2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
33 import java.util.ArrayList;
34 import java.util.Date;
35 import java.util.HashSet;
36 import java.util.Iterator;
37 import java.util.List;
38 import java.util.Locale;
40 import java.util.SortedSet;
42 import org.forester.application.support_transfer;
43 import org.forester.archaeopteryx.TreePanelUtil;
44 import org.forester.development.DevelopmentTools;
45 import org.forester.evoinference.TestPhylogenyReconstruction;
46 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
47 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
48 import org.forester.go.TestGo;
49 import org.forester.io.parsers.FastaParser;
50 import org.forester.io.parsers.GeneralMsaParser;
51 import org.forester.io.parsers.HmmscanPerDomainTableParser;
52 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
53 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
54 import org.forester.io.parsers.nexus.NexusCharactersParser;
55 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
56 import org.forester.io.parsers.nhx.NHXParser;
57 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
58 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
59 import org.forester.io.parsers.tol.TolParser;
60 import org.forester.io.parsers.util.ParserUtils;
61 import org.forester.io.writers.PhylogenyWriter;
62 import org.forester.io.writers.SequenceWriter;
63 import org.forester.msa.BasicMsa;
64 import org.forester.msa.Mafft;
65 import org.forester.msa.Msa;
66 import org.forester.msa.MsaInferrer;
67 import org.forester.msa.MsaMethods;
68 import org.forester.pccx.TestPccx;
69 import org.forester.phylogeny.Phylogeny;
70 import org.forester.phylogeny.PhylogenyBranch;
71 import org.forester.phylogeny.PhylogenyMethods;
72 import org.forester.phylogeny.PhylogenyNode;
73 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
74 import org.forester.phylogeny.data.Accession;
75 import org.forester.phylogeny.data.Accession.Source;
76 import org.forester.phylogeny.data.BinaryCharacters;
77 import org.forester.phylogeny.data.BranchWidth;
78 import org.forester.phylogeny.data.Confidence;
79 import org.forester.phylogeny.data.Distribution;
80 import org.forester.phylogeny.data.DomainArchitecture;
81 import org.forester.phylogeny.data.Event;
82 import org.forester.phylogeny.data.Identifier;
83 import org.forester.phylogeny.data.PhylogenyData;
84 import org.forester.phylogeny.data.PhylogenyDataUtil;
85 import org.forester.phylogeny.data.Polygon;
86 import org.forester.phylogeny.data.PropertiesMap;
87 import org.forester.phylogeny.data.Property;
88 import org.forester.phylogeny.data.Property.AppliesTo;
89 import org.forester.phylogeny.data.ProteinDomain;
90 import org.forester.phylogeny.data.Taxonomy;
91 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
92 import org.forester.phylogeny.factories.PhylogenyFactory;
93 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
94 import org.forester.protein.BasicDomain;
95 import org.forester.protein.BasicProtein;
96 import org.forester.protein.Domain;
97 import org.forester.protein.Protein;
98 import org.forester.protein.ProteinId;
99 import org.forester.rio.TestRIO;
100 import org.forester.sdi.SDI;
101 import org.forester.sdi.SDIR;
102 import org.forester.sdi.TestGSDI;
103 import org.forester.sequence.BasicSequence;
104 import org.forester.sequence.Sequence;
105 import org.forester.species.BasicSpecies;
106 import org.forester.species.Species;
107 import org.forester.surfacing.TestSurfacing;
108 import org.forester.tools.ConfidenceAssessor;
109 import org.forester.tools.SupportCount;
110 import org.forester.tools.TreeSplitMatrix;
111 import org.forester.util.AsciiHistogram;
112 import org.forester.util.BasicDescriptiveStatistics;
113 import org.forester.util.BasicTable;
114 import org.forester.util.BasicTableParser;
115 import org.forester.util.DescriptiveStatistics;
116 import org.forester.util.ForesterConstants;
117 import org.forester.util.ForesterUtil;
118 import org.forester.util.GeneralTable;
119 import org.forester.util.SequenceAccessionTools;
120 import org.forester.ws.seqdb.SequenceDatabaseEntry;
121 import org.forester.ws.seqdb.SequenceDbWsTools;
122 import org.forester.ws.seqdb.UniProtTaxonomy;
123 import org.forester.ws.wabi.TxSearch;
124 import org.forester.ws.wabi.TxSearch.RANKS;
125 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
126 import org.forester.ws.wabi.TxSearch.TAX_RANK;
128 @SuppressWarnings( "unused")
129 public final class Test {
131 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
132 + ForesterUtil.getFileSeparator() + "resources"
133 + ForesterUtil.getFileSeparator();
134 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
135 + ForesterUtil.getFileSeparator() + "test_data"
136 + ForesterUtil.getFileSeparator();
137 private final static boolean PERFORM_DB_TESTS = false;
138 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
139 + ForesterConstants.PHYLO_XML_VERSION + "/"
140 + ForesterConstants.PHYLO_XML_XSD;
141 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
142 + ForesterConstants.PHYLO_XML_VERSION + "/"
143 + ForesterConstants.PHYLO_XML_XSD;
144 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
145 private final static double ZERO_DIFF = 1.0E-9;
147 public static boolean isEqual( final double a, final double b ) {
148 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
151 public static void main( final String[] args ) {
152 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
153 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
155 Locale.setDefault( Locale.US );
156 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
159 System.out.print( "[Test if directory with files for testing exists/is readable: " );
160 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
161 System.out.println( "OK.]" );
164 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
165 System.out.println( "Testing aborted." );
168 System.out.print( "[Test if resources directory exists/is readable: " );
169 if ( testDir( PATH_TO_RESOURCES ) ) {
170 System.out.println( "OK.]" );
173 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
174 System.out.println( "Testing aborted." );
177 final long start_time = new Date().getTime();
178 System.out.print( "Basic node methods: " );
179 if ( Test.testBasicNodeMethods() ) {
180 System.out.println( "OK." );
184 System.out.println( "failed." );
187 System.out.print( "Protein id: " );
188 if ( !testProteinId() ) {
189 System.out.println( "failed." );
195 System.out.println( "OK." );
196 System.out.print( "Species: " );
197 if ( !testSpecies() ) {
198 System.out.println( "failed." );
204 System.out.println( "OK." );
205 System.out.print( "Basic domain: " );
206 if ( !testBasicDomain() ) {
207 System.out.println( "failed." );
213 System.out.println( "OK." );
214 System.out.print( "Basic protein: " );
215 if ( !testBasicProtein() ) {
216 System.out.println( "failed." );
222 System.out.println( "OK." );
223 System.out.print( "Sequence writer: " );
224 if ( testSequenceWriter() ) {
225 System.out.println( "OK." );
229 System.out.println( "failed." );
232 System.out.print( "Sequence id parsing: " );
233 if ( testSequenceIdParsing() ) {
234 System.out.println( "OK." );
238 System.out.println( "failed." );
241 System.out.print( "UniProtKB id extraction: " );
242 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
243 System.out.println( "OK." );
247 System.out.println( "failed." );
250 System.out.print( "Sequence DB tools 1: " );
251 if ( testSequenceDbWsTools1() ) {
252 System.out.println( "OK." );
256 System.out.println( "failed." );
259 if ( PERFORM_DB_TESTS ) {
260 System.out.print( "Ebi Entry Retrieval: " );
261 if ( Test.testEbiEntryRetrieval() ) {
262 System.out.println( "OK." );
266 System.out.println( "failed." );
271 if ( PERFORM_DB_TESTS ) {
272 System.out.print( "Sequence DB tools 2: " );
273 if ( testSequenceDbWsTools2() ) {
274 System.out.println( "OK." );
278 System.out.println( "failed." );
284 System.out.print( "Hmmscan output parser: " );
285 if ( testHmmscanOutputParser() ) {
286 System.out.println( "OK." );
290 System.out.println( "failed." );
294 System.out.print( "Overlap removal: " );
295 if ( !org.forester.test.Test.testOverlapRemoval() ) {
296 System.out.println( "failed." );
302 System.out.println( "OK." );
303 System.out.print( "Engulfing overlap removal: " );
304 if ( !Test.testEngulfingOverlapRemoval() ) {
305 System.out.println( "failed." );
311 System.out.println( "OK." );
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." );
883 if ( PERFORM_DB_TESTS ) {
884 System.out.print( "Uniprot Entry Retrieval: " );
885 if ( Test.testUniprotEntryRetrieval() ) {
886 System.out.println( "OK." );
890 System.out.println( "failed." );
894 if ( PERFORM_DB_TESTS ) {
895 System.out.print( "Uniprot Taxonomy Search: " );
896 if ( Test.testUniprotTaxonomySearch() ) {
897 System.out.println( "OK." );
901 System.out.println( "failed." );
907 final String os = ForesterUtil.OS_NAME.toLowerCase();
908 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
909 path = "/usr/local/bin/mafft";
911 else if ( os.indexOf( "win" ) >= 0 ) {
912 path = "C:\\Program Files\\mafft-win\\mafft.bat";
916 if ( !MsaInferrer.isInstalled( path ) ) {
917 path = "/usr/bin/mafft";
919 if ( !MsaInferrer.isInstalled( path ) ) {
920 path = "/usr/local/bin/mafft";
923 if ( MsaInferrer.isInstalled( path ) ) {
924 System.out.print( "MAFFT (external program): " );
925 if ( Test.testMafft( path ) ) {
926 System.out.println( "OK." );
930 System.out.println( "failed [will not count towards failed tests]" );
934 System.out.print( "Next nodes with collapsed: " );
935 if ( Test.testNextNodeWithCollapsing() ) {
936 System.out.println( "OK." );
940 System.out.println( "failed." );
943 System.out.print( "Simple MSA quality: " );
944 if ( Test.testMsaQualityMethod() ) {
945 System.out.println( "OK." );
949 System.out.println( "failed." );
952 System.out.print( "NHX parsing from URL: " );
953 if ( Test.testNHXparsingFromURL() ) {
954 System.out.println( "OK." );
958 System.out.println( "failed." );
961 System.out.print( "phyloXML parsing from URL: " );
962 if ( Test.testPhyloXMLparsingFromURL() ) {
963 System.out.println( "OK." );
967 System.out.println( "failed." );
970 System.out.print( "TreeBase parsing from URL: " );
971 if ( Test.testTreeBaseReading() ) {
972 System.out.println( "OK." );
976 System.out.println( "failed." );
979 System.out.println();
980 final Runtime rt = java.lang.Runtime.getRuntime();
981 final long free_memory = rt.freeMemory() / 1000000;
982 final long total_memory = rt.totalMemory() / 1000000;
983 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
984 + free_memory + "MB, total memory: " + total_memory + "MB)" );
985 System.out.println();
986 System.out.println( "Successful tests: " + succeeded );
987 System.out.println( "Failed tests: " + failed );
988 System.out.println();
990 System.out.println( "OK." );
993 System.out.println( "Not OK." );
997 public static boolean testEngulfingOverlapRemoval() {
999 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1000 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
1001 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
1002 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1003 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1004 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1005 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1006 final List<Boolean> covered = new ArrayList<Boolean>();
1007 covered.add( true ); // 0
1008 covered.add( false ); // 1
1009 covered.add( true ); // 2
1010 covered.add( false ); // 3
1011 covered.add( true ); // 4
1012 covered.add( true ); // 5
1013 covered.add( false ); // 6
1014 covered.add( true ); // 7
1015 covered.add( true ); // 8
1016 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
1019 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
1022 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
1025 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
1028 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
1031 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
1034 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
1037 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1038 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
1039 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
1040 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
1041 abc.addProteinDomain( a );
1042 abc.addProteinDomain( b );
1043 abc.addProteinDomain( c );
1044 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
1045 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
1046 if ( abc.getNumberOfProteinDomains() != 3 ) {
1049 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
1052 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
1055 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
1058 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
1061 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1062 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
1063 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
1064 final Protein def = new BasicProtein( "def", "nemve", 0 );
1065 def.addProteinDomain( d );
1066 def.addProteinDomain( e );
1067 def.addProteinDomain( f );
1068 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
1069 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
1070 if ( def.getNumberOfProteinDomains() != 3 ) {
1073 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
1076 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
1079 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
1082 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
1085 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
1089 catch ( final Exception e ) {
1090 e.printStackTrace( System.out );
1096 public static final boolean testPhyloXMLparsingFromURL() {
1098 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1099 final URL u = new URL( s );
1100 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1101 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1102 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1106 catch ( final Exception e ) {
1107 e.printStackTrace();
1112 public static final boolean testTreeBaseReading() {
1114 final String s = "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr825?format=nexus";
1115 final URL u = new URL( s );
1116 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1117 parser.setReplaceUnderscores( true );
1118 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1119 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1120 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1124 catch ( final Exception e ) {
1125 e.printStackTrace();
1130 public static final boolean testNHXparsingFromURL() {
1132 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1133 final URL u = new URL( s );
1134 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1135 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1136 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1139 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1140 System.out.println( phys[ 0 ].toNewHampshire() );
1143 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1144 System.out.println( phys[ 1 ].toNewHampshire() );
1147 final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
1148 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1151 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1152 System.out.println( phys2[ 0 ].toNewHampshire() );
1155 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1156 final NHXParser p = new NHXParser();
1157 final URL u2 = new URL( s );
1159 if ( !p.hasNext() ) {
1162 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1165 if ( !p.hasNext() ) {
1169 if ( !p.hasNext() ) {
1172 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1175 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1179 if ( !p.hasNext() ) {
1182 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1185 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1189 catch ( final Exception e ) {
1190 e.printStackTrace();
1195 public static boolean testOverlapRemoval() {
1197 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1198 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1199 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1200 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1201 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1202 final List<Boolean> covered = new ArrayList<Boolean>();
1203 covered.add( true ); // 0
1204 covered.add( false ); // 1
1205 covered.add( true ); // 2
1206 covered.add( false ); // 3
1207 covered.add( true ); // 4
1208 covered.add( true ); // 5
1209 covered.add( false ); // 6
1210 covered.add( true ); // 7
1211 covered.add( true ); // 8
1212 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1215 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1218 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1221 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1224 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1227 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1228 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1229 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1230 ab.addProteinDomain( a );
1231 ab.addProteinDomain( b );
1232 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1233 if ( ab.getNumberOfProteinDomains() != 2 ) {
1236 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1239 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1242 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1243 if ( ab.getNumberOfProteinDomains() != 2 ) {
1246 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1249 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1250 final Domain d = new BasicDomain( "d",
1257 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1258 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1259 cde.addProteinDomain( c );
1260 cde.addProteinDomain( d );
1261 cde.addProteinDomain( e );
1262 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1263 if ( cde.getNumberOfProteinDomains() != 3 ) {
1266 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1269 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1270 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1271 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1272 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1273 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1274 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1275 fghi.addProteinDomain( f );
1276 fghi.addProteinDomain( g );
1277 fghi.addProteinDomain( h );
1278 fghi.addProteinDomain( i );
1279 fghi.addProteinDomain( i );
1280 fghi.addProteinDomain( i );
1281 fghi.addProteinDomain( i2 );
1282 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1283 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1286 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1289 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1292 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1293 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1296 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1299 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1300 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1301 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1302 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1303 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1304 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1305 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1306 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1307 jklm.addProteinDomain( j );
1308 jklm.addProteinDomain( k );
1309 jklm.addProteinDomain( l );
1310 jklm.addProteinDomain( m );
1311 jklm.addProteinDomain( m0 );
1312 jklm.addProteinDomain( m1 );
1313 jklm.addProteinDomain( m2 );
1314 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1315 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1318 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1321 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1324 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1325 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1328 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1331 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1332 final Protein od = new BasicProtein( "od", "varanus", 0 );
1333 od.addProteinDomain( only );
1334 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1335 if ( od.getNumberOfProteinDomains() != 1 ) {
1338 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1342 catch ( final Exception e ) {
1343 e.printStackTrace( System.out );
1349 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1350 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1354 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1355 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1358 private static boolean testAminoAcidSequence() {
1360 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1361 if ( aa1.getLength() != 13 ) {
1364 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1367 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1370 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1373 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1374 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
1377 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1378 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1381 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1382 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1386 catch ( final Exception e ) {
1387 e.printStackTrace();
1393 private static boolean testBasicDomain() {
1395 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1396 if ( !pd.getDomainId().equals( "id" ) ) {
1399 if ( pd.getNumber() != 1 ) {
1402 if ( pd.getTotalCount() != 4 ) {
1405 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1408 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1409 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1410 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1411 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1412 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1413 if ( !a1.equals( a1 ) ) {
1416 if ( !a1.equals( a1_copy ) ) {
1419 if ( !a1.equals( a1_equal ) ) {
1422 if ( !a1.equals( a2 ) ) {
1425 if ( a1.equals( a3 ) ) {
1428 if ( a1.compareTo( a1 ) != 0 ) {
1431 if ( a1.compareTo( a1_copy ) != 0 ) {
1434 if ( a1.compareTo( a1_equal ) != 0 ) {
1437 if ( a1.compareTo( a2 ) != 0 ) {
1440 if ( a1.compareTo( a3 ) == 0 ) {
1444 catch ( final Exception e ) {
1445 e.printStackTrace( System.out );
1451 private static boolean testBasicNodeMethods() {
1453 if ( PhylogenyNode.getNodeCount() != 0 ) {
1456 final PhylogenyNode n1 = new PhylogenyNode();
1457 final PhylogenyNode n2 = PhylogenyNode
1458 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1459 final PhylogenyNode n3 = PhylogenyNode
1460 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1461 final PhylogenyNode n4 = PhylogenyNode
1462 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1463 if ( n1.isHasAssignedEvent() ) {
1466 if ( PhylogenyNode.getNodeCount() != 4 ) {
1469 if ( n3.getIndicator() != 0 ) {
1472 if ( n3.getNumberOfExternalNodes() != 1 ) {
1475 if ( !n3.isExternal() ) {
1478 if ( !n3.isRoot() ) {
1481 if ( !n4.getName().equals( "n4" ) ) {
1485 catch ( final Exception e ) {
1486 e.printStackTrace( System.out );
1492 private static boolean testBasicPhyloXMLparsing() {
1494 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1495 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1496 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1498 if ( xml_parser.getErrorCount() > 0 ) {
1499 System.out.println( xml_parser.getErrorMessages().toString() );
1502 if ( phylogenies_0.length != 4 ) {
1505 final Phylogeny t1 = phylogenies_0[ 0 ];
1506 final Phylogeny t2 = phylogenies_0[ 1 ];
1507 final Phylogeny t3 = phylogenies_0[ 2 ];
1508 final Phylogeny t4 = phylogenies_0[ 3 ];
1509 if ( t1.getNumberOfExternalNodes() != 1 ) {
1512 if ( !t1.isRooted() ) {
1515 if ( t1.isRerootable() ) {
1518 if ( !t1.getType().equals( "gene_tree" ) ) {
1521 if ( t2.getNumberOfExternalNodes() != 2 ) {
1524 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1527 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1530 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1533 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1536 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1539 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1542 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1543 .startsWith( "actgtgggggt" ) ) {
1546 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1547 .startsWith( "ctgtgatgcat" ) ) {
1550 if ( t3.getNumberOfExternalNodes() != 4 ) {
1553 if ( !t1.getName().equals( "t1" ) ) {
1556 if ( !t2.getName().equals( "t2" ) ) {
1559 if ( !t3.getName().equals( "t3" ) ) {
1562 if ( !t4.getName().equals( "t4" ) ) {
1565 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1568 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1571 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1574 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1575 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1578 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1581 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1584 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1587 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1588 .equals( "apoptosis" ) ) {
1591 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1592 .equals( "GO:0006915" ) ) {
1595 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1596 .equals( "UniProtKB" ) ) {
1599 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1600 .equals( "experimental" ) ) {
1603 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1604 .equals( "function" ) ) {
1607 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1608 .getValue() != 1 ) {
1611 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1612 .getType().equals( "ml" ) ) {
1615 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1616 .equals( "apoptosis" ) ) {
1619 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1620 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1623 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1624 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1627 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1628 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1631 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1632 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1635 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1636 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1639 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1640 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1643 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1644 .equals( "GO:0005829" ) ) {
1647 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1648 .equals( "intracellular organelle" ) ) {
1651 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1654 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1655 .equals( "UniProt link" ) ) ) {
1658 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1661 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1662 if ( x.size() != 4 ) {
1666 for( final Accession acc : x ) {
1668 if ( !acc.getSource().equals( "KEGG" ) ) {
1671 if ( !acc.getValue().equals( "hsa:596" ) ) {
1678 catch ( final Exception e ) {
1679 e.printStackTrace( System.out );
1685 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1687 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1688 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1689 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1690 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1693 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1695 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1697 if ( xml_parser.getErrorCount() > 0 ) {
1698 System.out.println( xml_parser.getErrorMessages().toString() );
1701 if ( phylogenies_0.length != 4 ) {
1704 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1705 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1706 if ( phylogenies_t1.length != 1 ) {
1709 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1710 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1713 if ( !t1_rt.isRooted() ) {
1716 if ( t1_rt.isRerootable() ) {
1719 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1722 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1723 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1724 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1725 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1728 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1731 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1734 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1737 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1738 .startsWith( "actgtgggggt" ) ) {
1741 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1742 .startsWith( "ctgtgatgcat" ) ) {
1745 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1746 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1747 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1748 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1749 if ( phylogenies_1.length != 1 ) {
1752 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1753 if ( !t3_rt.getName().equals( "t3" ) ) {
1756 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1759 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1762 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1765 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1768 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1769 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1772 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1775 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1778 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1779 .equals( "UniProtKB" ) ) {
1782 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1783 .equals( "apoptosis" ) ) {
1786 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1787 .equals( "GO:0006915" ) ) {
1790 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1791 .equals( "UniProtKB" ) ) {
1794 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1795 .equals( "experimental" ) ) {
1798 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1799 .equals( "function" ) ) {
1802 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1803 .getValue() != 1 ) {
1806 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1807 .getType().equals( "ml" ) ) {
1810 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1811 .equals( "apoptosis" ) ) {
1814 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1815 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1818 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1819 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1822 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1823 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1826 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1827 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1830 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1831 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1834 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1835 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1838 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1839 .equals( "GO:0005829" ) ) {
1842 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1843 .equals( "intracellular organelle" ) ) {
1846 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1849 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1850 .equals( "UniProt link" ) ) ) {
1853 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1856 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1859 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1860 .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." ) ) ) {
1863 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1866 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1869 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1872 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1875 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1876 .equals( "ncbi" ) ) {
1879 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1882 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1883 .getName().equals( "B" ) ) {
1886 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1887 .getFrom() != 21 ) {
1890 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1893 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1894 .getLength() != 24 ) {
1897 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1898 .getConfidence() != 2144 ) {
1901 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1902 .equals( "pfam" ) ) {
1905 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1908 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1911 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1914 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1917 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1918 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1921 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1924 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1927 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1930 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1933 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1936 if ( taxbb.getSynonyms().size() != 2 ) {
1939 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1942 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1945 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1948 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1951 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1954 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1955 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1958 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1961 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1964 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1967 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1970 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1973 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1976 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1980 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1983 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1984 .equalsIgnoreCase( "435" ) ) {
1987 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1990 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1991 .equalsIgnoreCase( "443.7" ) ) {
1994 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1997 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2000 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2001 .equalsIgnoreCase( "433" ) ) {
2004 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2005 .getCrossReferences();
2006 if ( x.size() != 4 ) {
2010 for( final Accession acc : x ) {
2012 if ( !acc.getSource().equals( "KEGG" ) ) {
2015 if ( !acc.getValue().equals( "hsa:596" ) ) {
2022 catch ( final Exception e ) {
2023 e.printStackTrace( System.out );
2029 private static boolean testBasicPhyloXMLparsingValidating() {
2031 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2032 PhyloXmlParser xml_parser = null;
2034 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2036 catch ( final Exception e ) {
2037 // Do nothing -- means were not running from jar.
