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.archaeopteryx.webservices.WebserviceUtil;
45 import org.forester.development.DevelopmentTools;
46 import org.forester.evoinference.TestPhylogenyReconstruction;
47 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
48 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
49 import org.forester.go.TestGo;
50 import org.forester.io.parsers.FastaParser;
51 import org.forester.io.parsers.GeneralMsaParser;
52 import org.forester.io.parsers.HmmscanPerDomainTableParser;
53 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
54 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
55 import org.forester.io.parsers.nexus.NexusCharactersParser;
56 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
57 import org.forester.io.parsers.nhx.NHXParser;
58 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
59 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
60 import org.forester.io.parsers.tol.TolParser;
61 import org.forester.io.parsers.util.ParserUtils;
62 import org.forester.io.writers.PhylogenyWriter;
63 import org.forester.io.writers.SequenceWriter;
64 import org.forester.msa.BasicMsa;
65 import org.forester.msa.Mafft;
66 import org.forester.msa.Msa;
67 import org.forester.msa.MsaInferrer;
68 import org.forester.msa.MsaMethods;
69 import org.forester.pccx.TestPccx;
70 import org.forester.phylogeny.Phylogeny;
71 import org.forester.phylogeny.PhylogenyBranch;
72 import org.forester.phylogeny.PhylogenyMethods;
73 import org.forester.phylogeny.PhylogenyNode;
74 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
75 import org.forester.phylogeny.data.Accession;
76 import org.forester.phylogeny.data.Accession.Source;
77 import org.forester.phylogeny.data.BinaryCharacters;
78 import org.forester.phylogeny.data.BranchWidth;
79 import org.forester.phylogeny.data.Confidence;
80 import org.forester.phylogeny.data.Distribution;
81 import org.forester.phylogeny.data.DomainArchitecture;
82 import org.forester.phylogeny.data.Event;
83 import org.forester.phylogeny.data.Identifier;
84 import org.forester.phylogeny.data.PhylogenyData;
85 import org.forester.phylogeny.data.PhylogenyDataUtil;
86 import org.forester.phylogeny.data.Polygon;
87 import org.forester.phylogeny.data.PropertiesMap;
88 import org.forester.phylogeny.data.Property;
89 import org.forester.phylogeny.data.Property.AppliesTo;
90 import org.forester.phylogeny.data.ProteinDomain;
91 import org.forester.phylogeny.data.Taxonomy;
92 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
93 import org.forester.phylogeny.factories.PhylogenyFactory;
94 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
95 import org.forester.protein.BasicDomain;
96 import org.forester.protein.BasicProtein;
97 import org.forester.protein.Domain;
98 import org.forester.protein.Protein;
99 import org.forester.protein.ProteinId;
100 import org.forester.rio.TestRIO;
101 import org.forester.sdi.SDI;
102 import org.forester.sdi.SDIR;
103 import org.forester.sdi.TestGSDI;
104 import org.forester.sequence.BasicSequence;
105 import org.forester.sequence.Sequence;
106 import org.forester.species.BasicSpecies;
107 import org.forester.species.Species;
108 import org.forester.surfacing.TestSurfacing;
109 import org.forester.tools.ConfidenceAssessor;
110 import org.forester.tools.SupportCount;
111 import org.forester.tools.TreeSplitMatrix;
112 import org.forester.util.AsciiHistogram;
113 import org.forester.util.BasicDescriptiveStatistics;
114 import org.forester.util.BasicTable;
115 import org.forester.util.BasicTableParser;
116 import org.forester.util.DescriptiveStatistics;
117 import org.forester.util.ForesterConstants;
118 import org.forester.util.ForesterUtil;
119 import org.forester.util.GeneralTable;
120 import org.forester.util.SequenceAccessionTools;
121 import org.forester.ws.seqdb.SequenceDatabaseEntry;
122 import org.forester.ws.seqdb.SequenceDbWsTools;
123 import org.forester.ws.seqdb.UniProtTaxonomy;
124 import org.forester.ws.wabi.TxSearch;
125 import org.forester.ws.wabi.TxSearch.RANKS;
