parser.setReplaceUnderscores( false );
1546 parser.setGuessRootedness( true );
1547 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1548 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1549 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1552 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1556 catch ( final Exception e ) {
1557 e.printStackTrace();
1562 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1563 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1567 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1568 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1571 private static boolean testAminoAcidSequence() {
1573 final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1574 if ( aa1.getLength() != 13 ) {
1577 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1580 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1583 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1586 final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1587 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
1590 final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1591 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1594 final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1595 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1599 catch ( final Exception e ) {
1600 e.printStackTrace();
1606 private static boolean testBasicDomain() {
1608 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1609 if ( !pd.getDomainId().equals( "id" ) ) {
1612 if ( pd.getNumber() != 1 ) {
1615 if ( pd.getTotalCount() != 4 ) {
1618 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1621 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1622 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1623 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1624 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1625 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1626 if ( !a1.equals( a1 ) ) {
1629 if ( !a1.equals( a1_copy ) ) {
1632 if ( !a1.equals( a1_equal ) ) {
1635 if ( !a1.equals( a2 ) ) {
1638 if ( a1.equals( a3 ) ) {
1641 if ( a1.compareTo( a1 ) != 0 ) {
1644 if ( a1.compareTo( a1_copy ) != 0 ) {
1647 if ( a1.compareTo( a1_equal ) != 0 ) {
1650 if ( a1.compareTo( a2 ) != 0 ) {
1653 if ( a1.compareTo( a3 ) == 0 ) {
1657 catch ( final Exception e ) {
1658 e.printStackTrace( System.out );
1664 private static boolean testBasicNodeMethods() {
1666 if ( PhylogenyNode.getNodeCount() != 0 ) {
1669 final PhylogenyNode n1 = new PhylogenyNode();
1670 final PhylogenyNode n2 = PhylogenyNode
1671 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1672 final PhylogenyNode n3 = PhylogenyNode
1673 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1674 final PhylogenyNode n4 = PhylogenyNode
1675 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1676 if ( n1.isHasAssignedEvent() ) {
1679 if ( PhylogenyNode.getNodeCount() != 4 ) {
1682 if ( n3.getIndicator() != 0 ) {
1685 if ( n3.getNumberOfExternalNodes() != 1 ) {
1688 if ( !n3.isExternal() ) {
1691 if ( !n3.isRoot() ) {
1694 if ( !n4.getName().equals( "n4" ) ) {
1698 catch ( final Exception e ) {
1699 e.printStackTrace( System.out );
1705 private static boolean testBasicPhyloXMLparsing() {
1707 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1708 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1709 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1711 if ( xml_parser.getErrorCount() > 0 ) {
1712 System.out.println( xml_parser.getErrorMessages().toString() );
1715 if ( phylogenies_0.length != 4 ) {
1718 final Phylogeny t1 = phylogenies_0[ 0 ];
1719 final Phylogeny t2 = phylogenies_0[ 1 ];
1720 final Phylogeny t3 = phylogenies_0[ 2 ];
1721 final Phylogeny t4 = phylogenies_0[ 3 ];
1722 if ( t1.getNumberOfExternalNodes() != 1 ) {
1725 if ( !t1.isRooted() ) {
1728 if ( t1.isRerootable() ) {
1731 if ( !t1.getType().equals( "gene_tree" ) ) {
1734 if ( t2.getNumberOfExternalNodes() != 2 ) {
1737 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1740 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1743 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1746 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1749 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1752 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1755 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1756 .startsWith( "actgtgggggt" ) ) {
1759 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1760 .startsWith( "ctgtgatgcat" ) ) {
1763 if ( t3.getNumberOfExternalNodes() != 4 ) {
1766 if ( !t1.getName().equals( "t1" ) ) {
1769 if ( !t2.getName().equals( "t2" ) ) {
1772 if ( !t3.getName().equals( "t3" ) ) {
1775 if ( !t4.getName().equals( "t4" ) ) {
1778 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1781 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1784 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1787 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1788 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1791 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1794 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1797 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1800 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1801 .equals( "apoptosis" ) ) {
1804 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1805 .equals( "GO:0006915" ) ) {
1808 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1809 .equals( "UniProtKB" ) ) {
1812 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1813 .equals( "experimental" ) ) {
1816 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1817 .equals( "function" ) ) {
1820 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1821 .getValue() != 1 ) {
1824 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1825 .getType().equals( "ml" ) ) {
1828 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1829 .equals( "apoptosis" ) ) {
1832 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1833 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1836 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1837 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1840 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1841 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1844 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1845 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1848 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1849 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1852 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1853 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1856 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1857 .equals( "GO:0005829" ) ) {
1860 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1861 .equals( "intracellular organelle" ) ) {
1864 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1867 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1868 .equals( "UniProt link" ) ) ) {
1871 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1874 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1875 if ( x.size() != 4 ) {
1879 for( final Accession acc : x ) {
1881 if ( !acc.getSource().equals( "KEGG" ) ) {
1884 if ( !acc.getValue().equals( "hsa:596" ) ) {
1891 catch ( final Exception e ) {
1892 e.printStackTrace( System.out );
1898 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1900 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1901 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1902 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1903 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1906 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1908 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1910 if ( xml_parser.getErrorCount() > 0 ) {
1911 System.out.println( xml_parser.getErrorMessages().toString() );
1914 if ( phylogenies_0.length != 4 ) {
1917 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1918 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1919 if ( phylogenies_t1.length != 1 ) {
1922 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1923 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1926 if ( !t1_rt.isRooted() ) {
1929 if ( t1_rt.isRerootable() ) {
1932 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1935 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1936 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1937 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1938 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1941 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1944 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1947 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1950 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1951 .startsWith( "actgtgggggt" ) ) {
1954 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1955 .startsWith( "ctgtgatgcat" ) ) {
1958 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1959 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1960 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1961 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1962 if ( phylogenies_1.length != 1 ) {
1965 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1966 if ( !t3_rt.getName().equals( "t3" ) ) {
1969 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1972 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1975 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1978 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1981 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1982 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1985 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1988 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1991 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1992 .equals( "UniProtKB" ) ) {
1995 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1996 .equals( "apoptosis" ) ) {
1999 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
2000 .equals( "GO:0006915" ) ) {
2003 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
2004 .equals( "UniProtKB" ) ) {
2007 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
2008 .equals( "experimental" ) ) {
2011 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
2012 .equals( "function" ) ) {
2015 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2016 .getValue() != 1 ) {
2019 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2020 .getType().equals( "ml" ) ) {
2023 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2024 .equals( "apoptosis" ) ) {
2027 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2028 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
2031 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2032 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
2035 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2036 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
2039 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2040 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
2043 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2044 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
2047 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2048 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
2051 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
2052 .equals( "GO:0005829" ) ) {
2055 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
2056 .equals( "intracellular organelle" ) ) {
2059 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
2062 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
2063 .equals( "UniProt link" ) ) ) {
2066 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
2069 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
2072 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
2073 .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." ) ) ) {
2076 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
2079 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
2082 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
2085 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
2088 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
2089 .equals( "ncbi" ) ) {
2092 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
2095 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2096 .getName().equals( "B" ) ) {
2099 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2100 .getFrom() != 21 ) {
2103 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
2106 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2107 .getLength() != 24 ) {
2110 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2111 .getConfidence() != 2144 ) {
2114 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2115 .equals( "pfam" ) ) {
2118 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2121 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2124 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2127 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2130 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2131 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2134 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2137 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2140 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2143 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2146 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2149 if ( taxbb.getSynonyms().size() != 2 ) {
2152 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2155 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2158 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2161 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2164 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2167 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2168 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2171 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2174 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2177 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2180 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2183 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2186 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2189 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2192 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2195 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2196 .equalsIgnoreCase( "435" ) ) {
2199 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2202 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2203 .equalsIgnoreCase( "443.7" ) ) {
2206 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2209 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2212 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2213 .equalsIgnoreCase( "433" ) ) {
2216 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2217 .getCrossReferences();
2218 if ( x.size() != 4 ) {
2222 for( final Accession acc : x ) {
2224 if ( !acc.getSource().equals( "KEGG" ) ) {
2227 if ( !acc.getValue().equals( "hsa:596" ) ) {
2234 catch ( final Exception e ) {
2235 e.printStackTrace( System.out );
2241 private static boolean testBasicPhyloXMLparsingValidating() {
2243 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2244 PhyloXmlParser xml_parser = null;
2246 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2248 catch ( final Exception e ) {
2249 // Do nothing -- means were not running from jar.
2251 if ( xml_parser == null ) {
2252 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2253 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2254 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2257 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2260 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2262 if ( xml_parser.getErrorCount() > 0 ) {
2263 System.out.println( xml_parser.getErrorMessages().toString() );
2266 if ( phylogenies_0.length != 4 ) {
2269 final Phylogeny t1 = phylogenies_0[ 0 ];
2270 final Phylogeny t2 = phylogenies_0[ 1 ];
2271 final Phylogeny t3 = phylogenies_0[ 2 ];
2272 final Phylogeny t4 = phylogenies_0[ 3 ];
2273 if ( !t1.getName().equals( "t1" ) ) {
2276 if ( !t2.getName().equals( "t2" ) ) {
2279 if ( !t3.getName().equals( "t3" ) ) {
2282 if ( !t4.getName().equals( "t4" ) ) {
2285 if ( t1.getNumberOfExternalNodes() != 1 ) {
2288 if ( t2.getNumberOfExternalNodes() != 2 ) {
2291 if ( t3.getNumberOfExternalNodes() != 4 ) {
2294 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2295 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2296 if ( xml_parser.getErrorCount() > 0 ) {
2297 System.out.println( "errors:" );
2298 System.out.println( xml_parser.getErrorMessages().toString() );
2301 if ( phylogenies_1.length != 4 ) {
2304 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2306 if ( xml_parser.getErrorCount() > 0 ) {
2307 System.out.println( "errors:" );
2308 System.out.println( xml_parser.getErrorMessages().toString() );
2311 if ( phylogenies_2.length != 1 ) {
2314 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2317 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2319 if ( xml_parser.getErrorCount() > 0 ) {
2320 System.out.println( xml_parser.getErrorMessages().toString() );
2323 if ( phylogenies_3.length != 2 ) {
2326 final Phylogeny a = phylogenies_3[ 0 ];
2327 if ( !a.getName().equals( "tree 4" ) ) {
2330 if ( a.getNumberOfExternalNodes() != 3 ) {
2333 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2336 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2339 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2341 if ( xml_parser.getErrorCount() > 0 ) {
2342 System.out.println( xml_parser.getErrorMessages().toString() );
2345 if ( phylogenies_4.length != 1 ) {
2348 final Phylogeny s = phylogenies_4[ 0 ];
2349 if ( s.getNumberOfExternalNodes() != 6 ) {
2352 s.getNode( "first" );
2354 s.getNode( "\"<a'b&c'd\">\"" );
2355 s.getNode( "'''\"" );
2356 s.getNode( "\"\"\"" );
2357 s.getNode( "dick & doof" );
2359 catch ( final Exception e ) {
2360 e.printStackTrace( System.out );
2366 private static boolean testBasicProtein() {
2368 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2369 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2370 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2371 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2372 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2373 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2374 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2375 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2376 p0.addProteinDomain( y );
2377 p0.addProteinDomain( e );
2378 p0.addProteinDomain( b );
2379 p0.addProteinDomain( c );
2380 p0.addProteinDomain( d );
2381 p0.addProteinDomain( a );
2382 p0.addProteinDomain( x );
2383 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2386 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2390 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2391 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2392 aa0.addProteinDomain( a1 );
2393 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2396 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2400 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2401 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2402 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2403 aa1.addProteinDomain( a11 );
2404 aa1.addProteinDomain( a12 );
2405 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2408 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2411 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2412 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2415 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2418 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2421 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2422 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2425 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2428 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2431 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2434 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2435 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2438 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2441 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2444 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2447 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2448 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2451 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2454 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2457 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2461 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2462 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2463 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2464 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2465 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2466 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2467 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2468 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2469 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2470 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2471 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2472 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2473 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2474 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2475 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2476 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2477 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2478 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2479 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2480 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2481 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2482 p00.addProteinDomain( y0 );
2483 p00.addProteinDomain( e0 );
2484 p00.addProteinDomain( b0 );
2485 p00.addProteinDomain( c0 );
2486 p00.addProteinDomain( d0 );
2487 p00.addProteinDomain( a0 );
2488 p00.addProteinDomain( x0 );
2489 p00.addProteinDomain( y1 );
2490 p00.addProteinDomain( y2 );
2491 p00.addProteinDomain( y3 );
2492 p00.addProteinDomain( e1 );
2493 p00.addProteinDomain( e2 );
2494 p00.addProteinDomain( e3 );
2495 p00.addProteinDomain( e4 );
2496 p00.addProteinDomain( e5 );
2497 p00.addProteinDomain( z0 );
2498 p00.addProteinDomain( z1 );
2499 p00.addProteinDomain( z2 );
2500 p00.addProteinDomain( zz0 );
2501 p00.addProteinDomain( zz1 );
2502 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2505 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2508 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2511 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2514 if ( !p00.toDomainArchitectureString( "~", 7, "" ).equals( "a~b~c~d~e~e~e~e~e~e~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2517 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2518 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2519 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2520 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2521 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2522 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2523 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2524 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2525 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2526 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2527 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2528 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2529 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2530 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2531 p.addProteinDomain( B15 );
2532 p.addProteinDomain( C50 );
2533 p.addProteinDomain( A60 );
2534 p.addProteinDomain( A30 );
2535 p.addProteinDomain( C70 );
2536 p.addProteinDomain( B35 );
2537 p.addProteinDomain( B40 );
2538 p.addProteinDomain( A0 );
2539 p.addProteinDomain( A10 );
2540 p.addProteinDomain( A20 );
2541 p.addProteinDomain( B25 );
2542 p.addProteinDomain( D80 );
2543 List<String> domains_ids = new ArrayList<String>();
2544 domains_ids.add( "A" );
2545 domains_ids.add( "B" );
2546 domains_ids.add( "C" );
2547 if ( !p.contains( domains_ids, false ) ) {
2550 if ( !p.contains( domains_ids, true ) ) {
2553 domains_ids.add( "X" );
2554 if ( p.contains( domains_ids, false ) ) {
2557 if ( p.contains( domains_ids, true ) ) {
2560 domains_ids = new ArrayList<String>();
2561 domains_ids.add( "A" );
2562 domains_ids.add( "C" );
2563 domains_ids.add( "D" );
2564 if ( !p.contains( domains_ids, false ) ) {
2567 if ( !p.contains( domains_ids, true ) ) {
2570 domains_ids = new ArrayList<String>();
2571 domains_ids.add( "A" );
2572 domains_ids.add( "D" );
2573 domains_ids.add( "C" );
2574 if ( !p.contains( domains_ids, false ) ) {
2577 if ( p.contains( domains_ids, true ) ) {
2580 domains_ids = new ArrayList<String>();
2581 domains_ids.add( "A" );
2582 domains_ids.add( "A" );
2583 domains_ids.add( "B" );
2584 if ( !p.contains( domains_ids, false ) ) {
2587 if ( !p.contains( domains_ids, true ) ) {
2590 domains_ids = new ArrayList<String>();
2591 domains_ids.add( "A" );
2592 domains_ids.add( "A" );
2593 domains_ids.add( "A" );
2594 domains_ids.add( "B" );
2595 domains_ids.add( "B" );
2596 if ( !p.contains( domains_ids, false ) ) {
2599 if ( !p.contains( domains_ids, true ) ) {
2602 domains_ids = new ArrayList<String>();
2603 domains_ids.add( "A" );
2604 domains_ids.add( "A" );
2605 domains_ids.add( "B" );
2606 domains_ids.add( "A" );
2607 domains_ids.add( "B" );
2608 domains_ids.add( "B" );
2609 domains_ids.add( "A" );
2610 domains_ids.add( "B" );
2611 domains_ids.add( "C" );
2612 domains_ids.add( "A" );
2613 domains_ids.add( "C" );
2614 domains_ids.add( "D" );
2615 if ( !p.contains( domains_ids, false ) ) {
2618 if ( p.contains( domains_ids, true ) ) {
2622 catch ( final Exception e ) {
2623 e.printStackTrace( System.out );
2629 private static boolean testBasicTable() {
2631 final BasicTable<String> t0 = new BasicTable<String>();
2632 if ( t0.getNumberOfColumns() != 0 ) {
2635 if ( t0.getNumberOfRows() != 0 ) {
2638 t0.setValue( 3, 2, "23" );
2639 t0.setValue( 10, 1, "error" );
2640 t0.setValue( 10, 1, "110" );
2641 t0.setValue( 9, 1, "19" );
2642 t0.setValue( 1, 10, "101" );
2643 t0.setValue( 10, 10, "1010" );
2644 t0.setValue( 100, 10, "10100" );
2645 t0.setValue( 0, 0, "00" );
2646 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2649 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2652 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2655 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2658 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2661 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2664 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2667 if ( t0.getNumberOfColumns() != 101 ) {
2670 if ( t0.getNumberOfRows() != 11 ) {
2673 if ( t0.getValueAsString( 49, 4 ) != null ) {
2676 final String l = ForesterUtil.getLineSeparator();
2677 final StringBuffer source = new StringBuffer();
2678 source.append( "" + l );
2679 source.append( "# 1 1 1 1 1 1 1 1" + l );
2680 source.append( " 00 01 02 03" + l );
2681 source.append( " 10 11 12 13 " + l );
2682 source.append( "20 21 22 23 " + l );
2683 source.append( " 30 31 32 33" + l );
2684 source.append( "40 41 42 43" + l );
2685 source.append( " # 1 1 1 1 1 " + l );
2686 source.append( "50 51 52 53 54" + l );
2687 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2688 if ( t1.getNumberOfColumns() != 5 ) {
2691 if ( t1.getNumberOfRows() != 6 ) {
2694 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2697 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2700 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2703 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2706 final StringBuffer source1 = new StringBuffer();
2707 source1.append( "" + l );
2708 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2709 source1.append( " 00; 01 ;02;03" + l );
2710 source1.append( " 10; 11; 12; 13 " + l );
2711 source1.append( "20; 21; 22; 23 " + l );
2712 source1.append( " 30; 31; 32; 33" + l );
2713 source1.append( "40;41;42;43" + l );
2714 source1.append( " # 1 1 1 1 1 " + l );
2715 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2716 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2717 if ( t2.getNumberOfColumns() != 5 ) {
2720 if ( t2.getNumberOfRows() != 6 ) {
2723 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2726 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2729 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2732 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2735 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2738 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2741 final StringBuffer source2 = new StringBuffer();
2742 source2.append( "" + l );
2743 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2744 source2.append( " 00; 01 ;02;03" + l );
2745 source2.append( " 10; 11; 12; 13 " + l );
2746 source2.append( "20; 21; 22; 23 " + l );
2747 source2.append( " " + l );
2748 source2.append( " 30; 31; 32; 33" + l );
2749 source2.append( "40;41;42;43" + l );
2750 source2.append( " comment: 1 1 1 1 1 " + l );
2751 source2.append( ";;;50 ; 52; 53;;54 " + l );
2752 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2758 if ( tl.size() != 2 ) {
2761 final BasicTable<String> t3 = tl.get( 0 );
2762 final BasicTable<String> t4 = tl.get( 1 );
2763 if ( t3.getNumberOfColumns() != 4 ) {
2766 if ( t3.getNumberOfRows() != 3 ) {
2769 if ( t4.getNumberOfColumns() != 4 ) {
2772 if ( t4.getNumberOfRows() != 3 ) {
2775 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2778 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2782 catch ( final Exception e ) {
2783 e.printStackTrace( System.out );
2789 private static boolean testBasicTolXMLparsing() {
2791 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2792 final TolParser parser = new TolParser();
2793 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2794 if ( parser.getErrorCount() > 0 ) {
2795 System.out.println( parser.getErrorMessages().toString() );
2798 if ( phylogenies_0.length != 1 ) {
2801 final Phylogeny t1 = phylogenies_0[ 0 ];
2802 if ( t1.getNumberOfExternalNodes() != 5 ) {
2805 if ( !t1.isRooted() ) {
2808 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2811 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2814 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2817 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2820 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2821 if ( parser.getErrorCount() > 0 ) {
2822 System.out.println( parser.getErrorMessages().toString() );
2825 if ( phylogenies_1.length != 1 ) {
2828 final Phylogeny t2 = phylogenies_1[ 0 ];
2829 if ( t2.getNumberOfExternalNodes() != 664 ) {
2832 if ( !t2.isRooted() ) {
2835 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2838 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2841 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2844 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2847 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2850 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2851 .equals( "Aquifex" ) ) {
2854 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2855 if ( parser.getErrorCount() > 0 ) {
2856 System.out.println( parser.getErrorMessages().toString() );
2859 if ( phylogenies_2.length != 1 ) {
2862 final Phylogeny t3 = phylogenies_2[ 0 ];
2863 if ( t3.getNumberOfExternalNodes() != 184 ) {
2866 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2869 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2872 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2875 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2876 if ( parser.getErrorCount() > 0 ) {
2877 System.out.println( parser.getErrorMessages().toString() );
2880 if ( phylogenies_3.length != 1 ) {
2883 final Phylogeny t4 = phylogenies_3[ 0 ];
2884 if ( t4.getNumberOfExternalNodes() != 1 ) {
2887 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2890 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2893 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2896 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2897 if ( parser.getErrorCount() > 0 ) {
2898 System.out.println( parser.getErrorMessages().toString() );
2901 if ( phylogenies_4.length != 1 ) {
2904 final Phylogeny t5 = phylogenies_4[ 0 ];
2905 if ( t5.getNumberOfExternalNodes() != 13 ) {
2908 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2911 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2914 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2918 catch ( final Exception e ) {
2919 e.printStackTrace( System.out );
2925 private static boolean testBasicTreeMethods() {
2927 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2928 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2929 if ( t2.getNumberOfExternalNodes() != 4 ) {
2932 if ( t2.getHeight() != 8.5 ) {
2935 if ( !t2.isCompletelyBinary() ) {
2938 if ( t2.isEmpty() ) {
2941 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2942 if ( t3.getNumberOfExternalNodes() != 5 ) {
2945 if ( t3.getHeight() != 11 ) {
2948 if ( t3.isCompletelyBinary() ) {
2951 final PhylogenyNode n = t3.getNode( "ABC" );