2039 if ( xml_parser == null ) {
2040 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2041 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2042 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2045 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2048 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2050 if ( xml_parser.getErrorCount() > 0 ) {
2051 System.out.println( xml_parser.getErrorMessages().toString() );
2054 if ( phylogenies_0.length != 4 ) {
2057 final Phylogeny t1 = phylogenies_0[ 0 ];
2058 final Phylogeny t2 = phylogenies_0[ 1 ];
2059 final Phylogeny t3 = phylogenies_0[ 2 ];
2060 final Phylogeny t4 = phylogenies_0[ 3 ];
2061 if ( !t1.getName().equals( "t1" ) ) {
2064 if ( !t2.getName().equals( "t2" ) ) {
2067 if ( !t3.getName().equals( "t3" ) ) {
2070 if ( !t4.getName().equals( "t4" ) ) {
2073 if ( t1.getNumberOfExternalNodes() != 1 ) {
2076 if ( t2.getNumberOfExternalNodes() != 2 ) {
2079 if ( t3.getNumberOfExternalNodes() != 4 ) {
2082 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2083 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2084 if ( xml_parser.getErrorCount() > 0 ) {
2085 System.out.println( "errors:" );
2086 System.out.println( xml_parser.getErrorMessages().toString() );
2089 if ( phylogenies_1.length != 4 ) {
2092 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2094 if ( xml_parser.getErrorCount() > 0 ) {
2095 System.out.println( "errors:" );
2096 System.out.println( xml_parser.getErrorMessages().toString() );
2099 if ( phylogenies_2.length != 1 ) {
2102 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2105 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2107 if ( xml_parser.getErrorCount() > 0 ) {
2108 System.out.println( xml_parser.getErrorMessages().toString() );
2111 if ( phylogenies_3.length != 2 ) {
2114 final Phylogeny a = phylogenies_3[ 0 ];
2115 if ( !a.getName().equals( "tree 4" ) ) {
2118 if ( a.getNumberOfExternalNodes() != 3 ) {
2121 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2124 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2127 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2129 if ( xml_parser.getErrorCount() > 0 ) {
2130 System.out.println( xml_parser.getErrorMessages().toString() );
2133 if ( phylogenies_4.length != 1 ) {
2136 final Phylogeny s = phylogenies_4[ 0 ];
2137 if ( s.getNumberOfExternalNodes() != 6 ) {
2140 s.getNode( "first" );
2142 s.getNode( "\"<a'b&c'd\">\"" );
2143 s.getNode( "'''\"" );
2144 s.getNode( "\"\"\"" );
2145 s.getNode( "dick & doof" );
2147 catch ( final Exception e ) {
2148 e.printStackTrace( System.out );
2154 private static boolean testBasicProtein() {
2156 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2157 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2158 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2159 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2160 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2161 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2162 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2163 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2164 p0.addProteinDomain( y );
2165 p0.addProteinDomain( e );
2166 p0.addProteinDomain( b );
2167 p0.addProteinDomain( c );
2168 p0.addProteinDomain( d );
2169 p0.addProteinDomain( a );
2170 p0.addProteinDomain( x );
2171 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2174 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2178 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2179 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2180 aa0.addProteinDomain( a1 );
2181 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2184 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2188 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2189 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2190 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2191 aa1.addProteinDomain( a11 );
2192 aa1.addProteinDomain( a12 );
2193 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2196 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2199 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2200 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2203 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2206 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2209 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2210 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2213 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2216 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2219 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2222 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2223 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2226 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2229 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2232 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2235 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2236 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2239 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2242 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2245 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2249 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2250 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2251 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2252 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2253 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2254 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2255 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2256 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2257 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2258 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2259 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2260 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2261 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2262 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2263 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2264 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2265 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2266 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2267 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2268 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2269 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2270 p00.addProteinDomain( y0 );
2271 p00.addProteinDomain( e0 );
2272 p00.addProteinDomain( b0 );
2273 p00.addProteinDomain( c0 );
2274 p00.addProteinDomain( d0 );
2275 p00.addProteinDomain( a0 );
2276 p00.addProteinDomain( x0 );
2277 p00.addProteinDomain( y1 );
2278 p00.addProteinDomain( y2 );
2279 p00.addProteinDomain( y3 );
2280 p00.addProteinDomain( e1 );
2281 p00.addProteinDomain( e2 );
2282 p00.addProteinDomain( e3 );
2283 p00.addProteinDomain( e4 );
2284 p00.addProteinDomain( e5 );
2285 p00.addProteinDomain( z0 );
2286 p00.addProteinDomain( z1 );
2287 p00.addProteinDomain( z2 );
2288 p00.addProteinDomain( zz0 );
2289 p00.addProteinDomain( zz1 );
2290 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2293 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2296 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2299 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2302 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" ) ) {
2305 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2306 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2307 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2308 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2309 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2310 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2311 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2312 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2313 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2314 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2315 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2316 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2317 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2318 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2319 p.addProteinDomain( B15 );
2320 p.addProteinDomain( C50 );
2321 p.addProteinDomain( A60 );
2322 p.addProteinDomain( A30 );
2323 p.addProteinDomain( C70 );
2324 p.addProteinDomain( B35 );
2325 p.addProteinDomain( B40 );
2326 p.addProteinDomain( A0 );
2327 p.addProteinDomain( A10 );
2328 p.addProteinDomain( A20 );
2329 p.addProteinDomain( B25 );
2330 p.addProteinDomain( D80 );
2331 List<String> domains_ids = new ArrayList<String>();
2332 domains_ids.add( "A" );
2333 domains_ids.add( "B" );
2334 domains_ids.add( "C" );
2335 if ( !p.contains( domains_ids, false ) ) {
2338 if ( !p.contains( domains_ids, true ) ) {
2341 domains_ids.add( "X" );
2342 if ( p.contains( domains_ids, false ) ) {
2345 if ( p.contains( domains_ids, true ) ) {
2348 domains_ids = new ArrayList<String>();
2349 domains_ids.add( "A" );
2350 domains_ids.add( "C" );
2351 domains_ids.add( "D" );
2352 if ( !p.contains( domains_ids, false ) ) {
2355 if ( !p.contains( domains_ids, true ) ) {
2358 domains_ids = new ArrayList<String>();
2359 domains_ids.add( "A" );
2360 domains_ids.add( "D" );
2361 domains_ids.add( "C" );
2362 if ( !p.contains( domains_ids, false ) ) {
2365 if ( p.contains( domains_ids, true ) ) {
2368 domains_ids = new ArrayList<String>();
2369 domains_ids.add( "A" );
2370 domains_ids.add( "A" );
2371 domains_ids.add( "B" );
2372 if ( !p.contains( domains_ids, false ) ) {
2375 if ( !p.contains( domains_ids, true ) ) {
2378 domains_ids = new ArrayList<String>();
2379 domains_ids.add( "A" );
2380 domains_ids.add( "A" );
2381 domains_ids.add( "A" );
2382 domains_ids.add( "B" );
2383 domains_ids.add( "B" );
2384 if ( !p.contains( domains_ids, false ) ) {
2387 if ( !p.contains( domains_ids, true ) ) {
2390 domains_ids = new ArrayList<String>();
2391 domains_ids.add( "A" );
2392 domains_ids.add( "A" );
2393 domains_ids.add( "B" );
2394 domains_ids.add( "A" );
2395 domains_ids.add( "B" );
2396 domains_ids.add( "B" );
2397 domains_ids.add( "A" );
2398 domains_ids.add( "B" );
2399 domains_ids.add( "C" );
2400 domains_ids.add( "A" );
2401 domains_ids.add( "C" );
2402 domains_ids.add( "D" );
2403 if ( !p.contains( domains_ids, false ) ) {
2406 if ( p.contains( domains_ids, true ) ) {
2410 catch ( final Exception e ) {
2411 e.printStackTrace( System.out );
2417 private static boolean testBasicTable() {
2419 final BasicTable<String> t0 = new BasicTable<String>();
2420 if ( t0.getNumberOfColumns() != 0 ) {
2423 if ( t0.getNumberOfRows() != 0 ) {
2426 t0.setValue( 3, 2, "23" );
2427 t0.setValue( 10, 1, "error" );
2428 t0.setValue( 10, 1, "110" );
2429 t0.setValue( 9, 1, "19" );
2430 t0.setValue( 1, 10, "101" );
2431 t0.setValue( 10, 10, "1010" );
2432 t0.setValue( 100, 10, "10100" );
2433 t0.setValue( 0, 0, "00" );
2434 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2437 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2440 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2443 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2446 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2449 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2452 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2455 if ( t0.getNumberOfColumns() != 101 ) {
2458 if ( t0.getNumberOfRows() != 11 ) {
2461 if ( t0.getValueAsString( 49, 4 ) != null ) {
2464 final String l = ForesterUtil.getLineSeparator();
2465 final StringBuffer source = new StringBuffer();
2466 source.append( "" + l );
2467 source.append( "# 1 1 1 1 1 1 1 1" + l );
2468 source.append( " 00 01 02 03" + l );
2469 source.append( " 10 11 12 13 " + l );
2470 source.append( "20 21 22 23 " + l );
2471 source.append( " 30 31 32 33" + l );
2472 source.append( "40 41 42 43" + l );
2473 source.append( " # 1 1 1 1 1 " + l );
2474 source.append( "50 51 52 53 54" + l );
2475 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2476 if ( t1.getNumberOfColumns() != 5 ) {
2479 if ( t1.getNumberOfRows() != 6 ) {
2482 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2485 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2488 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2491 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2494 final StringBuffer source1 = new StringBuffer();
2495 source1.append( "" + l );
2496 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2497 source1.append( " 00; 01 ;02;03" + l );
2498 source1.append( " 10; 11; 12; 13 " + l );
2499 source1.append( "20; 21; 22; 23 " + l );
2500 source1.append( " 30; 31; 32; 33" + l );
2501 source1.append( "40;41;42;43" + l );
2502 source1.append( " # 1 1 1 1 1 " + l );
2503 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2504 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2505 if ( t2.getNumberOfColumns() != 5 ) {
2508 if ( t2.getNumberOfRows() != 6 ) {
2511 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2514 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2517 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2520 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2523 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2526 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2529 final StringBuffer source2 = new StringBuffer();
2530 source2.append( "" + l );
2531 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2532 source2.append( " 00; 01 ;02;03" + l );
2533 source2.append( " 10; 11; 12; 13 " + l );
2534 source2.append( "20; 21; 22; 23 " + l );
2535 source2.append( " " + l );
2536 source2.append( " 30; 31; 32; 33" + l );
2537 source2.append( "40;41;42;43" + l );
2538 source2.append( " comment: 1 1 1 1 1 " + l );
2539 source2.append( ";;;50 ; 52; 53;;54 " + l );
2540 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2546 if ( tl.size() != 2 ) {
2549 final BasicTable<String> t3 = tl.get( 0 );
2550 final BasicTable<String> t4 = tl.get( 1 );
2551 if ( t3.getNumberOfColumns() != 4 ) {
2554 if ( t3.getNumberOfRows() != 3 ) {
2557 if ( t4.getNumberOfColumns() != 4 ) {
2560 if ( t4.getNumberOfRows() != 3 ) {
2563 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2566 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2570 catch ( final Exception e ) {
2571 e.printStackTrace( System.out );
2577 private static boolean testBasicTolXMLparsing() {
2579 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2580 final TolParser parser = new TolParser();
2581 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2582 if ( parser.getErrorCount() > 0 ) {
2583 System.out.println( parser.getErrorMessages().toString() );
2586 if ( phylogenies_0.length != 1 ) {
2589 final Phylogeny t1 = phylogenies_0[ 0 ];
2590 if ( t1.getNumberOfExternalNodes() != 5 ) {
2593 if ( !t1.isRooted() ) {
2596 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2599 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2602 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2605 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2608 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2609 if ( parser.getErrorCount() > 0 ) {
2610 System.out.println( parser.getErrorMessages().toString() );
2613 if ( phylogenies_1.length != 1 ) {
2616 final Phylogeny t2 = phylogenies_1[ 0 ];
2617 if ( t2.getNumberOfExternalNodes() != 664 ) {
2620 if ( !t2.isRooted() ) {
2623 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2626 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2629 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2632 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2635 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2638 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2639 .equals( "Aquifex" ) ) {
2642 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2643 if ( parser.getErrorCount() > 0 ) {
2644 System.out.println( parser.getErrorMessages().toString() );
2647 if ( phylogenies_2.length != 1 ) {
2650 final Phylogeny t3 = phylogenies_2[ 0 ];
2651 if ( t3.getNumberOfExternalNodes() != 184 ) {
2654 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2657 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2660 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2663 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2664 if ( parser.getErrorCount() > 0 ) {
2665 System.out.println( parser.getErrorMessages().toString() );
2668 if ( phylogenies_3.length != 1 ) {
2671 final Phylogeny t4 = phylogenies_3[ 0 ];
2672 if ( t4.getNumberOfExternalNodes() != 1 ) {
2675 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2678 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2681 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2684 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2685 if ( parser.getErrorCount() > 0 ) {
2686 System.out.println( parser.getErrorMessages().toString() );
2689 if ( phylogenies_4.length != 1 ) {
2692 final Phylogeny t5 = phylogenies_4[ 0 ];
2693 if ( t5.getNumberOfExternalNodes() != 13 ) {
2696 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2699 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2702 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2706 catch ( final Exception e ) {
2707 e.printStackTrace( System.out );
2713 private static boolean testBasicTreeMethods() {
2715 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2716 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2717 if ( t2.getNumberOfExternalNodes() != 4 ) {
2720 if ( t2.getHeight() != 8.5 ) {
2723 if ( !t2.isCompletelyBinary() ) {
2726 if ( t2.isEmpty() ) {
2729 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2730 if ( t3.getNumberOfExternalNodes() != 5 ) {
2733 if ( t3.getHeight() != 11 ) {
2736 if ( t3.isCompletelyBinary() ) {
2739 final PhylogenyNode n = t3.getNode( "ABC" );
2740 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 ];
2741 if ( t4.getNumberOfExternalNodes() != 9 ) {
2744 if ( t4.getHeight() != 11 ) {
2747 if ( t4.isCompletelyBinary() ) {
2750 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)" );
2751 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2752 if ( t5.getNumberOfExternalNodes() != 8 ) {
2755 if ( t5.getHeight() != 15 ) {
2758 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)" );
2759 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2760 if ( t6.getHeight() != 15 ) {
2763 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)" );
2764 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2765 if ( t7.getHeight() != 15 ) {
2768 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)" );
2769 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2770 if ( t8.getNumberOfExternalNodes() != 10 ) {
2773 if ( t8.getHeight() != 15 ) {
2776 final char[] a9 = new char[] { 'a' };
2777 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2778 if ( t9.getHeight() != 0 ) {
2781 final char[] a10 = new char[] { 'a', ':', '6' };
2782 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2783 if ( t10.getHeight() != 6 ) {
2787 catch ( final Exception e ) {
2788 e.printStackTrace( System.out );
2794 private static boolean testConfidenceAssessor() {
2796 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2797 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2798 final Phylogeny[] ev0 = factory
2799 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2801 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2802 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2805 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2808 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2809 final Phylogeny[] ev1 = factory
2810 .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)));",
2812 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2813 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2816 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2819 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2820 final Phylogeny[] ev_b = factory
2821 .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",
2823 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2824 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2827 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2831 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2832 final Phylogeny[] ev1x = factory
2833 .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)));",
2835 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2836 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2839 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2842 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2843 final Phylogeny[] ev_bx = factory
2844 .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",
2846 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2847 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2850 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2854 final Phylogeny[] t2 = factory
2855 .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);",
2857 final Phylogeny[] ev2 = factory
2858 .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);",
2860 for( final Phylogeny target : t2 ) {
2861 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2864 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2865 new NHXParser() )[ 0 ];
2866 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2867 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2868 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2871 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2874 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2878 catch ( final Exception e ) {
2879 e.printStackTrace();
2885 private static boolean testCopyOfNodeData() {
2887 final PhylogenyNode n1 = PhylogenyNode
2888 .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]" );
2889 final PhylogenyNode n2 = n1.copyNodeData();
2890 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2894 catch ( final Exception e ) {
2895 e.printStackTrace();
2901 private static boolean testCreateBalancedPhylogeny() {
2903 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
2904 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
2907 if ( p0.getNumberOfExternalNodes() != 15625 ) {
2910 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
2911 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
2914 if ( p1.getNumberOfExternalNodes() != 100 ) {
2918 catch ( final Exception e ) {
2919 e.printStackTrace();
2925 private static boolean testCreateUriForSeqWeb() {
2927 final PhylogenyNode n = new PhylogenyNode();
2928 n.setName( "tr|B3RJ64" );
2929 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
2932 n.setName( "B0LM41_HUMAN" );
2933 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
2936 n.setName( "NP_001025424" );
2937 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
2940 n.setName( "_NM_001030253-" );
2941 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
2944 n.setName( "XM_002122186" );
2945 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
2948 n.setName( "dgh_AAA34956_gdg" );
2949 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2952 n.setName( "AAA34956" );
2953 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2956 n.setName( "GI:394892" );
2957 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2958 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2961 n.setName( "gi_394892" );
2962 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2963 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2966 n.setName( "gi6335_gi_394892_56635_Gi_43" );
2967 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2968 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2971 n.setName( "P12345" );
2972 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2973 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2976 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
2977 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2978 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2982 catch ( final Exception e ) {
2983 e.printStackTrace( System.out );
2989 private static boolean testDataObjects() {
2991 final Confidence s0 = new Confidence();
2992 final Confidence s1 = new Confidence();
2993 if ( !s0.isEqual( s1 ) ) {
2996 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2997 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2998 if ( s2.isEqual( s1 ) ) {
3001 if ( !s2.isEqual( s3 ) ) {
3004 final Confidence s4 = ( Confidence ) s3.copy();
3005 if ( !s4.isEqual( s3 ) ) {
3012 final Taxonomy t1 = new Taxonomy();
3013 final Taxonomy t2 = new Taxonomy();
3014 final Taxonomy t3 = new Taxonomy();
3015 final Taxonomy t4 = new Taxonomy();
3016 final Taxonomy t5 = new Taxonomy();
3017 t1.setIdentifier( new Identifier( "ecoli" ) );
3018 t1.setTaxonomyCode( "ECOLI" );
3019 t1.setScientificName( "E. coli" );
3020 t1.setCommonName( "coli" );
3021 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3022 if ( !t1.isEqual( t0 ) ) {
3025 t2.setIdentifier( new Identifier( "ecoli" ) );
3026 t2.setTaxonomyCode( "OTHER" );
3027 t2.setScientificName( "what" );
3028 t2.setCommonName( "something" );
3029 if ( !t1.isEqual( t2 ) ) {
3032 t2.setIdentifier( new Identifier( "nemve" ) );
3033 if ( t1.isEqual( t2 ) ) {
3036 t1.setIdentifier( null );
3037 t3.setTaxonomyCode( "ECOLI" );
3038 t3.setScientificName( "what" );
3039 t3.setCommonName( "something" );
3040 if ( !t1.isEqual( t3 ) ) {
3043 t1.setIdentifier( null );
3044 t1.setTaxonomyCode( "" );
3045 t4.setScientificName( "E. ColI" );
3046 t4.setCommonName( "something" );
3047 if ( !t1.isEqual( t4 ) ) {
3050 t4.setScientificName( "B. subtilis" );
3051 t4.setCommonName( "something" );
3052 if ( t1.isEqual( t4 ) ) {
3055 t1.setIdentifier( null );
3056 t1.setTaxonomyCode( "" );
3057 t1.setScientificName( "" );
3058 t5.setCommonName( "COLI" );
3059 if ( !t1.isEqual( t5 ) ) {
3062 t5.setCommonName( "vibrio" );
3063 if ( t1.isEqual( t5 ) ) {
3068 final Identifier id0 = new Identifier( "123", "pfam" );
3069 final Identifier id1 = ( Identifier ) id0.copy();
3070 if ( !id1.isEqual( id1 ) ) {
3073 if ( !id1.isEqual( id0 ) ) {
3076 if ( !id0.isEqual( id1 ) ) {
3083 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3084 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3085 if ( !pd1.isEqual( pd1 ) ) {
3088 if ( !pd1.isEqual( pd0 ) ) {
3093 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3094 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3095 if ( !pd3.isEqual( pd3 ) ) {
3098 if ( !pd2.isEqual( pd3 ) ) {
3101 if ( !pd0.isEqual( pd3 ) ) {
3106 // DomainArchitecture
3107 // ------------------
3108 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3109 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3110 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3111 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3112 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3113 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3118 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3119 if ( ds0.getNumberOfDomains() != 4 ) {
3122 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3123 if ( !ds0.isEqual( ds0 ) ) {
3126 if ( !ds0.isEqual( ds1 ) ) {
3129 if ( ds1.getNumberOfDomains() != 4 ) {
3132 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3137 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3138 if ( ds0.isEqual( ds2 ) ) {
3144 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3145 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3146 System.out.println( ds3.toNHX() );
3149 if ( ds3.getNumberOfDomains() != 3 ) {
3154 final Event e1 = new Event( Event.EventType.fusion );
3155 if ( e1.isDuplication() ) {
3158 if ( !e1.isFusion() ) {
3161 if ( !e1.asText().toString().equals( "fusion" ) ) {
3164 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3167 final Event e11 = new Event( Event.EventType.fusion );
3168 if ( !e11.isEqual( e1 ) ) {
3171 if ( !e11.toNHX().toString().equals( "" ) ) {
3174 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3175 if ( e2.isDuplication() ) {
3178 if ( !e2.isSpeciationOrDuplication() ) {
3181 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3184 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3187 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3190 if ( e11.isEqual( e2 ) ) {
3193 final Event e2c = ( Event ) e2.copy();
3194 if ( !e2c.isEqual( e2 ) ) {
3197 Event e3 = new Event( 1, 2, 3 );
3198 if ( e3.isDuplication() ) {
3201 if ( e3.isSpeciation() ) {
3204 if ( e3.isGeneLoss() ) {
3207 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3210 final Event e3c = ( Event ) e3.copy();
3211 final Event e3cc = ( Event ) e3c.copy();
3212 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3216 if ( !e3c.isEqual( e3cc ) ) {
3219 Event e4 = new Event( 1, 2, 3 );
3220 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3223 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3226 final Event e4c = ( Event ) e4.copy();
3228 final Event e4cc = ( Event ) e4c.copy();
3229 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3232 if ( !e4c.isEqual( e4cc ) ) {
3235 final Event e5 = new Event();
3236 if ( !e5.isUnassigned() ) {
3239 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3242 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3245 final Event e6 = new Event( 1, 0, 0 );
3246 if ( !e6.asText().toString().equals( "duplication" ) ) {
3249 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3252 final Event e7 = new Event( 0, 1, 0 );
3253 if ( !e7.asText().toString().equals( "speciation" ) ) {
3256 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3259 final Event e8 = new Event( 0, 0, 1 );
3260 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3263 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3267 catch ( final Exception e ) {
3268 e.printStackTrace( System.out );
3274 private static boolean testDeletionOfExternalNodes() {
3276 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3277 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3278 final PhylogenyWriter w = new PhylogenyWriter();
3279 if ( t0.isEmpty() ) {
3282 if ( t0.getNumberOfExternalNodes() != 1 ) {
3285 t0.deleteSubtree( t0.getNode( "A" ), false );
3286 if ( t0.getNumberOfExternalNodes() != 0 ) {
3289 if ( !t0.isEmpty() ) {
3292 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3293 if ( t1.getNumberOfExternalNodes() != 2 ) {
3296 t1.deleteSubtree( t1.getNode( "A" ), false );
3297 if ( t1.getNumberOfExternalNodes() != 1 ) {
3300 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3303 t1.deleteSubtree( t1.getNode( "B" ), false );
3304 if ( t1.getNumberOfExternalNodes() != 1 ) {
3307 t1.deleteSubtree( t1.getNode( "r" ), false );
3308 if ( !t1.isEmpty() ) {
3311 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3312 if ( t2.getNumberOfExternalNodes() != 3 ) {
3315 t2.deleteSubtree( t2.getNode( "B" ), false );
3316 if ( t2.getNumberOfExternalNodes() != 2 ) {
3319 t2.toNewHampshireX();
3320 PhylogenyNode n = t2.getNode( "A" );
3321 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3324 t2.deleteSubtree( t2.getNode( "A" ), false );
3325 if ( t2.getNumberOfExternalNodes() != 2 ) {
3328 t2.deleteSubtree( t2.getNode( "C" ), true );
3329 if ( t2.getNumberOfExternalNodes() != 1 ) {
3332 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3333 if ( t3.getNumberOfExternalNodes() != 4 ) {
3336 t3.deleteSubtree( t3.getNode( "B" ), true );
3337 if ( t3.getNumberOfExternalNodes() != 3 ) {
3340 n = t3.getNode( "A" );
3341 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3344 n = n.getNextExternalNode();
3345 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3348 t3.deleteSubtree( t3.getNode( "A" ), true );
3349 if ( t3.getNumberOfExternalNodes() != 2 ) {
3352 n = t3.getNode( "C" );
3353 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3356 t3.deleteSubtree( t3.getNode( "C" ), true );
3357 if ( t3.getNumberOfExternalNodes() != 1 ) {
3360 t3.deleteSubtree( t3.getNode( "D" ), true );
3361 if ( t3.getNumberOfExternalNodes() != 0 ) {
3364 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3365 if ( t4.getNumberOfExternalNodes() != 6 ) {
3368 t4.deleteSubtree( t4.getNode( "B2" ), true );
3369 if ( t4.getNumberOfExternalNodes() != 5 ) {
3372 String s = w.toNewHampshire( t4, false, true ).toString();
3373 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3376 t4.deleteSubtree( t4.getNode( "B11" ), true );
3377 if ( t4.getNumberOfExternalNodes() != 4 ) {
3380 t4.deleteSubtree( t4.getNode( "C" ), true );
3381 if ( t4.getNumberOfExternalNodes() != 3 ) {
3384 n = t4.getNode( "A" );
3385 n = n.getNextExternalNode();
3386 if ( !n.getName().equals( "B12" ) ) {
3389 n = n.getNextExternalNode();
3390 if ( !n.getName().equals( "D" ) ) {
3393 s = w.toNewHampshire( t4, false, true ).toString();
3394 if ( !s.equals( "((A,B12),D);" ) ) {
3397 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3398 t5.deleteSubtree( t5.getNode( "A" ), true );
3399 if ( t5.getNumberOfExternalNodes() != 5 ) {
3402 s = w.toNewHampshire( t5, false, true ).toString();