126 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
127 import org.forester.ws.wabi.TxSearch.TAX_RANK;
129 @SuppressWarnings( "unused")
130 public final class Test {
132 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
133 + ForesterUtil.getFileSeparator() + "resources"
134 + ForesterUtil.getFileSeparator();
135 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
136 + ForesterUtil.getFileSeparator() + "test_data"
137 + ForesterUtil.getFileSeparator();
138 private final static boolean PERFORM_DB_TESTS = false;
139 private static final boolean PERFORM_WEB_TREE_ACCESS = true;
140 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
141 + ForesterConstants.PHYLO_XML_VERSION + "/"
142 + ForesterConstants.PHYLO_XML_XSD;
143 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
144 + ForesterConstants.PHYLO_XML_VERSION + "/"
145 + ForesterConstants.PHYLO_XML_XSD;
146 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
147 private final static double ZERO_DIFF = 1.0E-9;
149 public static boolean isEqual( final double a, final double b ) {
150 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
153 public static void main( final String[] args ) {
154 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
155 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
157 Locale.setDefault( Locale.US );
158 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
161 System.out.print( "[Test if directory with files for testing exists/is readable: " );
162 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
163 System.out.println( "OK.]" );
166 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
167 System.out.println( "Testing aborted." );
170 System.out.print( "[Test if resources directory exists/is readable: " );
171 if ( testDir( PATH_TO_RESOURCES ) ) {
172 System.out.println( "OK.]" );
175 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
176 System.out.println( "Testing aborted." );
179 final long start_time = new Date().getTime();
180 System.out.print( "Basic node methods: " );
181 if ( Test.testBasicNodeMethods() ) {
182 System.out.println( "OK." );
186 System.out.println( "failed." );
189 System.out.print( "Protein id: " );
190 if ( !testProteinId() ) {
191 System.out.println( "failed." );
197 System.out.println( "OK." );
198 System.out.print( "Species: " );
199 if ( !testSpecies() ) {
200 System.out.println( "failed." );
206 System.out.println( "OK." );
207 System.out.print( "Basic domain: " );
208 if ( !testBasicDomain() ) {
209 System.out.println( "failed." );
215 System.out.println( "OK." );
216 System.out.print( "Basic protein: " );
217 if ( !testBasicProtein() ) {
218 System.out.println( "failed." );
224 System.out.println( "OK." );
225 System.out.print( "Sequence writer: " );
226 if ( testSequenceWriter() ) {
227 System.out.println( "OK." );
231 System.out.println( "failed." );
234 System.out.print( "Sequence id parsing: " );
235 if ( testSequenceIdParsing() ) {
236 System.out.println( "OK." );
240 System.out.println( "failed." );
243 System.out.print( "UniProtKB id extraction: " );
244 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
245 System.out.println( "OK." );
249 System.out.println( "failed." );
252 System.out.print( "Sequence DB tools 1: " );
253 if ( testSequenceDbWsTools1() ) {
254 System.out.println( "OK." );
258 System.out.println( "failed." );
261 System.out.print( "Hmmscan output parser: " );
262 if ( testHmmscanOutputParser() ) {
263 System.out.println( "OK." );
267 System.out.println( "failed." );
270 System.out.print( "Overlap removal: " );
271 if ( !org.forester.test.Test.testOverlapRemoval() ) {
272 System.out.println( "failed." );
278 System.out.println( "OK." );
279 System.out.print( "Engulfing overlap removal: " );
280 if ( !Test.testEngulfingOverlapRemoval() ) {
281 System.out.println( "failed." );
287 System.out.println( "OK." );
288 System.out.print( "Taxonomy code extraction: " );
289 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
290 System.out.println( "OK." );
294 System.out.println( "failed." );