2952 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 ];
2953 if ( t4.getNumberOfExternalNodes() != 9 ) {
2956 if ( t4.getHeight() != 11 ) {
2959 if ( t4.isCompletelyBinary() ) {
2962 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)" );
2963 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2964 if ( t5.getNumberOfExternalNodes() != 8 ) {
2967 if ( t5.getHeight() != 15 ) {
2970 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)" );
2971 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2972 if ( t6.getHeight() != 15 ) {
2975 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)" );
2976 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2977 if ( t7.getHeight() != 15 ) {
2980 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)" );
2981 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2982 if ( t8.getNumberOfExternalNodes() != 10 ) {
2985 if ( t8.getHeight() != 15 ) {
2988 final char[] a9 = new char[] { 'a' };
2989 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2990 if ( t9.getHeight() != 0 ) {
2993 final char[] a10 = new char[] { 'a', ':', '6' };
2994 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2995 if ( t10.getHeight() != 6 ) {
2999 catch ( final Exception e ) {
3000 e.printStackTrace( System.out );
3006 private static boolean testConfidenceAssessor() {
3008 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3009 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3010 final Phylogeny[] ev0 = factory
3011 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
3013 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
3014 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3017 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3020 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3021 final Phylogeny[] ev1 = factory
3022 .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)));",
3024 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
3025 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
3028 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3031 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3032 final Phylogeny[] ev_b = factory
3033 .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",
3035 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
3036 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
3039 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3043 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3044 final Phylogeny[] ev1x = factory
3045 .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)));",
3047 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
3048 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3051 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3054 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3055 final Phylogeny[] ev_bx = factory
3056 .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",
3058 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
3059 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3062 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3065 final Phylogeny[] t2 = factory
3066 .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);",
3068 final Phylogeny[] ev2 = factory
3069 .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);",
3071 for( final Phylogeny target : t2 ) {
3072 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
3074 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
3075 new NHXParser() )[ 0 ];
3076 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
3077 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
3078 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3081 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
3084 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3088 catch ( final Exception e ) {
3089 e.printStackTrace();
3095 private static boolean testCopyOfNodeData() {
3097 final PhylogenyNode n1 = PhylogenyNode
3098 .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]" );
3099 final PhylogenyNode n2 = n1.copyNodeData();
3100 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
3104 catch ( final Exception e ) {
3105 e.printStackTrace();
3111 private static boolean testCreateBalancedPhylogeny() {
3113 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3114 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3117 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3120 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3121 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3124 if ( p1.getNumberOfExternalNodes() != 100 ) {
3128 catch ( final Exception e ) {
3129 e.printStackTrace();
3135 private static boolean testCreateUriForSeqWeb() {
3137 final PhylogenyNode n = new PhylogenyNode();
3138 n.setName( "tr|B3RJ64" );
3139 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3142 n.setName( "B0LM41_HUMAN" );
3143 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3146 n.setName( "NP_001025424" );
3147 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3150 n.setName( "_NM_001030253-" );
3151 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3154 n.setName( "XM_002122186" );
3155 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3158 n.setName( "dgh_AAA34956_gdg" );
3159 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3162 n.setName( "AAA34956" );
3163 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3166 n.setName( "GI:394892" );
3167 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3168 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3171 n.setName( "gi_394892" );
3172 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3173 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3176 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3177 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3178 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3181 n.setName( "P12345" );
3182 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3183 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3186 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3187 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3188 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3192 catch ( final Exception e ) {
3193 e.printStackTrace( System.out );
3199 private static boolean testDataObjects() {
3201 final Confidence s0 = new Confidence();
3202 final Confidence s1 = new Confidence();
3203 if ( !s0.isEqual( s1 ) ) {
3206 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3207 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3208 if ( s2.isEqual( s1 ) ) {
3211 if ( !s2.isEqual( s3 ) ) {
3214 final Confidence s4 = ( Confidence ) s3.copy();
3215 if ( !s4.isEqual( s3 ) ) {
3222 final Taxonomy t1 = new Taxonomy();
3223 final Taxonomy t2 = new Taxonomy();
3224 final Taxonomy t3 = new Taxonomy();
3225 final Taxonomy t4 = new Taxonomy();
3226 final Taxonomy t5 = new Taxonomy();
3227 t1.setIdentifier( new Identifier( "ecoli" ) );
3228 t1.setTaxonomyCode( "ECOLI" );
3229 t1.setScientificName( "E. coli" );
3230 t1.setCommonName( "coli" );
3231 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3232 if ( !t1.isEqual( t0 ) ) {
3235 t2.setIdentifier( new Identifier( "ecoli" ) );
3236 t2.setTaxonomyCode( "OTHER" );
3237 t2.setScientificName( "what" );
3238 t2.setCommonName( "something" );
3239 if ( !t1.isEqual( t2 ) ) {
3242 t2.setIdentifier( new Identifier( "nemve" ) );
3243 if ( t1.isEqual( t2 ) ) {
3246 t1.setIdentifier( null );
3247 t3.setTaxonomyCode( "ECOLI" );
3248 t3.setScientificName( "what" );
3249 t3.setCommonName( "something" );
3250 if ( !t1.isEqual( t3 ) ) {
3253 t1.setIdentifier( null );
3254 t1.setTaxonomyCode( "" );
3255 t4.setScientificName( "E. ColI" );
3256 t4.setCommonName( "something" );
3257 if ( !t1.isEqual( t4 ) ) {
3260 t4.setScientificName( "B. subtilis" );
3261 t4.setCommonName( "something" );
3262 if ( t1.isEqual( t4 ) ) {
3265 t1.setIdentifier( null );
3266 t1.setTaxonomyCode( "" );
3267 t1.setScientificName( "" );
3268 t5.setCommonName( "COLI" );
3269 if ( !t1.isEqual( t5 ) ) {
3272 t5.setCommonName( "vibrio" );
3273 if ( t1.isEqual( t5 ) ) {
3278 final Identifier id0 = new Identifier( "123", "pfam" );
3279 final Identifier id1 = ( Identifier ) id0.copy();
3280 if ( !id1.isEqual( id1 ) ) {
3283 if ( !id1.isEqual( id0 ) ) {
3286 if ( !id0.isEqual( id1 ) ) {
3293 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3294 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3295 if ( !pd1.isEqual( pd1 ) ) {
3298 if ( !pd1.isEqual( pd0 ) ) {
3303 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3304 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3305 if ( !pd3.isEqual( pd3 ) ) {
3308 if ( !pd2.isEqual( pd3 ) ) {
3311 if ( !pd0.isEqual( pd3 ) ) {
3316 // DomainArchitecture
3317 // ------------------
3318 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3319 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3320 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3321 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3322 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3323 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3328 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3329 if ( ds0.getNumberOfDomains() != 4 ) {
3332 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3333 if ( !ds0.isEqual( ds0 ) ) {
3336 if ( !ds0.isEqual( ds1 ) ) {
3339 if ( ds1.getNumberOfDomains() != 4 ) {
3342 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3347 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3348 if ( ds0.isEqual( ds2 ) ) {
3354 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3355 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3356 System.out.println( ds3.toNHX() );
3359 if ( ds3.getNumberOfDomains() != 3 ) {
3364 final Event e1 = new Event( Event.EventType.fusion );
3365 if ( e1.isDuplication() ) {
3368 if ( !e1.isFusion() ) {
3371 if ( !e1.asText().toString().equals( "fusion" ) ) {
3374 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3377 final Event e11 = new Event( Event.EventType.fusion );
3378 if ( !e11.isEqual( e1 ) ) {
3381 if ( !e11.toNHX().toString().equals( "" ) ) {
3384 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3385 if ( e2.isDuplication() ) {
3388 if ( !e2.isSpeciationOrDuplication() ) {
3391 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3394 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3397 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3400 if ( e11.isEqual( e2 ) ) {
3403 final Event e2c = ( Event ) e2.copy();
3404 if ( !e2c.isEqual( e2 ) ) {
3407 Event e3 = new Event( 1, 2, 3 );
3408 if ( e3.isDuplication() ) {
3411 if ( e3.isSpeciation() ) {
3414 if ( e3.isGeneLoss() ) {
3417 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3420 final Event e3c = ( Event ) e3.copy();
3421 final Event e3cc = ( Event ) e3c.copy();
3422 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3426 if ( !e3c.isEqual( e3cc ) ) {
3429 Event e4 = new Event( 1, 2, 3 );
3430 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3433 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3436 final Event e4c = ( Event ) e4.copy();
3438 final Event e4cc = ( Event ) e4c.copy();
3439 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3442 if ( !e4c.isEqual( e4cc ) ) {
3445 final Event e5 = new Event();
3446 if ( !e5.isUnassigned() ) {
3449 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3452 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3455 final Event e6 = new Event( 1, 0, 0 );
3456 if ( !e6.asText().toString().equals( "duplication" ) ) {
3459 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3462 final Event e7 = new Event( 0, 1, 0 );
3463 if ( !e7.asText().toString().equals( "speciation" ) ) {
3466 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3469 final Event e8 = new Event( 0, 0, 1 );
3470 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3473 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3477 catch ( final Exception e ) {
3478 e.printStackTrace( System.out );
3484 private static boolean testDeletionOfExternalNodes() {
3486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3487 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3488 final PhylogenyWriter w = new PhylogenyWriter();
3489 if ( t0.isEmpty() ) {
3492 if ( t0.getNumberOfExternalNodes() != 1 ) {
3495 t0.deleteSubtree( t0.getNode( "A" ), false );
3496 if ( t0.getNumberOfExternalNodes() != 0 ) {
3499 if ( !t0.isEmpty() ) {
3502 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3503 if ( t1.getNumberOfExternalNodes() != 2 ) {
3506 t1.deleteSubtree( t1.getNode( "A" ), false );
3507 if ( t1.getNumberOfExternalNodes() != 1 ) {
3510 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3513 t1.deleteSubtree( t1.getNode( "B" ), false );
3514 if ( t1.getNumberOfExternalNodes() != 1 ) {
3517 t1.deleteSubtree( t1.getNode( "r" ), false );
3518 if ( !t1.isEmpty() ) {
3521 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3522 if ( t2.getNumberOfExternalNodes() != 3 ) {
3525 t2.deleteSubtree( t2.getNode( "B" ), false );
3526 if ( t2.getNumberOfExternalNodes() != 2 ) {
3529 t2.toNewHampshireX();
3530 PhylogenyNode n = t2.getNode( "A" );
3531 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3534 t2.deleteSubtree( t2.getNode( "A" ), false );
3535 if ( t2.getNumberOfExternalNodes() != 2 ) {
3538 t2.deleteSubtree( t2.getNode( "C" ), true );
3539 if ( t2.getNumberOfExternalNodes() != 1 ) {
3542 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3543 if ( t3.getNumberOfExternalNodes() != 4 ) {
3546 t3.deleteSubtree( t3.getNode( "B" ), true );
3547 if ( t3.getNumberOfExternalNodes() != 3 ) {
3550 n = t3.getNode( "A" );
3551 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3554 n = n.getNextExternalNode();
3555 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3558 t3.deleteSubtree( t3.getNode( "A" ), true );
3559 if ( t3.getNumberOfExternalNodes() != 2 ) {
3562 n = t3.getNode( "C" );
3563 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3566 t3.deleteSubtree( t3.getNode( "C" ), true );
3567 if ( t3.getNumberOfExternalNodes() != 1 ) {
3570 t3.deleteSubtree( t3.getNode( "D" ), true );
3571 if ( t3.getNumberOfExternalNodes() != 0 ) {
3574 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3575 if ( t4.getNumberOfExternalNodes() != 6 ) {
3578 t4.deleteSubtree( t4.getNode( "B2" ), true );
3579 if ( t4.getNumberOfExternalNodes() != 5 ) {
3582 String s = w.toNewHampshire( t4, true ).toString();
3583 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3586 t4.deleteSubtree( t4.getNode( "B11" ), true );
3587 if ( t4.getNumberOfExternalNodes() != 4 ) {
3590 t4.deleteSubtree( t4.getNode( "C" ), true );
3591 if ( t4.getNumberOfExternalNodes() != 3 ) {
3594 n = t4.getNode( "A" );
3595 n = n.getNextExternalNode();
3596 if ( !n.getName().equals( "B12" ) ) {
3599 n = n.getNextExternalNode();
3600 if ( !n.getName().equals( "D" ) ) {
3603 s = w.toNewHampshire( t4, true ).toString();
3604 if ( !s.equals( "((A,B12),D);" ) ) {
3607 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3608 t5.deleteSubtree( t5.getNode( "A" ), true );
3609 if ( t5.getNumberOfExternalNodes() != 5 ) {
3612 s = w.toNewHampshire( t5, true ).toString();
3613 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3616 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3617 t6.deleteSubtree( t6.getNode( "B11" ), true );
3618 if ( t6.getNumberOfExternalNodes() != 5 ) {
3621 s = w.toNewHampshire( t6, false ).toString();
3622 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3625 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3626 t7.deleteSubtree( t7.getNode( "B12" ), true );
3627 if ( t7.getNumberOfExternalNodes() != 5 ) {
3630 s = w.toNewHampshire( t7, true ).toString();
3631 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3634 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3635 t8.deleteSubtree( t8.getNode( "B2" ), true );
3636 if ( t8.getNumberOfExternalNodes() != 5 ) {
3639 s = w.toNewHampshire( t8, false ).toString();
3640 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3643 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3644 t9.deleteSubtree( t9.getNode( "C" ), true );
3645 if ( t9.getNumberOfExternalNodes() != 5 ) {
3648 s = w.toNewHampshire( t9, true ).toString();
3649 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3652 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3653 t10.deleteSubtree( t10.getNode( "D" ), true );
3654 if ( t10.getNumberOfExternalNodes() != 5 ) {
3657 s = w.toNewHampshire( t10, true ).toString();
3658 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3661 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3662 t11.deleteSubtree( t11.getNode( "A" ), true );
3663 if ( t11.getNumberOfExternalNodes() != 2 ) {
3666 s = w.toNewHampshire( t11, true ).toString();
3667 if ( !s.equals( "(B,C);" ) ) {
3670 t11.deleteSubtree( t11.getNode( "C" ), true );
3671 if ( t11.getNumberOfExternalNodes() != 1 ) {
3674 s = w.toNewHampshire( t11, false ).toString();
3675 if ( !s.equals( "B;" ) ) {
3678 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3679 t12.deleteSubtree( t12.getNode( "B2" ), true );
3680 if ( t12.getNumberOfExternalNodes() != 8 ) {
3683 s = w.toNewHampshire( t12, true ).toString();
3684 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3687 t12.deleteSubtree( t12.getNode( "B3" ), true );
3688 if ( t12.getNumberOfExternalNodes() != 7 ) {
3691 s = w.toNewHampshire( t12, true ).toString();
3692 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3695 t12.deleteSubtree( t12.getNode( "C3" ), true );
3696 if ( t12.getNumberOfExternalNodes() != 6 ) {
3699 s = w.toNewHampshire( t12, true ).toString();
3700 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3703 t12.deleteSubtree( t12.getNode( "A1" ), true );
3704 if ( t12.getNumberOfExternalNodes() != 5 ) {
3707 s = w.toNewHampshire( t12, true ).toString();
3708 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3711 t12.deleteSubtree( t12.getNode( "B1" ), true );
3712 if ( t12.getNumberOfExternalNodes() != 4 ) {
3715 s = w.toNewHampshire( t12, true ).toString();
3716 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3719 t12.deleteSubtree( t12.getNode( "A3" ), true );
3720 if ( t12.getNumberOfExternalNodes() != 3 ) {
3723 s = w.toNewHampshire( t12, true ).toString();
3724 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3727 t12.deleteSubtree( t12.getNode( "A2" ), true );
3728 if ( t12.getNumberOfExternalNodes() != 2 ) {
3731 s = w.toNewHampshire( t12, true ).toString();
3732 if ( !s.equals( "(C1,C2);" ) ) {
3735 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3736 t13.deleteSubtree( t13.getNode( "D" ), true );
3737 if ( t13.getNumberOfExternalNodes() != 4 ) {
3740 s = w.toNewHampshire( t13, true ).toString();
3741 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3744 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3745 t14.deleteSubtree( t14.getNode( "E" ), true );
3746 if ( t14.getNumberOfExternalNodes() != 5 ) {
3749 s = w.toNewHampshire( t14, true ).toString();
3750 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3753 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3754 t15.deleteSubtree( t15.getNode( "B2" ), true );
3755 if ( t15.getNumberOfExternalNodes() != 11 ) {
3758 t15.deleteSubtree( t15.getNode( "B1" ), true );
3759 if ( t15.getNumberOfExternalNodes() != 10 ) {
3762 t15.deleteSubtree( t15.getNode( "B3" ), true );
3763 if ( t15.getNumberOfExternalNodes() != 9 ) {
3766 t15.deleteSubtree( t15.getNode( "B4" ), true );
3767 if ( t15.getNumberOfExternalNodes() != 8 ) {
3770 t15.deleteSubtree( t15.getNode( "A1" ), true );
3771 if ( t15.getNumberOfExternalNodes() != 7 ) {
3774 t15.deleteSubtree( t15.getNode( "C4" ), true );
3775 if ( t15.getNumberOfExternalNodes() != 6 ) {
3779 catch ( final Exception e ) {
3780 e.printStackTrace( System.out );
3786 private static boolean testDescriptiveStatistics() {
3788 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3789 dss1.addValue( 82 );
3790 dss1.addValue( 78 );
3791 dss1.addValue( 70 );
3792 dss1.addValue( 58 );
3793 dss1.addValue( 42 );
3794 if ( dss1.getN() != 5 ) {
3797 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3800 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3803 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3806 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3809 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3812 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3815 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3818 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3821 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3824 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3827 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3830 dss1.addValue( 123 );
3831 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3834 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3837 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3840 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3841 dss2.addValue( -1.85 );
3842 dss2.addValue( 57.5 );
3843 dss2.addValue( 92.78 );
3844 dss2.addValue( 57.78 );
3845 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3848 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3851 final double[] a = dss2.getDataAsDoubleArray();
3852 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3855 dss2.addValue( -100 );
3856 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3859 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3862 final double[] ds = new double[ 14 ];
3877 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3878 if ( bins.length != 4 ) {
3881 if ( bins[ 0 ] != 2 ) {
3884 if ( bins[ 1 ] != 3 ) {
3887 if ( bins[ 2 ] != 4 ) {
3890 if ( bins[ 3 ] != 5 ) {
3893 final double[] ds1 = new double[ 9 ];
3903 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3904 if ( bins1.length != 4 ) {
3907 if ( bins1[ 0 ] != 2 ) {
3910 if ( bins1[ 1 ] != 3 ) {
3913 if ( bins1[ 2 ] != 0 ) {
3916 if ( bins1[ 3 ] != 4 ) {
3919 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3920 if ( bins1_1.length != 3 ) {
3923 if ( bins1_1[ 0 ] != 3 ) {
3926 if ( bins1_1[ 1 ] != 2 ) {
3929 if ( bins1_1[ 2 ] != 4 ) {
3932 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3933 if ( bins1_2.length != 3 ) {
3936 if ( bins1_2[ 0 ] != 2 ) {
3939 if ( bins1_2[ 1 ] != 2 ) {
3942 if ( bins1_2[ 2 ] != 2 ) {
3945 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3959 dss3.addValue( 10 );
3960 dss3.addValue( 10 );
3961 dss3.addValue( 10 );
3962 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3963 histo.toStringBuffer( 10, '=', 40, 5 );
3964 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3966 catch ( final Exception e ) {
3967 e.printStackTrace( System.out );
3973 private static boolean testDir( final String file ) {
3975 final File f = new File( file );
3976 if ( !f.exists() ) {
3979 if ( !f.isDirectory() ) {
3982 if ( !f.canRead() ) {
3986 catch ( final Exception e ) {
3992 private static boolean testEbiEntryRetrieval() {
3994 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3995 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3996 System.out.println( entry.getAccession() );
3999 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
4000 System.out.println( entry.getTaxonomyScientificName() );
4003 if ( !entry.getSequenceName()
4004 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
4005 System.out.println( entry.getSequenceName() );
4008 if ( !entry.getGeneName().equals( "treX-like" ) ) {
4009 System.out.println( entry.getGeneName() );
4012 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
4013 System.out.println( entry.getTaxonomyIdentifier() );
4016 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
4017 System.out.println( entry.getAnnotations().first().getRefValue() );
4020 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
4021 System.out.println( entry.getAnnotations().first().getRefSource() );
4024 if ( entry.getCrossReferences().size() != 5 ) {
4027 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
4028 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
4031 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
4032 System.out.println( entry1.getTaxonomyScientificName() );
4035 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
4036 System.out.println( entry1.getSequenceName() );
4039 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
4040 System.out.println( entry1.getTaxonomyIdentifier() );
4043 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
4044 System.out.println( entry1.getGeneName() );
4047 if ( entry1.getCrossReferences().size() != 6 ) {
4050 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
4051 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
4054 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4055 System.out.println( entry2.getTaxonomyScientificName() );
4058 if ( !entry2.getSequenceName()
4059 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
4060 System.out.println( entry2.getSequenceName() );
4063 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
4064 System.out.println( entry2.getTaxonomyIdentifier() );
4067 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
4068 System.out.println( entry2.getGeneName() );
4071 if ( entry2.getCrossReferences().size() != 3 ) {
4075 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
4076 if ( !entry3.getAccession().equals( "HM043801" ) ) {
4079 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
4080 System.out.println( entry3.getTaxonomyScientificName() );
4083 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
4084 System.out.println( entry3.getSequenceName() );
4087 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
4088 System.out.println( entry3.getTaxonomyIdentifier() );
4091 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
4092 System.out.println( entry3.getSequenceSymbol() );
4095 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
4098 if ( entry3.getCrossReferences().size() < 7 ) {
4101 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
4102 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4105 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4106 System.out.println( entry4.getTaxonomyScientificName() );
4109 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4110 System.out.println( entry4.getSequenceName() );
4113 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4114 System.out.println( entry4.getTaxonomyIdentifier() );
4117 if ( !entry4.getGeneName().equals( "ras" ) ) {
4118 System.out.println( entry4.getGeneName() );
4121 // if ( !entry4.getChromosome().equals( "ras" ) ) {
4122 // System.out.println( entry4.getChromosome() );
4125 // if ( !entry4.getMap().equals( "ras" ) ) {
4126 // System.out.println( entry4.getMap() );
4132 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
4133 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
4136 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4137 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4140 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4141 System.out.println( entry5.getTaxonomyScientificName() );
4144 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4145 System.out.println( entry5.getSequenceName() );
4148 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4149 System.out.println( entry5.getTaxonomyIdentifier() );
4153 catch ( final IOException e ) {
4154 System.out.println();
4155 System.out.println( "the following might be due to absence internet connection:" );
4156 e.printStackTrace( System.out );
4159 catch ( final Exception e ) {
4160 e.printStackTrace();
4166 private static boolean testExternalNodeRelatedMethods() {
4168 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4169 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4170 PhylogenyNode n = t1.getNode( "A" );
4171 n = n.getNextExternalNode();
4172 if ( !n.getName().equals( "B" ) ) {
4175 n = n.getNextExternalNode();
4176 if ( !n.getName().equals( "C" ) ) {
4179 n = n.getNextExternalNode();
4180 if ( !n.getName().equals( "D" ) ) {
4183 n = t1.getNode( "B" );
4184 while ( !n.isLastExternalNode() ) {
4185 n = n.getNextExternalNode();
4187 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4188 n = t2.getNode( "A" );
4189 n = n.getNextExternalNode();
4190 if ( !n.getName().equals( "B" ) ) {
4193 n = n.getNextExternalNode();
4194 if ( !n.getName().equals( "C" ) ) {
4197 n = n.getNextExternalNode();
4198 if ( !n.getName().equals( "D" ) ) {
4201 n = t2.getNode( "B" );
4202 while ( !n.isLastExternalNode() ) {
4203 n = n.getNextExternalNode();
4205 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4206 n = t3.getNode( "A" );
4207 n = n.getNextExternalNode();
4208 if ( !n.getName().equals( "B" ) ) {
4211 n = n.getNextExternalNode();
4212 if ( !n.getName().equals( "C" ) ) {
4215 n = n.getNextExternalNode();
4216 if ( !n.getName().equals( "D" ) ) {
4219 n = n.getNextExternalNode();
4220 if ( !n.getName().equals( "E" ) ) {
4223 n = n.getNextExternalNode();
4224 if ( !n.getName().equals( "F" ) ) {
4227 n = n.getNextExternalNode();
4228 if ( !n.getName().equals( "G" ) ) {
4231 n = n.getNextExternalNode();
4232 if ( !n.getName().equals( "H" ) ) {
4235 n = t3.getNode( "B" );
4236 while ( !n.isLastExternalNode() ) {
4237 n = n.getNextExternalNode();
4239 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4240 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4241 final PhylogenyNode node = iter.next();
4243 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4244 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4245 final PhylogenyNode node = iter.next();
4247 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4248 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4249 if ( !iter.next().getName().equals( "A" ) ) {
4252 if ( !iter.next().getName().equals( "B" ) ) {
4255 if ( !iter.next().getName().equals( "C" ) ) {
4258 if ( !iter.next().getName().equals( "D" ) ) {
4261 if ( !iter.next().getName().equals( "E" ) ) {
4264 if ( !iter.next().getName().equals( "F" ) ) {
4267 if ( iter.hasNext() ) {
4271 catch ( final Exception e ) {
4272 e.printStackTrace( System.out );
4278 private static boolean testExtractSNFromNodeName() {
4280 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4283 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4286 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4289 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4290 .equals( "Mus musculus musculus" ) ) {
4293 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4294 .equals( "Mus musculus musculus" ) ) {
4297 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4298 .equals( "Mus musculus musculus" ) ) {
4301 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4302 .equals( "Mus musculus musculus" ) ) {
4305 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4308 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4309 .equals( "Mus musculus musculus" ) ) {
4312 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4313 .equals( "Mus musculus musculus" ) ) {
4316 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4319 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4322 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4325 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4328 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4329 .equals( "Mus musculus musculus" ) ) {
4332 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4335 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4338 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4341 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4344 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4347 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4350 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4353 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4356 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4357 .equals( "Mus musculus" ) ) {
4360 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4361 .equals( "Mus musculus" ) ) {
4364 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4367 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4368 .equals( "Mus musculus musculus" ) ) {
4371 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4372 .equals( "Mus musculus musculus" ) ) {
4375 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4376 .equals( "Mus musculus musculus" ) ) {
4379 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4382 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4383 .equals( "Pilostyles mexicana" ) ) {
4386 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4387 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4390 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4391 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4394 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4395 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4398 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4399 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4402 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4403 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4406 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4407 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4410 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