3403 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3406 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3407 t6.deleteSubtree( t6.getNode( "B11" ), true );
3408 if ( t6.getNumberOfExternalNodes() != 5 ) {
3411 s = w.toNewHampshire( t6, false, false ).toString();
3412 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3415 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3416 t7.deleteSubtree( t7.getNode( "B12" ), true );
3417 if ( t7.getNumberOfExternalNodes() != 5 ) {
3420 s = w.toNewHampshire( t7, false, true ).toString();
3421 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3424 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3425 t8.deleteSubtree( t8.getNode( "B2" ), true );
3426 if ( t8.getNumberOfExternalNodes() != 5 ) {
3429 s = w.toNewHampshire( t8, false, false ).toString();
3430 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3433 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3434 t9.deleteSubtree( t9.getNode( "C" ), true );
3435 if ( t9.getNumberOfExternalNodes() != 5 ) {
3438 s = w.toNewHampshire( t9, false, true ).toString();
3439 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3442 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3443 t10.deleteSubtree( t10.getNode( "D" ), true );
3444 if ( t10.getNumberOfExternalNodes() != 5 ) {
3447 s = w.toNewHampshire( t10, false, true ).toString();
3448 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3451 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3452 t11.deleteSubtree( t11.getNode( "A" ), true );
3453 if ( t11.getNumberOfExternalNodes() != 2 ) {
3456 s = w.toNewHampshire( t11, false, true ).toString();
3457 if ( !s.equals( "(B,C);" ) ) {
3460 t11.deleteSubtree( t11.getNode( "C" ), true );
3461 if ( t11.getNumberOfExternalNodes() != 1 ) {
3464 s = w.toNewHampshire( t11, false, false ).toString();
3465 if ( !s.equals( "B;" ) ) {
3468 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3469 t12.deleteSubtree( t12.getNode( "B2" ), true );
3470 if ( t12.getNumberOfExternalNodes() != 8 ) {
3473 s = w.toNewHampshire( t12, false, true ).toString();
3474 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3477 t12.deleteSubtree( t12.getNode( "B3" ), true );
3478 if ( t12.getNumberOfExternalNodes() != 7 ) {
3481 s = w.toNewHampshire( t12, false, true ).toString();
3482 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3485 t12.deleteSubtree( t12.getNode( "C3" ), true );
3486 if ( t12.getNumberOfExternalNodes() != 6 ) {
3489 s = w.toNewHampshire( t12, false, true ).toString();
3490 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3493 t12.deleteSubtree( t12.getNode( "A1" ), true );
3494 if ( t12.getNumberOfExternalNodes() != 5 ) {
3497 s = w.toNewHampshire( t12, false, true ).toString();
3498 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3501 t12.deleteSubtree( t12.getNode( "B1" ), true );
3502 if ( t12.getNumberOfExternalNodes() != 4 ) {
3505 s = w.toNewHampshire( t12, false, true ).toString();
3506 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3509 t12.deleteSubtree( t12.getNode( "A3" ), true );
3510 if ( t12.getNumberOfExternalNodes() != 3 ) {
3513 s = w.toNewHampshire( t12, false, true ).toString();
3514 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3517 t12.deleteSubtree( t12.getNode( "A2" ), true );
3518 if ( t12.getNumberOfExternalNodes() != 2 ) {
3521 s = w.toNewHampshire( t12, false, true ).toString();
3522 if ( !s.equals( "(C1,C2);" ) ) {
3525 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3526 t13.deleteSubtree( t13.getNode( "D" ), true );
3527 if ( t13.getNumberOfExternalNodes() != 4 ) {
3530 s = w.toNewHampshire( t13, false, true ).toString();
3531 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3534 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3535 t14.deleteSubtree( t14.getNode( "E" ), true );
3536 if ( t14.getNumberOfExternalNodes() != 5 ) {
3539 s = w.toNewHampshire( t14, false, true ).toString();
3540 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3543 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3544 t15.deleteSubtree( t15.getNode( "B2" ), true );
3545 if ( t15.getNumberOfExternalNodes() != 11 ) {
3548 t15.deleteSubtree( t15.getNode( "B1" ), true );
3549 if ( t15.getNumberOfExternalNodes() != 10 ) {
3552 t15.deleteSubtree( t15.getNode( "B3" ), true );
3553 if ( t15.getNumberOfExternalNodes() != 9 ) {
3556 t15.deleteSubtree( t15.getNode( "B4" ), true );
3557 if ( t15.getNumberOfExternalNodes() != 8 ) {
3560 t15.deleteSubtree( t15.getNode( "A1" ), true );
3561 if ( t15.getNumberOfExternalNodes() != 7 ) {
3564 t15.deleteSubtree( t15.getNode( "C4" ), true );
3565 if ( t15.getNumberOfExternalNodes() != 6 ) {
3569 catch ( final Exception e ) {
3570 e.printStackTrace( System.out );
3576 private static boolean testDescriptiveStatistics() {
3578 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3579 dss1.addValue( 82 );
3580 dss1.addValue( 78 );
3581 dss1.addValue( 70 );
3582 dss1.addValue( 58 );
3583 dss1.addValue( 42 );
3584 if ( dss1.getN() != 5 ) {
3587 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3590 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3593 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3596 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3599 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3602 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3605 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3608 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3611 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3614 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3617 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3620 dss1.addValue( 123 );
3621 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3624 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3627 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3630 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3631 dss2.addValue( -1.85 );
3632 dss2.addValue( 57.5 );
3633 dss2.addValue( 92.78 );
3634 dss2.addValue( 57.78 );
3635 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3638 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3641 final double[] a = dss2.getDataAsDoubleArray();
3642 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3645 dss2.addValue( -100 );
3646 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3649 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3652 final double[] ds = new double[ 14 ];
3667 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3668 if ( bins.length != 4 ) {
3671 if ( bins[ 0 ] != 2 ) {
3674 if ( bins[ 1 ] != 3 ) {
3677 if ( bins[ 2 ] != 4 ) {
3680 if ( bins[ 3 ] != 5 ) {
3683 final double[] ds1 = new double[ 9 ];
3693 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3694 if ( bins1.length != 4 ) {
3697 if ( bins1[ 0 ] != 2 ) {
3700 if ( bins1[ 1 ] != 3 ) {
3703 if ( bins1[ 2 ] != 0 ) {
3706 if ( bins1[ 3 ] != 4 ) {
3709 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3710 if ( bins1_1.length != 3 ) {
3713 if ( bins1_1[ 0 ] != 3 ) {
3716 if ( bins1_1[ 1 ] != 2 ) {
3719 if ( bins1_1[ 2 ] != 4 ) {
3722 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3723 if ( bins1_2.length != 3 ) {
3726 if ( bins1_2[ 0 ] != 2 ) {
3729 if ( bins1_2[ 1 ] != 2 ) {
3732 if ( bins1_2[ 2 ] != 2 ) {
3735 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3749 dss3.addValue( 10 );
3750 dss3.addValue( 10 );
3751 dss3.addValue( 10 );
3752 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3753 histo.toStringBuffer( 10, '=', 40, 5 );
3754 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3756 catch ( final Exception e ) {
3757 e.printStackTrace( System.out );
3763 private static boolean testDir( final String file ) {
3765 final File f = new File( file );
3766 if ( !f.exists() ) {
3769 if ( !f.isDirectory() ) {
3772 if ( !f.canRead() ) {
3776 catch ( final Exception e ) {
3782 private static boolean testEbiEntryRetrieval() {
3784 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3785 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3786 System.out.println( entry.getAccession() );
3789 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
3790 System.out.println( entry.getTaxonomyScientificName() );
3793 if ( !entry.getSequenceName()
3794 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
3795 System.out.println( entry.getSequenceName() );
3798 // if ( !entry.getSequenceSymbol().equals( "" ) ) {
3799 // System.out.println( entry.getSequenceSymbol() );
3802 if ( !entry.getGeneName().equals( "treX-like" ) ) {
3803 System.out.println( entry.getGeneName() );
3806 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
3807 System.out.println( entry.getTaxonomyIdentifier() );
3810 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
3811 System.out.println( entry.getAnnotations().first().getRefValue() );
3814 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
3815 System.out.println( entry.getAnnotations().first().getRefSource() );
3818 if ( entry.getCrossReferences().size() != 5 ) {
3822 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
3823 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
3826 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
3827 System.out.println( entry1.getTaxonomyScientificName() );
3830 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
3831 System.out.println( entry1.getSequenceName() );
3834 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
3835 System.out.println( entry1.getTaxonomyIdentifier() );
3838 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
3839 System.out.println( entry1.getGeneName() );
3842 if ( entry1.getCrossReferences().size() != 6 ) {
3846 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
3847 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
3850 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
3851 System.out.println( entry2.getTaxonomyScientificName() );
3854 if ( !entry2.getSequenceName()
3855 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
3856 System.out.println( entry2.getSequenceName() );
3859 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
3860 System.out.println( entry2.getTaxonomyIdentifier() );
3863 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
3864 System.out.println( entry2.getGeneName() );
3867 if ( entry2.getCrossReferences().size() != 3 ) {
3871 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
3872 if ( !entry3.getAccession().equals( "HM043801" ) ) {
3875 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
3876 System.out.println( entry3.getTaxonomyScientificName() );
3879 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
3880 System.out.println( entry3.getSequenceName() );
3883 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
3884 System.out.println( entry3.getTaxonomyIdentifier() );
3887 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
3888 System.out.println( entry3.getSequenceSymbol() );
3891 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
3894 if ( entry3.getCrossReferences().size() != 8 ) {
3899 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
3900 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
3903 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
3904 System.out.println( entry4.getTaxonomyScientificName() );
3907 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
3908 System.out.println( entry4.getSequenceName() );
3911 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
3912 System.out.println( entry4.getTaxonomyIdentifier() );
3915 if ( !entry4.getGeneName().equals( "ras" ) ) {
3916 System.out.println( entry4.getGeneName() );
3919 // if ( !entry4.getChromosome().equals( "ras" ) ) {
3920 // System.out.println( entry4.getChromosome() );
3923 // if ( !entry4.getMap().equals( "ras" ) ) {
3924 // System.out.println( entry4.getMap() );
3930 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
3931 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
3934 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
3935 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
3938 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
3939 System.out.println( entry5.getTaxonomyScientificName() );
3942 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
3943 System.out.println( entry5.getSequenceName() );
3946 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
3947 System.out.println( entry5.getTaxonomyIdentifier() );
3951 catch ( final IOException e ) {
3952 System.out.println();
3953 System.out.println( "the following might be due to absence internet connection:" );
3954 e.printStackTrace( System.out );
3957 catch ( final Exception e ) {
3958 e.printStackTrace();
3964 private static boolean testExternalNodeRelatedMethods() {
3966 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3967 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3968 PhylogenyNode n = t1.getNode( "A" );
3969 n = n.getNextExternalNode();
3970 if ( !n.getName().equals( "B" ) ) {
3973 n = n.getNextExternalNode();
3974 if ( !n.getName().equals( "C" ) ) {
3977 n = n.getNextExternalNode();
3978 if ( !n.getName().equals( "D" ) ) {
3981 n = t1.getNode( "B" );
3982 while ( !n.isLastExternalNode() ) {
3983 n = n.getNextExternalNode();
3985 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
3986 n = t2.getNode( "A" );
3987 n = n.getNextExternalNode();
3988 if ( !n.getName().equals( "B" ) ) {
3991 n = n.getNextExternalNode();
3992 if ( !n.getName().equals( "C" ) ) {
3995 n = n.getNextExternalNode();
3996 if ( !n.getName().equals( "D" ) ) {
3999 n = t2.getNode( "B" );
4000 while ( !n.isLastExternalNode() ) {
4001 n = n.getNextExternalNode();
4003 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4004 n = t3.getNode( "A" );
4005 n = n.getNextExternalNode();
4006 if ( !n.getName().equals( "B" ) ) {
4009 n = n.getNextExternalNode();
4010 if ( !n.getName().equals( "C" ) ) {
4013 n = n.getNextExternalNode();
4014 if ( !n.getName().equals( "D" ) ) {
4017 n = n.getNextExternalNode();
4018 if ( !n.getName().equals( "E" ) ) {
4021 n = n.getNextExternalNode();
4022 if ( !n.getName().equals( "F" ) ) {
4025 n = n.getNextExternalNode();
4026 if ( !n.getName().equals( "G" ) ) {
4029 n = n.getNextExternalNode();
4030 if ( !n.getName().equals( "H" ) ) {
4033 n = t3.getNode( "B" );
4034 while ( !n.isLastExternalNode() ) {
4035 n = n.getNextExternalNode();
4037 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4038 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4039 final PhylogenyNode node = iter.next();
4041 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4042 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4043 final PhylogenyNode node = iter.next();
4045 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4046 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4047 if ( !iter.next().getName().equals( "A" ) ) {
4050 if ( !iter.next().getName().equals( "B" ) ) {
4053 if ( !iter.next().getName().equals( "C" ) ) {
4056 if ( !iter.next().getName().equals( "D" ) ) {
4059 if ( !iter.next().getName().equals( "E" ) ) {
4062 if ( !iter.next().getName().equals( "F" ) ) {
4065 if ( iter.hasNext() ) {
4069 catch ( final Exception e ) {
4070 e.printStackTrace( System.out );
4076 private static boolean testExtractSNFromNodeName() {
4078 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4081 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
4082 .equals( "Mus musculus musculus" ) ) {
4085 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
4086 .equals( "Mus musculus musculus" ) ) {
4089 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
4092 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
4093 .equals( "Mus musculus" ) ) {
4096 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4099 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus" )
4100 .equals( "Mus musculus musculus" ) ) {
4103 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4107 catch ( final Exception e ) {
4108 e.printStackTrace( System.out );
4114 private static boolean testExtractTaxonomyCodeFromNodeName() {
4116 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4119 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4120 .equals( "SOYBN" ) ) {
4123 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4124 .equals( "ARATH" ) ) {
4127 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4128 .equals( "ARATH" ) ) {
4131 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4134 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4137 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4140 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4141 .equals( "SOYBN" ) ) {
4144 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4145 .equals( "SOYBN" ) ) {
4148 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4149 .equals( "SOYBN" ) ) {
4152 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4153 .equals( "SOYBN" ) ) {
4156 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4157 .equals( "SOYBN" ) ) {
4160 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4161 .equals( "SOYBN" ) ) {
4164 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4165 .equals( "SOYBN" ) ) {
4168 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4169 .equals( "SOYBN" ) ) {
4172 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4175 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4176 .equals( "SOYBN" ) ) {
4179 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4180 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4183 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4184 .equals( "9YX45" ) ) {
4187 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4188 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4189 .equals( "MOUSE" ) ) {
4192 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4193 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4194 .equals( "MOUSE" ) ) {
4197 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4198 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4199 .equals( "MOUSE" ) ) {
4202 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4203 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4206 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4207 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4210 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4211 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4214 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4215 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4218 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4219 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4222 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4223 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4226 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4227 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4230 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4231 .equals( "RAT" ) ) {
4234 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4235 .equals( "PIG" ) ) {
4239 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4240 .equals( "MOUSE" ) ) {
4243 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4244 .equals( "MOUSE" ) ) {
4247 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4251 catch ( final Exception e ) {
4252 e.printStackTrace( System.out );
4258 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4260 PhylogenyNode n = new PhylogenyNode();
4261 n.setName( "tr|B3RJ64" );
4262 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4265 n.setName( "tr.B3RJ64" );
4266 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4269 n.setName( "tr=B3RJ64" );
4270 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4273 n.setName( "tr-B3RJ64" );
4274 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4277 n.setName( "tr/B3RJ64" );
4278 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4281 n.setName( "tr\\B3RJ64" );
4282 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4285 n.setName( "tr_B3RJ64" );
4286 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4289 n.setName( " tr|B3RJ64 " );
4290 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4293 n.setName( "-tr|B3RJ64-" );
4294 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4297 n.setName( "-tr=B3RJ64-" );
4298 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4301 n.setName( "_tr=B3RJ64_" );
4302 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4305 n.setName( " tr_tr|B3RJ64_sp|123 " );
4306 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4309 n.setName( "B3RJ64" );
4310 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4313 n.setName( "sp|B3RJ64" );
4314 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4317 n.setName( "sp|B3RJ64C" );
4318 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4321 n.setName( "sp B3RJ64" );
4322 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4325 n.setName( "sp|B3RJ6X" );
4326 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4329 n.setName( "sp|B3RJ6" );
4330 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4333 n.setName( "K1PYK7_CRAGI" );
4334 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4337 n.setName( "K1PYK7_PEA" );
4338 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4341 n.setName( "K1PYK7_RAT" );
4342 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4345 n.setName( "K1PYK7_PIG" );
4346 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4349 n.setName( "~K1PYK7_PIG~" );
4350 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4353 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4354 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4357 n.setName( "K1PYKX_CRAGI" );
4358 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4361 n.setName( "XXXXX_CRAGI" );
4362 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4365 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4366 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4369 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4370 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4373 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4374 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4377 n = new PhylogenyNode();
4378 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4379 seq.setSymbol( "K1PYK7_CRAGI" );
4380 n.getNodeData().addSequence( seq );
4381 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4384 seq.setSymbol( "tr|B3RJ64" );
4385 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4388 n = new PhylogenyNode();
4389 seq = new org.forester.phylogeny.data.Sequence();
4390 seq.setName( "K1PYK7_CRAGI" );
4391 n.getNodeData().addSequence( seq );
4392 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4395 seq.setName( "tr|B3RJ64" );
4396 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4399 n = new PhylogenyNode();
4400 seq = new org.forester.phylogeny.data.Sequence();
4401 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4402 n.getNodeData().addSequence( seq );
4403 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4406 n = new PhylogenyNode();
4407 seq = new org.forester.phylogeny.data.Sequence();
4408 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4409 n.getNodeData().addSequence( seq );
4410 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4414 n = new PhylogenyNode();
4415 n.setName( "ACP19736" );
4416 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4419 n = new PhylogenyNode();
4420 n.setName( "|ACP19736|" );
4421 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4425 catch ( final Exception e ) {
4426 e.printStackTrace( System.out );
4432 private static boolean testFastaParser() {
4434 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4437 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4440 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4441 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4444 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4447 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4450 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
4453 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4456 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4460 catch ( final Exception e ) {
4461 e.printStackTrace();
4467 private static boolean testGenbankAccessorParsing() {
4468 //The format for GenBank Accession numbers are:
4469 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4470 //Protein: 3 letters + 5 numerals
4471 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4472 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4475 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4478 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4481 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4484 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4487 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4490 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4493 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4496 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4499 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4502 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4505 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4508 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4511 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4517 private static boolean testGeneralMsaParser() {
4519 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4520 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4521 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4522 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4523 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4524 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4525 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4526 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4527 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4530 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4533 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4536 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4539 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4542 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4545 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4548 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4551 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4554 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4557 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4560 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4563 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
4564 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4567 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4570 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4573 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
4574 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
4577 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
4580 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
4583 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
4584 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4587 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4590 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4594 catch ( final Exception e ) {
4595 e.printStackTrace();
4601 private static boolean testGeneralTable() {
4603 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
4604 t0.setValue( 3, 2, "23" );
4605 t0.setValue( 10, 1, "error" );
4606 t0.setValue( 10, 1, "110" );
4607 t0.setValue( 9, 1, "19" );
4608 t0.setValue( 1, 10, "101" );
4609 t0.setValue( 10, 10, "1010" );
4610 t0.setValue( 100, 10, "10100" );
4611 t0.setValue( 0, 0, "00" );
4612 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
4615 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
4618 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
4621 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
4624 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
4627 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
4630 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
4633 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
4636 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
4639 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
4640 t1.setValue( "3", "2", "23" );
4641 t1.setValue( "10", "1", "error" );
4642 t1.setValue( "10", "1", "110" );
4643 t1.setValue( "9", "1", "19" );
4644 t1.setValue( "1", "10", "101" );
4645 t1.setValue( "10", "10", "1010" );
4646 t1.setValue( "100", "10", "10100" );
4647 t1.setValue( "0", "0", "00" );
4648 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
4649 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
4652 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
4655 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
4658 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
4661 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
4664 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
4667 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
4670 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
4673 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
4676 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
4680 catch ( final Exception e ) {
4681 e.printStackTrace( System.out );
4687 private static boolean testGetDistance() {
4689 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4690 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",
4691 new NHXParser() )[ 0 ];
4692 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
4695 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
4698 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
4701 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
4704 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
4707 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
4710 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
4713 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
4716 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
4719 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
4722 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
4725 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
4728 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
4731 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
4734 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
4737 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
4740 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
4743 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
4746 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
4749 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
4752 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
4755 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
4758 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
4761 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
4764 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
4767 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
4770 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
4773 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
4776 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
4779 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
4782 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
4785 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",
4786 new NHXParser() )[ 0 ];
4787 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
4790 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
4793 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
4796 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
4799 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
4802 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
4805 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
4808 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
4811 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
4814 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
4817 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
4821 catch ( final Exception e ) {
4822 e.printStackTrace( System.out );
4828 private static boolean testGetLCA() {
4830 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4831 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
4832 new NHXParser() )[ 0 ];
4833 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
4834 if ( !A.getName().equals( "A" ) ) {
4837 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
4838 if ( !gh.getName().equals( "gh" ) ) {
4841 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
4842 if ( !ab.getName().equals( "ab" ) ) {
4845 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
4846 if ( !ab2.getName().equals( "ab" ) ) {
4849 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
4850 if ( !gh2.getName().equals( "gh" ) ) {
4853 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
4854 if ( !gh3.getName().equals( "gh" ) ) {
4857 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
4858 if ( !abc.getName().equals( "abc" ) ) {
4861 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
4862 if ( !abc2.getName().equals( "abc" ) ) {