297 System.out.print( "SN extraction: " );
298 if ( Test.testExtractSNFromNodeName() ) {
299 System.out.println( "OK." );
303 System.out.println( "failed." );
306 System.out.print( "Taxonomy extraction (general): " );
307 if ( Test.testTaxonomyExtraction() ) {
308 System.out.println( "OK." );
312 System.out.println( "failed." );
315 System.out.print( "Uri for Aptx web sequence accession: " );
316 if ( Test.testCreateUriForSeqWeb() ) {
317 System.out.println( "OK." );
321 System.out.println( "failed." );
324 System.out.print( "Basic node construction and parsing of NHX (node level): " );
325 if ( Test.testNHXNodeParsing() ) {
326 System.out.println( "OK." );
330 System.out.println( "failed." );
333 System.out.print( "NHX parsing iterating: " );
334 if ( Test.testNHParsingIter() ) {
335 System.out.println( "OK." );
339 System.out.println( "failed." );
342 System.out.print( "NH parsing: " );
343 if ( Test.testNHParsing() ) {
344 System.out.println( "OK." );
348 System.out.println( "failed." );
351 System.out.print( "Conversion to NHX (node level): " );
352 if ( Test.testNHXconversion() ) {
353 System.out.println( "OK." );
357 System.out.println( "failed." );
360 System.out.print( "NHX parsing: " );
361 if ( Test.testNHXParsing() ) {
362 System.out.println( "OK." );
366 System.out.println( "failed." );
369 System.out.print( "NHX parsing with quotes: " );
370 if ( Test.testNHXParsingQuotes() ) {
371 System.out.println( "OK." );
375 System.out.println( "failed." );
378 System.out.print( "NHX parsing (MrBayes): " );
379 if ( Test.testNHXParsingMB() ) {
380 System.out.println( "OK." );
384 System.out.println( "failed." );
387 System.out.print( "Nexus characters parsing: " );
388 if ( Test.testNexusCharactersParsing() ) {
389 System.out.println( "OK." );
393 System.out.println( "failed." );
396 System.out.print( "Nexus tree parsing iterating: " );
397 if ( Test.testNexusTreeParsingIterating() ) {
398 System.out.println( "OK." );
402 System.out.println( "failed." );
405 System.out.print( "Nexus tree parsing: " );
406 if ( Test.testNexusTreeParsing() ) {
407 System.out.println( "OK." );
411 System.out.println( "failed." );
414 System.out.print( "Nexus tree parsing (translating): " );
415 if ( Test.testNexusTreeParsingTranslating() ) {
416 System.out.println( "OK." );
420 System.out.println( "failed." );
423 System.out.print( "Nexus matrix parsing: " );
424 if ( Test.testNexusMatrixParsing() ) {
425 System.out.println( "OK." );
429 System.out.println( "failed." );
432 System.out.print( "Basic phyloXML parsing: " );
433 if ( Test.testBasicPhyloXMLparsing() ) {
434 System.out.println( "OK." );
438 System.out.println( "failed." );
441 System.out.print( "Basic phyloXML parsing (validating against schema): " );
442 if ( testBasicPhyloXMLparsingValidating() ) {
443 System.out.println( "OK." );
447 System.out.println( "failed." );
450 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
451 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
452 System.out.println( "OK." );
456 System.out.println( "failed." );
459 System.out.print( "phyloXML Distribution Element: " );
460 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
461 System.out.println( "OK." );
465 System.out.println( "failed." );
468 System.out.print( "Tol XML parsing: " );
469 if ( Test.testBasicTolXMLparsing() ) {
470 System.out.println( "OK." );
474 System.out.println( "failed." );
477 System.out.print( "Copying of node data: " );
478 if ( Test.testCopyOfNodeData() ) {
479 System.out.println( "OK." );
483 System.out.println( "failed." );
486 System.out.print( "Tree copy: " );
487 if ( Test.testTreeCopy() ) {
488 System.out.println( "OK." );
492 System.out.println( "failed." );
495 System.out.print( "Basic tree methods: " );
496 if ( Test.testBasicTreeMethods() ) {
497 System.out.println( "OK." );
501 System.out.println( "failed." );
504 System.out.print( "Tree methods: " );
505 if ( Test.testTreeMethods() ) {
506 System.out.println( "OK." );
510 System.out.println( "failed." );
513 System.out.print( "Postorder Iterator: " );