4411 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4414 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
4415 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4418 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
4419 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4422 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4423 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4426 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4427 .equals( "Escherichia coli (strain K12)" ) ) {
4430 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4431 .equals( "Escherichia coli (strain K12)" ) ) {
4434 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4435 .equals( "Escherichia coli (str. K12)" ) ) {
4438 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4439 .equals( "Escherichia coli (str. K12)" ) ) {
4442 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4443 .equals( "Escherichia coli (str. K12)" ) ) {
4446 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4447 .equals( "Escherichia coli (var. K12)" ) ) {
4450 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4451 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4454 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4455 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4459 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4460 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4463 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4464 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4468 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4469 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4472 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4473 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4476 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4477 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4480 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4483 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4486 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4489 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4490 .equals( "Macrocera sp." ) ) {
4493 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4496 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4497 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4500 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
4501 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4504 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
4505 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4508 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
4509 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4513 catch ( final Exception e ) {
4514 e.printStackTrace( System.out );
4520 private static boolean testExtractTaxonomyDataFromNodeName() {
4522 PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
4523 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4526 n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
4527 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4530 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
4531 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4534 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" );
4535 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4538 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" );
4539 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4542 n = new PhylogenyNode( "HNRPR_HUMAN" );
4543 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4546 n = new PhylogenyNode( "HNRPR_HUMAN_X" );
4547 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4551 catch ( final Exception e ) {
4552 e.printStackTrace( System.out );
4558 private static boolean testExtractTaxonomyCodeFromNodeName() {
4560 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4563 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4564 .equals( "SOYBN" ) ) {
4567 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4568 .equals( "ARATH" ) ) {
4571 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4572 .equals( "ARATH" ) ) {
4575 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4578 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4581 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4584 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4585 .equals( "SOYBN" ) ) {
4588 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4589 .equals( "SOYBN" ) ) {
4592 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4593 .equals( "SOYBN" ) ) {
4596 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4597 .equals( "SOYBN" ) ) {
4600 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4601 .equals( "SOYBN" ) ) {
4604 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4605 .equals( "SOYBN" ) ) {
4608 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4609 .equals( "SOYBN" ) ) {
4612 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4613 .equals( "SOYBN" ) ) {
4616 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4619 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4620 .equals( "SOYBN" ) ) {
4623 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4624 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4627 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4628 .equals( "9YX45" ) ) {
4631 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4632 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4633 .equals( "MOUSE" ) ) {
4636 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4637 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4638 .equals( "MOUSE" ) ) {
4641 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4642 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4643 .equals( "MOUSE" ) ) {
4646 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4647 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4650 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4651 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4654 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4655 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4658 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4659 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4662 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4663 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4666 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4667 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4670 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4671 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4674 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4675 .equals( "RAT" ) ) {
4678 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4679 .equals( "PIG" ) ) {
4683 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4684 .equals( "MOUSE" ) ) {
4687 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4688 .equals( "MOUSE" ) ) {
4691 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4695 catch ( final Exception e ) {
4696 e.printStackTrace( System.out );
4702 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4704 PhylogenyNode n = new PhylogenyNode();
4705 n.setName( "tr|B3RJ64" );
4706 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4709 n.setName( "tr.B3RJ64" );
4710 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4713 n.setName( "tr=B3RJ64" );
4714 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4717 n.setName( "tr-B3RJ64" );
4718 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4721 n.setName( "tr/B3RJ64" );
4722 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4725 n.setName( "tr\\B3RJ64" );
4726 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4729 n.setName( "tr_B3RJ64" );
4730 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4733 n.setName( " tr|B3RJ64 " );
4734 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4737 n.setName( "-tr|B3RJ64-" );
4738 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4741 n.setName( "-tr=B3RJ64-" );
4742 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4745 n.setName( "_tr=B3RJ64_" );
4746 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4749 n.setName( " tr_tr|B3RJ64_sp|123 " );
4750 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4753 n.setName( "B3RJ64" );
4754 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4757 n.setName( "sp|B3RJ64" );
4758 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4761 n.setName( "sp|B3RJ64C" );
4762 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4765 n.setName( "sp B3RJ64" );
4766 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4769 n.setName( "sp|B3RJ6X" );
4770 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4773 n.setName( "sp|B3RJ6" );
4774 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4777 n.setName( "K1PYK7_CRAGI" );
4778 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4781 n.setName( "K1PYK7_PEA" );
4782 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4785 n.setName( "K1PYK7_RAT" );
4786 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4789 n.setName( "K1PYK7_PIG" );
4790 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4793 n.setName( "~K1PYK7_PIG~" );
4794 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4797 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4798 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4801 n.setName( "K1PYKX_CRAGI" );
4802 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4805 n.setName( "XXXXX_CRAGI" );
4806 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4809 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4810 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4813 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4814 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4817 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4818 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4821 n = new PhylogenyNode();
4822 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4823 seq.setSymbol( "K1PYK7_CRAGI" );
4824 n.getNodeData().addSequence( seq );
4825 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4828 seq.setSymbol( "tr|B3RJ64" );
4829 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4832 n = new PhylogenyNode();
4833 seq = new org.forester.phylogeny.data.Sequence();
4834 seq.setName( "K1PYK7_CRAGI" );
4835 n.getNodeData().addSequence( seq );
4836 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4839 seq.setName( "tr|B3RJ64" );
4840 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4843 n = new PhylogenyNode();
4844 seq = new org.forester.phylogeny.data.Sequence();
4845 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4846 n.getNodeData().addSequence( seq );
4847 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4850 n = new PhylogenyNode();
4851 seq = new org.forester.phylogeny.data.Sequence();
4852 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4853 n.getNodeData().addSequence( seq );
4854 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4858 n = new PhylogenyNode();
4859 n.setName( "ACP19736" );
4860 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4863 n = new PhylogenyNode();
4864 n.setName( "|ACP19736|" );
4865 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4869 catch ( final Exception e ) {
4870 e.printStackTrace( System.out );
4876 private static boolean testFastaParser() {
4878 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4881 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4884 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4885 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4888 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4891 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4894 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
4897 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4900 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4904 catch ( final Exception e ) {
4905 e.printStackTrace();
4911 private static boolean testGenbankAccessorParsing() {
4912 //The format for GenBank Accession numbers are:
4913 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4914 //Protein: 3 letters + 5 numerals
4915 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4916 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4919 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4922 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4925 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4928 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4931 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4934 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4937 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4940 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4943 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4946 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4949 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4952 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4955 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4961 private static boolean testGeneralMsaParser() {
4963 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4964 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4965 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4966 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4967 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4968 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4969 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4970 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4971 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4974 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4977 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4980 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4983 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4986 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4989 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4992 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4995 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4998 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
5001 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
5004 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5007 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
5008 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5011 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5014 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5017 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
5018 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
5021 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
5024 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
5027 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
5028 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5031 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5034 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5038 catch ( final Exception e ) {
5039 e.printStackTrace();
5045 private static boolean testGeneralTable() {
5047 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
5048 t0.setValue( 3, 2, "23" );
5049 t0.setValue( 10, 1, "error" );
5050 t0.setValue( 10, 1, "110" );
5051 t0.setValue( 9, 1, "19" );
5052 t0.setValue( 1, 10, "101" );
5053 t0.setValue( 10, 10, "1010" );
5054 t0.setValue( 100, 10, "10100" );
5055 t0.setValue( 0, 0, "00" );
5056 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
5059 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
5062 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
5065 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
5068 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
5071 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
5074 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
5077 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
5080 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
5083 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
5084 t1.setValue( "3", "2", "23" );
5085 t1.setValue( "10", "1", "error" );
5086 t1.setValue( "10", "1", "110" );
5087 t1.setValue( "9", "1", "19" );
5088 t1.setValue( "1", "10", "101" );
5089 t1.setValue( "10", "10", "1010" );
5090 t1.setValue( "100", "10", "10100" );
5091 t1.setValue( "0", "0", "00" );
5092 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
5093 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
5096 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
5099 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
5102 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
5105 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
5108 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
5111 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
5114 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
5117 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
5120 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
5124 catch ( final Exception e ) {
5125 e.printStackTrace( System.out );
5131 private static boolean testGetDistance() {
5133 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5134 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",
5135 new NHXParser() )[ 0 ];
5136 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
5139 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5142 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5145 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5148 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5151 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5154 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5157 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5160 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5163 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5166 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5169 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5172 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5175 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5178 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5181 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5184 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5187 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5190 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5193 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5196 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5199 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5202 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5205 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5208 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5211 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5214 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5217 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5220 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5223 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5226 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5229 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",
5230 new NHXParser() )[ 0 ];
5231 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5234 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5237 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5240 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5243 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5246 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5249 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5252 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5255 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5258 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5261 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5265 catch ( final Exception e ) {
5266 e.printStackTrace( System.out );
5272 private static boolean testGetLCA() {
5274 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5275 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5276 new NHXParser() )[ 0 ];
5277 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5278 if ( !A.getName().equals( "A" ) ) {
5281 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5282 if ( !gh.getName().equals( "gh" ) ) {
5285 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5286 if ( !ab.getName().equals( "ab" ) ) {
5289 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5290 if ( !ab2.getName().equals( "ab" ) ) {
5293 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5294 if ( !gh2.getName().equals( "gh" ) ) {
5297 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5298 if ( !gh3.getName().equals( "gh" ) ) {
5301 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5302 if ( !abc.getName().equals( "abc" ) ) {
5305 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5306 if ( !abc2.getName().equals( "abc" ) ) {
5309 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5310 if ( !abcd.getName().equals( "abcd" ) ) {
5313 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5314 if ( !abcd2.getName().equals( "abcd" ) ) {
5317 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5318 if ( !abcdef.getName().equals( "abcdef" ) ) {
5321 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5322 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5325 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5326 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5329 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5330 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5333 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5334 if ( !abcde.getName().equals( "abcde" ) ) {
5337 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5338 if ( !abcde2.getName().equals( "abcde" ) ) {
5341 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5342 if ( !r.getName().equals( "abcdefgh" ) ) {
5345 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5346 if ( !r2.getName().equals( "abcdefgh" ) ) {
5349 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5350 if ( !r3.getName().equals( "abcdefgh" ) ) {
5353 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5354 if ( !abcde3.getName().equals( "abcde" ) ) {
5357 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5358 if ( !abcde4.getName().equals( "abcde" ) ) {
5361 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5362 if ( !ab3.getName().equals( "ab" ) ) {
5365 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5366 if ( !ab4.getName().equals( "ab" ) ) {
5369 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5370 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5371 if ( !cd.getName().equals( "cd" ) ) {
5374 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5375 if ( !cd2.getName().equals( "cd" ) ) {
5378 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5379 if ( !cde.getName().equals( "cde" ) ) {
5382 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5383 if ( !cde2.getName().equals( "cde" ) ) {
5386 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5387 if ( !cdef.getName().equals( "cdef" ) ) {
5390 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5391 if ( !cdef2.getName().equals( "cdef" ) ) {
5394 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5395 if ( !cdef3.getName().equals( "cdef" ) ) {
5398 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5399 if ( !rt.getName().equals( "r" ) ) {
5402 final Phylogeny p3 = factory
5403 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5404 new NHXParser() )[ 0 ];
5405 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5406 if ( !bc_3.getName().equals( "bc" ) ) {
5409 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5410 if ( !ac_3.getName().equals( "abc" ) ) {
5413 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5414 if ( !ad_3.getName().equals( "abcde" ) ) {
5417 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5418 if ( !af_3.getName().equals( "abcdef" ) ) {
5421 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5422 if ( !ag_3.getName().equals( "" ) ) {
5425 if ( !ag_3.isRoot() ) {
5428 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5429 if ( !al_3.getName().equals( "" ) ) {
5432 if ( !al_3.isRoot() ) {
5435 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5436 if ( !kl_3.getName().equals( "" ) ) {
5439 if ( !kl_3.isRoot() ) {
5442 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5443 if ( !fl_3.getName().equals( "" ) ) {
5446 if ( !fl_3.isRoot() ) {
5449 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5450 if ( !gk_3.getName().equals( "ghijk" ) ) {
5453 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5454 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5455 if ( !r_4.getName().equals( "r" ) ) {
5458 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5459 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5460 if ( !r_5.getName().equals( "root" ) ) {
5463 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5464 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5465 if ( !r_6.getName().equals( "rot" ) ) {
5468 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5469 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5470 if ( !r_7.getName().equals( "rott" ) ) {
5474 catch ( final Exception e ) {
5475 e.printStackTrace( System.out );
5481 private static boolean testGetLCA2() {
5483 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5484 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5485 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5486 PhylogenyMethods.preOrderReId( p_a );
5487 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5488 p_a.getNode( "a" ) );
5489 if ( !p_a_1.getName().equals( "a" ) ) {
5492 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5493 PhylogenyMethods.preOrderReId( p_b );
5494 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5495 p_b.getNode( "a" ) );
5496 if ( !p_b_1.getName().equals( "b" ) ) {
5499 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5500 p_b.getNode( "b" ) );
5501 if ( !p_b_2.getName().equals( "b" ) ) {
5504 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5505 PhylogenyMethods.preOrderReId( p_c );
5506 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5507 p_c.getNode( "a" ) );
5508 if ( !p_c_1.getName().equals( "b" ) ) {
5511 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5512 p_c.getNode( "c" ) );
5513 if ( !p_c_2.getName().equals( "c" ) ) {
5514 System.out.println( p_c_2.getName() );
5518 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5519 p_c.getNode( "b" ) );
5520 if ( !p_c_3.getName().equals( "b" ) ) {
5523 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5524 p_c.getNode( "a" ) );
5525 if ( !p_c_4.getName().equals( "c" ) ) {
5528 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5529 new NHXParser() )[ 0 ];
5530 PhylogenyMethods.preOrderReId( p1 );
5531 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5532 p1.getNode( "A" ) );
5533 if ( !A.getName().equals( "A" ) ) {
5536 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5537 p1.getNode( "gh" ) );
5538 if ( !gh.getName().equals( "gh" ) ) {
5541 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5542 p1.getNode( "B" ) );
5543 if ( !ab.getName().equals( "ab" ) ) {
5546 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5547 p1.getNode( "A" ) );
5548 if ( !ab2.getName().equals( "ab" ) ) {
5551 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5552 p1.getNode( "G" ) );
5553 if ( !gh2.getName().equals( "gh" ) ) {
5556 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5557 p1.getNode( "H" ) );
5558 if ( !gh3.getName().equals( "gh" ) ) {
5561 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5562 p1.getNode( "A" ) );
5563 if ( !abc.getName().equals( "abc" ) ) {
5566 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5567 p1.getNode( "C" ) );
5568 if ( !abc2.getName().equals( "abc" ) ) {
5571 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5572 p1.getNode( "D" ) );
5573 if ( !abcd.getName().equals( "abcd" ) ) {
5576 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5577 p1.getNode( "A" ) );
5578 if ( !abcd2.getName().equals( "abcd" ) ) {
5581 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5582 p1.getNode( "F" ) );
5583 if ( !abcdef.getName().equals( "abcdef" ) ) {
5586 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5587 p1.getNode( "A" ) );
5588 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5591 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5592 p1.getNode( "F" ) );
5593 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5596 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5597 p1.getNode( "ab" ) );
5598 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5601 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5602 p1.getNode( "E" ) );
5603 if ( !abcde.getName().equals( "abcde" ) ) {
5606 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5607 p1.getNode( "A" ) );
5608 if ( !abcde2.getName().equals( "abcde" ) ) {
5611 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5612 p1.getNode( "abcdefgh" ) );
5613 if ( !r.getName().equals( "abcdefgh" ) ) {
5616 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5617 p1.getNode( "H" ) );
5618 if ( !r2.getName().equals( "abcdefgh" ) ) {
5621 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5622 p1.getNode( "A" ) );
5623 if ( !r3.getName().equals( "abcdefgh" ) ) {
5626 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5627 p1.getNode( "abcde" ) );
5628 if ( !abcde3.getName().equals( "abcde" ) ) {
5631 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5632 p1.getNode( "E" ) );
5633 if ( !abcde4.getName().equals( "abcde" ) ) {
5636 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5637 p1.getNode( "B" ) );
5638 if ( !ab3.getName().equals( "ab" ) ) {
5641 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5642 p1.getNode( "ab" ) );
5643 if ( !ab4.getName().equals( "ab" ) ) {
5646 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5647 PhylogenyMethods.preOrderReId( p2 );
5648 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5649 p2.getNode( "d" ) );
5650 if ( !cd.getName().equals( "cd" ) ) {
5653 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5654 p2.getNode( "c" ) );
5655 if ( !cd2.getName().equals( "cd" ) ) {
5658 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5659 p2.getNode( "e" ) );
5660 if ( !cde.getName().equals( "cde" ) ) {
5663 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5664 p2.getNode( "c" ) );
5665 if ( !cde2.getName().equals( "cde" ) ) {
5668 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5669 p2.getNode( "f" ) );
5670 if ( !cdef.getName().equals( "cdef" ) ) {
5673 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5674 p2.getNode( "f" ) );
5675 if ( !cdef2.getName().equals( "cdef" ) ) {
5678 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5679 p2.getNode( "d" ) );
5680 if ( !cdef3.getName().equals( "cdef" ) ) {
5683 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5684 p2.getNode( "a" ) );
5685 if ( !rt.getName().equals( "r" ) ) {
5688 final Phylogeny p3 = factory
5689 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5690 new NHXParser() )[ 0 ];
5691 PhylogenyMethods.preOrderReId( p3 );
5692 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5693 p3.getNode( "c" ) );
5694 if ( !bc_3.getName().equals( "bc" ) ) {
5697 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5698 p3.getNode( "c" ) );
5699 if ( !ac_3.getName().equals( "abc" ) ) {
5702 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5703 p3.getNode( "d" ) );
5704 if ( !ad_3.getName().equals( "abcde" ) ) {
5707 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5708 p3.getNode( "f" ) );
5709 if ( !af_3.getName().equals( "abcdef" ) ) {
5712 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5713 p3.getNode( "g" ) );
5714 if ( !ag_3.getName().equals( "" ) ) {
5717 if ( !ag_3.isRoot() ) {
5720 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5721 p3.getNode( "l" ) );
5722 if ( !al_3.getName().equals( "" ) ) {
5725 if ( !al_3.isRoot() ) {
5728 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5729 p3.getNode( "l" ) );
5730 if ( !kl_3.getName().equals( "" ) ) {
5733 if ( !kl_3.isRoot() ) {
5736 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5737 p3.getNode( "l" ) );
5738 if ( !fl_3.getName().equals( "" ) ) {
5741 if ( !fl_3.isRoot() ) {
5744 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5745 p3.getNode( "k" ) );
5746 if ( !gk_3.getName().equals( "ghijk" ) ) {
5749 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5750 PhylogenyMethods.preOrderReId( p4 );
5751 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5752 p4.getNode( "c" ) );
5753 if ( !r_4.getName().equals( "r" ) ) {
5756 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5757 PhylogenyMethods.preOrderReId( p5 );
5758 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5759 p5.getNode( "c" ) );
5760 if ( !r_5.getName().equals( "root" ) ) {
5763 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5764 PhylogenyMethods.preOrderReId( p6 );
5765 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5766 p6.getNode( "a" ) );
5767 if ( !r_6.getName().equals( "rot" ) ) {
5770 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5771 PhylogenyMethods.preOrderReId( p7 );