4865 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
4866 if ( !abcd.getName().equals( "abcd" ) ) {
4869 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
4870 if ( !abcd2.getName().equals( "abcd" ) ) {
4873 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
4874 if ( !abcdef.getName().equals( "abcdef" ) ) {
4877 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
4878 if ( !abcdef2.getName().equals( "abcdef" ) ) {
4881 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
4882 if ( !abcdef3.getName().equals( "abcdef" ) ) {
4885 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
4886 if ( !abcdef4.getName().equals( "abcdef" ) ) {
4889 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
4890 if ( !abcde.getName().equals( "abcde" ) ) {
4893 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
4894 if ( !abcde2.getName().equals( "abcde" ) ) {
4897 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
4898 if ( !r.getName().equals( "abcdefgh" ) ) {
4901 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
4902 if ( !r2.getName().equals( "abcdefgh" ) ) {
4905 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
4906 if ( !r3.getName().equals( "abcdefgh" ) ) {
4909 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
4910 if ( !abcde3.getName().equals( "abcde" ) ) {
4913 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
4914 if ( !abcde4.getName().equals( "abcde" ) ) {
4917 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
4918 if ( !ab3.getName().equals( "ab" ) ) {
4921 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
4922 if ( !ab4.getName().equals( "ab" ) ) {
4925 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
4926 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
4927 if ( !cd.getName().equals( "cd" ) ) {
4930 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
4931 if ( !cd2.getName().equals( "cd" ) ) {
4934 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
4935 if ( !cde.getName().equals( "cde" ) ) {
4938 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
4939 if ( !cde2.getName().equals( "cde" ) ) {
4942 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
4943 if ( !cdef.getName().equals( "cdef" ) ) {
4946 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
4947 if ( !cdef2.getName().equals( "cdef" ) ) {
4950 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
4951 if ( !cdef3.getName().equals( "cdef" ) ) {
4954 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
4955 if ( !rt.getName().equals( "r" ) ) {
4958 final Phylogeny p3 = factory
4959 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
4960 new NHXParser() )[ 0 ];
4961 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
4962 if ( !bc_3.getName().equals( "bc" ) ) {
4965 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
4966 if ( !ac_3.getName().equals( "abc" ) ) {
4969 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
4970 if ( !ad_3.getName().equals( "abcde" ) ) {
4973 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
4974 if ( !af_3.getName().equals( "abcdef" ) ) {
4977 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
4978 if ( !ag_3.getName().equals( "" ) ) {
4981 if ( !ag_3.isRoot() ) {
4984 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
4985 if ( !al_3.getName().equals( "" ) ) {
4988 if ( !al_3.isRoot() ) {
4991 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
4992 if ( !kl_3.getName().equals( "" ) ) {
4995 if ( !kl_3.isRoot() ) {
4998 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
4999 if ( !fl_3.getName().equals( "" ) ) {
5002 if ( !fl_3.isRoot() ) {
5005 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5006 if ( !gk_3.getName().equals( "ghijk" ) ) {
5009 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5010 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5011 if ( !r_4.getName().equals( "r" ) ) {
5014 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5015 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5016 if ( !r_5.getName().equals( "root" ) ) {
5019 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5020 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5021 if ( !r_6.getName().equals( "rot" ) ) {
5024 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5025 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5026 if ( !r_7.getName().equals( "rott" ) ) {
5030 catch ( final Exception e ) {
5031 e.printStackTrace( System.out );
5037 private static boolean testGetLCA2() {
5039 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5040 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5041 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5042 PhylogenyMethods.preOrderReId( p_a );
5043 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5044 p_a.getNode( "a" ) );
5045 if ( !p_a_1.getName().equals( "a" ) ) {
5048 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5049 PhylogenyMethods.preOrderReId( p_b );
5050 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5051 p_b.getNode( "a" ) );
5052 if ( !p_b_1.getName().equals( "b" ) ) {
5055 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5056 p_b.getNode( "b" ) );
5057 if ( !p_b_2.getName().equals( "b" ) ) {
5060 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5061 PhylogenyMethods.preOrderReId( p_c );
5062 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5063 p_c.getNode( "a" ) );
5064 if ( !p_c_1.getName().equals( "b" ) ) {
5067 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5068 p_c.getNode( "c" ) );
5069 if ( !p_c_2.getName().equals( "c" ) ) {
5070 System.out.println( p_c_2.getName() );
5074 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5075 p_c.getNode( "b" ) );
5076 if ( !p_c_3.getName().equals( "b" ) ) {
5079 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5080 p_c.getNode( "a" ) );
5081 if ( !p_c_4.getName().equals( "c" ) ) {
5084 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5085 new NHXParser() )[ 0 ];
5086 PhylogenyMethods.preOrderReId( p1 );
5087 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5088 p1.getNode( "A" ) );
5089 if ( !A.getName().equals( "A" ) ) {
5092 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5093 p1.getNode( "gh" ) );
5094 if ( !gh.getName().equals( "gh" ) ) {
5097 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5098 p1.getNode( "B" ) );
5099 if ( !ab.getName().equals( "ab" ) ) {
5102 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5103 p1.getNode( "A" ) );
5104 if ( !ab2.getName().equals( "ab" ) ) {
5107 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5108 p1.getNode( "G" ) );
5109 if ( !gh2.getName().equals( "gh" ) ) {
5112 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5113 p1.getNode( "H" ) );
5114 if ( !gh3.getName().equals( "gh" ) ) {
5117 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5118 p1.getNode( "A" ) );
5119 if ( !abc.getName().equals( "abc" ) ) {
5122 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5123 p1.getNode( "C" ) );
5124 if ( !abc2.getName().equals( "abc" ) ) {
5127 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5128 p1.getNode( "D" ) );
5129 if ( !abcd.getName().equals( "abcd" ) ) {
5132 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5133 p1.getNode( "A" ) );
5134 if ( !abcd2.getName().equals( "abcd" ) ) {
5137 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5138 p1.getNode( "F" ) );
5139 if ( !abcdef.getName().equals( "abcdef" ) ) {
5142 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5143 p1.getNode( "A" ) );
5144 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5147 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5148 p1.getNode( "F" ) );
5149 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5152 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5153 p1.getNode( "ab" ) );
5154 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5157 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5158 p1.getNode( "E" ) );
5159 if ( !abcde.getName().equals( "abcde" ) ) {
5162 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5163 p1.getNode( "A" ) );
5164 if ( !abcde2.getName().equals( "abcde" ) ) {
5167 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5168 p1.getNode( "abcdefgh" ) );
5169 if ( !r.getName().equals( "abcdefgh" ) ) {
5172 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5173 p1.getNode( "H" ) );
5174 if ( !r2.getName().equals( "abcdefgh" ) ) {
5177 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5178 p1.getNode( "A" ) );
5179 if ( !r3.getName().equals( "abcdefgh" ) ) {
5182 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5183 p1.getNode( "abcde" ) );
5184 if ( !abcde3.getName().equals( "abcde" ) ) {
5187 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5188 p1.getNode( "E" ) );
5189 if ( !abcde4.getName().equals( "abcde" ) ) {
5192 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5193 p1.getNode( "B" ) );
5194 if ( !ab3.getName().equals( "ab" ) ) {
5197 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5198 p1.getNode( "ab" ) );
5199 if ( !ab4.getName().equals( "ab" ) ) {
5202 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5203 PhylogenyMethods.preOrderReId( p2 );
5204 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5205 p2.getNode( "d" ) );
5206 if ( !cd.getName().equals( "cd" ) ) {
5209 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5210 p2.getNode( "c" ) );
5211 if ( !cd2.getName().equals( "cd" ) ) {
5214 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5215 p2.getNode( "e" ) );
5216 if ( !cde.getName().equals( "cde" ) ) {
5219 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5220 p2.getNode( "c" ) );
5221 if ( !cde2.getName().equals( "cde" ) ) {
5224 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5225 p2.getNode( "f" ) );
5226 if ( !cdef.getName().equals( "cdef" ) ) {
5229 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5230 p2.getNode( "f" ) );
5231 if ( !cdef2.getName().equals( "cdef" ) ) {
5234 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5235 p2.getNode( "d" ) );
5236 if ( !cdef3.getName().equals( "cdef" ) ) {
5239 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5240 p2.getNode( "a" ) );
5241 if ( !rt.getName().equals( "r" ) ) {
5244 final Phylogeny p3 = factory
5245 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5246 new NHXParser() )[ 0 ];
5247 PhylogenyMethods.preOrderReId( p3 );
5248 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5249 p3.getNode( "c" ) );
5250 if ( !bc_3.getName().equals( "bc" ) ) {
5253 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5254 p3.getNode( "c" ) );
5255 if ( !ac_3.getName().equals( "abc" ) ) {
5258 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5259 p3.getNode( "d" ) );
5260 if ( !ad_3.getName().equals( "abcde" ) ) {
5263 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5264 p3.getNode( "f" ) );
5265 if ( !af_3.getName().equals( "abcdef" ) ) {
5268 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5269 p3.getNode( "g" ) );
5270 if ( !ag_3.getName().equals( "" ) ) {
5273 if ( !ag_3.isRoot() ) {
5276 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5277 p3.getNode( "l" ) );
5278 if ( !al_3.getName().equals( "" ) ) {
5281 if ( !al_3.isRoot() ) {
5284 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5285 p3.getNode( "l" ) );
5286 if ( !kl_3.getName().equals( "" ) ) {
5289 if ( !kl_3.isRoot() ) {
5292 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5293 p3.getNode( "l" ) );
5294 if ( !fl_3.getName().equals( "" ) ) {
5297 if ( !fl_3.isRoot() ) {
5300 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5301 p3.getNode( "k" ) );
5302 if ( !gk_3.getName().equals( "ghijk" ) ) {
5305 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5306 PhylogenyMethods.preOrderReId( p4 );
5307 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5308 p4.getNode( "c" ) );
5309 if ( !r_4.getName().equals( "r" ) ) {
5312 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5313 PhylogenyMethods.preOrderReId( p5 );
5314 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5315 p5.getNode( "c" ) );
5316 if ( !r_5.getName().equals( "root" ) ) {
5319 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5320 PhylogenyMethods.preOrderReId( p6 );
5321 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5322 p6.getNode( "a" ) );
5323 if ( !r_6.getName().equals( "rot" ) ) {
5326 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5327 PhylogenyMethods.preOrderReId( p7 );
5328 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5329 p7.getNode( "e" ) );
5330 if ( !r_7.getName().equals( "rott" ) ) {
5333 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5334 p7.getNode( "a" ) );
5335 if ( !r_71.getName().equals( "rott" ) ) {
5338 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5339 p7.getNode( "rott" ) );
5340 if ( !r_72.getName().equals( "rott" ) ) {
5343 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5344 p7.getNode( "a" ) );
5345 if ( !r_73.getName().equals( "rott" ) ) {
5348 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5349 p7.getNode( "rott" ) );
5350 if ( !r_74.getName().equals( "rott" ) ) {
5353 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5354 p7.getNode( "e" ) );
5355 if ( !r_75.getName().equals( "e" ) ) {
5359 catch ( final Exception e ) {
5360 e.printStackTrace( System.out );
5366 private static boolean testHmmscanOutputParser() {
5367 final String test_dir = Test.PATH_TO_TEST_DATA;
5369 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5370 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5372 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5373 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5374 final List<Protein> proteins = parser2.parse();
5375 if ( parser2.getProteinsEncountered() != 4 ) {
5378 if ( proteins.size() != 4 ) {
5381 if ( parser2.getDomainsEncountered() != 69 ) {
5384 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5387 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5390 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5393 final Protein p1 = proteins.get( 0 );
5394 if ( p1.getNumberOfProteinDomains() != 15 ) {
5397 if ( p1.getLength() != 850 ) {
5400 final Protein p2 = proteins.get( 1 );
5401 if ( p2.getNumberOfProteinDomains() != 51 ) {
5404 if ( p2.getLength() != 1291 ) {
5407 final Protein p3 = proteins.get( 2 );
5408 if ( p3.getNumberOfProteinDomains() != 2 ) {
5411 final Protein p4 = proteins.get( 3 );
5412 if ( p4.getNumberOfProteinDomains() != 1 ) {
5415 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5418 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5421 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5424 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5427 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5430 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5433 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5437 catch ( final Exception e ) {
5438 e.printStackTrace( System.out );
5444 private static boolean testLastExternalNodeMethods() {
5446 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5447 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5448 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5449 final PhylogenyNode n1 = t0.getNode( "A" );
5450 if ( n1.isLastExternalNode() ) {
5453 final PhylogenyNode n2 = t0.getNode( "B" );
5454 if ( n2.isLastExternalNode() ) {
5457 final PhylogenyNode n3 = t0.getNode( "C" );
5458 if ( n3.isLastExternalNode() ) {
5461 final PhylogenyNode n4 = t0.getNode( "D" );
5462 if ( !n4.isLastExternalNode() ) {
5466 catch ( final Exception e ) {
5467 e.printStackTrace( System.out );
5473 private static boolean testLevelOrderIterator() {
5475 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5476 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5477 PhylogenyNodeIterator it0;
5478 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5481 for( it0.reset(); it0.hasNext(); ) {
5484 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5485 if ( !it.next().getName().equals( "r" ) ) {
5488 if ( !it.next().getName().equals( "ab" ) ) {
5491 if ( !it.next().getName().equals( "cd" ) ) {
5494 if ( !it.next().getName().equals( "A" ) ) {
5497 if ( !it.next().getName().equals( "B" ) ) {
5500 if ( !it.next().getName().equals( "C" ) ) {
5503 if ( !it.next().getName().equals( "D" ) ) {
5506 if ( it.hasNext() ) {
5509 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",
5510 new NHXParser() )[ 0 ];
5511 PhylogenyNodeIterator it2;
5512 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5515 for( it2.reset(); it2.hasNext(); ) {
5518 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5519 if ( !it3.next().getName().equals( "r" ) ) {
5522 if ( !it3.next().getName().equals( "abc" ) ) {
5525 if ( !it3.next().getName().equals( "defg" ) ) {
5528 if ( !it3.next().getName().equals( "A" ) ) {
5531 if ( !it3.next().getName().equals( "B" ) ) {
5534 if ( !it3.next().getName().equals( "C" ) ) {
5537 if ( !it3.next().getName().equals( "D" ) ) {
5540 if ( !it3.next().getName().equals( "E" ) ) {
5543 if ( !it3.next().getName().equals( "F" ) ) {
5546 if ( !it3.next().getName().equals( "G" ) ) {
5549 if ( !it3.next().getName().equals( "1" ) ) {
5552 if ( !it3.next().getName().equals( "2" ) ) {
5555 if ( !it3.next().getName().equals( "3" ) ) {
5558 if ( !it3.next().getName().equals( "4" ) ) {
5561 if ( !it3.next().getName().equals( "5" ) ) {
5564 if ( !it3.next().getName().equals( "6" ) ) {
5567 if ( !it3.next().getName().equals( "f1" ) ) {
5570 if ( !it3.next().getName().equals( "f2" ) ) {
5573 if ( !it3.next().getName().equals( "f3" ) ) {
5576 if ( !it3.next().getName().equals( "a" ) ) {
5579 if ( !it3.next().getName().equals( "b" ) ) {
5582 if ( !it3.next().getName().equals( "f21" ) ) {
5585 if ( !it3.next().getName().equals( "X" ) ) {
5588 if ( !it3.next().getName().equals( "Y" ) ) {
5591 if ( !it3.next().getName().equals( "Z" ) ) {
5594 if ( it3.hasNext() ) {
5597 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
5598 PhylogenyNodeIterator it4;
5599 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
5602 for( it4.reset(); it4.hasNext(); ) {
5605 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
5606 if ( !it5.next().getName().equals( "r" ) ) {
5609 if ( !it5.next().getName().equals( "A" ) ) {
5612 if ( !it5.next().getName().equals( "B" ) ) {
5615 if ( !it5.next().getName().equals( "C" ) ) {
5618 if ( !it5.next().getName().equals( "D" ) ) {
5621 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
5622 PhylogenyNodeIterator it6;
5623 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
5626 for( it6.reset(); it6.hasNext(); ) {
5629 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
5630 if ( !it7.next().getName().equals( "A" ) ) {
5633 if ( it.hasNext() ) {
5637 catch ( final Exception e ) {
5638 e.printStackTrace( System.out );
5644 private static boolean testMafft( final String path ) {
5646 final List<String> opts = new ArrayList<String>();
5647 opts.add( "--maxiterate" );
5649 opts.add( "--localpair" );
5650 opts.add( "--quiet" );
5652 final MsaInferrer mafft = Mafft.createInstance( path );
5653 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
5654 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
5657 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
5661 catch ( final Exception e ) {
5662 e.printStackTrace( System.out );
5668 private static boolean testMidpointrooting() {
5670 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5671 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
5672 PhylogenyMethods.midpointRoot( t0 );
5673 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
5676 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
5679 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
5683 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",
5684 new NHXParser() )[ 0 ];
5685 if ( !t1.isRooted() ) {
5688 PhylogenyMethods.midpointRoot( t1 );
5689 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5692 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5695 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5698 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5701 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5704 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5707 t1.reRoot( t1.getNode( "A" ) );
5708 PhylogenyMethods.midpointRoot( t1 );
5709 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5712 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5715 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5718 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5721 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5725 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5729 catch ( final Exception e ) {
5730 e.printStackTrace( System.out );
5736 private static boolean testMsaQualityMethod() {
5738 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
5739 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
5740 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
5741 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
5742 final List<Sequence> l = new ArrayList<Sequence>();
5747 final Msa msa = BasicMsa.createInstance( l );
5748 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
5751 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
5754 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
5757 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
5760 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
5763 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
5766 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
5770 catch ( final Exception e ) {
5771 e.printStackTrace( System.out );
5777 private static boolean testNextNodeWithCollapsing() {
5779 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5781 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
5782 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5783 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
5784 t0.getNode( "cd" ).setCollapse( true );
5785 t0.getNode( "cde" ).setCollapse( true );
5786 n = t0.getFirstExternalNode();
5787 while ( n != null ) {
5789 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5791 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5794 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5797 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
5800 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
5803 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
5806 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
5810 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5811 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
5812 t1.getNode( "ab" ).setCollapse( true );
5813 t1.getNode( "cd" ).setCollapse( true );
5814 t1.getNode( "cde" ).setCollapse( true );
5815 n = t1.getNode( "ab" );
5816 ext = new ArrayList<PhylogenyNode>();
5817 while ( n != null ) {
5819 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5821 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5824 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5827 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5830 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
5833 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
5839 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5840 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
5841 t2.getNode( "ab" ).setCollapse( true );
5842 t2.getNode( "cd" ).setCollapse( true );
5843 t2.getNode( "cde" ).setCollapse( true );
5844 t2.getNode( "c" ).setCollapse( true );
5845 t2.getNode( "d" ).setCollapse( true );
5846 t2.getNode( "e" ).setCollapse( true );
5847 t2.getNode( "gh" ).setCollapse( true );
5848 n = t2.getNode( "ab" );
5849 ext = new ArrayList<PhylogenyNode>();
5850 while ( n != null ) {
5852 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5854 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5857 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5860 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5863 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
5869 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5870 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
5871 t3.getNode( "ab" ).setCollapse( true );
5872 t3.getNode( "cd" ).setCollapse( true );
5873 t3.getNode( "cde" ).setCollapse( true );
5874 t3.getNode( "c" ).setCollapse( true );
5875 t3.getNode( "d" ).setCollapse( true );
5876 t3.getNode( "e" ).setCollapse( true );
5877 t3.getNode( "gh" ).setCollapse( true );
5878 t3.getNode( "fgh" ).setCollapse( true );
5879 n = t3.getNode( "ab" );
5880 ext = new ArrayList<PhylogenyNode>();
5881 while ( n != null ) {
5883 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5885 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5888 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5891 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
5897 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5898 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
5899 t4.getNode( "ab" ).setCollapse( true );
5900 t4.getNode( "cd" ).setCollapse( true );
5901 t4.getNode( "cde" ).setCollapse( true );
5902 t4.getNode( "c" ).setCollapse( true );
5903 t4.getNode( "d" ).setCollapse( true );
5904 t4.getNode( "e" ).setCollapse( true );
5905 t4.getNode( "gh" ).setCollapse( true );
5906 t4.getNode( "fgh" ).setCollapse( true );
5907 t4.getNode( "abcdefgh" ).setCollapse( true );
5908 n = t4.getNode( "abcdefgh" );
5909 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
5914 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5915 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
5917 n = t5.getFirstExternalNode();
5918 while ( n != null ) {
5920 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5922 if ( ext.size() != 8 ) {
5925 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5928 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5931 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5934 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5937 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5940 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5943 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
5946 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
5951 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5952 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
5954 t6.getNode( "ab" ).setCollapse( true );
5955 n = t6.getNode( "ab" );
5956 while ( n != null ) {
5958 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5960 if ( ext.size() != 7 ) {
5963 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5966 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5969 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5972 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5975 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5978 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5981 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5986 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5987 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
5989 t7.getNode( "cd" ).setCollapse( true );
5990 n = t7.getNode( "a" );
5991 while ( n != null ) {
5993 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5995 if ( ext.size() != 7 ) {
5998 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6001 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6004 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6007 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6010 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6013 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6016 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6021 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6022 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6024 t8.getNode( "cd" ).setCollapse( true );
6025 t8.getNode( "c" ).setCollapse( true );
6026 t8.getNode( "d" ).setCollapse( true );
6027 n = t8.getNode( "a" );
6028 while ( n != null ) {
6030 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6032 if ( ext.size() != 7 ) {
6035 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6038 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6041 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6042 System.out.println( "2 fail" );
6045 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6048 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6051 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6054 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6059 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6060 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6062 t9.getNode( "gh" ).setCollapse( true );
6063 n = t9.getNode( "a" );
6064 while ( n != null ) {
6066 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6068 if ( ext.size() != 7 ) {
6071 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6074 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6077 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6080 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6083 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6086 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6089 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6094 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6095 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6097 t10.getNode( "gh" ).setCollapse( true );
6098 t10.getNode( "g" ).setCollapse( true );
6099 t10.getNode( "h" ).setCollapse( true );
6100 n = t10.getNode( "a" );
6101 while ( n != null ) {
6103 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6105 if ( ext.size() != 7 ) {
6108 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6111 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6114 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6117 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6120 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6123 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6126 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6131 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6132 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6134 t11.getNode( "gh" ).setCollapse( true );
6135 t11.getNode( "fgh" ).setCollapse( true );
6136 n = t11.getNode( "a" );
6137 while ( n != null ) {
6139 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6141 if ( ext.size() != 6 ) {
6144 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6147 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6150 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6153 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6156 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6159 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6164 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6165 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6167 t12.getNode( "gh" ).setCollapse( true );
6168 t12.getNode( "fgh" ).setCollapse( true );
6169 t12.getNode( "g" ).setCollapse( true );
6170 t12.getNode( "h" ).setCollapse( true );
6171 t12.getNode( "f" ).setCollapse( true );
6172 n = t12.getNode( "a" );
6173 while ( n != null ) {
6175 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6177 if ( ext.size() != 6 ) {
6180 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6183 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6186 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6189 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6192 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6195 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6200 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6201 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6203 t13.getNode( "ab" ).setCollapse( true );
6204 t13.getNode( "b" ).setCollapse( true );
6205 t13.getNode( "fgh" ).setCollapse( true );
6206 t13.getNode( "gh" ).setCollapse( true );
6207 n = t13.getNode( "ab" );
6208 while ( n != null ) {
6210 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6212 if ( ext.size() != 5 ) {
6215 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6218 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6221 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6224 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6227 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6232 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6233 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6235 t14.getNode( "ab" ).setCollapse( true );
6236 t14.getNode( "a" ).setCollapse( true );
6237 t14.getNode( "fgh" ).setCollapse( true );
6238 t14.getNode( "gh" ).setCollapse( true );
6239 n = t14.getNode( "ab" );
6240 while ( n != null ) {
6242 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6244 if ( ext.size() != 5 ) {
6247 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6250 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6253 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6256 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6259 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6264 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" );
6265 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6267 t15.getNode( "ab" ).setCollapse( true );