514 if ( Test.testPostOrderIterator() ) {
515 System.out.println( "OK." );
519 System.out.println( "failed." );
522 System.out.print( "Preorder Iterator: " );
523 if ( Test.testPreOrderIterator() ) {
524 System.out.println( "OK." );
528 System.out.println( "failed." );
531 System.out.print( "Levelorder Iterator: " );
532 if ( Test.testLevelOrderIterator() ) {
533 System.out.println( "OK." );
537 System.out.println( "failed." );
540 System.out.print( "Re-id methods: " );
541 if ( Test.testReIdMethods() ) {
542 System.out.println( "OK." );
546 System.out.println( "failed." );
549 System.out.print( "Methods on last external nodes: " );
550 if ( Test.testLastExternalNodeMethods() ) {
551 System.out.println( "OK." );
555 System.out.println( "failed." );
558 System.out.print( "Methods on external nodes: " );
559 if ( Test.testExternalNodeRelatedMethods() ) {
560 System.out.println( "OK." );
564 System.out.println( "failed." );
567 System.out.print( "Deletion of external nodes: " );
568 if ( Test.testDeletionOfExternalNodes() ) {
569 System.out.println( "OK." );
573 System.out.println( "failed." );
576 System.out.print( "Subtree deletion: " );
577 if ( Test.testSubtreeDeletion() ) {
578 System.out.println( "OK." );
582 System.out.println( "failed." );
585 System.out.print( "Phylogeny branch: " );
586 if ( Test.testPhylogenyBranch() ) {
587 System.out.println( "OK." );
591 System.out.println( "failed." );
594 System.out.print( "Rerooting: " );
595 if ( Test.testRerooting() ) {
596 System.out.println( "OK." );
600 System.out.println( "failed." );
603 System.out.print( "Mipoint rooting: " );
604 if ( Test.testMidpointrooting() ) {
605 System.out.println( "OK." );
609 System.out.println( "failed." );
612 System.out.print( "Node removal: " );
613 if ( Test.testNodeRemoval() ) {
614 System.out.println( "OK." );
618 System.out.println( "failed." );
621 System.out.print( "Support count: " );
622 if ( Test.testSupportCount() ) {
623 System.out.println( "OK." );
627 System.out.println( "failed." );
630 System.out.print( "Support transfer: " );
631 if ( Test.testSupportTransfer() ) {
632 System.out.println( "OK." );
636 System.out.println( "failed." );
639 System.out.print( "Finding of LCA: " );
640 if ( Test.testGetLCA() ) {
641 System.out.println( "OK." );
645 System.out.println( "failed." );
648 System.out.print( "Finding of LCA 2: " );
649 if ( Test.testGetLCA2() ) {
650 System.out.println( "OK." );
654 System.out.println( "failed." );
657 System.out.print( "Calculation of distance between nodes: " );
658 if ( Test.testGetDistance() ) {
659 System.out.println( "OK." );
663 System.out.println( "failed." );
666 System.out.print( "Descriptive statistics: " );
667 if ( Test.testDescriptiveStatistics() ) {
668 System.out.println( "OK." );
672 System.out.println( "failed." );
675 System.out.print( "Data objects and methods: " );
676 if ( Test.testDataObjects() ) {
677 System.out.println( "OK." );
681 System.out.println( "failed." );
684 System.out.print( "Properties map: " );
685 if ( Test.testPropertiesMap() ) {
686 System.out.println( "OK." );
690 System.out.println( "failed." );
693 System.out.print( "SDIse: " );
694 if ( Test.testSDIse() ) {
695 System.out.println( "OK." );
699 System.out.println( "failed." );
702 System.out.print( "SDIunrooted: " );
703 if ( Test.testSDIunrooted() ) {
704 System.out.println( "OK." );
708 System.out.println( "failed." );
711 System.out.print( "GSDI: " );
712 if ( TestGSDI.test() ) {
713 System.out.println( "OK." );
717 System.out.println( "failed." );
720 System.out.print( "RIO: " );
721 if ( TestRIO.test() ) {
722 System.out.println( "OK." );
726 System.out.println( "failed." );
729 System.out.print( "Phylogeny reconstruction:" );
730 System.out.println();
731 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
732 System.out.println( "OK." );
736 System.out.println( "failed." );
739 System.out.print( "Analysis of domain architectures: " );
740 System.out.println();
741 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