5772 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5773 p7.getNode( "e" ) );
5774 if ( !r_7.getName().equals( "rott" ) ) {
5777 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5778 p7.getNode( "a" ) );
5779 if ( !r_71.getName().equals( "rott" ) ) {
5782 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5783 p7.getNode( "rott" ) );
5784 if ( !r_72.getName().equals( "rott" ) ) {
5787 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5788 p7.getNode( "a" ) );
5789 if ( !r_73.getName().equals( "rott" ) ) {
5792 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5793 p7.getNode( "rott" ) );
5794 if ( !r_74.getName().equals( "rott" ) ) {
5797 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5798 p7.getNode( "e" ) );
5799 if ( !r_75.getName().equals( "e" ) ) {
5803 catch ( final Exception e ) {
5804 e.printStackTrace( System.out );
5810 private static boolean testHmmscanOutputParser() {
5811 final String test_dir = Test.PATH_TO_TEST_DATA;
5813 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5814 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5816 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5817 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5818 final List<Protein> proteins = parser2.parse();
5819 if ( parser2.getProteinsEncountered() != 4 ) {
5822 if ( proteins.size() != 4 ) {
5825 if ( parser2.getDomainsEncountered() != 69 ) {
5828 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5831 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5834 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5837 final Protein p1 = proteins.get( 0 );
5838 if ( p1.getNumberOfProteinDomains() != 15 ) {
5841 if ( p1.getLength() != 850 ) {
5844 final Protein p2 = proteins.get( 1 );
5845 if ( p2.getNumberOfProteinDomains() != 51 ) {
5848 if ( p2.getLength() != 1291 ) {
5851 final Protein p3 = proteins.get( 2 );
5852 if ( p3.getNumberOfProteinDomains() != 2 ) {
5855 final Protein p4 = proteins.get( 3 );
5856 if ( p4.getNumberOfProteinDomains() != 1 ) {
5859 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5862 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5865 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5868 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5871 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5874 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5877 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5881 catch ( final Exception e ) {
5882 e.printStackTrace( System.out );
5888 private static boolean testLastExternalNodeMethods() {
5890 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5891 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5892 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5893 final PhylogenyNode n1 = t0.getNode( "A" );
5894 if ( n1.isLastExternalNode() ) {
5897 final PhylogenyNode n2 = t0.getNode( "B" );
5898 if ( n2.isLastExternalNode() ) {
5901 final PhylogenyNode n3 = t0.getNode( "C" );
5902 if ( n3.isLastExternalNode() ) {
5905 final PhylogenyNode n4 = t0.getNode( "D" );
5906 if ( !n4.isLastExternalNode() ) {
5910 catch ( final Exception e ) {
5911 e.printStackTrace( System.out );
5917 private static boolean testLevelOrderIterator() {
5919 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5920 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5921 PhylogenyNodeIterator it0;
5922 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5925 for( it0.reset(); it0.hasNext(); ) {
5928 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5929 if ( !it.next().getName().equals( "r" ) ) {
5932 if ( !it.next().getName().equals( "ab" ) ) {
5935 if ( !it.next().getName().equals( "cd" ) ) {
5938 if ( !it.next().getName().equals( "A" ) ) {
5941 if ( !it.next().getName().equals( "B" ) ) {
5944 if ( !it.next().getName().equals( "C" ) ) {
5947 if ( !it.next().getName().equals( "D" ) ) {
5950 if ( it.hasNext() ) {
5953 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",
5954 new NHXParser() )[ 0 ];
5955 PhylogenyNodeIterator it2;
5956 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5959 for( it2.reset(); it2.hasNext(); ) {
5962 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5963 if ( !it3.next().getName().equals( "r" ) ) {
5966 if ( !it3.next().getName().equals( "abc" ) ) {
5969 if ( !it3.next().getName().equals( "defg" ) ) {
5972 if ( !it3.next().getName().equals( "A" ) ) {
5975 if ( !it3.next().getName().equals( "B" ) ) {
5978 if ( !it3.next().getName().equals( "C" ) ) {
5981 if ( !it3.next().getName().equals( "D" ) ) {
5984 if ( !it3.next().getName().equals( "E" ) ) {
5987 if ( !it3.next().getName().equals( "F" ) ) {
5990 if ( !it3.next().getName().equals( "G" ) ) {
5993 if ( !it3.next().getName().equals( "1" ) ) {
5996 if ( !it3.next().getName().equals( "2" ) ) {
5999 if ( !it3.next().getName().equals( "3" ) ) {
6002 if ( !it3.next().getName().equals( "4" ) ) {
6005 if ( !it3.next().getName().equals( "5" ) ) {
6008 if ( !it3.next().getName().equals( "6" ) ) {
6011 if ( !it3.next().getName().equals( "f1" ) ) {
6014 if ( !it3.next().getName().equals( "f2" ) ) {
6017 if ( !it3.next().getName().equals( "f3" ) ) {
6020 if ( !it3.next().getName().equals( "a" ) ) {
6023 if ( !it3.next().getName().equals( "b" ) ) {
6026 if ( !it3.next().getName().equals( "f21" ) ) {
6029 if ( !it3.next().getName().equals( "X" ) ) {
6032 if ( !it3.next().getName().equals( "Y" ) ) {
6035 if ( !it3.next().getName().equals( "Z" ) ) {
6038 if ( it3.hasNext() ) {
6041 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
6042 PhylogenyNodeIterator it4;
6043 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
6046 for( it4.reset(); it4.hasNext(); ) {
6049 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
6050 if ( !it5.next().getName().equals( "r" ) ) {
6053 if ( !it5.next().getName().equals( "A" ) ) {
6056 if ( !it5.next().getName().equals( "B" ) ) {
6059 if ( !it5.next().getName().equals( "C" ) ) {
6062 if ( !it5.next().getName().equals( "D" ) ) {
6065 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
6066 PhylogenyNodeIterator it6;
6067 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
6070 for( it6.reset(); it6.hasNext(); ) {
6073 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
6074 if ( !it7.next().getName().equals( "A" ) ) {
6077 if ( it.hasNext() ) {
6081 catch ( final Exception e ) {
6082 e.printStackTrace( System.out );
6088 private static boolean testMafft( final String path ) {
6090 final List<String> opts = new ArrayList<String>();
6091 opts.add( "--maxiterate" );
6093 opts.add( "--localpair" );
6094 opts.add( "--quiet" );
6096 final MsaInferrer mafft = Mafft.createInstance( path );
6097 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
6098 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
6101 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
6105 catch ( final Exception e ) {
6106 e.printStackTrace( System.out );
6112 private static boolean testMidpointrooting() {
6114 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6115 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
6116 PhylogenyMethods.midpointRoot( t0 );
6117 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
6120 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
6123 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
6127 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",
6128 new NHXParser() )[ 0 ];
6129 if ( !t1.isRooted() ) {
6132 PhylogenyMethods.midpointRoot( t1 );
6133 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6136 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6139 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6142 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6145 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6148 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6151 t1.reRoot( t1.getNode( "A" ) );
6152 PhylogenyMethods.midpointRoot( t1 );
6153 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6156 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6159 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6162 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6165 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6169 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6173 catch ( final Exception e ) {
6174 e.printStackTrace( System.out );
6180 private static boolean testMsaQualityMethod() {
6182 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6183 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6184 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6185 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6186 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6191 final Msa msa = BasicMsa.createInstance( l );
6192 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6195 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6198 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6201 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6204 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6207 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6210 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6214 catch ( final Exception e ) {
6215 e.printStackTrace( System.out );
6221 private static boolean testMsaEntropy() {
6223 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
6224 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
6225 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
6226 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
6227 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6232 final Msa msa = BasicMsa.createInstance( l );
6233 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
6234 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
6235 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
6236 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
6237 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
6238 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
6239 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
6240 System.out.println();
6241 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
6242 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
6243 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
6244 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
6245 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
6246 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
6247 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
6248 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6249 l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
6250 l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
6251 l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
6252 l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
6253 l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
6254 l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
6255 l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
6256 l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
6257 l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
6258 l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
6259 l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
6260 l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
6261 l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
6262 l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
6263 l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
6264 l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
6265 l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
6266 l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
6267 l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
6268 l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
6269 l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
6270 l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
6271 final Msa msa2 = BasicMsa.createInstance( l2 );
6272 System.out.println();
6273 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
6274 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
6275 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
6277 catch ( final Exception e ) {
6278 e.printStackTrace( System.out );
6284 private static boolean testDeleteableMsa() {
6286 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
6287 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
6288 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
6289 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
6290 final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
6291 final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
6292 final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
6299 final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
6300 dmsa0.deleteRow( "b", false );
6301 if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
6304 dmsa0.deleteRow( "e", false );
6305 dmsa0.deleteRow( "a", false );
6306 dmsa0.deleteRow( "f", false );
6307 if ( dmsa0.getLength() != 4 ) {
6310 if ( dmsa0.getNumberOfSequences() != 2 ) {
6313 if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
6316 if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
6319 if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
6322 if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
6325 if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
6328 dmsa0.deleteRow( "c", false );
6329 dmsa0.deleteRow( "d", false );
6330 if ( dmsa0.getNumberOfSequences() != 0 ) {
6334 final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
6335 final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
6336 final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
6337 final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
6338 final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
6339 final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
6340 final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
6347 final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
6348 dmsa1.deleteGapOnlyColumns();
6349 dmsa1.deleteRow( "a", false );
6350 dmsa1.deleteRow( "f", false );
6351 dmsa1.deleteRow( "d", false );
6352 dmsa1.deleteGapOnlyColumns();
6353 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
6356 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
6359 if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
6362 dmsa1.deleteRow( "c", false );
6363 dmsa1.deleteGapOnlyColumns();
6364 final Writer w0 = new StringWriter();
6365 dmsa1.write( w0, MSA_FORMAT.FASTA );
6366 final Writer w1 = new StringWriter();
6367 dmsa1.write( w1, MSA_FORMAT.PHYLIP );
6368 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
6371 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
6374 final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
6375 final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
6376 final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
6377 final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
6378 final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
6379 final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
6380 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6387 final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
6388 dmsa2.deleteGapColumns( 0.5 );
6389 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
6392 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
6395 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
6398 dmsa2.deleteGapColumns( 0.2 );
6399 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
6402 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
6405 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
6408 dmsa2.deleteGapColumns( 0 );
6409 dmsa2.deleteRow( "a", false );
6410 dmsa2.deleteRow( "b", false );
6411 dmsa2.deleteRow( "f", false );
6412 dmsa2.deleteRow( "e", false );
6413 dmsa2.setIdentifier( 0, "new_c" );
6414 dmsa2.setIdentifier( 1, "new_d" );
6415 dmsa2.setResidueAt( 0, 0, 'x' );
6416 final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
6417 if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
6420 final Writer w = new StringWriter();
6421 dmsa2.write( w, MSA_FORMAT.PHYLIP );
6422 final String phylip = w.toString();
6423 if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
6424 System.out.println( phylip );
6427 final Writer w2 = new StringWriter();
6428 dmsa2.write( w2, MSA_FORMAT.FASTA );
6429 final String fasta = w2.toString();
6430 if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
6431 System.out.println( fasta );
6435 catch ( final Exception e ) {
6436 e.printStackTrace( System.out );
6442 private static boolean testNextNodeWithCollapsing() {
6444 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6446 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6447 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6448 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6449 t0.getNode( "cd" ).setCollapse( true );
6450 t0.getNode( "cde" ).setCollapse( true );
6451 n = t0.getFirstExternalNode();
6452 while ( n != null ) {
6454 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6456 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6459 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6462 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6465 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6468 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6471 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6475 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6476 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6477 t1.getNode( "ab" ).setCollapse( true );
6478 t1.getNode( "cd" ).setCollapse( true );
6479 t1.getNode( "cde" ).setCollapse( true );
6480 n = t1.getNode( "ab" );
6481 ext = new ArrayList<PhylogenyNode>();
6482 while ( n != null ) {
6484 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6486 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6489 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6492 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6495 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6498 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6502 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6503 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6504 t2.getNode( "ab" ).setCollapse( true );
6505 t2.getNode( "cd" ).setCollapse( true );
6506 t2.getNode( "cde" ).setCollapse( true );
6507 t2.getNode( "c" ).setCollapse( true );
6508 t2.getNode( "d" ).setCollapse( true );
6509 t2.getNode( "e" ).setCollapse( true );
6510 t2.getNode( "gh" ).setCollapse( true );
6511 n = t2.getNode( "ab" );
6512 ext = new ArrayList<PhylogenyNode>();
6513 while ( n != null ) {
6515 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6517 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6520 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6523 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6526 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6530 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6531 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6532 t3.getNode( "ab" ).setCollapse( true );
6533 t3.getNode( "cd" ).setCollapse( true );
6534 t3.getNode( "cde" ).setCollapse( true );
6535 t3.getNode( "c" ).setCollapse( true );
6536 t3.getNode( "d" ).setCollapse( true );
6537 t3.getNode( "e" ).setCollapse( true );
6538 t3.getNode( "gh" ).setCollapse( true );
6539 t3.getNode( "fgh" ).setCollapse( true );
6540 n = t3.getNode( "ab" );
6541 ext = new ArrayList<PhylogenyNode>();
6542 while ( n != null ) {
6544 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6546 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6549 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6552 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6556 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6557 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6558 t4.getNode( "ab" ).setCollapse( true );
6559 t4.getNode( "cd" ).setCollapse( true );
6560 t4.getNode( "cde" ).setCollapse( true );
6561 t4.getNode( "c" ).setCollapse( true );
6562 t4.getNode( "d" ).setCollapse( true );
6563 t4.getNode( "e" ).setCollapse( true );
6564 t4.getNode( "gh" ).setCollapse( true );
6565 t4.getNode( "fgh" ).setCollapse( true );
6566 t4.getNode( "abcdefgh" ).setCollapse( true );
6567 n = t4.getNode( "abcdefgh" );
6568 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6571 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6572 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6574 n = t5.getFirstExternalNode();
6575 while ( n != null ) {
6577 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6579 if ( ext.size() != 8 ) {
6582 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6585 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6588 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6591 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6594 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6597 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6600 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6603 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6606 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6607 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6609 t6.getNode( "ab" ).setCollapse( true );
6610 n = t6.getNode( "ab" );
6611 while ( n != null ) {
6613 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6615 if ( ext.size() != 7 ) {
6618 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6621 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6624 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6627 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6630 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6633 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6636 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6639 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6640 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6642 t7.getNode( "cd" ).setCollapse( true );
6643 n = t7.getNode( "a" );
6644 while ( n != null ) {
6646 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6648 if ( ext.size() != 7 ) {
6651 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6654 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6657 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6660 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6663 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6666 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6669 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6672 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6673 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6675 t8.getNode( "cd" ).setCollapse( true );
6676 t8.getNode( "c" ).setCollapse( true );
6677 t8.getNode( "d" ).setCollapse( true );
6678 n = t8.getNode( "a" );
6679 while ( n != null ) {
6681 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6683 if ( ext.size() != 7 ) {
6686 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6689 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6692 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6693 System.out.println( "2 fail" );
6696 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6699 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6702 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6705 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6708 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6709 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6711 t9.getNode( "gh" ).setCollapse( true );
6712 n = t9.getNode( "a" );
6713 while ( n != null ) {
6715 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6717 if ( ext.size() != 7 ) {
6720 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6723 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6726 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6729 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6732 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6735 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6738 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6741 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6742 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6744 t10.getNode( "gh" ).setCollapse( true );
6745 t10.getNode( "g" ).setCollapse( true );
6746 t10.getNode( "h" ).setCollapse( true );
6747 n = t10.getNode( "a" );
6748 while ( n != null ) {
6750 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6752 if ( ext.size() != 7 ) {
6755 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6758 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6761 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6764 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6767 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6770 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6773 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6776 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6777 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6779 t11.getNode( "gh" ).setCollapse( true );
6780 t11.getNode( "fgh" ).setCollapse( true );
6781 n = t11.getNode( "a" );
6782 while ( n != null ) {
6784 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6786 if ( ext.size() != 6 ) {
6789 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6792 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6795 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6798 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6801 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6804 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6807 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6808 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6810 t12.getNode( "gh" ).setCollapse( true );
6811 t12.getNode( "fgh" ).setCollapse( true );
6812 t12.getNode( "g" ).setCollapse( true );
6813 t12.getNode( "h" ).setCollapse( true );
6814 t12.getNode( "f" ).setCollapse( true );
6815 n = t12.getNode( "a" );
6816 while ( n != null ) {
6818 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6820 if ( ext.size() != 6 ) {
6823 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6826 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6829 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6832 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6835 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6838 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6841 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6842 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6844 t13.getNode( "ab" ).setCollapse( true );
6845 t13.getNode( "b" ).setCollapse( true );
6846 t13.getNode( "fgh" ).setCollapse( true );
6847 t13.getNode( "gh" ).setCollapse( true );
6848 n = t13.getNode( "ab" );
6849 while ( n != null ) {
6851 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6853 if ( ext.size() != 5 ) {
6856 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6859 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6862 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6865 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6868 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6871 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6872 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6874 t14.getNode( "ab" ).setCollapse( true );
6875 t14.getNode( "a" ).setCollapse( true );
6876 t14.getNode( "fgh" ).setCollapse( true );
6877 t14.getNode( "gh" ).setCollapse( true );
6878 n = t14.getNode( "ab" );
6879 while ( n != null ) {
6881 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6883 if ( ext.size() != 5 ) {
6886 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6889 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6892 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6895 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6898 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6901 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" );
6902 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6904 t15.getNode( "ab" ).setCollapse( true );
6905 t15.getNode( "a" ).setCollapse( true );
6906 t15.getNode( "fgh" ).setCollapse( true );
6907 t15.getNode( "gh" ).setCollapse( true );
6908 n = t15.getNode( "ab" );
6909 while ( n != null ) {
6911 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6913 if ( ext.size() != 6 ) {
6916 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6919 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6922 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6925 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6928 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6931 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6936 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" );
6937 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6939 t16.getNode( "ab" ).setCollapse( true );
6940 t16.getNode( "a" ).setCollapse( true );
6941 t16.getNode( "fgh" ).setCollapse( true );
6942 t16.getNode( "gh" ).setCollapse( true );
6943 t16.getNode( "cd" ).setCollapse( true );
6944 t16.getNode( "cde" ).setCollapse( true );
6945 t16.getNode( "d" ).setCollapse( true );
6946 t16.getNode( "x" ).setCollapse( true );
6947 n = t16.getNode( "ab" );
6948 while ( n != null ) {
6950 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6952 if ( ext.size() != 4 ) {
6955 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6958 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6961 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6964 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6968 catch ( final Exception e ) {
6969 e.printStackTrace( System.out );
6975 private static boolean testNexusCharactersParsing() {
6977 final NexusCharactersParser parser = new NexusCharactersParser();
6978 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6980 String[] labels = parser.getCharStateLabels();
6981 if ( labels.length != 7 ) {
6984 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6987 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6990 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6993 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6996 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6999 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7002 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7005 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7007 labels = parser.getCharStateLabels();
7008 if ( labels.length != 7 ) {
7011 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7014 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7017 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7020 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7023 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7026 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7029 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7033 catch ( final Exception e ) {
7034 e.printStackTrace( System.out );
7040 private static boolean testNexusMatrixParsing() {
7042 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
7043 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
7045 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
7046 if ( m.getNumberOfCharacters() != 9 ) {
7049 if ( m.getNumberOfIdentifiers() != 5 ) {
7052 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
7055 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
7058 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
7061 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
7064 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
7067 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
7070 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
7073 // if ( labels.length != 7 ) {
7076 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7079 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7082 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7085 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7088 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7091 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7094 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7097 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7099 // labels = parser.getCharStateLabels();
7100 // if ( labels.length != 7 ) {
7103 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7106 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7109 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7112 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7115 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7118 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7121 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7125 catch ( final Exception e ) {
7126 e.printStackTrace( System.out );
7132 private static boolean testNexusTreeParsing() {
7134 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7135 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7136 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
7137 if ( phylogenies.length != 1 ) {
7140 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
7143 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7147 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
7148 if ( phylogenies.length != 1 ) {
7151 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7154 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