6268 t15.getNode( "a" ).setCollapse( true );
6269 t15.getNode( "fgh" ).setCollapse( true );
6270 t15.getNode( "gh" ).setCollapse( true );
6271 n = t15.getNode( "ab" );
6272 while ( n != null ) {
6274 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6276 if ( ext.size() != 6 ) {
6279 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6282 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6285 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6288 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6291 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6294 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6299 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" );
6300 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6302 t16.getNode( "ab" ).setCollapse( true );
6303 t16.getNode( "a" ).setCollapse( true );
6304 t16.getNode( "fgh" ).setCollapse( true );
6305 t16.getNode( "gh" ).setCollapse( true );
6306 t16.getNode( "cd" ).setCollapse( true );
6307 t16.getNode( "cde" ).setCollapse( true );
6308 t16.getNode( "d" ).setCollapse( true );
6309 t16.getNode( "x" ).setCollapse( true );
6310 n = t16.getNode( "ab" );
6311 while ( n != null ) {
6313 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6315 if ( ext.size() != 4 ) {
6318 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6321 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6324 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6327 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6331 catch ( final Exception e ) {
6332 e.printStackTrace( System.out );
6338 private static boolean testNexusCharactersParsing() {
6340 final NexusCharactersParser parser = new NexusCharactersParser();
6341 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6343 String[] labels = parser.getCharStateLabels();
6344 if ( labels.length != 7 ) {
6347 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6350 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6353 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6356 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6359 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6362 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6365 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6368 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6370 labels = parser.getCharStateLabels();
6371 if ( labels.length != 7 ) {
6374 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6377 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6380 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6383 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6386 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6389 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6392 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6396 catch ( final Exception e ) {
6397 e.printStackTrace( System.out );
6403 private static boolean testNexusMatrixParsing() {
6405 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
6406 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
6408 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
6409 if ( m.getNumberOfCharacters() != 9 ) {
6412 if ( m.getNumberOfIdentifiers() != 5 ) {
6415 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
6418 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
6421 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
6424 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
6427 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
6430 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
6433 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
6436 // if ( labels.length != 7 ) {
6439 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6442 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6445 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6448 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6451 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6454 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6457 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6460 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6462 // labels = parser.getCharStateLabels();
6463 // if ( labels.length != 7 ) {
6466 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6469 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6472 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6475 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6478 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6481 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6484 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6488 catch ( final Exception e ) {
6489 e.printStackTrace( System.out );
6495 private static boolean testNexusTreeParsing() {
6497 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6498 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6499 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
6500 if ( phylogenies.length != 1 ) {
6503 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
6506 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6510 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
6511 if ( phylogenies.length != 1 ) {
6514 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6517 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
6521 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
6522 if ( phylogenies.length != 1 ) {
6525 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6528 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6531 if ( phylogenies[ 0 ].isRooted() ) {
6535 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
6536 if ( phylogenies.length != 18 ) {
6539 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6542 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
6545 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
6548 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
6551 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
6554 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
6557 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
6560 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
6563 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
6566 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
6569 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
6572 if ( phylogenies[ 8 ].isRooted() ) {
6575 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
6578 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
6581 if ( !phylogenies[ 9 ].isRooted() ) {
6584 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
6587 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
6590 if ( !phylogenies[ 10 ].isRooted() ) {
6593 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
6596 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
6599 if ( phylogenies[ 11 ].isRooted() ) {
6602 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
6605 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
6608 if ( !phylogenies[ 12 ].isRooted() ) {
6611 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
6614 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
6617 if ( !phylogenies[ 13 ].isRooted() ) {
6620 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
6623 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
6626 if ( !phylogenies[ 14 ].isRooted() ) {
6629 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
6632 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
6635 if ( phylogenies[ 15 ].isRooted() ) {
6638 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
6641 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
6644 if ( !phylogenies[ 16 ].isRooted() ) {
6647 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
6650 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
6653 if ( phylogenies[ 17 ].isRooted() ) {
6656 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
6659 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
6661 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
6662 if ( phylogenies.length != 9 ) {
6665 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
6666 .getDistanceToParent() ) ) {
6669 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
6670 .getDistanceToParent() ) ) {
6673 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
6676 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
6679 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
6682 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
6685 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
6689 catch ( final Exception e ) {
6690 e.printStackTrace( System.out );
6696 private static boolean testNexusTreeParsingIterating() {
6698 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
6699 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
6700 if ( !p.hasNext() ) {
6703 Phylogeny phy = p.next();
6704 if ( phy == null ) {
6707 if ( phy.getNumberOfExternalNodes() != 25 ) {
6710 if ( !phy.getName().equals( "" ) ) {
6713 if ( p.hasNext() ) {
6717 if ( phy != null ) {
6722 if ( !p.hasNext() ) {
6726 if ( phy == null ) {
6729 if ( phy.getNumberOfExternalNodes() != 25 ) {
6732 if ( !phy.getName().equals( "" ) ) {
6735 if ( p.hasNext() ) {
6739 if ( phy != null ) {
6743 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
6744 if ( !p.hasNext() ) {
6748 if ( phy == null ) {
6751 if ( phy.getNumberOfExternalNodes() != 10 ) {
6754 if ( !phy.getName().equals( "name" ) ) {
6757 if ( p.hasNext() ) {
6761 if ( phy != null ) {
6766 if ( !p.hasNext() ) {
6770 if ( phy == null ) {
6773 if ( phy.getNumberOfExternalNodes() != 10 ) {
6776 if ( !phy.getName().equals( "name" ) ) {
6779 if ( p.hasNext() ) {
6783 if ( phy != null ) {
6787 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
6788 if ( !p.hasNext() ) {
6792 if ( phy == null ) {
6795 if ( phy.getNumberOfExternalNodes() != 3 ) {
6798 if ( !phy.getName().equals( "" ) ) {
6801 if ( phy.isRooted() ) {
6804 if ( p.hasNext() ) {
6808 if ( phy != null ) {
6813 if ( !p.hasNext() ) {
6817 if ( phy == null ) {
6820 if ( phy.getNumberOfExternalNodes() != 3 ) {
6823 if ( !phy.getName().equals( "" ) ) {
6826 if ( p.hasNext() ) {
6830 if ( phy != null ) {
6834 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
6835 if ( !p.hasNext() ) {
6840 if ( phy == null ) {
6843 if ( phy.getNumberOfExternalNodes() != 10 ) {
6846 if ( !phy.getName().equals( "tree 0" ) ) {
6850 if ( !p.hasNext() ) {
6854 if ( phy == null ) {
6857 if ( phy.getNumberOfExternalNodes() != 10 ) {
6860 if ( !phy.getName().equals( "tree 1" ) ) {
6864 if ( !p.hasNext() ) {
6868 if ( phy == null ) {
6871 if ( phy.getNumberOfExternalNodes() != 3 ) {
6872 System.out.println( phy.toString() );
6875 if ( !phy.getName().equals( "" ) ) {
6878 if ( phy.isRooted() ) {
6882 if ( !p.hasNext() ) {
6886 if ( phy == null ) {
6889 if ( phy.getNumberOfExternalNodes() != 4 ) {
6892 if ( !phy.getName().equals( "" ) ) {
6895 if ( !phy.isRooted() ) {
6899 if ( !p.hasNext() ) {
6903 if ( phy == null ) {
6906 if ( phy.getNumberOfExternalNodes() != 5 ) {
6907 System.out.println( phy.getNumberOfExternalNodes() );
6910 if ( !phy.getName().equals( "" ) ) {
6913 if ( !phy.isRooted() ) {
6917 if ( !p.hasNext() ) {
6921 if ( phy == null ) {
6924 if ( phy.getNumberOfExternalNodes() != 3 ) {
6927 if ( !phy.getName().equals( "" ) ) {
6930 if ( phy.isRooted() ) {
6934 if ( !p.hasNext() ) {
6938 if ( phy == null ) {
6941 if ( phy.getNumberOfExternalNodes() != 2 ) {
6944 if ( !phy.getName().equals( "" ) ) {
6947 if ( !phy.isRooted() ) {
6951 if ( !p.hasNext() ) {
6955 if ( phy.getNumberOfExternalNodes() != 3 ) {
6958 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6961 if ( !phy.isRooted() ) {
6965 if ( !p.hasNext() ) {
6969 if ( phy.getNumberOfExternalNodes() != 3 ) {
6972 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
6975 if ( !phy.getName().equals( "tree 8" ) ) {
6979 if ( !p.hasNext() ) {
6983 if ( phy.getNumberOfExternalNodes() != 3 ) {
6986 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
6989 if ( !phy.getName().equals( "tree 9" ) ) {
6993 if ( !p.hasNext() ) {
6997 if ( phy.getNumberOfExternalNodes() != 3 ) {
7000 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7003 if ( !phy.getName().equals( "tree 10" ) ) {
7006 if ( !phy.isRooted() ) {
7010 if ( !p.hasNext() ) {
7014 if ( phy.getNumberOfExternalNodes() != 3 ) {
7017 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7020 if ( !phy.getName().equals( "tree 11" ) ) {
7023 if ( phy.isRooted() ) {
7027 if ( !p.hasNext() ) {
7031 if ( phy.getNumberOfExternalNodes() != 3 ) {
7034 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7037 if ( !phy.getName().equals( "tree 12" ) ) {
7040 if ( !phy.isRooted() ) {
7044 if ( !p.hasNext() ) {
7048 if ( phy.getNumberOfExternalNodes() != 3 ) {
7051 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7054 if ( !phy.getName().equals( "tree 13" ) ) {
7057 if ( !phy.isRooted() ) {
7061 if ( !p.hasNext() ) {
7065 if ( phy.getNumberOfExternalNodes() != 10 ) {
7066 System.out.println( phy.getNumberOfExternalNodes() );
7071 .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;" ) ) {
7072 System.out.println( phy.toNewHampshire() );
7075 if ( !phy.getName().equals( "tree 14" ) ) {
7078 if ( !phy.isRooted() ) {
7082 if ( !p.hasNext() ) {
7086 if ( phy.getNumberOfExternalNodes() != 10 ) {
7087 System.out.println( phy.getNumberOfExternalNodes() );
7092 .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;" ) ) {
7093 System.out.println( phy.toNewHampshire() );
7096 if ( !phy.getName().equals( "tree 15" ) ) {
7099 if ( phy.isRooted() ) {
7103 if ( !p.hasNext() ) {
7107 if ( phy.getNumberOfExternalNodes() != 10 ) {
7108 System.out.println( phy.getNumberOfExternalNodes() );
7113 .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;" ) ) {
7114 System.out.println( phy.toNewHampshire() );
7117 if ( !phy.getName().equals( "tree 16" ) ) {
7120 if ( !phy.isRooted() ) {
7124 if ( !p.hasNext() ) {
7128 if ( phy.getNumberOfExternalNodes() != 10 ) {
7129 System.out.println( phy.getNumberOfExternalNodes() );
7134 .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;" ) ) {
7135 System.out.println( phy.toNewHampshire() );
7138 if ( !phy.getName().equals( "tree 17" ) ) {
7141 if ( phy.isRooted() ) {
7145 if ( p.hasNext() ) {
7149 if ( phy != null ) {
7154 if ( !p.hasNext() ) {
7158 if ( phy == null ) {
7161 if ( phy.getNumberOfExternalNodes() != 10 ) {
7164 if ( !phy.getName().equals( "tree 0" ) ) {
7168 if ( !p.hasNext() ) {
7172 if ( phy == null ) {
7175 if ( phy.getNumberOfExternalNodes() != 10 ) {
7178 if ( !phy.getName().equals( "tree 1" ) ) {
7182 if ( !p.hasNext() ) {
7186 if ( phy == null ) {
7189 if ( phy.getNumberOfExternalNodes() != 3 ) {
7192 if ( !phy.getName().equals( "" ) ) {
7195 if ( phy.isRooted() ) {
7199 if ( !p.hasNext() ) {
7203 if ( phy == null ) {
7206 if ( phy.getNumberOfExternalNodes() != 4 ) {
7209 if ( !phy.getName().equals( "" ) ) {
7212 if ( !phy.isRooted() ) {
7216 if ( !p.hasNext() ) {
7220 if ( phy == null ) {
7223 if ( phy.getNumberOfExternalNodes() != 5 ) {
7224 System.out.println( phy.getNumberOfExternalNodes() );
7227 if ( !phy.getName().equals( "" ) ) {
7230 if ( !phy.isRooted() ) {
7234 if ( !p.hasNext() ) {
7238 if ( phy == null ) {
7241 if ( phy.getNumberOfExternalNodes() != 3 ) {
7244 if ( !phy.getName().equals( "" ) ) {
7247 if ( phy.isRooted() ) {
7251 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7252 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7254 if ( !p2.hasNext() ) {
7258 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7261 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7265 if ( !p2.hasNext() ) {
7270 if ( !p2.hasNext() ) {
7275 if ( !p2.hasNext() ) {
7280 if ( !p2.hasNext() ) {
7285 if ( !p2.hasNext() ) {
7290 if ( !p2.hasNext() ) {
7295 if ( !p2.hasNext() ) {
7300 if ( !p2.hasNext() ) {
7304 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7307 if ( p2.hasNext() ) {
7311 if ( phy != null ) {
7316 if ( !p2.hasNext() ) {
7320 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7323 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7327 catch ( final Exception e ) {
7328 e.printStackTrace( System.out );
7334 private static boolean testNexusTreeParsingTranslating() {
7336 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7337 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7338 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7339 if ( phylogenies.length != 1 ) {
7342 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7345 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7348 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7351 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7354 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7355 .equals( "Aranaeus" ) ) {
7359 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7360 if ( phylogenies.length != 3 ) {
7363 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7366 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7369 if ( phylogenies[ 0 ].isRooted() ) {
7372 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7375 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7378 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7379 .equals( "Aranaeus" ) ) {
7382 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7385 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7388 if ( phylogenies[ 1 ].isRooted() ) {
7391 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7394 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7397 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7398 .equals( "Aranaeus" ) ) {
7401 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7404 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7407 if ( !phylogenies[ 2 ].isRooted() ) {
7410 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7413 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7416 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7417 .equals( "Aranaeus" ) ) {
7421 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
7422 if ( phylogenies.length != 3 ) {
7425 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7428 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7431 if ( phylogenies[ 0 ].isRooted() ) {
7434 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7437 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7440 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7441 .equals( "Aranaeus" ) ) {
7444 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7447 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7450 if ( phylogenies[ 1 ].isRooted() ) {
7453 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7456 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7459 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7460 .equals( "Aranaeus" ) ) {
7463 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7466 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7469 if ( !phylogenies[ 2 ].isRooted() ) {
7472 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7475 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7478 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7479 .equals( "Aranaeus" ) ) {
7483 catch ( final Exception e ) {
7484 e.printStackTrace( System.out );
7490 private static boolean testNHParsing() {
7492 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7493 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
7494 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
7497 final NHXParser nhxp = new NHXParser();
7498 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
7499 nhxp.setReplaceUnderscores( true );
7500 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
7501 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
7504 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
7507 final Phylogeny p1b = factory
7508 .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 ",
7509 new NHXParser() )[ 0 ];
7510 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
7513 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
7516 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
7517 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
7518 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
7519 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
7520 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
7521 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
7522 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
7523 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
7524 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
7525 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
7526 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
7527 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
7528 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
7530 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
7533 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
7536 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
7539 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
7542 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
7543 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
7544 final String p16_S = "((A,B),C)";
7545 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
7546 if ( p16.length != 1 ) {
7549 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
7552 final String p17_S = "(C,(A,B))";
7553 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
7554 if ( p17.length != 1 ) {
7557 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
7560 final String p18_S = "((A,B),(C,D))";
7561 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
7562 if ( p18.length != 1 ) {
7565 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
7568 final String p19_S = "(((A,B),C),D)";
7569 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
7570 if ( p19.length != 1 ) {
7573 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
7576 final String p20_S = "(A,(B,(C,D)))";
7577 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
7578 if ( p20.length != 1 ) {
7581 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
7584 final String p21_S = "(A,(B,(C,(D,E))))";
7585 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
7586 if ( p21.length != 1 ) {
7589 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
7592 final String p22_S = "((((A,B),C),D),E)";
7593 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
7594 if ( p22.length != 1 ) {
7597 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
7600 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7601 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
7602 if ( p23.length != 1 ) {
7603 System.out.println( "xl=" + p23.length );
7607 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
7610 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7611 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
7612 if ( p24.length != 1 ) {
7615 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
7618 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7619 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7620 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
7621 if ( p241.length != 2 ) {
7624 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
7627 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
7630 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
7631 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
7632 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
7633 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
7634 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
7635 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
7636 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
7637 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
7638 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
7639 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
7642 final String p26_S = "(A,B)ab";
7643 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
7644 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
7647 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7648 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
7649 if ( p27s.length != 1 ) {
7650 System.out.println( "xxl=" + p27s.length );
7654 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7655 System.out.println( p27s[ 0 ].toNewHampshireX() );
7659 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
7661 if ( p27.length != 1 ) {
7662 System.out.println( "yl=" + p27.length );
7666 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7667 System.out.println( p27[ 0 ].toNewHampshireX() );
7671 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7672 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7673 final String p28_S3 = "(A,B)ab";
7674 final String p28_S4 = "((((A,B),C),D),;E;)";
7675 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
7677 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
7680 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
7683 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
7686 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
7689 if ( p28.length != 4 ) {
7692 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";
7693 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
7694 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
7697 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";
7698 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
7699 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
7702 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
7703 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
7704 if ( ( p32.length != 0 ) ) {
7707 final String p33_S = "A";
7708 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
7709 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
7712 final String p34_S = "B;";
7713 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
7714 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
7717 final String p35_S = "B:0.2";
7718 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
7719 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
7722 final String p36_S = "(A)";
7723 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
7724 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
7727 final String p37_S = "((A))";
7728 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
7729 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
7732 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7733 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
7734 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
7737 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7738 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
7739 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
7742 final String p40_S = "(A,B,C)";
7743 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
7744 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
7747 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
7748 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
7749 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
7752 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
7753 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
7754 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
7757 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)";
7758 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
7759 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
7762 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)))";
7763 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
7764 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
7767 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
7768 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
7769 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
7772 final String p46_S = "";
7773 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
7774 if ( p46.length != 0 ) {
7777 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
7778 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7781 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7782 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7785 final Phylogeny p49 = factory
7786 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
7787 new NHXParser() )[ 0 ];
7788 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7791 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7792 if ( p50.getNode( "A" ) == null ) {
7795 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7796 .equals( "((A,B)ab:2.0[88],C);" ) ) {
7799 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
7802 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
7803 .equals( "((A,B)88:2.0,C);" ) ) {
7806 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7807 if ( p51.getNode( "A(A" ) == null ) {
7810 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7811 if ( p52.getNode( "A(A" ) == null ) {
7814 final Phylogeny p53 = factory
7815 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
7816 new NHXParser() )[ 0 ];
7817 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
7821 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
7822 if ( p54.getNode( "A" ) == null ) {
7825 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7826 .equals( "((A,B)[88],C);" ) ) {
7830 catch ( final Exception e ) {
7831 e.printStackTrace( System.out );
7837 private static boolean testNHParsingIter() {
7839 final String p0_str = "(A,B);";
7840 final NHXParser p = new NHXParser();
7841 p.setSource( p0_str );
7842 if ( !p.hasNext() ) {
7845 final Phylogeny p0 = p.next();
7846 if ( !p0.toNewHampshire().equals( p0_str ) ) {
7847 System.out.println( p0.toNewHampshire() );
7850 if ( p.hasNext() ) {
7853 if ( p.next() != null ) {
7857 final String p00_str = "(A,B)root;";
7858 p.setSource( p00_str );
7859 final Phylogeny p00 = p.next();
7860 if ( !p00.toNewHampshire().equals( p00_str ) ) {
7861 System.out.println( p00.toNewHampshire() );
7865 final String p000_str = "A;";
7866 p.setSource( p000_str );
7867 final Phylogeny p000 = p.next();
7868 if ( !p000.toNewHampshire().equals( p000_str ) ) {
7869 System.out.println( p000.toNewHampshire() );
7873 final String p0000_str = "A";
7874 p.setSource( p0000_str );
7875 final Phylogeny p0000 = p.next();
7876 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
7877 System.out.println( p0000.toNewHampshire() );
7881 p.setSource( "(A)" );
7882 final Phylogeny p00000 = p.next();
7883 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
7884 System.out.println( p00000.toNewHampshire() );
7888 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
7889 p.setSource( p1_str );
7890 if ( !p.hasNext() ) {
7893 final Phylogeny p1_0 = p.next();
7894 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
7895 System.out.println( p1_0.toNewHampshire() );
7898 if ( !p.hasNext() ) {
7901 final Phylogeny p1_1 = p.next();
7902 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
7903 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
7906 if ( !p.hasNext() ) {
7909 final Phylogeny p1_2 = p.next();
7910 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
7911 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
7914 if ( !p.hasNext() ) {
7917 final Phylogeny p1_3 = p.next();
7918 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
7919 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
7922 if ( p.hasNext() ) {
7925 if ( p.next() != null ) {
7929 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
7930 p.setSource( p2_str );
7931 if ( !p.hasNext() ) {
7934 Phylogeny p2_0 = p.next();
7935 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7936 System.out.println( p2_0.toNewHampshire() );
7939 if ( !p.hasNext() ) {
7942 Phylogeny p2_1 = p.next();
7943 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7944 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7947 if ( !p.hasNext() ) {
7950 Phylogeny p2_2 = p.next();
7951 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
7952 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
7955 if ( !p.hasNext() ) {
7958 Phylogeny p2_3 = p.next();
7959 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
7960 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
7963 if ( !p.hasNext() ) {
7966 Phylogeny p2_4 = p.next();
7967 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
7968 System.out.println( "(X) != " + p2_4.toNewHampshire() );
7971 if ( p.hasNext() ) {
7974 if ( p.next() != null ) {
7979 if ( !p.hasNext() ) {
7983 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7984 System.out.println( p2_0.toNewHampshire() );
7987 if ( !p.hasNext() ) {
7991 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7992 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7995 if ( !p.hasNext() ) {
7999 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8000 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8003 if ( !p.hasNext() ) {
8007 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8008 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8011 if ( !p.hasNext() ) {
8015 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8016 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8019 if ( p.hasNext() ) {