7158 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
7159 if ( phylogenies.length != 1 ) {
7162 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7165 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7168 if ( phylogenies[ 0 ].isRooted() ) {
7172 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
7173 if ( phylogenies.length != 18 ) {
7176 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7179 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
7182 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
7185 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
7188 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7191 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
7194 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
7197 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
7200 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
7203 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
7206 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
7209 if ( phylogenies[ 8 ].isRooted() ) {
7212 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
7215 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
7218 if ( !phylogenies[ 9 ].isRooted() ) {
7221 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
7224 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
7227 if ( !phylogenies[ 10 ].isRooted() ) {
7230 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
7233 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
7236 if ( phylogenies[ 11 ].isRooted() ) {
7239 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
7242 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
7245 if ( !phylogenies[ 12 ].isRooted() ) {
7248 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
7251 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
7254 if ( !phylogenies[ 13 ].isRooted() ) {
7257 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
7260 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
7263 if ( !phylogenies[ 14 ].isRooted() ) {
7266 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
7269 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
7272 if ( phylogenies[ 15 ].isRooted() ) {
7275 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
7278 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
7281 if ( !phylogenies[ 16 ].isRooted() ) {
7284 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
7287 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
7290 if ( phylogenies[ 17 ].isRooted() ) {
7293 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
7296 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7298 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
7299 if ( phylogenies.length != 9 ) {
7302 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
7303 .getDistanceToParent() ) ) {
7306 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
7307 .getDistanceToParent() ) ) {
7310 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
7313 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7316 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7319 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7322 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7326 catch ( final Exception e ) {
7327 e.printStackTrace( System.out );
7333 private static boolean testNexusTreeParsingIterating() {
7335 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7336 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7337 if ( !p.hasNext() ) {
7340 Phylogeny phy = p.next();
7341 if ( phy == null ) {
7344 if ( phy.getNumberOfExternalNodes() != 25 ) {
7347 if ( !phy.getName().equals( "" ) ) {
7350 if ( p.hasNext() ) {
7354 if ( phy != null ) {
7358 if ( !p.hasNext() ) {
7362 if ( phy == null ) {
7365 if ( phy.getNumberOfExternalNodes() != 25 ) {
7368 if ( !phy.getName().equals( "" ) ) {
7371 if ( p.hasNext() ) {
7375 if ( phy != null ) {
7378 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7379 if ( !p.hasNext() ) {
7383 if ( phy == null ) {
7386 if ( phy.getNumberOfExternalNodes() != 10 ) {
7389 if ( !phy.getName().equals( "name" ) ) {
7392 if ( p.hasNext() ) {
7396 if ( phy != null ) {
7400 if ( !p.hasNext() ) {
7404 if ( phy == null ) {
7407 if ( phy.getNumberOfExternalNodes() != 10 ) {
7410 if ( !phy.getName().equals( "name" ) ) {
7413 if ( p.hasNext() ) {
7417 if ( phy != null ) {
7420 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7421 if ( !p.hasNext() ) {
7425 if ( phy == null ) {
7428 if ( phy.getNumberOfExternalNodes() != 3 ) {
7431 if ( !phy.getName().equals( "" ) ) {
7434 if ( phy.isRooted() ) {
7437 if ( p.hasNext() ) {
7441 if ( phy != null ) {
7446 if ( !p.hasNext() ) {
7450 if ( phy == null ) {
7453 if ( phy.getNumberOfExternalNodes() != 3 ) {
7456 if ( !phy.getName().equals( "" ) ) {
7459 if ( p.hasNext() ) {
7463 if ( phy != null ) {
7467 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7468 if ( !p.hasNext() ) {
7473 if ( phy == null ) {
7476 if ( phy.getNumberOfExternalNodes() != 10 ) {
7479 if ( !phy.getName().equals( "tree 0" ) ) {
7483 if ( !p.hasNext() ) {
7487 if ( phy == null ) {
7490 if ( phy.getNumberOfExternalNodes() != 10 ) {
7493 if ( !phy.getName().equals( "tree 1" ) ) {
7497 if ( !p.hasNext() ) {
7501 if ( phy == null ) {
7504 if ( phy.getNumberOfExternalNodes() != 3 ) {
7505 System.out.println( phy.toString() );
7508 if ( !phy.getName().equals( "" ) ) {
7511 if ( phy.isRooted() ) {
7515 if ( !p.hasNext() ) {
7519 if ( phy == null ) {
7522 if ( phy.getNumberOfExternalNodes() != 4 ) {
7525 if ( !phy.getName().equals( "" ) ) {
7528 if ( !phy.isRooted() ) {
7532 if ( !p.hasNext() ) {
7536 if ( phy == null ) {
7539 if ( phy.getNumberOfExternalNodes() != 5 ) {
7540 System.out.println( phy.getNumberOfExternalNodes() );
7543 if ( !phy.getName().equals( "" ) ) {
7546 if ( !phy.isRooted() ) {
7550 if ( !p.hasNext() ) {
7554 if ( phy == null ) {
7557 if ( phy.getNumberOfExternalNodes() != 3 ) {
7560 if ( !phy.getName().equals( "" ) ) {
7563 if ( phy.isRooted() ) {
7567 if ( !p.hasNext() ) {
7571 if ( phy == null ) {
7574 if ( phy.getNumberOfExternalNodes() != 2 ) {
7577 if ( !phy.getName().equals( "" ) ) {
7580 if ( !phy.isRooted() ) {
7584 if ( !p.hasNext() ) {
7588 if ( phy.getNumberOfExternalNodes() != 3 ) {
7591 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7594 if ( !phy.isRooted() ) {
7598 if ( !p.hasNext() ) {
7602 if ( phy.getNumberOfExternalNodes() != 3 ) {
7605 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7608 if ( !phy.getName().equals( "tree 8" ) ) {
7612 if ( !p.hasNext() ) {
7616 if ( phy.getNumberOfExternalNodes() != 3 ) {
7619 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7622 if ( !phy.getName().equals( "tree 9" ) ) {
7626 if ( !p.hasNext() ) {
7630 if ( phy.getNumberOfExternalNodes() != 3 ) {
7633 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7636 if ( !phy.getName().equals( "tree 10" ) ) {
7639 if ( !phy.isRooted() ) {
7643 if ( !p.hasNext() ) {
7647 if ( phy.getNumberOfExternalNodes() != 3 ) {
7650 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7653 if ( !phy.getName().equals( "tree 11" ) ) {
7656 if ( phy.isRooted() ) {
7660 if ( !p.hasNext() ) {
7664 if ( phy.getNumberOfExternalNodes() != 3 ) {
7667 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7670 if ( !phy.getName().equals( "tree 12" ) ) {
7673 if ( !phy.isRooted() ) {
7677 if ( !p.hasNext() ) {
7681 if ( phy.getNumberOfExternalNodes() != 3 ) {
7684 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7687 if ( !phy.getName().equals( "tree 13" ) ) {
7690 if ( !phy.isRooted() ) {
7694 if ( !p.hasNext() ) {
7698 if ( phy.getNumberOfExternalNodes() != 10 ) {
7699 System.out.println( phy.getNumberOfExternalNodes() );
7704 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7705 System.out.println( phy.toNewHampshire() );
7708 if ( !phy.getName().equals( "tree 14" ) ) {
7711 if ( !phy.isRooted() ) {
7715 if ( !p.hasNext() ) {
7719 if ( phy.getNumberOfExternalNodes() != 10 ) {
7720 System.out.println( phy.getNumberOfExternalNodes() );
7725 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7726 System.out.println( phy.toNewHampshire() );
7729 if ( !phy.getName().equals( "tree 15" ) ) {
7732 if ( phy.isRooted() ) {
7736 if ( !p.hasNext() ) {
7740 if ( phy.getNumberOfExternalNodes() != 10 ) {
7741 System.out.println( phy.getNumberOfExternalNodes() );
7746 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7747 System.out.println( phy.toNewHampshire() );
7750 if ( !phy.getName().equals( "tree 16" ) ) {
7753 if ( !phy.isRooted() ) {
7757 if ( !p.hasNext() ) {
7761 if ( phy.getNumberOfExternalNodes() != 10 ) {
7762 System.out.println( phy.getNumberOfExternalNodes() );
7767 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7768 System.out.println( phy.toNewHampshire() );
7771 if ( !phy.getName().equals( "tree 17" ) ) {
7774 if ( phy.isRooted() ) {
7778 if ( p.hasNext() ) {
7782 if ( phy != null ) {
7787 if ( !p.hasNext() ) {
7791 if ( phy == null ) {
7794 if ( phy.getNumberOfExternalNodes() != 10 ) {
7797 if ( !phy.getName().equals( "tree 0" ) ) {
7801 if ( !p.hasNext() ) {
7805 if ( phy == null ) {
7808 if ( phy.getNumberOfExternalNodes() != 10 ) {
7811 if ( !phy.getName().equals( "tree 1" ) ) {
7815 if ( !p.hasNext() ) {
7819 if ( phy == null ) {
7822 if ( phy.getNumberOfExternalNodes() != 3 ) {
7825 if ( !phy.getName().equals( "" ) ) {
7828 if ( phy.isRooted() ) {
7832 if ( !p.hasNext() ) {
7836 if ( phy == null ) {
7839 if ( phy.getNumberOfExternalNodes() != 4 ) {
7842 if ( !phy.getName().equals( "" ) ) {
7845 if ( !phy.isRooted() ) {
7849 if ( !p.hasNext() ) {
7853 if ( phy == null ) {
7856 if ( phy.getNumberOfExternalNodes() != 5 ) {
7857 System.out.println( phy.getNumberOfExternalNodes() );
7860 if ( !phy.getName().equals( "" ) ) {
7863 if ( !phy.isRooted() ) {
7867 if ( !p.hasNext() ) {
7871 if ( phy == null ) {
7874 if ( phy.getNumberOfExternalNodes() != 3 ) {
7877 if ( !phy.getName().equals( "" ) ) {
7880 if ( phy.isRooted() ) {
7884 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7885 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7887 if ( !p2.hasNext() ) {
7891 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7894 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7898 if ( !p2.hasNext() ) {
7903 if ( !p2.hasNext() ) {
7908 if ( !p2.hasNext() ) {
7913 if ( !p2.hasNext() ) {
7918 if ( !p2.hasNext() ) {
7923 if ( !p2.hasNext() ) {
7928 if ( !p2.hasNext() ) {
7933 if ( !p2.hasNext() ) {
7937 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7940 if ( p2.hasNext() ) {
7944 if ( phy != null ) {
7949 if ( !p2.hasNext() ) {
7953 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7956 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7960 catch ( final Exception e ) {
7961 e.printStackTrace( System.out );
7967 private static boolean testNexusTreeParsingTranslating() {
7969 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7970 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7971 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7972 if ( phylogenies.length != 1 ) {
7975 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7978 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7981 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7984 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7987 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7988 .equals( "Aranaeus" ) ) {
7992 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7993 if ( phylogenies.length != 3 ) {
7996 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7999 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8002 if ( phylogenies[ 0 ].isRooted() ) {
8005 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8008 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8011 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8012 .equals( "Aranaeus" ) ) {
8015 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8018 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8021 if ( phylogenies[ 1 ].isRooted() ) {
8024 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8027 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8030 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8031 .equals( "Aranaeus" ) ) {
8034 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8037 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8040 if ( !phylogenies[ 2 ].isRooted() ) {
8043 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8046 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8049 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8050 .equals( "Aranaeus" ) ) {
8054 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
8055 if ( phylogenies.length != 3 ) {
8058 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8061 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8064 if ( phylogenies[ 0 ].isRooted() ) {
8067 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8070 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8073 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8074 .equals( "Aranaeus" ) ) {
8077 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8080 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8083 if ( phylogenies[ 1 ].isRooted() ) {
8086 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8089 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8092 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8093 .equals( "Aranaeus" ) ) {
8096 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8099 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8102 if ( !phylogenies[ 2 ].isRooted() ) {
8105 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8108 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8111 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8112 .equals( "Aranaeus" ) ) {
8115 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
8116 if ( phylogenies.length != 3 ) {
8119 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
8124 catch ( final Exception e ) {
8125 e.printStackTrace( System.out );
8131 private static boolean testNHParsing() {
8133 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8134 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
8135 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
8138 final NHXParser nhxp = new NHXParser();
8139 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
8140 nhxp.setReplaceUnderscores( true );
8141 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
8142 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
8145 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
8148 final Phylogeny p1b = factory
8149 .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 ",
8150 new NHXParser() )[ 0 ];
8151 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
8154 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
8157 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
8158 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
8159 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
8160 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
8161 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
8162 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
8163 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
8164 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
8165 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
8166 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
8167 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
8168 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
8169 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
8171 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
8174 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
8177 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
8180 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
8183 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
8184 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
8185 final String p16_S = "((A,B),C)";
8186 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
8187 if ( p16.length != 1 ) {
8190 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
8193 final String p17_S = "(C,(A,B))";
8194 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
8195 if ( p17.length != 1 ) {
8198 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
8201 final String p18_S = "((A,B),(C,D))";
8202 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
8203 if ( p18.length != 1 ) {
8206 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
8209 final String p19_S = "(((A,B),C),D)";
8210 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
8211 if ( p19.length != 1 ) {
8214 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
8217 final String p20_S = "(A,(B,(C,D)))";
8218 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
8219 if ( p20.length != 1 ) {
8222 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
8225 final String p21_S = "(A,(B,(C,(D,E))))";
8226 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
8227 if ( p21.length != 1 ) {
8230 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
8233 final String p22_S = "((((A,B),C),D),E)";
8234 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
8235 if ( p22.length != 1 ) {
8238 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
8241 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8242 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
8243 if ( p23.length != 1 ) {
8244 System.out.println( "xl=" + p23.length );
8248 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
8251 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8252 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
8253 if ( p24.length != 1 ) {
8256 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
8259 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8260 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8261 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
8262 if ( p241.length != 2 ) {
8265 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
8268 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
8271 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
8272 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
8273 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
8274 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
8275 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
8276 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
8277 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
8278 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
8279 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
8280 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
8283 final String p26_S = "(A,B)ab";
8284 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
8285 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
8288 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8289 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
8290 if ( p27s.length != 1 ) {
8291 System.out.println( "xxl=" + p27s.length );
8295 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8296 System.out.println( p27s[ 0 ].toNewHampshireX() );
8300 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
8302 if ( p27.length != 1 ) {
8303 System.out.println( "yl=" + p27.length );
8307 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8308 System.out.println( p27[ 0 ].toNewHampshireX() );
8312 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8313 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8314 final String p28_S3 = "(A,B)ab";
8315 final String p28_S4 = "((((A,B),C),D),;E;)";
8316 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
8318 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
8321 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
8324 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
8327 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
8330 if ( p28.length != 4 ) {
8333 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";
8334 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8335 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8338 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";
8339 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8340 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8343 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8344 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8345 if ( ( p32.length != 0 ) ) {
8348 final String p33_S = "A";
8349 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8350 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8353 final String p34_S = "B;";
8354 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8355 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8358 final String p35_S = "B:0.2";
8359 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8360 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8363 final String p36_S = "(A)";
8364 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8365 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8368 final String p37_S = "((A))";
8369 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8370 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8373 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8374 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8375 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8378 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8379 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8380 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8383 final String p40_S = "(A,B,C)";
8384 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8385 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8388 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8389 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8390 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8393 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8394 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8395 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8398 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)";
8399 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8400 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8403 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)))";
8404 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8405 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8408 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8409 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8410 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8413 final String p46_S = "";
8414 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8415 if ( p46.length != 0 ) {
8418 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8419 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8422 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8423 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8426 final Phylogeny p49 = factory
8427 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8428 new NHXParser() )[ 0 ];
8429 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8432 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8433 if ( p50.getNode( "A" ) == null ) {
8436 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8437 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8440 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8443 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8444 .equals( "((A,B)88:2.0,C);" ) ) {
8447 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8448 if ( p51.getNode( "A(A" ) == null ) {
8451 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8452 if ( p52.getNode( "A(A" ) == null ) {
8455 final Phylogeny p53 = factory
8456 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8457 new NHXParser() )[ 0 ];
8458 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8461 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8462 if ( p54.getNode( "A" ) == null ) {
8465 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8468 final Phylogeny p55 = factory
8469 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
8470 new NHXParser() )[ 0 ];
8473 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,lcl|HPV66_L1.1x:0.0798012);" ) ) {
8474 System.out.println( p55.toNewHampshire() );
8477 final Phylogeny p56 = factory
8478 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
8479 new NHXParser() )[ 0 ];
8482 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8483 System.out.println( p56.toNewHampshire() );
8486 final Phylogeny p57 = factory
8487 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
8488 new NHXParser() )[ 0 ];
8491 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8492 System.out.println( p56.toNewHampshire() );
8495 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8496 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8497 if ( !p58.toNewHampshire().equals( s58 ) ) {
8498 System.out.println( p58.toNewHampshire() );
8501 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8502 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8503 if ( !p59.toNewHampshire().equals( s59 ) ) {
8504 System.out.println( p59.toNewHampshire() );
8507 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8508 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8509 if ( !p60.toNewHampshire().equals( s60 ) ) {
8510 System.out.println( p60.toNewHampshire() );
8513 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8514 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8515 if ( !p61.toNewHampshire()
8516 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8517 System.out.println( p61.toNewHampshire() );
8521 catch ( final Exception e ) {
8522 e.printStackTrace( System.out );
8528 private static boolean testNHParsingIter() {
8530 final String p0_str = "(A,B);";
8531 final NHXParser p = new NHXParser();
8532 p.setSource( p0_str );
8533 if ( !p.hasNext() ) {
8536 final Phylogeny p0 = p.next();
8537 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8538 System.out.println( p0.toNewHampshire() );
8541 if ( p.hasNext() ) {
8544 if ( p.next() != null ) {
8548 final String p00_str = "(A,B)root;";
8549 p.setSource( p00_str );
8550 final Phylogeny p00 = p.next();
8551 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8552 System.out.println( p00.toNewHampshire() );
8556 final String p000_str = "A;";
8557 p.setSource( p000_str );
8558 final Phylogeny p000 = p.next();
8559 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8560 System.out.println( p000.toNewHampshire() );
8564 final String p0000_str = "A";
8565 p.setSource( p0000_str );
8566 final Phylogeny p0000 = p.next();
8567 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8568 System.out.println( p0000.toNewHampshire() );
8572 p.setSource( "(A)" );
8573 final Phylogeny p00000 = p.next();
8574 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8575 System.out.println( p00000.toNewHampshire() );
8579 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8580 p.setSource( p1_str );
8581 if ( !p.hasNext() ) {
8584 final Phylogeny p1_0 = p.next();
8585 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8586 System.out.println( p1_0.toNewHampshire() );
8589 if ( !p.hasNext() ) {
8592 final Phylogeny p1_1 = p.next();
8593 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8594 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8597 if ( !p.hasNext() ) {
8600 final Phylogeny p1_2 = p.next();
8601 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8602 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8605 if ( !p.hasNext() ) {
8608 final Phylogeny p1_3 = p.next();
8609 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8610 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8613 if ( p.hasNext() ) {
8616 if ( p.next() != null ) {
8620 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8621 p.setSource( p2_str );
8622 if ( !p.hasNext() ) {
8625 Phylogeny p2_0 = p.next();
8626 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8627 System.out.println( p2_0.toNewHampshire() );
8630 if ( !p.hasNext() ) {
8633 Phylogeny p2_1 = p.next();
8634 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8635 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8638 if ( !p.hasNext() ) {
8641 Phylogeny p2_2 = p.next();
8642 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8643 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8646 if ( !p.hasNext() ) {
8649 Phylogeny p2_3 = p.next();
8650 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8651 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8654 if ( !p.hasNext() ) {
8657 Phylogeny p2_4 = p.next();
8658 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8659 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8662 if ( p.hasNext() ) {
8665 if ( p.next() != null ) {
8670 if ( !p.hasNext() ) {
8674 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8675 System.out.println( p2_0.toNewHampshire() );
8678 if ( !p.hasNext() ) {
8682 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8683 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8686 if ( !p.hasNext() ) {
8690 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8691 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8694 if ( !p.hasNext() ) {
8698 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8699 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8702 if ( !p.hasNext() ) {
8706 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8707 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8710 if ( p.hasNext() ) {
8713 if ( p.next() != null ) {
8717 final String p3_str = "((A,B),C)abc";
8718 p.setSource( p3_str );
8719 if ( !p.hasNext() ) {
8722 final Phylogeny p3_0 = p.next();
8723 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8726 if ( p.hasNext() ) {
8729 if ( p.next() != null ) {
8733 final String p4_str = "((A,B)ab,C)abc";
8734 p.setSource( p4_str );
8735 if ( !p.hasNext() ) {
8738 final Phylogeny p4_0 = p.next();
8739 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8742 if ( p.hasNext() ) {
8745 if ( p.next() != null ) {
8749 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8750 p.setSource( p5_str );
8751 if ( !p.hasNext() ) {
8754 final Phylogeny p5_0 = p.next();
8755 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8758 if ( p.hasNext() ) {
8761 if ( p.next() != null ) {
8765 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8766 p.setSource( p6_str );
8767 if ( !p.hasNext() ) {
8770 Phylogeny p6_0 = p.next();
8771 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8774 if ( p.hasNext() ) {
8777 if ( p.next() != null ) {
8781 if ( !p.hasNext() ) {
8785 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8788 if ( p.hasNext() ) {
8791 if ( p.next() != null ) {
8795 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8796 p.setSource( p7_str );
8797 if ( !p.hasNext() ) {
8800 Phylogeny p7_0 = p.next();
8801 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8804 if ( p.hasNext() ) {
8807 if ( p.next() != null ) {
8811 if ( !p.hasNext() ) {
8815 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8818 if ( p.hasNext() ) {
8821 if ( p.next() != null ) {
8825 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8826 p.setSource( p8_str );
8827 if ( !p.hasNext() ) {
8830 Phylogeny p8_0 = p.next();
8831 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8834 if ( !p.hasNext() ) {
8837 if ( !p.hasNext() ) {
8840 Phylogeny p8_1 = p.next();
8841 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8844 if ( p.hasNext() ) {
8847 if ( p.next() != null ) {
8851 if ( !p.hasNext() ) {
8855 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8858 if ( !p.hasNext() ) {
8862 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8865 if ( p.hasNext() ) {
8868 if ( p.next() != null ) {
8874 if ( p.hasNext() ) {
8878 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8879 if ( !p.hasNext() ) {
8882 Phylogeny p_27 = p.next();
8883 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8884 System.out.println( p_27.toNewHampshireX() );
8888 if ( p.hasNext() ) {
8891 if ( p.next() != null ) {
8895 if ( !p.hasNext() ) {
8899 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8900 System.out.println( p_27.toNewHampshireX() );
8904 if ( p.hasNext() ) {
8907 if ( p.next() != null ) {
8911 final String p30_str = "(A,B);(C,D)";
8912 final NHXParser p30 = new NHXParser();
8913 p30.setSource( p30_str );
8914 if ( !p30.hasNext() ) {
8917 Phylogeny phy30 = p30.next();
8918 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8919 System.out.println( phy30.toNewHampshire() );
8922 if ( !p30.hasNext() ) {
8925 Phylogeny phy301 = p30.next();
8926 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8927 System.out.println( phy301.toNewHampshire() );
8930 if ( p30.hasNext() ) {
8933 if ( p30.hasNext() ) {
8936 if ( p30.next() != null ) {
8939 if ( p30.next() != null ) {
8943 if ( !p30.hasNext() ) {
8947 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8948 System.out.println( phy30.toNewHampshire() );
8951 if ( !p30.hasNext() ) {
8954 phy301 = p30.next();
8955 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8956 System.out.println( phy301.toNewHampshire() );
8959 if ( p30.hasNext() ) {
8962 if ( p30.hasNext() ) {
8965 if ( p30.next() != null ) {
8968 if ( p30.next() != null ) {