8022 if ( p.next() != null ) {
8026 final String p3_str = "((A,B),C)abc";
8027 p.setSource( p3_str );
8028 if ( !p.hasNext() ) {
8031 final Phylogeny p3_0 = p.next();
8032 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8035 if ( p.hasNext() ) {
8038 if ( p.next() != null ) {
8042 final String p4_str = "((A,B)ab,C)abc";
8043 p.setSource( p4_str );
8044 if ( !p.hasNext() ) {
8047 final Phylogeny p4_0 = p.next();
8048 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8051 if ( p.hasNext() ) {
8054 if ( p.next() != null ) {
8058 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8059 p.setSource( p5_str );
8060 if ( !p.hasNext() ) {
8063 final Phylogeny p5_0 = p.next();
8064 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8067 if ( p.hasNext() ) {
8070 if ( p.next() != null ) {
8074 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8075 p.setSource( p6_str );
8076 if ( !p.hasNext() ) {
8079 Phylogeny p6_0 = p.next();
8080 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8083 if ( p.hasNext() ) {
8086 if ( p.next() != null ) {
8090 if ( !p.hasNext() ) {
8094 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8097 if ( p.hasNext() ) {
8100 if ( p.next() != null ) {
8104 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8105 p.setSource( p7_str );
8106 if ( !p.hasNext() ) {
8109 Phylogeny p7_0 = p.next();
8110 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8113 if ( p.hasNext() ) {
8116 if ( p.next() != null ) {
8120 if ( !p.hasNext() ) {
8124 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8127 if ( p.hasNext() ) {
8130 if ( p.next() != null ) {
8134 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8135 p.setSource( p8_str );
8136 if ( !p.hasNext() ) {
8139 Phylogeny p8_0 = p.next();
8140 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8143 if ( !p.hasNext() ) {
8146 if ( !p.hasNext() ) {
8149 Phylogeny p8_1 = p.next();
8150 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8153 if ( p.hasNext() ) {
8156 if ( p.next() != null ) {
8160 if ( !p.hasNext() ) {
8164 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8167 if ( !p.hasNext() ) {
8171 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8174 if ( p.hasNext() ) {
8177 if ( p.next() != null ) {
8183 if ( p.hasNext() ) {
8187 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8188 if ( !p.hasNext() ) {
8191 Phylogeny p_27 = p.next();
8192 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8193 System.out.println( p_27.toNewHampshireX() );
8197 if ( p.hasNext() ) {
8200 if ( p.next() != null ) {
8204 if ( !p.hasNext() ) {
8208 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8209 System.out.println( p_27.toNewHampshireX() );
8213 if ( p.hasNext() ) {
8216 if ( p.next() != null ) {
8220 final String p30_str = "(A,B);(C,D)";
8221 final NHXParser p30 = new NHXParser();
8222 p30.setSource( p30_str );
8223 if ( !p30.hasNext() ) {
8226 Phylogeny phy30 = p30.next();
8227 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8228 System.out.println( phy30.toNewHampshire() );
8231 if ( !p30.hasNext() ) {
8234 Phylogeny phy301 = p30.next();
8235 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8236 System.out.println( phy301.toNewHampshire() );
8239 if ( p30.hasNext() ) {
8242 if ( p30.hasNext() ) {
8245 if ( p30.next() != null ) {
8248 if ( p30.next() != null ) {
8252 if ( !p30.hasNext() ) {
8256 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8257 System.out.println( phy30.toNewHampshire() );
8260 if ( !p30.hasNext() ) {
8263 phy301 = p30.next();
8264 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8265 System.out.println( phy301.toNewHampshire() );
8268 if ( p30.hasNext() ) {
8271 if ( p30.hasNext() ) {
8274 if ( p30.next() != null ) {
8277 if ( p30.next() != null ) {
8281 catch ( final Exception e ) {
8282 e.printStackTrace( System.out );
8288 private static boolean testNHXconversion() {
8290 final PhylogenyNode n1 = new PhylogenyNode();
8291 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8292 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8293 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8294 final PhylogenyNode n5 = PhylogenyNode
8295 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8296 final PhylogenyNode n6 = PhylogenyNode
8297 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8298 if ( !n1.toNewHampshireX().equals( "" ) ) {
8301 if ( !n2.toNewHampshireX().equals( "" ) ) {
8304 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8307 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
8310 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
8313 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
8314 System.out.println( n6.toNewHampshireX() );
8318 catch ( final Exception e ) {
8319 e.printStackTrace( System.out );
8325 private static boolean testNHXNodeParsing() {
8327 final PhylogenyNode n1 = new PhylogenyNode();
8328 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8329 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8330 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8331 final PhylogenyNode n5 = PhylogenyNode
8332 .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]" );
8333 if ( !n3.getName().equals( "n3" ) ) {
8336 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8339 if ( n3.isDuplication() ) {
8342 if ( n3.isHasAssignedEvent() ) {
8345 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
8348 if ( !n4.getName().equals( "n4" ) ) {
8351 if ( n4.getDistanceToParent() != 0.01 ) {
8354 if ( !n5.getName().equals( "n5" ) ) {
8357 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
8360 if ( n5.getDistanceToParent() != 0.1 ) {
8363 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
8366 if ( !n5.isDuplication() ) {
8369 if ( !n5.isHasAssignedEvent() ) {
8372 final PhylogenyNode n8 = PhylogenyNode
8373 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
8374 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8375 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8378 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
8381 final PhylogenyNode n9 = PhylogenyNode
8382 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
8383 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8384 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
8387 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
8390 final PhylogenyNode n10 = PhylogenyNode
8391 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8392 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
8395 final PhylogenyNode n20 = PhylogenyNode
8396 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8397 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8400 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
8403 final PhylogenyNode n20x = PhylogenyNode
8404 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8405 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
8408 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
8411 final PhylogenyNode n20xx = PhylogenyNode
8412 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8413 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
8416 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
8419 final PhylogenyNode n20xxx = PhylogenyNode
8420 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8421 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
8424 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
8427 final PhylogenyNode n20xxxx = PhylogenyNode
8428 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8429 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
8432 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
8435 final PhylogenyNode n21 = PhylogenyNode
8436 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8437 if ( !n21.getName().equals( "N21_PIG" ) ) {
8440 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
8443 final PhylogenyNode n21x = PhylogenyNode
8444 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8445 if ( !n21x.getName().equals( "n21_PIG" ) ) {
8448 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
8451 final PhylogenyNode n22 = PhylogenyNode
8452 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8453 if ( !n22.getName().equals( "n22/PIG" ) ) {
8456 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
8459 final PhylogenyNode n23 = PhylogenyNode
8460 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8461 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
8464 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
8467 final PhylogenyNode a = PhylogenyNode
8468 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8469 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8472 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
8475 final PhylogenyNode c1 = PhylogenyNode
8476 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
8477 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8478 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
8481 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
8484 final PhylogenyNode c2 = PhylogenyNode
8485 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
8486 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8487 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
8490 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
8493 final PhylogenyNode e3 = PhylogenyNode
8494 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8495 if ( !e3.getName().equals( "n10_RAT~" ) ) {
8498 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
8501 final PhylogenyNode n11 = PhylogenyNode
8502 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
8503 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8504 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
8507 if ( n11.getDistanceToParent() != 0.4 ) {
8510 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
8513 final PhylogenyNode n12 = PhylogenyNode
8514 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
8515 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8516 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
8519 if ( n12.getDistanceToParent() != 0.4 ) {
8522 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
8525 final PhylogenyNode o = PhylogenyNode
8526 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8527 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
8530 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
8533 if ( n1.getName().compareTo( "" ) != 0 ) {
8536 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8539 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8542 if ( n2.getName().compareTo( "" ) != 0 ) {
8545 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8548 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8551 final PhylogenyNode n00 = PhylogenyNode
8552 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
8553 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
8556 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
8559 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
8560 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
8563 final PhylogenyNode n13 = PhylogenyNode
8564 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8565 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
8568 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
8571 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8574 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8577 final PhylogenyNode n14 = PhylogenyNode
8578 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8579 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
8582 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
8585 final PhylogenyNode n15 = PhylogenyNode
8586 .createInstanceFromNhxString( "something_wicked[123]",
8587 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8588 if ( !n15.getName().equals( "something_wicked" ) ) {
8591 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
8594 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
8597 final PhylogenyNode n16 = PhylogenyNode
8598 .createInstanceFromNhxString( "something_wicked2[9]",
8599 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8600 if ( !n16.getName().equals( "something_wicked2" ) ) {
8603 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
8606 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
8609 final PhylogenyNode n17 = PhylogenyNode
8610 .createInstanceFromNhxString( "something_wicked3[a]",
8611 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8612 if ( !n17.getName().equals( "something_wicked3" ) ) {
8615 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
8618 final PhylogenyNode n18 = PhylogenyNode
8619 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8620 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
8623 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
8626 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
8629 final PhylogenyNode n19 = PhylogenyNode
8630 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8631 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
8634 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8637 final PhylogenyNode n30 = PhylogenyNode
8638 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
8639 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8640 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
8643 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8646 final PhylogenyNode n31 = PhylogenyNode
8647 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
8648 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8649 if ( n31.getNodeData().isHasTaxonomy() ) {
8652 final PhylogenyNode n32 = PhylogenyNode
8653 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8654 if ( n32.getNodeData().isHasTaxonomy() ) {
8657 final PhylogenyNode n40 = PhylogenyNode
8658 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8659 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8662 final PhylogenyNode n41 = PhylogenyNode
8663 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8664 if ( n41.getNodeData().isHasTaxonomy() ) {
8667 final PhylogenyNode n42 = PhylogenyNode
8668 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8669 if ( n42.getNodeData().isHasTaxonomy() ) {
8672 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
8673 NHXParser.TAXONOMY_EXTRACTION.NO );
8674 if ( n43.getNodeData().isHasTaxonomy() ) {
8677 final PhylogenyNode n44 = PhylogenyNode
8678 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8679 if ( n44.getNodeData().isHasTaxonomy() ) {
8683 catch ( final Exception e ) {
8684 e.printStackTrace( System.out );
8690 private static boolean testNHXParsing() {
8692 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8693 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
8694 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
8697 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]";
8698 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
8699 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8702 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]";
8703 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
8704 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
8707 final Phylogeny[] p3 = factory
8708 .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]",
8710 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8713 final Phylogeny[] p4 = factory
8714 .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(]",
8716 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8719 final Phylogeny[] p5 = factory
8720 .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(((]",
8722 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8725 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)";
8726 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)";
8727 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
8728 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
8731 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)))";
8732 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)))";
8733 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
8734 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
8737 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]) ))[,,, ])))))))";
8738 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
8739 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
8740 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
8743 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
8744 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8747 final Phylogeny p10 = factory
8748 .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]",
8749 new NHXParser() )[ 0 ];
8750 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8754 catch ( final Exception e ) {
8755 e.printStackTrace( System.out );
8761 private static boolean testNHXParsingMB() {
8763 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8764 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
8765 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8766 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8767 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8768 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8769 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8770 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8771 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8772 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
8773 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
8776 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
8779 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
8780 0.1100000000000000e+00 ) ) {
8783 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
8786 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
8789 final Phylogeny p2 = factory
8790 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
8791 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8792 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8793 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8794 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8795 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8796 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8797 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8798 + "7.369400000000000e-02}])",
8799 new NHXParser() )[ 0 ];
8800 if ( p2.getNode( "1" ) == null ) {
8803 if ( p2.getNode( "2" ) == null ) {
8807 catch ( final Exception e ) {
8808 e.printStackTrace( System.out );
8815 private static boolean testNHXParsingQuotes() {
8817 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8818 final NHXParser p = new NHXParser();
8819 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
8820 if ( phylogenies_0.length != 5 ) {
8823 final Phylogeny phy = phylogenies_0[ 4 ];
8824 if ( phy.getNumberOfExternalNodes() != 7 ) {
8827 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
8830 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
8833 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
8834 .getScientificName().equals( "hsapiens" ) ) {
8837 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
8840 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
8843 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
8846 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
8849 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
8852 final NHXParser p1p = new NHXParser();
8853 p1p.setIgnoreQuotes( true );
8854 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
8855 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
8858 final NHXParser p2p = new NHXParser();
8859 p1p.setIgnoreQuotes( false );
8860 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
8861 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
8864 final NHXParser p3p = new NHXParser();
8865 p3p.setIgnoreQuotes( false );
8866 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
8867 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
8870 final NHXParser p4p = new NHXParser();
8871 p4p.setIgnoreQuotes( false );
8872 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
8873 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
8876 final Phylogeny p10 = factory
8877 .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]",
8878 new NHXParser() )[ 0 ];
8879 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]";
8880 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
8883 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
8884 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
8888 final Phylogeny p12 = factory
8889 .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]",
8890 new NHXParser() )[ 0 ];
8891 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]";
8892 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
8895 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
8896 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
8899 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;";
8900 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
8903 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
8904 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
8908 catch ( final Exception e ) {
8909 e.printStackTrace( System.out );
8915 private static boolean testNodeRemoval() {
8917 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8918 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
8919 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
8920 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
8923 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
8924 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
8925 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
8928 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
8929 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
8930 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
8934 catch ( final Exception e ) {
8935 e.printStackTrace( System.out );
8941 private static boolean testPhylogenyBranch() {
8943 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
8944 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
8945 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
8946 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
8947 if ( !a1b1.equals( a1b1 ) ) {
8950 if ( !a1b1.equals( b1a1 ) ) {
8953 if ( !b1a1.equals( a1b1 ) ) {
8956 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
8957 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
8958 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
8959 if ( a1_b1.equals( b1_a1 ) ) {
8962 if ( a1_b1.equals( a1_b1_ ) ) {
8965 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
8966 if ( !a1_b1.equals( b1_a1_ ) ) {
8969 if ( a1_b1_.equals( b1_a1_ ) ) {
8972 if ( !a1_b1_.equals( b1_a1 ) ) {
8976 catch ( final Exception e ) {
8977 e.printStackTrace( System.out );
8983 private static boolean testPhyloXMLparsingOfDistributionElement() {
8985 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8986 PhyloXmlParser xml_parser = null;
8988 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
8990 catch ( final Exception e ) {
8991 // Do nothing -- means were not running from jar.
8993 if ( xml_parser == null ) {
8994 xml_parser = PhyloXmlParser.createPhyloXmlParser();
8995 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
8996 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
8999 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9002 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9004 if ( xml_parser.getErrorCount() > 0 ) {
9005 System.out.println( xml_parser.getErrorMessages().toString() );
9008 if ( phylogenies_0.length != 1 ) {
9011 final Phylogeny t1 = phylogenies_0[ 0 ];
9012 PhylogenyNode n = null;
9013 Distribution d = null;
9014 n = t1.getNode( "root node" );
9015 if ( !n.getNodeData().isHasDistribution() ) {
9018 if ( n.getNodeData().getDistributions().size() != 1 ) {
9021 d = n.getNodeData().getDistribution();
9022 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9025 if ( d.getPoints().size() != 1 ) {
9028 if ( d.getPolygons() != null ) {
9031 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9034 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9037 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9040 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9043 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9046 n = t1.getNode( "node a" );
9047 if ( !n.getNodeData().isHasDistribution() ) {
9050 if ( n.getNodeData().getDistributions().size() != 2 ) {
9053 d = n.getNodeData().getDistribution( 1 );
9054 if ( !d.getDesc().equals( "San Diego" ) ) {
9057 if ( d.getPoints().size() != 1 ) {
9060 if ( d.getPolygons() != null ) {
9063 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9066 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9069 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9072 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9075 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9078 n = t1.getNode( "node bb" );
9079 if ( !n.getNodeData().isHasDistribution() ) {
9082 if ( n.getNodeData().getDistributions().size() != 1 ) {
9085 d = n.getNodeData().getDistribution( 0 );
9086 if ( d.getPoints().size() != 3 ) {
9089 if ( d.getPolygons().size() != 2 ) {
9092 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9095 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9098 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9101 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9104 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9107 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9110 Polygon p = d.getPolygons().get( 0 );
9111 if ( p.getPoints().size() != 3 ) {
9114 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9117 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9120 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9123 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9126 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9129 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9132 p = d.getPolygons().get( 1 );
9133 if ( p.getPoints().size() != 3 ) {
9136 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9139 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9142 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9146 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9147 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9148 if ( rt.length != 1 ) {
9151 final Phylogeny t1_rt = rt[ 0 ];
9152 n = t1_rt.getNode( "root node" );
9153 if ( !n.getNodeData().isHasDistribution() ) {
9156 if ( n.getNodeData().getDistributions().size() != 1 ) {
9159 d = n.getNodeData().getDistribution();
9160 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9163 if ( d.getPoints().size() != 1 ) {
9166 if ( d.getPolygons() != null ) {
9169 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9172 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9175 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9178 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9181 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9184 n = t1_rt.getNode( "node a" );
9185 if ( !n.getNodeData().isHasDistribution() ) {
9188 if ( n.getNodeData().getDistributions().size() != 2 ) {
9191 d = n.getNodeData().getDistribution( 1 );
9192 if ( !d.getDesc().equals( "San Diego" ) ) {
9195 if ( d.getPoints().size() != 1 ) {
9198 if ( d.getPolygons() != null ) {
9201 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9204 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9207 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9210 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9213 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9216 n = t1_rt.getNode( "node bb" );
9217 if ( !n.getNodeData().isHasDistribution() ) {
9220 if ( n.getNodeData().getDistributions().size() != 1 ) {
9223 d = n.getNodeData().getDistribution( 0 );
9224 if ( d.getPoints().size() != 3 ) {
9227 if ( d.getPolygons().size() != 2 ) {
9230 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9233 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9236 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9239 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9242 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9245 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9248 p = d.getPolygons().get( 0 );
9249 if ( p.getPoints().size() != 3 ) {
9252 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9255 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9258 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9261 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9264 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9267 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9270 p = d.getPolygons().get( 1 );
9271 if ( p.getPoints().size() != 3 ) {
9274 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9277 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9280 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9284 catch ( final Exception e ) {
9285 e.printStackTrace( System.out );
9291 private static boolean testPostOrderIterator() {
9293 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9294 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9295 PhylogenyNodeIterator it0;
9296 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
9299 for( it0.reset(); it0.hasNext(); ) {
9302 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
9303 final PhylogenyNodeIterator it = t1.iteratorPostorder();
9304 if ( !it.next().getName().equals( "A" ) ) {
9307 if ( !it.next().getName().equals( "B" ) ) {
9310 if ( !it.next().getName().equals( "ab" ) ) {
9313 if ( !it.next().getName().equals( "C" ) ) {
9316 if ( !it.next().getName().equals( "D" ) ) {
9319 if ( !it.next().getName().equals( "cd" ) ) {
9322 if ( !it.next().getName().equals( "abcd" ) ) {
9325 if ( !it.next().getName().equals( "E" ) ) {
9328 if ( !it.next().getName().equals( "F" ) ) {
9331 if ( !it.next().getName().equals( "ef" ) ) {
9334 if ( !it.next().getName().equals( "G" ) ) {
9337 if ( !it.next().getName().equals( "H" ) ) {
9340 if ( !it.next().getName().equals( "gh" ) ) {
9343 if ( !it.next().getName().equals( "efgh" ) ) {
9346 if ( !it.next().getName().equals( "r" ) ) {
9349 if ( it.hasNext() ) {
9353 catch ( final Exception e ) {
9354 e.printStackTrace( System.out );
9360 private static boolean testPreOrderIterator() {
9362 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9363 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9364 PhylogenyNodeIterator it0;
9365 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
9368 for( it0.reset(); it0.hasNext(); ) {
9371 PhylogenyNodeIterator it = t0.iteratorPreorder();
9372 if ( !it.next().getName().equals( "r" ) ) {
9375 if ( !it.next().getName().equals( "ab" ) ) {
9378 if ( !it.next().getName().equals( "A" ) ) {
9381 if ( !it.next().getName().equals( "B" ) ) {
9384 if ( !it.next().getName().equals( "cd" ) ) {
9387 if ( !it.next().getName().equals( "C" ) ) {
9390 if ( !it.next().getName().equals( "D" ) ) {
9393 if ( it.hasNext() ) {
9396 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
9397 it = t1.iteratorPreorder();
9398 if ( !it.next().getName().equals( "r" ) ) {
9401 if ( !it.next().getName().equals( "abcd" ) ) {
9404 if ( !it.next().getName().equals( "ab" ) ) {
9407 if ( !it.next().getName().equals( "A" ) ) {
9410 if ( !it.next().getName().equals( "B" ) ) {
9413 if ( !it.next().getName().equals( "cd" ) ) {
9416 if ( !it.next().getName().equals( "C" ) ) {
9419 if ( !it.next().getName().equals( "D" ) ) {
9422 if ( !it.next().getName().equals( "efgh" ) ) {
9425 if ( !it.next().getName().equals( "ef" ) ) {
9428 if ( !it.next().getName().equals( "E" ) ) {
9431 if ( !it.next().getName().equals( "F" ) ) {
9434 if ( !it.next().getName().equals( "gh" ) ) {
9437 if ( !it.next().getName().equals( "G" ) ) {
9440 if ( !it.next().getName().equals( "H" ) ) {
9443 if ( it.hasNext() ) {
9447 catch ( final Exception e ) {
9448 e.printStackTrace( System.out );
9454 private static boolean testPropertiesMap() {
9456 final PropertiesMap pm = new PropertiesMap();
9457 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9458 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9459 final Property p2 = new Property( "something:else",
9461 "improbable:research",
9464 pm.addProperty( p0 );
9465 pm.addProperty( p1 );
9466 pm.addProperty( p2 );
9467 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
9470 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
9473 if ( pm.getProperties().size() != 3 ) {
9476 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
9479 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9482 if ( pm.getProperties().size() != 3 ) {
9485 pm.removeProperty( "dimensions:diameter" );
9486 if ( pm.getProperties().size() != 2 ) {
9489 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
9492 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9496 catch ( final Exception e ) {
9497 e.printStackTrace( System.out );
9503 private static boolean testProteinId() {
9505 final ProteinId id1 = new ProteinId( "a" );
9506 final ProteinId id2 = new ProteinId( "a" );
9507 final ProteinId id3 = new ProteinId( "A" );