8972 catch ( final Exception e ) {
8973 e.printStackTrace( System.out );
8979 private static boolean testNHXconversion() {
8981 final PhylogenyNode n1 = new PhylogenyNode();
8982 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8983 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8984 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8985 final PhylogenyNode n5 = PhylogenyNode
8986 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8987 final PhylogenyNode n6 = PhylogenyNode
8988 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8989 if ( !n1.toNewHampshireX().equals( "" ) ) {
8992 if ( !n2.toNewHampshireX().equals( "" ) ) {
8995 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8998 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
9001 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
9004 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
9005 System.out.println( n6.toNewHampshireX() );
9008 final PhylogenyNode n7 = new PhylogenyNode();
9009 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
9010 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
9011 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
9012 System.out.println( n7
9013 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
9017 catch ( final Exception e ) {
9018 e.printStackTrace( System.out );
9024 private static boolean testNHXNodeParsing() {
9026 final PhylogenyNode n1 = new PhylogenyNode();
9027 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9028 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9029 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9030 final PhylogenyNode n5 = PhylogenyNode
9031 .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]" );
9032 if ( !n3.getName().equals( "n3" ) ) {
9035 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9038 if ( n3.isDuplication() ) {
9041 if ( n3.isHasAssignedEvent() ) {
9044 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
9047 if ( !n4.getName().equals( "n4" ) ) {
9050 if ( n4.getDistanceToParent() != 0.01 ) {
9053 if ( !n5.getName().equals( "n5" ) ) {
9056 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
9059 if ( n5.getDistanceToParent() != 0.1 ) {
9062 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
9065 if ( !n5.isDuplication() ) {
9068 if ( !n5.isHasAssignedEvent() ) {
9071 final PhylogenyNode n8 = PhylogenyNode
9072 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
9073 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9074 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9077 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
9080 final PhylogenyNode n9 = PhylogenyNode
9081 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
9082 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9083 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
9086 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
9089 final PhylogenyNode n10 = PhylogenyNode
9090 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9091 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
9094 final PhylogenyNode n20 = PhylogenyNode
9095 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9096 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9099 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
9102 final PhylogenyNode n20x = PhylogenyNode
9103 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9104 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
9107 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
9110 final PhylogenyNode n20xx = PhylogenyNode
9111 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9112 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
9115 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
9118 final PhylogenyNode n20xxx = PhylogenyNode
9119 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9120 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
9123 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
9126 final PhylogenyNode n20xxxx = PhylogenyNode
9127 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9128 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
9131 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
9134 final PhylogenyNode n21 = PhylogenyNode
9135 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9136 if ( !n21.getName().equals( "N21_PIG" ) ) {
9139 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
9142 final PhylogenyNode n21x = PhylogenyNode
9143 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9144 if ( !n21x.getName().equals( "n21_PIG" ) ) {
9147 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
9150 final PhylogenyNode n22 = PhylogenyNode
9151 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9152 if ( !n22.getName().equals( "n22/PIG" ) ) {
9155 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
9158 final PhylogenyNode n23 = PhylogenyNode
9159 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9160 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
9163 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
9166 final PhylogenyNode a = PhylogenyNode
9167 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9168 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9171 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
9174 final PhylogenyNode c1 = PhylogenyNode
9175 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
9176 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9177 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
9180 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
9183 final PhylogenyNode c2 = PhylogenyNode
9184 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
9185 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9186 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
9189 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
9192 final PhylogenyNode e3 = PhylogenyNode
9193 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9194 if ( !e3.getName().equals( "n10_RAT~" ) ) {
9197 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
9200 final PhylogenyNode n11 = PhylogenyNode
9201 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
9202 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9203 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
9206 if ( n11.getDistanceToParent() != 0.4 ) {
9209 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
9212 final PhylogenyNode n12 = PhylogenyNode
9213 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
9214 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9215 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
9218 if ( n12.getDistanceToParent() != 0.4 ) {
9221 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
9224 final PhylogenyNode o = PhylogenyNode
9225 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9226 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
9229 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
9232 if ( n1.getName().compareTo( "" ) != 0 ) {
9235 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9238 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9241 if ( n2.getName().compareTo( "" ) != 0 ) {
9244 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9247 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9250 final PhylogenyNode n00 = PhylogenyNode
9251 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
9252 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
9255 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
9258 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
9259 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
9262 final PhylogenyNode n13 = PhylogenyNode
9263 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9264 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
9267 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
9270 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9273 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9276 final PhylogenyNode n14 = PhylogenyNode
9277 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9278 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
9281 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
9284 final PhylogenyNode n15 = PhylogenyNode
9285 .createInstanceFromNhxString( "something_wicked[123]",
9286 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9287 if ( !n15.getName().equals( "something_wicked" ) ) {
9290 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
9293 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
9296 final PhylogenyNode n16 = PhylogenyNode
9297 .createInstanceFromNhxString( "something_wicked2[9]",
9298 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9299 if ( !n16.getName().equals( "something_wicked2" ) ) {
9302 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
9305 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
9308 final PhylogenyNode n17 = PhylogenyNode
9309 .createInstanceFromNhxString( "something_wicked3[a]",
9310 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9311 if ( !n17.getName().equals( "something_wicked3" ) ) {
9314 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
9317 final PhylogenyNode n18 = PhylogenyNode
9318 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9319 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
9322 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
9325 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
9328 final PhylogenyNode n19 = PhylogenyNode
9329 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9330 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9333 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9336 final PhylogenyNode n30 = PhylogenyNode
9337 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9338 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9339 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9342 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9345 final PhylogenyNode n31 = PhylogenyNode
9346 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9347 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9348 if ( n31.getNodeData().isHasTaxonomy() ) {
9351 final PhylogenyNode n32 = PhylogenyNode
9352 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9353 if ( n32.getNodeData().isHasTaxonomy() ) {
9356 final PhylogenyNode n40 = PhylogenyNode
9357 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9358 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9361 final PhylogenyNode n41 = PhylogenyNode
9362 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9363 if ( n41.getNodeData().isHasTaxonomy() ) {
9366 final PhylogenyNode n42 = PhylogenyNode
9367 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9368 if ( n42.getNodeData().isHasTaxonomy() ) {
9371 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9372 NHXParser.TAXONOMY_EXTRACTION.NO );
9373 if ( n43.getNodeData().isHasTaxonomy() ) {
9376 final PhylogenyNode n44 = PhylogenyNode
9377 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9378 if ( n44.getNodeData().isHasTaxonomy() ) {
9382 catch ( final Exception e ) {
9383 e.printStackTrace( System.out );
9389 private static boolean testNHXParsing() {
9391 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9392 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9393 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9396 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]";
9397 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9398 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9401 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]";
9402 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9403 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9406 final Phylogeny[] p3 = factory
9407 .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]",
9409 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9412 final Phylogeny[] p4 = factory
9413 .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(]",
9415 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9418 final Phylogeny[] p5 = factory
9419 .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(((]",
9421 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9424 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)";
9425 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)";
9426 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9427 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9430 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)))";
9431 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)))";
9432 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9433 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9436 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]) ))[,,, ])))))))";
9437 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9438 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9439 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9442 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9443 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9446 final Phylogeny p10 = factory
9447 .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]",
9448 new NHXParser() )[ 0 ];
9449 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9452 final Phylogeny p11 = factory
9453 .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]",
9454 new NHXParser() )[ 0 ];
9455 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9459 catch ( final Exception e ) {
9460 e.printStackTrace( System.out );
9466 private static boolean testNHXParsingMB() {
9468 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9469 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9470 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9471 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9472 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9473 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9474 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9475 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9476 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9477 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9478 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9481 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9484 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9485 0.1100000000000000e+00 ) ) {
9488 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9491 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9494 final Phylogeny p2 = factory
9495 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9496 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9497 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9498 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9499 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9500 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9501 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9502 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9503 + "7.369400000000000e-02}])",
9504 new NHXParser() )[ 0 ];
9505 if ( p2.getNode( "1" ) == null ) {
9508 if ( p2.getNode( "2" ) == null ) {
9512 catch ( final Exception e ) {
9513 e.printStackTrace( System.out );
9520 private static boolean testNHXParsingQuotes() {
9522 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9523 final NHXParser p = new NHXParser();
9524 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9525 if ( phylogenies_0.length != 5 ) {
9528 final Phylogeny phy = phylogenies_0[ 4 ];
9529 if ( phy.getNumberOfExternalNodes() != 7 ) {
9532 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9535 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9538 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9539 .getScientificName().equals( "hsapiens" ) ) {
9542 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9545 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9548 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9551 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9554 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9557 final NHXParser p1p = new NHXParser();
9558 p1p.setIgnoreQuotes( true );
9559 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9560 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9563 final NHXParser p2p = new NHXParser();
9564 p1p.setIgnoreQuotes( false );
9565 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9566 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9569 final NHXParser p3p = new NHXParser();
9570 p3p.setIgnoreQuotes( false );
9571 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9572 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9575 final NHXParser p4p = new NHXParser();
9576 p4p.setIgnoreQuotes( false );
9577 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9578 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9581 final Phylogeny p10 = factory
9582 .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]",
9583 new NHXParser() )[ 0 ];
9584 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]";
9585 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9588 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9589 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9592 final Phylogeny p12 = factory
9593 .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]",
9594 new NHXParser() )[ 0 ];
9595 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]";
9596 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9599 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9600 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9603 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;";
9604 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9607 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9608 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9612 catch ( final Exception e ) {
9613 e.printStackTrace( System.out );
9619 private static boolean testNodeRemoval() {
9621 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9622 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9623 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9624 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9627 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9628 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9629 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9632 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9633 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9634 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9638 catch ( final Exception e ) {
9639 e.printStackTrace( System.out );
9645 private static boolean testPhylogenyBranch() {
9647 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9648 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9649 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9650 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9651 if ( !a1b1.equals( a1b1 ) ) {
9654 if ( !a1b1.equals( b1a1 ) ) {
9657 if ( !b1a1.equals( a1b1 ) ) {
9660 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9661 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9662 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9663 if ( a1_b1.equals( b1_a1 ) ) {
9666 if ( a1_b1.equals( a1_b1_ ) ) {
9669 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9670 if ( !a1_b1.equals( b1_a1_ ) ) {
9673 if ( a1_b1_.equals( b1_a1_ ) ) {
9676 if ( !a1_b1_.equals( b1_a1 ) ) {
9680 catch ( final Exception e ) {
9681 e.printStackTrace( System.out );
9687 private static boolean testPhyloXMLparsingOfDistributionElement() {
9689 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9690 PhyloXmlParser xml_parser = null;
9692 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9694 catch ( final Exception e ) {
9695 // Do nothing -- means were not running from jar.
9697 if ( xml_parser == null ) {
9698 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9699 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9700 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9703 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9706 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9708 if ( xml_parser.getErrorCount() > 0 ) {
9709 System.out.println( xml_parser.getErrorMessages().toString() );
9712 if ( phylogenies_0.length != 1 ) {
9715 final Phylogeny t1 = phylogenies_0[ 0 ];
9716 PhylogenyNode n = null;
9717 Distribution d = null;
9718 n = t1.getNode( "root node" );
9719 if ( !n.getNodeData().isHasDistribution() ) {
9722 if ( n.getNodeData().getDistributions().size() != 1 ) {
9725 d = n.getNodeData().getDistribution();
9726 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9729 if ( d.getPoints().size() != 1 ) {
9732 if ( d.getPolygons() != null ) {
9735 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9738 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9741 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9744 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9747 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9750 n = t1.getNode( "node a" );
9751 if ( !n.getNodeData().isHasDistribution() ) {
9754 if ( n.getNodeData().getDistributions().size() != 2 ) {
9757 d = n.getNodeData().getDistribution( 1 );
9758 if ( !d.getDesc().equals( "San Diego" ) ) {
9761 if ( d.getPoints().size() != 1 ) {
9764 if ( d.getPolygons() != null ) {
9767 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9770 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9773 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9776 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9779 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9782 n = t1.getNode( "node bb" );
9783 if ( !n.getNodeData().isHasDistribution() ) {
9786 if ( n.getNodeData().getDistributions().size() != 1 ) {
9789 d = n.getNodeData().getDistribution( 0 );
9790 if ( d.getPoints().size() != 3 ) {
9793 if ( d.getPolygons().size() != 2 ) {
9796 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9799 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9802 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9805 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9808 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9811 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9814 Polygon p = d.getPolygons().get( 0 );
9815 if ( p.getPoints().size() != 3 ) {
9818 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9821 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9824 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9827 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9830 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9833 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9836 p = d.getPolygons().get( 1 );
9837 if ( p.getPoints().size() != 3 ) {
9840 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9843 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9846 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9850 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9851 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9852 if ( rt.length != 1 ) {
9855 final Phylogeny t1_rt = rt[ 0 ];
9856 n = t1_rt.getNode( "root node" );
9857 if ( !n.getNodeData().isHasDistribution() ) {
9860 if ( n.getNodeData().getDistributions().size() != 1 ) {
9863 d = n.getNodeData().getDistribution();
9864 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9867 if ( d.getPoints().size() != 1 ) {
9870 if ( d.getPolygons() != null ) {
9873 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9876 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9879 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9882 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9885 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9888 n = t1_rt.getNode( "node a" );
9889 if ( !n.getNodeData().isHasDistribution() ) {
9892 if ( n.getNodeData().getDistributions().size() != 2 ) {
9895 d = n.getNodeData().getDistribution( 1 );
9896 if ( !d.getDesc().equals( "San Diego" ) ) {
9899 if ( d.getPoints().size() != 1 ) {
9902 if ( d.getPolygons() != null ) {
9905 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9908 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9911 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9914 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9917 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9920 n = t1_rt.getNode( "node bb" );
9921 if ( !n.getNodeData().isHasDistribution() ) {
9924 if ( n.getNodeData().getDistributions().size() != 1 ) {
9927 d = n.getNodeData().getDistribution( 0 );
9928 if ( d.getPoints().size() != 3 ) {
9931 if ( d.getPolygons().size() != 2 ) {
9934 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9937 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9940 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9943 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9946 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9949 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9952 p = d.getPolygons().get( 0 );
9953 if ( p.getPoints().size() != 3 ) {
9956 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9959 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9962 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9965 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9968 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9971 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9974 p = d.getPolygons().get( 1 );
9975 if ( p.getPoints().size() != 3 ) {
9978 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9981 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9984 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9988 catch ( final Exception e ) {
9989 e.printStackTrace( System.out );
9995 private static boolean testPostOrderIterator() {
9997 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9998 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9999 PhylogenyNodeIterator it0;
10000 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
10003 for( it0.reset(); it0.hasNext(); ) {
10006 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10007 final PhylogenyNodeIterator it = t1.iteratorPostorder();
10008 if ( !it.next().getName().equals( "A" ) ) {
10011 if ( !it.next().getName().equals( "B" ) ) {
10014 if ( !it.next().getName().equals( "ab" ) ) {
10017 if ( !it.next().getName().equals( "C" ) ) {
10020 if ( !it.next().getName().equals( "D" ) ) {
10023 if ( !it.next().getName().equals( "cd" ) ) {
10026 if ( !it.next().getName().equals( "abcd" ) ) {
10029 if ( !it.next().getName().equals( "E" ) ) {
10032 if ( !it.next().getName().equals( "F" ) ) {
10035 if ( !it.next().getName().equals( "ef" ) ) {
10038 if ( !it.next().getName().equals( "G" ) ) {
10041 if ( !it.next().getName().equals( "H" ) ) {
10044 if ( !it.next().getName().equals( "gh" ) ) {
10047 if ( !it.next().getName().equals( "efgh" ) ) {
10050 if ( !it.next().getName().equals( "r" ) ) {
10053 if ( it.hasNext() ) {
10057 catch ( final Exception e ) {
10058 e.printStackTrace( System.out );
10064 private static boolean testPreOrderIterator() {
10066 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10067 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10068 PhylogenyNodeIterator it0;
10069 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
10072 for( it0.reset(); it0.hasNext(); ) {
10075 PhylogenyNodeIterator it = t0.iteratorPreorder();
10076 if ( !it.next().getName().equals( "r" ) ) {
10079 if ( !it.next().getName().equals( "ab" ) ) {
10082 if ( !it.next().getName().equals( "A" ) ) {
10085 if ( !it.next().getName().equals( "B" ) ) {
10088 if ( !it.next().getName().equals( "cd" ) ) {
10091 if ( !it.next().getName().equals( "C" ) ) {
10094 if ( !it.next().getName().equals( "D" ) ) {
10097 if ( it.hasNext() ) {
10100 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10101 it = t1.iteratorPreorder();
10102 if ( !it.next().getName().equals( "r" ) ) {
10105 if ( !it.next().getName().equals( "abcd" ) ) {
10108 if ( !it.next().getName().equals( "ab" ) ) {
10111 if ( !it.next().getName().equals( "A" ) ) {
10114 if ( !it.next().getName().equals( "B" ) ) {
10117 if ( !it.next().getName().equals( "cd" ) ) {
10120 if ( !it.next().getName().equals( "C" ) ) {
10123 if ( !it.next().getName().equals( "D" ) ) {
10126 if ( !it.next().getName().equals( "efgh" ) ) {
10129 if ( !it.next().getName().equals( "ef" ) ) {
10132 if ( !it.next().getName().equals( "E" ) ) {
10135 if ( !it.next().getName().equals( "F" ) ) {
10138 if ( !it.next().getName().equals( "gh" ) ) {
10141 if ( !it.next().getName().equals( "G" ) ) {
10144 if ( !it.next().getName().equals( "H" ) ) {
10147 if ( it.hasNext() ) {
10151 catch ( final Exception e ) {
10152 e.printStackTrace( System.out );
10158 private static boolean testPropertiesMap() {
10160 final PropertiesMap pm = new PropertiesMap();
10161 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10162 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10163 final Property p2 = new Property( "something:else",
10165 "improbable:research",
10168 pm.addProperty( p0 );
10169 pm.addProperty( p1 );
10170 pm.addProperty( p2 );
10171 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
10174 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
10177 if ( pm.getProperties().size() != 3 ) {
10180 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
10183 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10186 if ( pm.getProperties().size() != 3 ) {
10189 pm.removeProperty( "dimensions:diameter" );
10190 if ( pm.getProperties().size() != 2 ) {
10193 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
10196 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10200 catch ( final Exception e ) {
10201 e.printStackTrace( System.out );
10207 private static boolean testProteinId() {
10209 final ProteinId id1 = new ProteinId( "a" );
10210 final ProteinId id2 = new ProteinId( "a" );
10211 final ProteinId id3 = new ProteinId( "A" );
10212 final ProteinId id4 = new ProteinId( "b" );
10213 if ( !id1.equals( id1 ) ) {
10216 if ( id1.getId().equals( "x" ) ) {
10219 if ( id1.getId().equals( null ) ) {
10222 if ( !id1.equals( id2 ) ) {
10225 if ( id1.equals( id3 ) ) {
10228 if ( id1.hashCode() != id1.hashCode() ) {
10231 if ( id1.hashCode() != id2.hashCode() ) {
10234 if ( id1.hashCode() == id3.hashCode() ) {
10237 if ( id1.compareTo( id1 ) != 0 ) {
10240 if ( id1.compareTo( id2 ) != 0 ) {
10243 if ( id1.compareTo( id3 ) != 0 ) {
10246 if ( id1.compareTo( id4 ) >= 0 ) {
10249 if ( id4.compareTo( id1 ) <= 0 ) {
10252 if ( !id4.getId().equals( "b" ) ) {
10255 final ProteinId id5 = new ProteinId( " C " );
10256 if ( !id5.getId().equals( "C" ) ) {
10259 if ( id5.equals( id1 ) ) {
10263 catch ( final Exception e ) {
10264 e.printStackTrace( System.out );
10270 private static boolean testReIdMethods() {
10272 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10273 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
10274 final long count = PhylogenyNode.getNodeCount();
10275 p.levelOrderReID();
10276 if ( p.getNode( "r" ).getId() != count ) {
10279 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
10282 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
10285 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
10288 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
10291 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
10294 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
10297 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
10300 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
10303 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
10306 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
10309 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
10312 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
10315 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
10318 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
10322 catch ( final Exception e ) {
10323 e.printStackTrace( System.out );
10329 private static boolean testRerooting() {
10331 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10332 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",
10333 new NHXParser() )[ 0 ];
10334 if ( !t1.isRooted() ) {
10337 t1.reRoot( t1.getNode( "D" ) );
10338 t1.reRoot( t1.getNode( "CD" ) );
10339 t1.reRoot( t1.getNode( "A" ) );
10340 t1.reRoot( t1.getNode( "B" ) );
10341 t1.reRoot( t1.getNode( "AB" ) );
10342 t1.reRoot( t1.getNode( "D" ) );
10343 t1.reRoot( t1.getNode( "C" ) );
10344 t1.reRoot( t1.getNode( "CD" ) );
10345 t1.reRoot( t1.getNode( "A" ) );
10346 t1.reRoot( t1.getNode( "B" ) );
10347 t1.reRoot( t1.getNode( "AB" ) );
10348 t1.reRoot( t1.getNode( "D" ) );
10349 t1.reRoot( t1.getNode( "D" ) );
10350 t1.reRoot( t1.getNode( "C" ) );
10351 t1.reRoot( t1.getNode( "A" ) );
10352 t1.reRoot( t1.getNode( "B" ) );
10353 t1.reRoot( t1.getNode( "AB" ) );
10354 t1.reRoot( t1.getNode( "C" ) );
10355 t1.reRoot( t1.getNode( "D" ) );
10356 t1.reRoot( t1.getNode( "CD" ) );
10357 t1.reRoot( t1.getNode( "D" ) );
10358 t1.reRoot( t1.getNode( "A" ) );
10359 t1.reRoot( t1.getNode( "B" ) );
10360 t1.reRoot( t1.getNode( "AB" ) );
10361 t1.reRoot( t1.getNode( "C" ) );
10362 t1.reRoot( t1.getNode( "D" ) );
10363 t1.reRoot( t1.getNode( "CD" ) );
10364 t1.reRoot( t1.getNode( "D" ) );