9508 final ProteinId id4 = new ProteinId( "b" );
9509 if ( !id1.equals( id1 ) ) {
9512 if ( id1.getId().equals( "x" ) ) {
9515 if ( id1.getId().equals( null ) ) {
9518 if ( !id1.equals( id2 ) ) {
9521 if ( id1.equals( id3 ) ) {
9524 if ( id1.hashCode() != id1.hashCode() ) {
9527 if ( id1.hashCode() != id2.hashCode() ) {
9530 if ( id1.hashCode() == id3.hashCode() ) {
9533 if ( id1.compareTo( id1 ) != 0 ) {
9536 if ( id1.compareTo( id2 ) != 0 ) {
9539 if ( id1.compareTo( id3 ) != 0 ) {
9542 if ( id1.compareTo( id4 ) >= 0 ) {
9545 if ( id4.compareTo( id1 ) <= 0 ) {
9548 if ( !id4.getId().equals( "b" ) ) {
9551 final ProteinId id5 = new ProteinId( " C " );
9552 if ( !id5.getId().equals( "C" ) ) {
9555 if ( id5.equals( id1 ) ) {
9559 catch ( final Exception e ) {
9560 e.printStackTrace( System.out );
9566 private static boolean testReIdMethods() {
9568 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9569 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
9570 final long count = PhylogenyNode.getNodeCount();
9572 if ( p.getNode( "r" ).getId() != count ) {
9575 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
9578 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
9581 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
9584 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
9587 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
9590 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
9593 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
9596 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
9599 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
9602 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
9605 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
9608 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
9611 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
9614 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
9618 catch ( final Exception e ) {
9619 e.printStackTrace( System.out );
9625 private static boolean testRerooting() {
9627 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9628 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",
9629 new NHXParser() )[ 0 ];
9630 if ( !t1.isRooted() ) {
9633 t1.reRoot( t1.getNode( "D" ) );
9634 t1.reRoot( t1.getNode( "CD" ) );
9635 t1.reRoot( t1.getNode( "A" ) );
9636 t1.reRoot( t1.getNode( "B" ) );
9637 t1.reRoot( t1.getNode( "AB" ) );
9638 t1.reRoot( t1.getNode( "D" ) );
9639 t1.reRoot( t1.getNode( "C" ) );
9640 t1.reRoot( t1.getNode( "CD" ) );
9641 t1.reRoot( t1.getNode( "A" ) );
9642 t1.reRoot( t1.getNode( "B" ) );
9643 t1.reRoot( t1.getNode( "AB" ) );
9644 t1.reRoot( t1.getNode( "D" ) );
9645 t1.reRoot( t1.getNode( "D" ) );
9646 t1.reRoot( t1.getNode( "C" ) );
9647 t1.reRoot( t1.getNode( "A" ) );
9648 t1.reRoot( t1.getNode( "B" ) );
9649 t1.reRoot( t1.getNode( "AB" ) );
9650 t1.reRoot( t1.getNode( "C" ) );
9651 t1.reRoot( t1.getNode( "D" ) );
9652 t1.reRoot( t1.getNode( "CD" ) );
9653 t1.reRoot( t1.getNode( "D" ) );
9654 t1.reRoot( t1.getNode( "A" ) );
9655 t1.reRoot( t1.getNode( "B" ) );
9656 t1.reRoot( t1.getNode( "AB" ) );
9657 t1.reRoot( t1.getNode( "C" ) );
9658 t1.reRoot( t1.getNode( "D" ) );
9659 t1.reRoot( t1.getNode( "CD" ) );
9660 t1.reRoot( t1.getNode( "D" ) );
9661 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
9664 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
9667 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
9670 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
9673 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
9676 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
9679 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",
9680 new NHXParser() )[ 0 ];
9681 t2.reRoot( t2.getNode( "A" ) );
9682 t2.reRoot( t2.getNode( "D" ) );
9683 t2.reRoot( t2.getNode( "ABC" ) );
9684 t2.reRoot( t2.getNode( "A" ) );
9685 t2.reRoot( t2.getNode( "B" ) );
9686 t2.reRoot( t2.getNode( "D" ) );
9687 t2.reRoot( t2.getNode( "C" ) );
9688 t2.reRoot( t2.getNode( "ABC" ) );
9689 t2.reRoot( t2.getNode( "A" ) );
9690 t2.reRoot( t2.getNode( "B" ) );
9691 t2.reRoot( t2.getNode( "AB" ) );
9692 t2.reRoot( t2.getNode( "AB" ) );
9693 t2.reRoot( t2.getNode( "D" ) );
9694 t2.reRoot( t2.getNode( "C" ) );
9695 t2.reRoot( t2.getNode( "B" ) );
9696 t2.reRoot( t2.getNode( "AB" ) );
9697 t2.reRoot( t2.getNode( "D" ) );
9698 t2.reRoot( t2.getNode( "D" ) );
9699 t2.reRoot( t2.getNode( "ABC" ) );
9700 t2.reRoot( t2.getNode( "A" ) );
9701 t2.reRoot( t2.getNode( "B" ) );
9702 t2.reRoot( t2.getNode( "AB" ) );
9703 t2.reRoot( t2.getNode( "D" ) );
9704 t2.reRoot( t2.getNode( "C" ) );
9705 t2.reRoot( t2.getNode( "ABC" ) );
9706 t2.reRoot( t2.getNode( "A" ) );
9707 t2.reRoot( t2.getNode( "B" ) );
9708 t2.reRoot( t2.getNode( "AB" ) );
9709 t2.reRoot( t2.getNode( "D" ) );
9710 t2.reRoot( t2.getNode( "D" ) );
9711 t2.reRoot( t2.getNode( "C" ) );
9712 t2.reRoot( t2.getNode( "A" ) );
9713 t2.reRoot( t2.getNode( "B" ) );
9714 t2.reRoot( t2.getNode( "AB" ) );
9715 t2.reRoot( t2.getNode( "C" ) );
9716 t2.reRoot( t2.getNode( "D" ) );
9717 t2.reRoot( t2.getNode( "ABC" ) );
9718 t2.reRoot( t2.getNode( "D" ) );
9719 t2.reRoot( t2.getNode( "A" ) );
9720 t2.reRoot( t2.getNode( "B" ) );
9721 t2.reRoot( t2.getNode( "AB" ) );
9722 t2.reRoot( t2.getNode( "C" ) );
9723 t2.reRoot( t2.getNode( "D" ) );
9724 t2.reRoot( t2.getNode( "ABC" ) );
9725 t2.reRoot( t2.getNode( "D" ) );
9726 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9729 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9732 t2.reRoot( t2.getNode( "ABC" ) );
9733 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9736 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9739 t2.reRoot( t2.getNode( "AB" ) );
9740 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9743 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9746 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9749 t2.reRoot( t2.getNode( "AB" ) );
9750 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9753 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9756 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9759 t2.reRoot( t2.getNode( "D" ) );
9760 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9763 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9766 t2.reRoot( t2.getNode( "ABC" ) );
9767 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9770 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9773 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
9774 new NHXParser() )[ 0 ];
9775 t3.reRoot( t3.getNode( "B" ) );
9776 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9779 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9782 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9785 t3.reRoot( t3.getNode( "B" ) );
9786 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9789 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9792 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9795 t3.reRoot( t3.getRoot() );
9796 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9799 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9802 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9806 catch ( final Exception e ) {
9807 e.printStackTrace( System.out );
9813 private static boolean testSDIse() {
9815 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9816 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
9817 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
9818 gene1.setRooted( true );
9819 species1.setRooted( true );
9820 final SDI sdi = new SDI( gene1, species1 );
9821 if ( !gene1.getRoot().isDuplication() ) {
9824 final Phylogeny species2 = factory
9825 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9826 new NHXParser() )[ 0 ];
9827 final Phylogeny gene2 = factory
9828 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9829 new NHXParser() )[ 0 ];
9830 species2.setRooted( true );
9831 gene2.setRooted( true );
9832 final SDI sdi2 = new SDI( gene2, species2 );
9833 if ( sdi2.getDuplicationsSum() != 0 ) {
9836 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
9839 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
9842 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
9845 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
9848 if ( !gene2.getNode( "r" ).isSpeciation() ) {
9851 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
9854 final Phylogeny species3 = factory
9855 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9856 new NHXParser() )[ 0 ];
9857 final Phylogeny gene3 = factory
9858 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9859 new NHXParser() )[ 0 ];
9860 species3.setRooted( true );
9861 gene3.setRooted( true );
9862 final SDI sdi3 = new SDI( gene3, species3 );
9863 if ( sdi3.getDuplicationsSum() != 1 ) {
9866 if ( !gene3.getNode( "aa" ).isDuplication() ) {
9869 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
9872 final Phylogeny species4 = factory
9873 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9874 new NHXParser() )[ 0 ];
9875 final Phylogeny gene4 = factory
9876 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9877 new NHXParser() )[ 0 ];
9878 species4.setRooted( true );
9879 gene4.setRooted( true );
9880 final SDI sdi4 = new SDI( gene4, species4 );
9881 if ( sdi4.getDuplicationsSum() != 1 ) {
9884 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
9887 if ( !gene4.getNode( "abc" ).isDuplication() ) {
9890 if ( gene4.getNode( "abcd" ).isDuplication() ) {
9893 if ( species4.getNumberOfExternalNodes() != 6 ) {
9896 if ( gene4.getNumberOfExternalNodes() != 6 ) {
9899 final Phylogeny species5 = factory
9900 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9901 new NHXParser() )[ 0 ];
9902 final Phylogeny gene5 = factory
9903 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9904 new NHXParser() )[ 0 ];
9905 species5.setRooted( true );
9906 gene5.setRooted( true );
9907 final SDI sdi5 = new SDI( gene5, species5 );
9908 if ( sdi5.getDuplicationsSum() != 2 ) {
9911 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
9914 if ( !gene5.getNode( "adc" ).isDuplication() ) {
9917 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
9920 if ( species5.getNumberOfExternalNodes() != 6 ) {
9923 if ( gene5.getNumberOfExternalNodes() != 6 ) {
9926 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
9927 // Conjecture for Comparing Molecular Phylogenies"
9928 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
9929 final Phylogeny species6 = factory
9930 .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,"
9931 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9932 new NHXParser() )[ 0 ];
9933 final Phylogeny gene6 = factory
9934 .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,"
9935 + "((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,"
9936 + "(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;",
9937 new NHXParser() )[ 0 ];
9938 species6.setRooted( true );
9939 gene6.setRooted( true );
9940 final SDI sdi6 = new SDI( gene6, species6 );
9941 if ( sdi6.getDuplicationsSum() != 3 ) {
9944 if ( !gene6.getNode( "r" ).isDuplication() ) {
9947 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
9950 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
9953 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
9956 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
9959 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
9962 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
9965 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
9968 sdi6.computeMappingCostL();
9969 if ( sdi6.computeMappingCostL() != 17 ) {
9972 if ( species6.getNumberOfExternalNodes() != 9 ) {
9975 if ( gene6.getNumberOfExternalNodes() != 9 ) {
9978 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
9979 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
9980 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
9981 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
9982 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
9983 species7.setRooted( true );
9984 final Phylogeny gene7_1 = Test
9985 .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])" );
9986 gene7_1.setRooted( true );
9987 final SDI sdi7 = new SDI( gene7_1, species7 );
9988 if ( sdi7.getDuplicationsSum() != 0 ) {
9991 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
9994 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
9997 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10000 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10003 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10006 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10009 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10012 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10015 final Phylogeny gene7_2 = Test
10016 .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])" );
10017 gene7_2.setRooted( true );
10018 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10019 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10022 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10025 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10028 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10031 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10034 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10037 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10040 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10043 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10046 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10050 catch ( final Exception e ) {
10056 private static boolean testSDIunrooted() {
10058 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10059 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10060 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10061 final Iterator<PhylogenyBranch> iter = l.iterator();
10062 PhylogenyBranch br = iter.next();
10063 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10066 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10070 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10073 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10077 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10080 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10084 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10087 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10091 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10094 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10098 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10101 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10105 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10108 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10112 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10115 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10119 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10122 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10126 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10129 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10133 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10136 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10140 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10143 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10147 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10150 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10154 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10157 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10161 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10164 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10167 if ( iter.hasNext() ) {
10170 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10171 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10172 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10174 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10177 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10181 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10184 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10188 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10191 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10194 if ( iter1.hasNext() ) {
10197 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10198 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10199 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10201 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10204 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10208 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10211 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10215 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10218 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10221 if ( iter2.hasNext() ) {
10224 final Phylogeny species0 = factory
10225 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10226 new NHXParser() )[ 0 ];
10227 final Phylogeny gene1 = factory
10228 .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])",
10229 new NHXParser() )[ 0 ];
10230 species0.setRooted( true );
10231 gene1.setRooted( true );
10232 final SDIR sdi_unrooted = new SDIR();
10233 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10234 if ( sdi_unrooted.getCount() != 1 ) {
10237 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10240 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10243 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10246 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10249 final Phylogeny gene2 = factory
10250 .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])",
10251 new NHXParser() )[ 0 ];
10252 gene2.setRooted( true );
10253 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10254 if ( sdi_unrooted.getCount() != 1 ) {
10257 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10260 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10263 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10266 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10269 final Phylogeny species6 = factory
10270 .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,"
10271 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10272 new NHXParser() )[ 0 ];
10273 final Phylogeny gene6 = factory
10274 .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],"
10275 + "(((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],"
10276 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10277 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10278 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10279 new NHXParser() )[ 0 ];
10280 species6.setRooted( true );
10281 gene6.setRooted( true );
10282 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10283 if ( sdi_unrooted.getCount() != 1 ) {
10286 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10289 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10292 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10295 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10298 if ( !p6[ 0 ].getRoot().isDuplication() ) {
10301 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10304 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10307 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
10310 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10313 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
10316 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
10319 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10323 final Phylogeny species7 = factory
10324 .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,"
10325 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10326 new NHXParser() )[ 0 ];
10327 final Phylogeny gene7 = factory
10328 .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],"
10329 + "(((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],"
10330 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10331 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10332 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10333 new NHXParser() )[ 0 ];
10334 species7.setRooted( true );
10335 gene7.setRooted( true );
10336 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
10337 if ( sdi_unrooted.getCount() != 1 ) {
10340 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10343 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10346 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10349 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
10352 if ( !p7[ 0 ].getRoot().isDuplication() ) {
10355 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10358 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10361 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
10364 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10367 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
10370 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
10373 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10377 final Phylogeny species8 = factory
10378 .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,"
10379 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10380 new NHXParser() )[ 0 ];
10381 final Phylogeny gene8 = factory
10382 .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],"
10383 + "(((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],"
10384 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10385 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10386 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10387 new NHXParser() )[ 0 ];
10388 species8.setRooted( true );
10389 gene8.setRooted( true );
10390 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
10391 if ( sdi_unrooted.getCount() != 1 ) {
10394 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10397 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10400 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10403 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10406 if ( !p8[ 0 ].getRoot().isDuplication() ) {
10409 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10412 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10415 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
10418 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10421 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
10424 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
10427 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10432 catch ( final Exception e ) {
10433 e.printStackTrace( System.out );
10439 private static boolean testSequenceDbWsTools1() {
10441 final PhylogenyNode n = new PhylogenyNode();
10442 n.setName( "NP_001025424" );
10443 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
10444 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10445 || !acc.getValue().equals( "NP_001025424" ) ) {
10448 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
10449 acc = SequenceDbWsTools.obtainSeqAccession( n );
10450 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10451 || !acc.getValue().equals( "NP_001025424" ) ) {
10454 n.setName( "NP_001025424.1" );
10455 acc = SequenceDbWsTools.obtainSeqAccession( n );
10456 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10457 || !acc.getValue().equals( "NP_001025424" ) ) {
10460 n.setName( "NM_001030253" );
10461 acc = SequenceDbWsTools.obtainSeqAccession( n );
10462 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10463 || !acc.getValue().equals( "NM_001030253" ) ) {
10466 n.setName( "BCL2_HUMAN" );
10467 acc = SequenceDbWsTools.obtainSeqAccession( n );
10468 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10469 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
10470 System.out.println( acc.toString() );
10473 n.setName( "P10415" );
10474 acc = SequenceDbWsTools.obtainSeqAccession( n );
10475 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10476 || !acc.getValue().equals( "P10415" ) ) {
10477 System.out.println( acc.toString() );
10480 n.setName( " P10415 " );
10481 acc = SequenceDbWsTools.obtainSeqAccession( n );
10482 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10483 || !acc.getValue().equals( "P10415" ) ) {
10484 System.out.println( acc.toString() );
10487 n.setName( "_P10415|" );
10488 acc = SequenceDbWsTools.obtainSeqAccession( n );
10489 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10490 || !acc.getValue().equals( "P10415" ) ) {
10491 System.out.println( acc.toString() );
10494 n.setName( "AY695820" );
10495 acc = SequenceDbWsTools.obtainSeqAccession( n );
10496 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10497 || !acc.getValue().equals( "AY695820" ) ) {
10498 System.out.println( acc.toString() );
10501 n.setName( "_AY695820_" );
10502 acc = SequenceDbWsTools.obtainSeqAccession( n );
10503 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10504 || !acc.getValue().equals( "AY695820" ) ) {
10505 System.out.println( acc.toString() );
10508 n.setName( "AAA59452" );
10509 acc = SequenceDbWsTools.obtainSeqAccession( n );
10510 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10511 || !acc.getValue().equals( "AAA59452" ) ) {
10512 System.out.println( acc.toString() );
10515 n.setName( "_AAA59452_" );
10516 acc = SequenceDbWsTools.obtainSeqAccession( n );
10517 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10518 || !acc.getValue().equals( "AAA59452" ) ) {
10519 System.out.println( acc.toString() );
10522 n.setName( "AAA59452.1" );
10523 acc = SequenceDbWsTools.obtainSeqAccession( n );
10524 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10525 || !acc.getValue().equals( "AAA59452.1" ) ) {
10526 System.out.println( acc.toString() );
10529 n.setName( "_AAA59452.1_" );
10530 acc = SequenceDbWsTools.obtainSeqAccession( n );
10531 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10532 || !acc.getValue().equals( "AAA59452.1" ) ) {
10533 System.out.println( acc.toString() );
10536 n.setName( "GI:94894583" );
10537 acc = SequenceDbWsTools.obtainSeqAccession( n );
10538 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
10539 || !acc.getValue().equals( "94894583" ) ) {
10540 System.out.println( acc.toString() );
10543 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
10544 acc = SequenceDbWsTools.obtainSeqAccession( n );
10545 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
10546 || !acc.getValue().equals( "71845847" ) ) {
10547 System.out.println( acc.toString() );
10550 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
10551 acc = SequenceDbWsTools.obtainSeqAccession( n );
10552 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10553 || !acc.getValue().equals( "AAZ45343.1" ) ) {
10554 System.out.println( acc.toString() );
10558 catch ( final Exception e ) {
10564 private static boolean testSequenceDbWsTools2() {
10566 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
10567 SequenceDbWsTools.obtainSeqInformation( n1 );
10568 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
10571 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
10574 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10577 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
10580 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
10581 SequenceDbWsTools.obtainSeqInformation( n2 );
10582 if ( !n2.getNodeData().getSequence().getName()
10583 .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
10586 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
10589 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10592 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
10595 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
10596 SequenceDbWsTools.obtainSeqInformation( n3 );
10597 if ( !n3.getNodeData().getSequence().getName()
10598 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
10601 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
10604 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10607 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
10611 catch ( final IOException e ) {
10612 System.out.println();
10613 System.out.println( "the following might be due to absence internet connection:" );
10614 e.printStackTrace( System.out );
10617 catch ( final Exception e ) {
10618 e.printStackTrace();
10624 private static boolean testSequenceIdParsing() {
10626 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
10627 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10628 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10629 if ( id != null ) {
10630 System.out.println( "value =" + id.getValue() );
10631 System.out.println( "provider=" + id.getSource() );
10636 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
10637 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10638 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10639 if ( id != null ) {
10640 System.out.println( "value =" + id.getValue() );
10641 System.out.println( "provider=" + id.getSource() );
10646 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
10647 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10648 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10649 if ( id != null ) {
10650 System.out.println( "value =" + id.getValue() );
10651 System.out.println( "provider=" + id.getSource() );
10656 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
10657 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10658 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
10659 if ( id != null ) {
10660 System.out.println( "value =" + id.getValue() );
10661 System.out.println( "provider=" + id.getSource() );
10666 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
10667 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10668 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
10669 if ( id != null ) {
10670 System.out.println( "value =" + id.getValue() );
10671 System.out.println( "provider=" + id.getSource() );
10676 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
10677 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10678 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
10679 if ( id != null ) {
10680 System.out.println( "value =" + id.getValue() );
10681 System.out.println( "provider=" + id.getSource() );
10686 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
10687 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10688 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
10689 if ( id != null ) {
10690 System.out.println( "value =" + id.getValue() );
10691 System.out.println( "provider=" + id.getSource() );
10696 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
10697 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10698 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10699 if ( id != null ) {
10700 System.out.println( "value =" + id.getValue() );
10701 System.out.println( "provider=" + id.getSource() );
10706 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
10707 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10708 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10709 if ( id != null ) {
10710 System.out.println( "value =" + id.getValue() );
10711 System.out.println( "provider=" + id.getSource() );
10716 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
10717 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10718 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
10719 if ( id != null ) {
10720 System.out.println( "value =" + id.getValue() );
10721 System.out.println( "provider=" + id.getSource() );
10725 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
10726 if ( id != null ) {
10727 System.out.println( "value =" + id.getValue() );
10728 System.out.println( "provider=" + id.getSource() );
10732 catch ( final Exception e ) {
10733 e.printStackTrace( System.out );
10739 private static boolean testSequenceWriter() {
10741 final String n = ForesterUtil.LINE_SEPARATOR;
10742 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
10745 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
10748 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
10751 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
10754 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
10755 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
10758 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
10759 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
10763 catch ( final Exception e ) {
10764 e.printStackTrace();
10770 private static boolean testSpecies() {
10772 final Species s1 = new BasicSpecies( "a" );
10773 final Species s2 = new BasicSpecies( "a" );
10774 final Species s3 = new BasicSpecies( "A" );
10775 final Species s4 = new BasicSpecies( "b" );
10776 if ( !s1.equals( s1 ) ) {
10779 if ( s1.getSpeciesId().equals( "x" ) ) {
10782 if ( s1.getSpeciesId().equals( null ) ) {
10785 if ( !s1.equals( s2 ) ) {
10788 if ( s1.equals( s3 ) ) {
10791 if ( s1.hashCode() != s1.hashCode() ) {
10794 if ( s1.hashCode() != s2.hashCode() ) {
10797 if ( s1.hashCode() == s3.hashCode() ) {
10800 if ( s1.compareTo( s1 ) != 0 ) {
10803 if ( s1.compareTo( s2 ) != 0 ) {
10806 if ( s1.compareTo( s3 ) != 0 ) {
10809 if ( s1.compareTo( s4 ) >= 0 ) {
10812 if ( s4.compareTo( s1 ) <= 0 ) {
10815 if ( !s4.getSpeciesId().equals( "b" ) ) {