10365 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10368 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10371 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10374 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10377 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10380 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10383 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",
10384 new NHXParser() )[ 0 ];
10385 t2.reRoot( t2.getNode( "A" ) );
10386 t2.reRoot( t2.getNode( "D" ) );
10387 t2.reRoot( t2.getNode( "ABC" ) );
10388 t2.reRoot( t2.getNode( "A" ) );
10389 t2.reRoot( t2.getNode( "B" ) );
10390 t2.reRoot( t2.getNode( "D" ) );
10391 t2.reRoot( t2.getNode( "C" ) );
10392 t2.reRoot( t2.getNode( "ABC" ) );
10393 t2.reRoot( t2.getNode( "A" ) );
10394 t2.reRoot( t2.getNode( "B" ) );
10395 t2.reRoot( t2.getNode( "AB" ) );
10396 t2.reRoot( t2.getNode( "AB" ) );
10397 t2.reRoot( t2.getNode( "D" ) );
10398 t2.reRoot( t2.getNode( "C" ) );
10399 t2.reRoot( t2.getNode( "B" ) );
10400 t2.reRoot( t2.getNode( "AB" ) );
10401 t2.reRoot( t2.getNode( "D" ) );
10402 t2.reRoot( t2.getNode( "D" ) );
10403 t2.reRoot( t2.getNode( "ABC" ) );
10404 t2.reRoot( t2.getNode( "A" ) );
10405 t2.reRoot( t2.getNode( "B" ) );
10406 t2.reRoot( t2.getNode( "AB" ) );
10407 t2.reRoot( t2.getNode( "D" ) );
10408 t2.reRoot( t2.getNode( "C" ) );
10409 t2.reRoot( t2.getNode( "ABC" ) );
10410 t2.reRoot( t2.getNode( "A" ) );
10411 t2.reRoot( t2.getNode( "B" ) );
10412 t2.reRoot( t2.getNode( "AB" ) );
10413 t2.reRoot( t2.getNode( "D" ) );
10414 t2.reRoot( t2.getNode( "D" ) );
10415 t2.reRoot( t2.getNode( "C" ) );
10416 t2.reRoot( t2.getNode( "A" ) );
10417 t2.reRoot( t2.getNode( "B" ) );
10418 t2.reRoot( t2.getNode( "AB" ) );
10419 t2.reRoot( t2.getNode( "C" ) );
10420 t2.reRoot( t2.getNode( "D" ) );
10421 t2.reRoot( t2.getNode( "ABC" ) );
10422 t2.reRoot( t2.getNode( "D" ) );
10423 t2.reRoot( t2.getNode( "A" ) );
10424 t2.reRoot( t2.getNode( "B" ) );
10425 t2.reRoot( t2.getNode( "AB" ) );
10426 t2.reRoot( t2.getNode( "C" ) );
10427 t2.reRoot( t2.getNode( "D" ) );
10428 t2.reRoot( t2.getNode( "ABC" ) );
10429 t2.reRoot( t2.getNode( "D" ) );
10430 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10433 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10436 t2.reRoot( t2.getNode( "ABC" ) );
10437 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10440 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10443 t2.reRoot( t2.getNode( "AB" ) );
10444 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10447 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10450 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10453 t2.reRoot( t2.getNode( "AB" ) );
10454 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10457 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10460 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10463 t2.reRoot( t2.getNode( "D" ) );
10464 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10467 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10470 t2.reRoot( t2.getNode( "ABC" ) );
10471 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10474 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10477 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10478 new NHXParser() )[ 0 ];
10479 t3.reRoot( t3.getNode( "B" ) );
10480 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10483 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10486 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10489 t3.reRoot( t3.getNode( "B" ) );
10490 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10493 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10496 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10499 t3.reRoot( t3.getRoot() );
10500 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10503 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10506 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10510 catch ( final Exception e ) {
10511 e.printStackTrace( System.out );
10517 private static boolean testSDIse() {
10519 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10520 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10521 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10522 gene1.setRooted( true );
10523 species1.setRooted( true );
10524 final SDI sdi = new SDI( gene1, species1 );
10525 if ( !gene1.getRoot().isDuplication() ) {
10528 final Phylogeny species2 = factory
10529 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10530 new NHXParser() )[ 0 ];
10531 final Phylogeny gene2 = factory
10532 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10533 new NHXParser() )[ 0 ];
10534 species2.setRooted( true );
10535 gene2.setRooted( true );
10536 final SDI sdi2 = new SDI( gene2, species2 );
10537 if ( sdi2.getDuplicationsSum() != 0 ) {
10540 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10543 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10546 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10549 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10552 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10555 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10558 final Phylogeny species3 = factory
10559 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10560 new NHXParser() )[ 0 ];
10561 final Phylogeny gene3 = factory
10562 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10563 new NHXParser() )[ 0 ];
10564 species3.setRooted( true );
10565 gene3.setRooted( true );
10566 final SDI sdi3 = new SDI( gene3, species3 );
10567 if ( sdi3.getDuplicationsSum() != 1 ) {
10570 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10573 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10576 final Phylogeny species4 = factory
10577 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10578 new NHXParser() )[ 0 ];
10579 final Phylogeny gene4 = factory
10580 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10581 new NHXParser() )[ 0 ];
10582 species4.setRooted( true );
10583 gene4.setRooted( true );
10584 final SDI sdi4 = new SDI( gene4, species4 );
10585 if ( sdi4.getDuplicationsSum() != 1 ) {
10588 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10591 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10594 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10597 if ( species4.getNumberOfExternalNodes() != 6 ) {
10600 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10603 final Phylogeny species5 = factory
10604 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10605 new NHXParser() )[ 0 ];
10606 final Phylogeny gene5 = factory
10607 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10608 new NHXParser() )[ 0 ];
10609 species5.setRooted( true );
10610 gene5.setRooted( true );
10611 final SDI sdi5 = new SDI( gene5, species5 );
10612 if ( sdi5.getDuplicationsSum() != 2 ) {
10615 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10618 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10621 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10624 if ( species5.getNumberOfExternalNodes() != 6 ) {
10627 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10630 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10631 // Conjecture for Comparing Molecular Phylogenies"
10632 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10633 final Phylogeny species6 = factory
10634 .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,"
10635 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10636 new NHXParser() )[ 0 ];
10637 final Phylogeny gene6 = factory
10638 .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,"
10639 + "((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,"
10640 + "(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;",
10641 new NHXParser() )[ 0 ];
10642 species6.setRooted( true );
10643 gene6.setRooted( true );
10644 final SDI sdi6 = new SDI( gene6, species6 );
10645 if ( sdi6.getDuplicationsSum() != 3 ) {
10648 if ( !gene6.getNode( "r" ).isDuplication() ) {
10651 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10654 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10657 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10660 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10663 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10666 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10669 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10672 sdi6.computeMappingCostL();
10673 if ( sdi6.computeMappingCostL() != 17 ) {
10676 if ( species6.getNumberOfExternalNodes() != 9 ) {
10679 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10682 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10683 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10684 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10685 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10686 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10687 species7.setRooted( true );
10688 final Phylogeny gene7_1 = Test
10689 .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])" );
10690 gene7_1.setRooted( true );
10691 final SDI sdi7 = new SDI( gene7_1, species7 );
10692 if ( sdi7.getDuplicationsSum() != 0 ) {
10695 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10698 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10701 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10704 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10707 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10710 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10713 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10716 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10719 final Phylogeny gene7_2 = Test
10720 .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])" );
10721 gene7_2.setRooted( true );
10722 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10723 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10726 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10729 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10732 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10735 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10738 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10741 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10744 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10747 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10750 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10754 catch ( final Exception e ) {
10760 private static boolean testSDIunrooted() {
10762 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10763 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10764 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10765 final Iterator<PhylogenyBranch> iter = l.iterator();
10766 PhylogenyBranch br = iter.next();
10767 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10770 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10774 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10777 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10781 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10784 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10788 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10791 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10795 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10798 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10802 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10805 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10809 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10812 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10816 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10819 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10823 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10826 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10830 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10833 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10837 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10840 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10844 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10847 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10851 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10854 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10858 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10861 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10865 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10868 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10871 if ( iter.hasNext() ) {
10874 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10875 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10876 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10878 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10881 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10885 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10888 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10892 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10895 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10898 if ( iter1.hasNext() ) {
10901 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10902 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10903 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10905 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10908 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10912 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10915 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10919 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10922 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10925 if ( iter2.hasNext() ) {
10928 final Phylogeny species0 = factory
10929 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10930 new NHXParser() )[ 0 ];
10931 final Phylogeny gene1 = factory
10932 .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])",
10933 new NHXParser() )[ 0 ];
10934 species0.setRooted( true );
10935 gene1.setRooted( true );
10936 final SDIR sdi_unrooted = new SDIR();
10937 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10938 if ( sdi_unrooted.getCount() != 1 ) {
10941 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10944 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10947 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10950 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10953 final Phylogeny gene2 = factory
10954 .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])",
10955 new NHXParser() )[ 0 ];
10956 gene2.setRooted( true );
10957 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10958 if ( sdi_unrooted.getCount() != 1 ) {
10961 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10964 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10967 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10970 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10973 final Phylogeny species6 = factory
10974 .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,"
10975 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10976 new NHXParser() )[ 0 ];
10977 final Phylogeny gene6 = factory
10978 .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],"
10979 + "(((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],"
10980 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10981 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10982 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10983 new NHXParser() )[ 0 ];
10984 species6.setRooted( true );
10985 gene6.setRooted( true );
10986 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10987 if ( sdi_unrooted.getCount() != 1 ) {
10990 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10993 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10996 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10999 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11002 if ( !p6[ 0 ].getRoot().isDuplication() ) {
11005 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11008 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11011 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
11014 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11017 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
11020 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
11023 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11027 final Phylogeny species7 = factory
11028 .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,"
11029 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11030 new NHXParser() )[ 0 ];
11031 final Phylogeny gene7 = factory
11032 .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],"
11033 + "(((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],"
11034 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11035 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11036 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11037 new NHXParser() )[ 0 ];
11038 species7.setRooted( true );
11039 gene7.setRooted( true );
11040 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
11041 if ( sdi_unrooted.getCount() != 1 ) {
11044 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11047 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11050 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11053 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
11056 if ( !p7[ 0 ].getRoot().isDuplication() ) {
11059 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11062 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11065 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
11068 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11071 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
11074 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
11077 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11081 final Phylogeny species8 = factory
11082 .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,"
11083 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11084 new NHXParser() )[ 0 ];
11085 final Phylogeny gene8 = factory
11086 .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],"
11087 + "(((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],"
11088 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11089 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11090 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11091 new NHXParser() )[ 0 ];
11092 species8.setRooted( true );
11093 gene8.setRooted( true );
11094 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
11095 if ( sdi_unrooted.getCount() != 1 ) {
11098 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11101 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11104 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11107 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11110 if ( !p8[ 0 ].getRoot().isDuplication() ) {
11113 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11116 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11119 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
11122 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11125 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
11128 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
11131 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11136 catch ( final Exception e ) {
11137 e.printStackTrace( System.out );
11143 private static boolean testSequenceDbWsTools1() {
11145 final PhylogenyNode n = new PhylogenyNode();
11146 n.setName( "NP_001025424" );
11147 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11148 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11149 || !acc.getValue().equals( "NP_001025424" ) ) {
11152 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11153 acc = SequenceDbWsTools.obtainSeqAccession( n );
11154 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11155 || !acc.getValue().equals( "NP_001025424" ) ) {
11158 n.setName( "NP_001025424.1" );
11159 acc = SequenceDbWsTools.obtainSeqAccession( n );
11160 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11161 || !acc.getValue().equals( "NP_001025424" ) ) {
11164 n.setName( "NM_001030253" );
11165 acc = SequenceDbWsTools.obtainSeqAccession( n );
11166 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11167 || !acc.getValue().equals( "NM_001030253" ) ) {
11170 n.setName( "BCL2_HUMAN" );
11171 acc = SequenceDbWsTools.obtainSeqAccession( n );
11172 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11173 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11174 System.out.println( acc.toString() );
11177 n.setName( "P10415" );
11178 acc = SequenceDbWsTools.obtainSeqAccession( n );
11179 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11180 || !acc.getValue().equals( "P10415" ) ) {
11181 System.out.println( acc.toString() );
11184 n.setName( " P10415 " );
11185 acc = SequenceDbWsTools.obtainSeqAccession( n );
11186 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11187 || !acc.getValue().equals( "P10415" ) ) {
11188 System.out.println( acc.toString() );
11191 n.setName( "_P10415|" );
11192 acc = SequenceDbWsTools.obtainSeqAccession( n );
11193 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11194 || !acc.getValue().equals( "P10415" ) ) {
11195 System.out.println( acc.toString() );
11198 n.setName( "AY695820" );
11199 acc = SequenceDbWsTools.obtainSeqAccession( n );
11200 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11201 || !acc.getValue().equals( "AY695820" ) ) {
11202 System.out.println( acc.toString() );
11205 n.setName( "_AY695820_" );
11206 acc = SequenceDbWsTools.obtainSeqAccession( n );
11207 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11208 || !acc.getValue().equals( "AY695820" ) ) {
11209 System.out.println( acc.toString() );
11212 n.setName( "AAA59452" );
11213 acc = SequenceDbWsTools.obtainSeqAccession( n );
11214 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11215 || !acc.getValue().equals( "AAA59452" ) ) {
11216 System.out.println( acc.toString() );
11219 n.setName( "_AAA59452_" );
11220 acc = SequenceDbWsTools.obtainSeqAccession( n );
11221 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11222 || !acc.getValue().equals( "AAA59452" ) ) {
11223 System.out.println( acc.toString() );
11226 n.setName( "AAA59452.1" );
11227 acc = SequenceDbWsTools.obtainSeqAccession( n );
11228 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11229 || !acc.getValue().equals( "AAA59452.1" ) ) {
11230 System.out.println( acc.toString() );
11233 n.setName( "_AAA59452.1_" );
11234 acc = SequenceDbWsTools.obtainSeqAccession( n );
11235 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11236 || !acc.getValue().equals( "AAA59452.1" ) ) {
11237 System.out.println( acc.toString() );
11240 n.setName( "GI:94894583" );
11241 acc = SequenceDbWsTools.obtainSeqAccession( n );
11242 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11243 || !acc.getValue().equals( "94894583" ) ) {
11244 System.out.println( acc.toString() );
11247 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11248 acc = SequenceDbWsTools.obtainSeqAccession( n );
11249 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11250 || !acc.getValue().equals( "71845847" ) ) {
11251 System.out.println( acc.toString() );
11254 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11255 acc = SequenceDbWsTools.obtainSeqAccession( n );
11256 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11257 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11258 System.out.println( acc.toString() );
11262 catch ( final Exception e ) {
11268 private static boolean testSequenceDbWsTools2() {
11270 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11271 SequenceDbWsTools.obtainSeqInformation( n1 );
11272 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11275 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11278 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11281 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11284 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11285 SequenceDbWsTools.obtainSeqInformation( n2 );
11286 if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
11289 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11292 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11295 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11298 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11299 SequenceDbWsTools.obtainSeqInformation( n3 );
11300 if ( !n3.getNodeData().getSequence().getName()
11301 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11304 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11307 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11310 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11314 catch ( final IOException e ) {
11315 System.out.println();
11316 System.out.println( "the following might be due to absence internet connection:" );
11317 e.printStackTrace( System.out );
11320 catch ( final Exception e ) {
11321 e.printStackTrace();
11327 private static boolean testSequenceIdParsing() {
11329 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11330 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11331 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11332 if ( id != null ) {
11333 System.out.println( "value =" + id.getValue() );
11334 System.out.println( "provider=" + id.getSource() );
11338 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11339 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11340 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11341 if ( id != null ) {
11342 System.out.println( "value =" + id.getValue() );
11343 System.out.println( "provider=" + id.getSource() );
11347 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11348 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11349 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11350 if ( id != null ) {
11351 System.out.println( "value =" + id.getValue() );
11352 System.out.println( "provider=" + id.getSource() );
11356 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11357 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11358 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11359 if ( id != null ) {
11360 System.out.println( "value =" + id.getValue() );
11361 System.out.println( "provider=" + id.getSource() );
11365 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11366 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11367 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11368 if ( id != null ) {
11369 System.out.println( "value =" + id.getValue() );
11370 System.out.println( "provider=" + id.getSource() );
11374 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11375 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11376 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11377 if ( id != null ) {
11378 System.out.println( "value =" + id.getValue() );
11379 System.out.println( "provider=" + id.getSource() );
11383 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11384 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11385 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11386 if ( id != null ) {
11387 System.out.println( "value =" + id.getValue() );
11388 System.out.println( "provider=" + id.getSource() );
11392 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11393 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11394 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11395 if ( id != null ) {
11396 System.out.println( "value =" + id.getValue() );
11397 System.out.println( "provider=" + id.getSource() );
11401 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11402 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11403 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11404 if ( id != null ) {
11405 System.out.println( "value =" + id.getValue() );
11406 System.out.println( "provider=" + id.getSource() );
11410 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11411 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11412 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11413 if ( id != null ) {
11414 System.out.println( "value =" + id.getValue() );
11415 System.out.println( "provider=" + id.getSource() );
11419 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11420 if ( id != null ) {
11421 System.out.println( "value =" + id.getValue() );
11422 System.out.println( "provider=" + id.getSource() );
11425 id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
11426 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11427 || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
11428 if ( id != null ) {
11429 System.out.println( "value =" + id.getValue() );
11430 System.out.println( "provider=" + id.getSource() );
11434 id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
11435 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11436 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11437 if ( id != null ) {
11438 System.out.println( "value =" + id.getValue() );
11439 System.out.println( "provider=" + id.getSource() );
11443 id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
11444 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11445 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11446 if ( id != null ) {
11447 System.out.println( "value =" + id.getValue() );
11448 System.out.println( "provider=" + id.getSource() );
11452 id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
11453 if ( id != null ) {
11454 System.out.println( "value =" + id.getValue() );
11455 System.out.println( "provider=" + id.getSource() );
11459 catch ( final Exception e ) {
11460 e.printStackTrace( System.out );
11466 private static boolean testSequenceWriter() {
11468 final String n = ForesterUtil.LINE_SEPARATOR;
11469 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11472 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11475 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11478 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11481 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11482 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11485 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11486 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11490 catch ( final Exception e ) {
11491 e.printStackTrace();
11497 private static boolean testSpecies() {
11499 final Species s1 = new BasicSpecies( "a" );
11500 final Species s2 = new BasicSpecies( "a" );
11501 final Species s3 = new BasicSpecies( "A" );
11502 final Species s4 = new BasicSpecies( "b" );
11503 if ( !s1.equals( s1 ) ) {
11506 if ( s1.getSpeciesId().equals( "x" ) ) {
11509 if ( s1.getSpeciesId().equals( null ) ) {
11512 if ( !s1.equals( s2 ) ) {
11515 if ( s1.equals( s3 ) ) {
11518 if ( s1.hashCode() != s1.hashCode() ) {
11521 if ( s1.hashCode() != s2.hashCode() ) {
11524 if ( s1.hashCode() == s3.hashCode() ) {
11527 if ( s1.compareTo( s1 ) != 0 ) {
11530 if ( s1.compareTo( s2 ) != 0 ) {
11533 if ( s1.compareTo( s3 ) != 0 ) {
11536 if ( s1.compareTo( s4 ) >= 0 ) {
11539 if ( s4.compareTo( s1 ) <= 0 ) {
11542 if ( !s4.getSpeciesId().equals( "b" ) ) {
11545 final Species s5 = new BasicSpecies( " C " );
11546 if ( !s5.getSpeciesId().equals( "C" ) ) {
11549 if ( s5.equals( s1 ) ) {
11553 catch ( final Exception e ) {
11554 e.printStackTrace( System.out );
11560 private static boolean testSplit() {
11562 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11563 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11564 //Archaeopteryx.createApplication( p0 );
11565 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11566 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11567 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11568 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11569 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11570 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11571 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11572 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11573 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11574 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11575 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11576 // System.out.println( s0.toString() );
11578 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11581 if ( s0.match( query_nodes ) ) {
11584 query_nodes = new HashSet<PhylogenyNode>();
11585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11592 if ( !s0.match( query_nodes ) ) {
11596 query_nodes = new HashSet<PhylogenyNode>();
11597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11600 if ( !s0.match( query_nodes ) ) {
11604 query_nodes = new HashSet<PhylogenyNode>();
11605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11609 if ( !s0.match( query_nodes ) ) {
11613 query_nodes = new HashSet<PhylogenyNode>();
11614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11618 if ( !s0.match( query_nodes ) ) {
11622 query_nodes = new HashSet<PhylogenyNode>();
11623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11626 if ( !s0.match( query_nodes ) ) {
11629 query_nodes = new HashSet<PhylogenyNode>();
11630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11632 if ( !s0.match( query_nodes ) ) {
11635 query_nodes = new HashSet<PhylogenyNode>();
11636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11641 if ( !s0.match( query_nodes ) ) {
11644 query_nodes = new HashSet<PhylogenyNode>();