10818 final Species s5 = new BasicSpecies( " C " );
10819 if ( !s5.getSpeciesId().equals( "C" ) ) {
10822 if ( s5.equals( s1 ) ) {
10826 catch ( final Exception e ) {
10827 e.printStackTrace( System.out );
10833 private static boolean testSplit() {
10835 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10836 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
10837 //Archaeopteryx.createApplication( p0 );
10838 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
10839 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10840 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10841 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10842 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10843 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10844 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10845 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10846 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10847 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10848 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
10849 // System.out.println( s0.toString() );
10851 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
10852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10854 if ( s0.match( query_nodes ) ) {
10857 query_nodes = new HashSet<PhylogenyNode>();
10858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10864 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10865 if ( !s0.match( query_nodes ) ) {
10869 query_nodes = new HashSet<PhylogenyNode>();
10870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10873 if ( !s0.match( query_nodes ) ) {
10877 query_nodes = new HashSet<PhylogenyNode>();
10878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10882 if ( !s0.match( query_nodes ) ) {
10886 query_nodes = new HashSet<PhylogenyNode>();
10887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10890 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10891 if ( !s0.match( query_nodes ) ) {
10895 query_nodes = new HashSet<PhylogenyNode>();
10896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10899 if ( !s0.match( query_nodes ) ) {
10903 query_nodes = new HashSet<PhylogenyNode>();
10904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10906 if ( !s0.match( query_nodes ) ) {
10910 query_nodes = new HashSet<PhylogenyNode>();
10911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10916 if ( !s0.match( query_nodes ) ) {
10920 query_nodes = new HashSet<PhylogenyNode>();
10921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10924 if ( !s0.match( query_nodes ) ) {
10928 query_nodes = new HashSet<PhylogenyNode>();
10929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10933 if ( !s0.match( query_nodes ) ) {
10937 query_nodes = new HashSet<PhylogenyNode>();
10938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10940 if ( s0.match( query_nodes ) ) {
10944 query_nodes = new HashSet<PhylogenyNode>();
10945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10949 if ( s0.match( query_nodes ) ) {
10953 query_nodes = new HashSet<PhylogenyNode>();
10954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10959 if ( s0.match( query_nodes ) ) {
10963 query_nodes = new HashSet<PhylogenyNode>();
10964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10967 if ( s0.match( query_nodes ) ) {
10971 query_nodes = new HashSet<PhylogenyNode>();
10972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10974 if ( s0.match( query_nodes ) ) {
10978 query_nodes = new HashSet<PhylogenyNode>();
10979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10981 if ( s0.match( query_nodes ) ) {
10985 query_nodes = new HashSet<PhylogenyNode>();
10986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10988 if ( s0.match( query_nodes ) ) {
10992 query_nodes = new HashSet<PhylogenyNode>();
10993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10995 if ( s0.match( query_nodes ) ) {
10999 query_nodes = new HashSet<PhylogenyNode>();
11000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11002 if ( s0.match( query_nodes ) ) {
11006 query_nodes = new HashSet<PhylogenyNode>();
11007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11009 if ( s0.match( query_nodes ) ) {
11013 query_nodes = new HashSet<PhylogenyNode>();
11014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11017 if ( s0.match( query_nodes ) ) {
11021 query_nodes = new HashSet<PhylogenyNode>();
11022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11025 if ( s0.match( query_nodes ) ) {
11029 query_nodes = new HashSet<PhylogenyNode>();
11030 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11033 if ( s0.match( query_nodes ) ) {
11037 query_nodes = new HashSet<PhylogenyNode>();
11038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11042 if ( s0.match( query_nodes ) ) {
11046 // query_nodes = new HashSet<PhylogenyNode>();
11047 // query_nodes.add( new PhylogenyNode( "X" ) );
11048 // query_nodes.add( new PhylogenyNode( "Y" ) );
11049 // query_nodes.add( new PhylogenyNode( "A" ) );
11050 // query_nodes.add( new PhylogenyNode( "B" ) );
11051 // query_nodes.add( new PhylogenyNode( "C" ) );
11052 // query_nodes.add( new PhylogenyNode( "D" ) );
11053 // query_nodes.add( new PhylogenyNode( "E" ) );
11054 // query_nodes.add( new PhylogenyNode( "F" ) );
11055 // query_nodes.add( new PhylogenyNode( "G" ) );
11056 // if ( !s0.match( query_nodes ) ) {
11059 // query_nodes = new HashSet<PhylogenyNode>();
11060 // query_nodes.add( new PhylogenyNode( "X" ) );
11061 // query_nodes.add( new PhylogenyNode( "Y" ) );
11062 // query_nodes.add( new PhylogenyNode( "A" ) );
11063 // query_nodes.add( new PhylogenyNode( "B" ) );
11064 // query_nodes.add( new PhylogenyNode( "C" ) );
11065 // if ( !s0.match( query_nodes ) ) {
11069 // query_nodes = new HashSet<PhylogenyNode>();
11070 // query_nodes.add( new PhylogenyNode( "X" ) );
11071 // query_nodes.add( new PhylogenyNode( "Y" ) );
11072 // query_nodes.add( new PhylogenyNode( "D" ) );
11073 // query_nodes.add( new PhylogenyNode( "E" ) );
11074 // query_nodes.add( new PhylogenyNode( "F" ) );
11075 // query_nodes.add( new PhylogenyNode( "G" ) );
11076 // if ( !s0.match( query_nodes ) ) {
11080 // query_nodes = new HashSet<PhylogenyNode>();
11081 // query_nodes.add( new PhylogenyNode( "X" ) );
11082 // query_nodes.add( new PhylogenyNode( "Y" ) );
11083 // query_nodes.add( new PhylogenyNode( "A" ) );
11084 // query_nodes.add( new PhylogenyNode( "B" ) );
11085 // query_nodes.add( new PhylogenyNode( "C" ) );
11086 // query_nodes.add( new PhylogenyNode( "D" ) );
11087 // if ( !s0.match( query_nodes ) ) {
11091 // query_nodes = new HashSet<PhylogenyNode>();
11092 // query_nodes.add( new PhylogenyNode( "X" ) );
11093 // query_nodes.add( new PhylogenyNode( "Y" ) );
11094 // query_nodes.add( new PhylogenyNode( "E" ) );
11095 // query_nodes.add( new PhylogenyNode( "F" ) );
11096 // query_nodes.add( new PhylogenyNode( "G" ) );
11097 // if ( !s0.match( query_nodes ) ) {
11101 // query_nodes = new HashSet<PhylogenyNode>();
11102 // query_nodes.add( new PhylogenyNode( "X" ) );
11103 // query_nodes.add( new PhylogenyNode( "Y" ) );
11104 // query_nodes.add( new PhylogenyNode( "F" ) );
11105 // query_nodes.add( new PhylogenyNode( "G" ) );
11106 // if ( !s0.match( query_nodes ) ) {
11110 query_nodes = new HashSet<PhylogenyNode>();
11111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11115 if ( s0.match( query_nodes ) ) {
11119 query_nodes = new HashSet<PhylogenyNode>();
11120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11124 if ( s0.match( query_nodes ) ) {
11127 ///////////////////////////
11129 query_nodes = new HashSet<PhylogenyNode>();
11130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11134 if ( s0.match( query_nodes ) ) {
11138 query_nodes = new HashSet<PhylogenyNode>();
11139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11143 if ( s0.match( query_nodes ) ) {
11147 query_nodes = new HashSet<PhylogenyNode>();
11148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11151 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11152 if ( s0.match( query_nodes ) ) {
11156 query_nodes = new HashSet<PhylogenyNode>();
11157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11159 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11160 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11161 if ( s0.match( query_nodes ) ) {
11165 query_nodes = new HashSet<PhylogenyNode>();
11166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11169 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11170 if ( s0.match( query_nodes ) ) {
11174 query_nodes = new HashSet<PhylogenyNode>();
11175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11178 if ( s0.match( query_nodes ) ) {
11182 query_nodes = new HashSet<PhylogenyNode>();
11183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11188 if ( s0.match( query_nodes ) ) {
11192 query_nodes = new HashSet<PhylogenyNode>();
11193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11197 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11198 if ( s0.match( query_nodes ) ) {
11202 query_nodes = new HashSet<PhylogenyNode>();
11203 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11208 if ( s0.match( query_nodes ) ) {
11212 query_nodes = new HashSet<PhylogenyNode>();
11213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11217 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11218 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11219 if ( s0.match( query_nodes ) ) {
11223 catch ( final Exception e ) {
11224 e.printStackTrace();
11230 private static boolean testSplitStrict() {
11232 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11233 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11234 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11235 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11236 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11237 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11238 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11239 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11240 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11241 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11242 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11243 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11246 if ( s0.match( query_nodes ) ) {
11249 query_nodes = new HashSet<PhylogenyNode>();
11250 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11257 if ( !s0.match( query_nodes ) ) {
11261 query_nodes = new HashSet<PhylogenyNode>();
11262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11265 if ( !s0.match( query_nodes ) ) {
11269 query_nodes = new HashSet<PhylogenyNode>();
11270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11274 if ( !s0.match( query_nodes ) ) {
11278 query_nodes = new HashSet<PhylogenyNode>();
11279 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11280 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11282 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11283 if ( !s0.match( query_nodes ) ) {
11287 query_nodes = new HashSet<PhylogenyNode>();
11288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11290 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11291 if ( !s0.match( query_nodes ) ) {
11295 query_nodes = new HashSet<PhylogenyNode>();
11296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11298 if ( !s0.match( query_nodes ) ) {
11302 query_nodes = new HashSet<PhylogenyNode>();
11303 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11305 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11306 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11307 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11308 if ( !s0.match( query_nodes ) ) {
11312 query_nodes = new HashSet<PhylogenyNode>();
11313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11315 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11316 if ( !s0.match( query_nodes ) ) {
11320 query_nodes = new HashSet<PhylogenyNode>();
11321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11322 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11323 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11325 if ( !s0.match( query_nodes ) ) {
11329 query_nodes = new HashSet<PhylogenyNode>();
11330 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11332 if ( s0.match( query_nodes ) ) {
11336 query_nodes = new HashSet<PhylogenyNode>();
11337 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11338 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11341 if ( s0.match( query_nodes ) ) {
11345 query_nodes = new HashSet<PhylogenyNode>();
11346 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11351 if ( s0.match( query_nodes ) ) {
11355 query_nodes = new HashSet<PhylogenyNode>();
11356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11359 if ( s0.match( query_nodes ) ) {
11363 query_nodes = new HashSet<PhylogenyNode>();
11364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11366 if ( s0.match( query_nodes ) ) {
11370 query_nodes = new HashSet<PhylogenyNode>();
11371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11373 if ( s0.match( query_nodes ) ) {
11377 query_nodes = new HashSet<PhylogenyNode>();
11378 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11380 if ( s0.match( query_nodes ) ) {
11384 query_nodes = new HashSet<PhylogenyNode>();
11385 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11386 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11387 if ( s0.match( query_nodes ) ) {
11391 query_nodes = new HashSet<PhylogenyNode>();
11392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11394 if ( s0.match( query_nodes ) ) {
11398 query_nodes = new HashSet<PhylogenyNode>();
11399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11401 if ( s0.match( query_nodes ) ) {
11405 query_nodes = new HashSet<PhylogenyNode>();
11406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11407 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11409 if ( s0.match( query_nodes ) ) {
11413 query_nodes = new HashSet<PhylogenyNode>();
11414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11417 if ( s0.match( query_nodes ) ) {
11421 query_nodes = new HashSet<PhylogenyNode>();
11422 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11423 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11424 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11425 if ( s0.match( query_nodes ) ) {
11429 query_nodes = new HashSet<PhylogenyNode>();
11430 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11431 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11432 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11434 if ( s0.match( query_nodes ) ) {
11438 catch ( final Exception e ) {
11439 e.printStackTrace();
11445 private static boolean testSubtreeDeletion() {
11447 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11448 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
11449 t1.deleteSubtree( t1.getNode( "A" ), false );
11450 if ( t1.getNumberOfExternalNodes() != 5 ) {
11453 t1.toNewHampshireX();
11454 t1.deleteSubtree( t1.getNode( "E" ), false );
11455 if ( t1.getNumberOfExternalNodes() != 4 ) {
11458 t1.toNewHampshireX();
11459 t1.deleteSubtree( t1.getNode( "F" ), false );
11460 if ( t1.getNumberOfExternalNodes() != 3 ) {
11463 t1.toNewHampshireX();
11464 t1.deleteSubtree( t1.getNode( "D" ), false );
11465 t1.toNewHampshireX();
11466 if ( t1.getNumberOfExternalNodes() != 3 ) {
11469 t1.deleteSubtree( t1.getNode( "def" ), false );
11470 t1.toNewHampshireX();
11471 if ( t1.getNumberOfExternalNodes() != 2 ) {
11474 t1.deleteSubtree( t1.getNode( "B" ), false );
11475 t1.toNewHampshireX();
11476 if ( t1.getNumberOfExternalNodes() != 1 ) {
11479 t1.deleteSubtree( t1.getNode( "C" ), false );
11480 t1.toNewHampshireX();
11481 if ( t1.getNumberOfExternalNodes() != 1 ) {
11484 t1.deleteSubtree( t1.getNode( "abc" ), false );
11485 t1.toNewHampshireX();
11486 if ( t1.getNumberOfExternalNodes() != 1 ) {
11489 t1.deleteSubtree( t1.getNode( "r" ), false );
11490 if ( t1.getNumberOfExternalNodes() != 0 ) {
11493 if ( !t1.isEmpty() ) {
11496 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
11497 t2.deleteSubtree( t2.getNode( "A" ), false );
11498 t2.toNewHampshireX();
11499 if ( t2.getNumberOfExternalNodes() != 5 ) {
11502 t2.deleteSubtree( t2.getNode( "abc" ), false );
11503 t2.toNewHampshireX();
11504 if ( t2.getNumberOfExternalNodes() != 3 ) {
11507 t2.deleteSubtree( t2.getNode( "def" ), false );
11508 t2.toNewHampshireX();
11509 if ( t2.getNumberOfExternalNodes() != 1 ) {
11513 catch ( final Exception e ) {
11514 e.printStackTrace( System.out );
11520 private static boolean testSupportCount() {
11522 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11523 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
11524 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
11525 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
11526 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
11527 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
11528 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
11530 SupportCount.count( t0_1, phylogenies_1, true, false );
11531 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
11532 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
11533 + "(((((A,B),C),D),E),((F,G),X))"
11534 + "(((((A,Y),B),C),D),((F,G),E))"
11535 + "(((((A,B),C),D),E),(F,G))"
11536 + "(((((A,B),C),D),E),(F,G))"
11537 + "(((((A,B),C),D),E),(F,G))"
11538 + "(((((A,B),C),D),E),(F,G),Z)"
11539 + "(((((A,B),C),D),E),(F,G))"
11540 + "((((((A,B),C),D),E),F),G)"
11541 + "(((((X,Y),F,G),E),((A,B),C)),D)",
11543 SupportCount.count( t0_2, phylogenies_2, true, false );
11544 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
11545 while ( it.hasNext() ) {
11546 final PhylogenyNode n = it.next();
11547 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
11551 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
11552 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
11553 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
11554 SupportCount.count( t0_3, phylogenies_3, true, false );
11555 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
11556 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
11559 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
11562 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
11565 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
11568 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
11571 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
11574 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
11577 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
11580 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
11583 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
11586 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11587 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
11588 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
11589 SupportCount.count( t0_4, phylogenies_4, true, false );
11590 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
11591 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
11594 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
11597 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
11600 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
11603 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
11606 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
11609 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
11612 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
11615 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
11618 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
11621 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11622 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11623 double d = SupportCount.compare( b1, a, true, true, true );
11624 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
11627 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11628 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11629 d = SupportCount.compare( b2, a, true, true, true );
11630 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
11633 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11634 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
11635 d = SupportCount.compare( b3, a, true, true, true );
11636 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
11639 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
11640 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
11641 d = SupportCount.compare( b4, a, true, true, false );
11642 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
11646 catch ( final Exception e ) {
11647 e.printStackTrace( System.out );
11653 private static boolean testSupportTransfer() {
11655 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11656 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)",
11657 new NHXParser() )[ 0 ];
11658 final Phylogeny p2 = factory
11659 .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 ];
11660 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
11663 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
11666 support_transfer.moveBranchLengthsToBootstrap( p1 );
11667 support_transfer.transferSupportValues( p1, p2 );
11668 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
11671 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
11674 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
11677 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
11680 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
11683 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
11686 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
11689 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
11693 catch ( final Exception e ) {
11694 e.printStackTrace( System.out );
11700 private static boolean testTaxonomyExtraction() {
11702 final PhylogenyNode n0 = PhylogenyNode
11703 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11704 if ( n0.getNodeData().isHasTaxonomy() ) {
11707 final PhylogenyNode n1 = PhylogenyNode
11708 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11709 if ( n1.getNodeData().isHasTaxonomy() ) {
11710 System.out.println( n1.toString() );
11713 final PhylogenyNode n2x = PhylogenyNode
11714 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11715 if ( n2x.getNodeData().isHasTaxonomy() ) {
11718 final PhylogenyNode n3 = PhylogenyNode
11719 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11720 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11721 System.out.println( n3.toString() );
11724 final PhylogenyNode n4 = PhylogenyNode
11725 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11726 if ( n4.getNodeData().isHasTaxonomy() ) {
11727 System.out.println( n4.toString() );
11730 final PhylogenyNode n5 = PhylogenyNode
11731 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11732 if ( n5.getNodeData().isHasTaxonomy() ) {
11733 System.out.println( n5.toString() );
11736 final PhylogenyNode n6 = PhylogenyNode
11737 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11738 if ( n6.getNodeData().isHasTaxonomy() ) {
11739 System.out.println( n6.toString() );
11742 final PhylogenyNode n7 = PhylogenyNode
11743 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11744 if ( n7.getNodeData().isHasTaxonomy() ) {
11745 System.out.println( n7.toString() );
11748 final PhylogenyNode n8 = PhylogenyNode
11749 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11750 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11751 System.out.println( n8.toString() );
11754 final PhylogenyNode n9 = PhylogenyNode
11755 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11756 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11757 System.out.println( n9.toString() );
11760 final PhylogenyNode n10x = PhylogenyNode
11761 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11762 if ( n10x.getNodeData().isHasTaxonomy() ) {
11763 System.out.println( n10x.toString() );
11766 final PhylogenyNode n10xx = PhylogenyNode
11767 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11768 if ( n10xx.getNodeData().isHasTaxonomy() ) {
11769 System.out.println( n10xx.toString() );
11772 final PhylogenyNode n10 = PhylogenyNode
11773 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11774 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
11775 System.out.println( n10.toString() );
11778 final PhylogenyNode n11 = PhylogenyNode
11779 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11780 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
11781 System.out.println( n11.toString() );
11784 final PhylogenyNode n12 = PhylogenyNode
11785 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
11786 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11787 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
11788 System.out.println( n12.toString() );
11791 final PhylogenyNode n13 = PhylogenyNode
11792 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11793 if ( n13.getNodeData().isHasTaxonomy() ) {
11794 System.out.println( n13.toString() );
11798 catch ( final Exception e ) {
11799 e.printStackTrace( System.out );
11805 private static boolean testTreeCopy() {
11807 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
11808 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
11809 final Phylogeny t1 = t0.copy();
11810 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
11813 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
11816 t0.deleteSubtree( t0.getNode( "c" ), true );
11817 t0.deleteSubtree( t0.getNode( "a" ), true );
11818 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
11819 t0.getNode( "b" ).setName( "Bee" );
11820 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
11823 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
11826 t0.deleteSubtree( t0.getNode( "e" ), true );
11827 t0.deleteSubtree( t0.getNode( "Bee" ), true );
11828 t0.deleteSubtree( t0.getNode( "d" ), true );
11829 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
11833 catch ( final Exception e ) {
11834 e.printStackTrace();
11840 private static boolean testTreeMethods() {
11842 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11843 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
11844 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
11845 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
11846 System.out.println( t0.toNewHampshireX() );
11849 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
11850 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
11851 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
11854 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
11857 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
11861 catch ( final Exception e ) {
11862 e.printStackTrace( System.out );
11868 private static boolean testUniprotEntryRetrieval() {
11870 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
11871 if ( !entry.getAccession().equals( "P12345" ) ) {
11874 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
11877 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
11880 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
11883 if ( !entry.getGeneName().equals( "GOT2" ) ) {
11886 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
11890 catch ( final IOException e ) {
11891 System.out.println();
11892 System.out.println( "the following might be due to absence internet connection:" );
11893 e.printStackTrace( System.out );
11896 catch ( final Exception e ) {
11902 private static boolean testUniprotTaxonomySearch() {
11904 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
11906 if ( results.size() != 1 ) {
11909 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11912 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11915 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11918 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11921 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11925 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
11926 if ( results.size() != 1 ) {
11929 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11932 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11935 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11938 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11941 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11945 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
11946 if ( results.size() != 1 ) {
11949 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11952 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11955 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11958 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11961 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11965 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
11966 if ( results.size() != 1 ) {
11969 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11972 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11975 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11978 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11981 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11984 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
11987 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
11990 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11991 .equals( "Nematostella vectensis" ) ) {
11992 System.out.println( results.get( 0 ).getLineage() );
11997 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
11998 if ( results.size() != 1 ) {
12001 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12004 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12007 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12010 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12013 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12016 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12017 .equals( "Xenopus tropicalis" ) ) {
12018 System.out.println( results.get( 0 ).getLineage() );
12023 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12024 if ( results.size() != 1 ) {
12027 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12030 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12033 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12036 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12039 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12042 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12043 .equals( "Xenopus tropicalis" ) ) {
12044 System.out.println( results.get( 0 ).getLineage() );
12049 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12050 if ( results.size() != 1 ) {
12053 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12056 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12059 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12062 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12065 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12068 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12069 .equals( "Xenopus tropicalis" ) ) {
12070 System.out.println( results.get( 0 ).getLineage() );
12074 catch ( final IOException e ) {
12075 System.out.println();
12076 System.out.println( "the following might be due to absence internet connection:" );
12077 e.printStackTrace( System.out );
12080 catch ( final Exception e ) {
12086 private static boolean testWabiTxSearch() {
12088 String result = "";
12089 result = TxSearch.searchSimple( "nematostella" );
12090 result = TxSearch.getTxId( "nematostella" );
12091 if ( !result.equals( "45350" ) ) {
12094 result = TxSearch.getTxName( "45350" );
12095 if ( !result.equals( "Nematostella" ) ) {
12098 result = TxSearch.getTxId( "nematostella vectensis" );
12099 if ( !result.equals( "45351" ) ) {
12102 result = TxSearch.getTxName( "45351" );
12103 if ( !result.equals( "Nematostella vectensis" ) ) {
12106 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12107 if ( !result.equals( "536089" ) ) {
12110 result = TxSearch.getTxName( "536089" );
12111 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12114 final List<String> queries = new ArrayList<String>();
12115 queries.add( "Campylobacter coli" );
12116 queries.add( "Escherichia coli" );
12117 queries.add( "Arabidopsis" );
12118 queries.add( "Trichoplax" );
12119 queries.add( "Samanea saman" );
12120 queries.add( "Kluyveromyces marxianus" );
12121 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12122 queries.add( "Bornavirus parrot/PDD/2008" );
12123 final List<RANKS> ranks = new ArrayList<RANKS>();
12124 ranks.add( RANKS.SUPERKINGDOM );
12125 ranks.add( RANKS.KINGDOM );
12126 ranks.add( RANKS.FAMILY );
12127 ranks.add( RANKS.GENUS );
12128 ranks.add( RANKS.TRIBE );
12129 result = TxSearch.searchLineage( queries, ranks );
12130 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12131 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12133 catch ( final Exception e ) {
12134 System.out.println();
12135 System.out.println( "the following might be due to absence internet connection:" );
12136 e.printStackTrace( System.out );