11645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11648 if ( !s0.match( query_nodes ) ) {
11651 query_nodes = new HashSet<PhylogenyNode>();
11652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11656 if ( !s0.match( query_nodes ) ) {
11659 query_nodes = new HashSet<PhylogenyNode>();
11660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11662 if ( s0.match( query_nodes ) ) {
11665 query_nodes = new HashSet<PhylogenyNode>();
11666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11670 if ( s0.match( query_nodes ) ) {
11673 query_nodes = new HashSet<PhylogenyNode>();
11674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11679 if ( s0.match( query_nodes ) ) {
11682 query_nodes = new HashSet<PhylogenyNode>();
11683 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11686 if ( s0.match( query_nodes ) ) {
11689 query_nodes = new HashSet<PhylogenyNode>();
11690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11691 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11692 if ( s0.match( query_nodes ) ) {
11695 query_nodes = new HashSet<PhylogenyNode>();
11696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11698 if ( s0.match( query_nodes ) ) {
11701 query_nodes = new HashSet<PhylogenyNode>();
11702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11704 if ( s0.match( query_nodes ) ) {
11707 query_nodes = new HashSet<PhylogenyNode>();
11708 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11710 if ( s0.match( query_nodes ) ) {
11713 query_nodes = new HashSet<PhylogenyNode>();
11714 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11715 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11716 if ( s0.match( query_nodes ) ) {
11719 query_nodes = new HashSet<PhylogenyNode>();
11720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11722 if ( s0.match( query_nodes ) ) {
11725 query_nodes = new HashSet<PhylogenyNode>();
11726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11729 if ( s0.match( query_nodes ) ) {
11732 query_nodes = new HashSet<PhylogenyNode>();
11733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11736 if ( s0.match( query_nodes ) ) {
11739 query_nodes = new HashSet<PhylogenyNode>();
11740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11742 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11743 if ( s0.match( query_nodes ) ) {
11746 query_nodes = new HashSet<PhylogenyNode>();
11747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11751 if ( s0.match( query_nodes ) ) {
11755 // query_nodes = new HashSet<PhylogenyNode>();
11756 // query_nodes.add( new PhylogenyNode( "X" ) );
11757 // query_nodes.add( new PhylogenyNode( "Y" ) );
11758 // query_nodes.add( new PhylogenyNode( "A" ) );
11759 // query_nodes.add( new PhylogenyNode( "B" ) );
11760 // query_nodes.add( new PhylogenyNode( "C" ) );
11761 // query_nodes.add( new PhylogenyNode( "D" ) );
11762 // query_nodes.add( new PhylogenyNode( "E" ) );
11763 // query_nodes.add( new PhylogenyNode( "F" ) );
11764 // query_nodes.add( new PhylogenyNode( "G" ) );
11765 // if ( !s0.match( query_nodes ) ) {
11768 // query_nodes = new HashSet<PhylogenyNode>();
11769 // query_nodes.add( new PhylogenyNode( "X" ) );
11770 // query_nodes.add( new PhylogenyNode( "Y" ) );
11771 // query_nodes.add( new PhylogenyNode( "A" ) );
11772 // query_nodes.add( new PhylogenyNode( "B" ) );
11773 // query_nodes.add( new PhylogenyNode( "C" ) );
11774 // if ( !s0.match( query_nodes ) ) {
11778 // query_nodes = new HashSet<PhylogenyNode>();
11779 // query_nodes.add( new PhylogenyNode( "X" ) );
11780 // query_nodes.add( new PhylogenyNode( "Y" ) );
11781 // query_nodes.add( new PhylogenyNode( "D" ) );
11782 // query_nodes.add( new PhylogenyNode( "E" ) );
11783 // query_nodes.add( new PhylogenyNode( "F" ) );
11784 // query_nodes.add( new PhylogenyNode( "G" ) );
11785 // if ( !s0.match( query_nodes ) ) {
11789 // query_nodes = new HashSet<PhylogenyNode>();
11790 // query_nodes.add( new PhylogenyNode( "X" ) );
11791 // query_nodes.add( new PhylogenyNode( "Y" ) );
11792 // query_nodes.add( new PhylogenyNode( "A" ) );
11793 // query_nodes.add( new PhylogenyNode( "B" ) );
11794 // query_nodes.add( new PhylogenyNode( "C" ) );
11795 // query_nodes.add( new PhylogenyNode( "D" ) );
11796 // if ( !s0.match( query_nodes ) ) {
11800 // query_nodes = new HashSet<PhylogenyNode>();
11801 // query_nodes.add( new PhylogenyNode( "X" ) );
11802 // query_nodes.add( new PhylogenyNode( "Y" ) );
11803 // query_nodes.add( new PhylogenyNode( "E" ) );
11804 // query_nodes.add( new PhylogenyNode( "F" ) );
11805 // query_nodes.add( new PhylogenyNode( "G" ) );
11806 // if ( !s0.match( query_nodes ) ) {
11810 // query_nodes = new HashSet<PhylogenyNode>();
11811 // query_nodes.add( new PhylogenyNode( "X" ) );
11812 // query_nodes.add( new PhylogenyNode( "Y" ) );
11813 // query_nodes.add( new PhylogenyNode( "F" ) );
11814 // query_nodes.add( new PhylogenyNode( "G" ) );
11815 // if ( !s0.match( query_nodes ) ) {
11819 query_nodes = new HashSet<PhylogenyNode>();
11820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11821 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11824 if ( s0.match( query_nodes ) ) {
11828 query_nodes = new HashSet<PhylogenyNode>();
11829 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11833 if ( s0.match( query_nodes ) ) {
11836 ///////////////////////////
11838 query_nodes = new HashSet<PhylogenyNode>();
11839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11843 if ( s0.match( query_nodes ) ) {
11847 query_nodes = new HashSet<PhylogenyNode>();
11848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11852 if ( s0.match( query_nodes ) ) {
11856 query_nodes = new HashSet<PhylogenyNode>();
11857 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11861 if ( s0.match( query_nodes ) ) {
11865 query_nodes = new HashSet<PhylogenyNode>();
11866 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11867 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11868 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11870 if ( s0.match( query_nodes ) ) {
11874 query_nodes = new HashSet<PhylogenyNode>();
11875 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11876 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11879 if ( s0.match( query_nodes ) ) {
11883 query_nodes = new HashSet<PhylogenyNode>();
11884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11887 if ( s0.match( query_nodes ) ) {
11891 query_nodes = new HashSet<PhylogenyNode>();
11892 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11893 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11897 if ( s0.match( query_nodes ) ) {
11901 query_nodes = new HashSet<PhylogenyNode>();
11902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11907 if ( s0.match( query_nodes ) ) {
11911 query_nodes = new HashSet<PhylogenyNode>();
11912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11917 if ( s0.match( query_nodes ) ) {
11921 query_nodes = new HashSet<PhylogenyNode>();
11922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11928 if ( s0.match( query_nodes ) ) {
11932 catch ( final Exception e ) {
11933 e.printStackTrace();
11939 private static boolean testSplitStrict() {
11941 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11942 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11943 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11944 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11945 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11946 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11947 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11948 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11949 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11950 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11951 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11952 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11955 if ( s0.match( query_nodes ) ) {
11958 query_nodes = new HashSet<PhylogenyNode>();
11959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11960 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11961 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11962 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11966 if ( !s0.match( query_nodes ) ) {
11970 query_nodes = new HashSet<PhylogenyNode>();
11971 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11974 if ( !s0.match( query_nodes ) ) {
11978 query_nodes = new HashSet<PhylogenyNode>();
11979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11983 if ( !s0.match( query_nodes ) ) {
11987 query_nodes = new HashSet<PhylogenyNode>();
11988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11992 if ( !s0.match( query_nodes ) ) {
11996 query_nodes = new HashSet<PhylogenyNode>();
11997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12000 if ( !s0.match( query_nodes ) ) {
12004 query_nodes = new HashSet<PhylogenyNode>();
12005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12007 if ( !s0.match( query_nodes ) ) {
12011 query_nodes = new HashSet<PhylogenyNode>();
12012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12017 if ( !s0.match( query_nodes ) ) {
12021 query_nodes = new HashSet<PhylogenyNode>();
12022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12025 if ( !s0.match( query_nodes ) ) {
12029 query_nodes = new HashSet<PhylogenyNode>();
12030 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12034 if ( !s0.match( query_nodes ) ) {
12038 query_nodes = new HashSet<PhylogenyNode>();
12039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12041 if ( s0.match( query_nodes ) ) {
12045 query_nodes = new HashSet<PhylogenyNode>();
12046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12050 if ( s0.match( query_nodes ) ) {
12054 query_nodes = new HashSet<PhylogenyNode>();
12055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12060 if ( s0.match( query_nodes ) ) {
12064 query_nodes = new HashSet<PhylogenyNode>();
12065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12068 if ( s0.match( query_nodes ) ) {
12072 query_nodes = new HashSet<PhylogenyNode>();
12073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12075 if ( s0.match( query_nodes ) ) {
12079 query_nodes = new HashSet<PhylogenyNode>();
12080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12082 if ( s0.match( query_nodes ) ) {
12086 query_nodes = new HashSet<PhylogenyNode>();
12087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12089 if ( s0.match( query_nodes ) ) {
12093 query_nodes = new HashSet<PhylogenyNode>();
12094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12096 if ( s0.match( query_nodes ) ) {
12100 query_nodes = new HashSet<PhylogenyNode>();
12101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12103 if ( s0.match( query_nodes ) ) {
12107 query_nodes = new HashSet<PhylogenyNode>();
12108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12110 if ( s0.match( query_nodes ) ) {
12114 query_nodes = new HashSet<PhylogenyNode>();
12115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12118 if ( s0.match( query_nodes ) ) {
12122 query_nodes = new HashSet<PhylogenyNode>();
12123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12124 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12125 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12126 if ( s0.match( query_nodes ) ) {
12130 query_nodes = new HashSet<PhylogenyNode>();
12131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12134 if ( s0.match( query_nodes ) ) {
12138 query_nodes = new HashSet<PhylogenyNode>();
12139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12143 if ( s0.match( query_nodes ) ) {
12147 catch ( final Exception e ) {
12148 e.printStackTrace();
12154 private static boolean testSubtreeDeletion() {
12156 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12157 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12158 t1.deleteSubtree( t1.getNode( "A" ), false );
12159 if ( t1.getNumberOfExternalNodes() != 5 ) {
12162 t1.toNewHampshireX();
12163 t1.deleteSubtree( t1.getNode( "E" ), false );
12164 if ( t1.getNumberOfExternalNodes() != 4 ) {
12167 t1.toNewHampshireX();
12168 t1.deleteSubtree( t1.getNode( "F" ), false );
12169 if ( t1.getNumberOfExternalNodes() != 3 ) {
12172 t1.toNewHampshireX();
12173 t1.deleteSubtree( t1.getNode( "D" ), false );
12174 t1.toNewHampshireX();
12175 if ( t1.getNumberOfExternalNodes() != 3 ) {
12178 t1.deleteSubtree( t1.getNode( "def" ), false );
12179 t1.toNewHampshireX();
12180 if ( t1.getNumberOfExternalNodes() != 2 ) {
12183 t1.deleteSubtree( t1.getNode( "B" ), false );
12184 t1.toNewHampshireX();
12185 if ( t1.getNumberOfExternalNodes() != 1 ) {
12188 t1.deleteSubtree( t1.getNode( "C" ), false );
12189 t1.toNewHampshireX();
12190 if ( t1.getNumberOfExternalNodes() != 1 ) {
12193 t1.deleteSubtree( t1.getNode( "abc" ), false );
12194 t1.toNewHampshireX();
12195 if ( t1.getNumberOfExternalNodes() != 1 ) {
12198 t1.deleteSubtree( t1.getNode( "r" ), false );
12199 if ( t1.getNumberOfExternalNodes() != 0 ) {
12202 if ( !t1.isEmpty() ) {
12205 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12206 t2.deleteSubtree( t2.getNode( "A" ), false );
12207 t2.toNewHampshireX();
12208 if ( t2.getNumberOfExternalNodes() != 5 ) {
12211 t2.deleteSubtree( t2.getNode( "abc" ), false );
12212 t2.toNewHampshireX();
12213 if ( t2.getNumberOfExternalNodes() != 3 ) {
12216 t2.deleteSubtree( t2.getNode( "def" ), false );
12217 t2.toNewHampshireX();
12218 if ( t2.getNumberOfExternalNodes() != 1 ) {
12222 catch ( final Exception e ) {
12223 e.printStackTrace( System.out );
12229 private static boolean testSupportCount() {
12231 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12232 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
12233 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
12234 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
12235 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
12236 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
12237 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
12239 SupportCount.count( t0_1, phylogenies_1, true, false );
12240 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
12241 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
12242 + "(((((A,B),C),D),E),((F,G),X))"
12243 + "(((((A,Y),B),C),D),((F,G),E))"
12244 + "(((((A,B),C),D),E),(F,G))"
12245 + "(((((A,B),C),D),E),(F,G))"
12246 + "(((((A,B),C),D),E),(F,G))"
12247 + "(((((A,B),C),D),E),(F,G),Z)"
12248 + "(((((A,B),C),D),E),(F,G))"
12249 + "((((((A,B),C),D),E),F),G)"
12250 + "(((((X,Y),F,G),E),((A,B),C)),D)",
12252 SupportCount.count( t0_2, phylogenies_2, true, false );
12253 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
12254 while ( it.hasNext() ) {
12255 final PhylogenyNode n = it.next();
12256 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
12260 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
12261 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
12262 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
12263 SupportCount.count( t0_3, phylogenies_3, true, false );
12264 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
12265 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
12268 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
12271 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
12274 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
12277 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
12280 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
12283 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
12286 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
12289 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
12292 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
12295 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12296 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
12297 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
12298 SupportCount.count( t0_4, phylogenies_4, true, false );
12299 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
12300 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
12303 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
12306 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
12309 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
12312 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
12315 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
12318 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
12321 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
12324 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
12327 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
12330 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12331 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12332 double d = SupportCount.compare( b1, a, true, true, true );
12333 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12336 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12337 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12338 d = SupportCount.compare( b2, a, true, true, true );
12339 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12342 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12343 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12344 d = SupportCount.compare( b3, a, true, true, true );
12345 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12348 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12349 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12350 d = SupportCount.compare( b4, a, true, true, false );
12351 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12355 catch ( final Exception e ) {
12356 e.printStackTrace( System.out );
12362 private static boolean testSupportTransfer() {
12364 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12365 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)",
12366 new NHXParser() )[ 0 ];
12367 final Phylogeny p2 = factory
12368 .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 ];
12369 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12372 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12375 support_transfer.moveBranchLengthsToBootstrap( p1 );
12376 support_transfer.transferSupportValues( p1, p2 );
12377 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12380 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12383 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12386 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12389 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12392 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12395 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12398 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12402 catch ( final Exception e ) {
12403 e.printStackTrace( System.out );
12409 private static boolean testTaxonomyExtraction() {
12411 final PhylogenyNode n0 = PhylogenyNode
12412 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12413 if ( n0.getNodeData().isHasTaxonomy() ) {
12416 final PhylogenyNode n1 = PhylogenyNode
12417 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12418 if ( n1.getNodeData().isHasTaxonomy() ) {
12419 System.out.println( n1.toString() );
12422 final PhylogenyNode n2x = PhylogenyNode
12423 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12424 if ( n2x.getNodeData().isHasTaxonomy() ) {
12427 final PhylogenyNode n3 = PhylogenyNode
12428 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12429 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12430 System.out.println( n3.toString() );
12433 final PhylogenyNode n4 = PhylogenyNode
12434 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12435 if ( n4.getNodeData().isHasTaxonomy() ) {
12436 System.out.println( n4.toString() );
12439 final PhylogenyNode n5 = PhylogenyNode
12440 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12441 if ( n5.getNodeData().isHasTaxonomy() ) {
12442 System.out.println( n5.toString() );
12445 final PhylogenyNode n6 = PhylogenyNode
12446 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12447 if ( n6.getNodeData().isHasTaxonomy() ) {
12448 System.out.println( n6.toString() );
12451 final PhylogenyNode n7 = PhylogenyNode
12452 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12453 if ( n7.getNodeData().isHasTaxonomy() ) {
12454 System.out.println( n7.toString() );
12457 final PhylogenyNode n8 = PhylogenyNode
12458 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12459 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12460 System.out.println( n8.toString() );
12463 final PhylogenyNode n9 = PhylogenyNode
12464 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12465 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12466 System.out.println( n9.toString() );
12469 final PhylogenyNode n10x = PhylogenyNode
12470 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12471 if ( n10x.getNodeData().isHasTaxonomy() ) {
12472 System.out.println( n10x.toString() );
12475 final PhylogenyNode n10xx = PhylogenyNode
12476 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12477 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12478 System.out.println( n10xx.toString() );
12481 final PhylogenyNode n10 = PhylogenyNode
12482 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12483 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12484 System.out.println( n10.toString() );
12487 final PhylogenyNode n11 = PhylogenyNode
12488 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12489 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12490 System.out.println( n11.toString() );
12493 final PhylogenyNode n12 = PhylogenyNode
12494 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12495 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12496 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12497 System.out.println( n12.toString() );
12500 final PhylogenyNode n13 = PhylogenyNode
12501 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12502 if ( n13.getNodeData().isHasTaxonomy() ) {
12503 System.out.println( n13.toString() );
12506 final PhylogenyNode n14 = PhylogenyNode
12507 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12508 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12509 System.out.println( n14.toString() );
12512 final PhylogenyNode n15 = PhylogenyNode
12513 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12514 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12515 System.out.println( n15.toString() );
12518 final PhylogenyNode n16 = PhylogenyNode
12519 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12520 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12521 System.out.println( n16.toString() );
12524 final PhylogenyNode n17 = PhylogenyNode
12525 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12526 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12527 System.out.println( n17.toString() );
12530 final PhylogenyNode n18 = PhylogenyNode
12531 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12532 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12533 System.out.println( n18.toString() );
12536 final PhylogenyNode n19 = PhylogenyNode
12537 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12538 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12539 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12540 System.out.println( n19.toString() );
12543 final PhylogenyNode n20 = PhylogenyNode
12544 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12545 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12546 System.out.println( n20.toString() );
12549 final PhylogenyNode n21 = PhylogenyNode
12550 .createInstanceFromNhxString( "Mus musculus musculus K392",
12551 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12552 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12553 System.out.println( n21.toString() );
12556 final PhylogenyNode n23 = PhylogenyNode
12557 .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
12558 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12559 if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12560 System.out.println( n23.toString() );
12563 final PhylogenyNode n24 = PhylogenyNode
12564 .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12565 if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12566 System.out.println( n24.toString() );
12570 final PhylogenyNode n25 = PhylogenyNode
12571 .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
12572 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12573 if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
12574 System.out.println( n25.toString() );
12577 final PhylogenyNode n26 = PhylogenyNode
12578 .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
12579 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12580 if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12581 System.out.println( n26.toString() );
12584 final PhylogenyNode n27 = PhylogenyNode
12585 .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12586 if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12587 System.out.println( n27.toString() );
12591 catch ( final Exception e ) {
12592 e.printStackTrace( System.out );
12598 private static boolean testTreeCopy() {
12600 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12601 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12602 final Phylogeny t1 = t0.copy();
12603 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12606 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12609 t0.deleteSubtree( t0.getNode( "c" ), true );
12610 t0.deleteSubtree( t0.getNode( "a" ), true );
12611 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12612 t0.getNode( "b" ).setName( "Bee" );
12613 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12616 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12619 t0.deleteSubtree( t0.getNode( "e" ), true );
12620 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12621 t0.deleteSubtree( t0.getNode( "d" ), true );
12622 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12626 catch ( final Exception e ) {
12627 e.printStackTrace();
12633 private static boolean testTreeMethods() {
12635 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12636 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12637 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12638 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12639 System.out.println( t0.toNewHampshireX() );
12642 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12643 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12644 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12647 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12650 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12654 catch ( final Exception e ) {
12655 e.printStackTrace( System.out );
12661 private static boolean testUniprotEntryRetrieval() {
12663 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
12664 if ( !entry.getAccession().equals( "P12345" ) ) {
12667 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12670 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12673 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12676 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12679 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12683 .getMolecularSequence()
12684 .getMolecularSequenceAsString()
12685 .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
12686 || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
12687 System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
12691 catch ( final IOException e ) {
12692 System.out.println();
12693 System.out.println( "the following might be due to absence internet connection:" );
12694 e.printStackTrace( System.out );
12697 catch ( final Exception e ) {
12703 private static boolean testUniprotTaxonomySearch() {
12705 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12707 if ( results.size() != 1 ) {
12710 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12713 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12716 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12719 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12722 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12726 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12727 if ( results.size() != 1 ) {
12730 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12733 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12736 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12739 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12742 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12746 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12747 if ( results.size() != 1 ) {
12750 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12753 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12756 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12759 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12762 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12766 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12767 if ( results.size() != 1 ) {
12770 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12773 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12776 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12779 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12782 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12785 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12788 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12791 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12792 .equals( "Nematostella vectensis" ) ) {
12793 System.out.println( results.get( 0 ).getLineage() );
12798 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12799 if ( results.size() != 1 ) {
12802 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12805 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12808 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12811 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12814 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12817 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12818 .equals( "Xenopus tropicalis" ) ) {
12819 System.out.println( results.get( 0 ).getLineage() );
12824 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12825 if ( results.size() != 1 ) {
12828 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12831 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12834 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12837 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12840 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12843 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12844 .equals( "Xenopus tropicalis" ) ) {
12845 System.out.println( results.get( 0 ).getLineage() );
12850 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12851 if ( results.size() != 1 ) {
12854 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12857 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12860 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12863 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12866 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12869 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12870 .equals( "Xenopus tropicalis" ) ) {
12871 System.out.println( results.get( 0 ).getLineage() );
12875 catch ( final IOException e ) {
12876 System.out.println();
12877 System.out.println( "the following might be due to absence internet connection:" );
12878 e.printStackTrace( System.out );
12881 catch ( final Exception e ) {
12887 private static boolean testWabiTxSearch() {
12889 String result = "";
12890 result = TxSearch.searchSimple( "nematostella" );
12891 result = TxSearch.getTxId( "nematostella" );
12892 if ( !result.equals( "45350" ) ) {
12895 result = TxSearch.getTxName( "45350" );
12896 if ( !result.equals( "Nematostella" ) ) {
12899 result = TxSearch.getTxId( "nematostella vectensis" );
12900 if ( !result.equals( "45351" ) ) {
12903 result = TxSearch.getTxName( "45351" );
12904 if ( !result.equals( "Nematostella vectensis" ) ) {
12907 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12908 if ( !result.equals( "536089" ) ) {
12911 result = TxSearch.getTxName( "536089" );
12912 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12915 final List<String> queries = new ArrayList<String>();
12916 queries.add( "Campylobacter coli" );
12917 queries.add( "Escherichia coli" );
12918 queries.add( "Arabidopsis" );
12919 queries.add( "Trichoplax" );
12920 queries.add( "Samanea saman" );
12921 queries.add( "Kluyveromyces marxianus" );
12922 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12923 queries.add( "Bornavirus parrot/PDD/2008" );
12924 final List<RANKS> ranks = new ArrayList<RANKS>();
12925 ranks.add( RANKS.SUPERKINGDOM );
12926 ranks.add( RANKS.KINGDOM );
12927 ranks.add( RANKS.FAMILY );
12928 ranks.add( RANKS.GENUS );
12929 ranks.add( RANKS.TRIBE );
12930 result = TxSearch.searchLineage( queries, ranks );
12931 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12932 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12934 catch ( final Exception e ) {
12935 System.out.println();
12936 System.out.println( "the following might be due to absence internet connection:" );
12937 e.printStackTrace( System.out );