742 System.out.println( "OK." );
746 System.out.println( "failed." );
749 System.out.print( "GO: " );
750 System.out.println();
751 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
752 System.out.println( "OK." );
756 System.out.println( "failed." );
759 System.out.print( "Modeling tools: " );
760 if ( TestPccx.test() ) {
761 System.out.println( "OK." );
765 System.out.println( "failed." );
768 System.out.print( "Split Matrix strict: " );
769 if ( Test.testSplitStrict() ) {
770 System.out.println( "OK." );
774 System.out.println( "failed." );
777 System.out.print( "Split Matrix: " );
778 if ( Test.testSplit() ) {
779 System.out.println( "OK." );
783 System.out.println( "failed." );
786 System.out.print( "Confidence Assessor: " );
787 if ( Test.testConfidenceAssessor() ) {
788 System.out.println( "OK." );
792 System.out.println( "failed." );
795 System.out.print( "Basic table: " );
796 if ( Test.testBasicTable() ) {
797 System.out.println( "OK." );
801 System.out.println( "failed." );
804 System.out.print( "General table: " );
805 if ( Test.testGeneralTable() ) {
806 System.out.println( "OK." );
810 System.out.println( "failed." );
813 System.out.print( "Amino acid sequence: " );
814 if ( Test.testAminoAcidSequence() ) {
815 System.out.println( "OK." );
819 System.out.println( "failed." );
822 System.out.print( "General MSA parser: " );
823 if ( Test.testGeneralMsaParser() ) {
824 System.out.println( "OK." );
828 System.out.println( "failed." );
831 System.out.print( "Fasta parser for msa: " );
832 if ( Test.testFastaParser() ) {
833 System.out.println( "OK." );
837 System.out.println( "failed." );
840 System.out.print( "Creation of balanced phylogeny: " );
841 if ( Test.testCreateBalancedPhylogeny() ) {
842 System.out.println( "OK." );
846 System.out.println( "failed." );
849 System.out.print( "Genbank accessor parsing: " );
850 if ( Test.testGenbankAccessorParsing() ) {
851 System.out.println( "OK." );
855 System.out.println( "failed." );
859 final String os = ForesterUtil.OS_NAME.toLowerCase();
860 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
861 path = "/usr/local/bin/mafft";
863 else if ( os.indexOf( "win" ) >= 0 ) {
864 path = "C:\\Program Files\\mafft-win\\mafft.bat";
868 if ( !MsaInferrer.isInstalled( path ) ) {
869 path = "/usr/bin/mafft";
871 if ( !MsaInferrer.isInstalled( path ) ) {
872 path = "/usr/local/bin/mafft";
875 if ( MsaInferrer.isInstalled( path ) ) {
876 System.out.print( "MAFFT (external program): " );
877 if ( Test.testMafft( path ) ) {
878 System.out.println( "OK." );
882 System.out.println( "failed [will not count towards failed tests]" );
885 System.out.print( "Next nodes with collapsed: " );
886 if ( Test.testNextNodeWithCollapsing() ) {
887 System.out.println( "OK." );
891 System.out.println( "failed." );
894 System.out.print( "Simple MSA quality: " );
895 if ( Test.testMsaQualityMethod() ) {
896 System.out.println( "OK." );
900 System.out.println( "failed." );
903 if ( PERFORM_DB_TESTS ) {
904 System.out.print( "Uniprot Entry Retrieval: " );
905 if ( Test.testUniprotEntryRetrieval() ) {
906 System.out.println( "OK." );
910 System.out.println( "failed." );
913 System.out.print( "Ebi Entry Retrieval: " );
914 if ( Test.testEbiEntryRetrieval() ) {
915 System.out.println( "OK." );
919 System.out.println( "failed." );
922 System.out.print( "Sequence DB tools 2: " );
923 if ( testSequenceDbWsTools2() ) {
924 System.out.println( "OK." );
928 System.out.println( "failed." );
932 System.out.print( "Uniprot Taxonomy Search: " );
933 if ( Test.testUniprotTaxonomySearch() ) {
934 System.out.println( "OK." );
938 System.out.println( "failed." );
942 if ( PERFORM_WEB_TREE_ACCESS ) {
943 System.out.print( "NHX parsing from URL: " );
944 if ( Test.testNHXparsingFromURL() ) {
945 System.out.println( "OK." );
949 System.out.println( "failed." );
952 System.out.print( "phyloXML parsing from URL: " );
953 if ( Test.testPhyloXMLparsingFromURL() ) {
954 System.out.println( "OK." );
958 System.out.println( "failed." );
961 System.out.print( "TreeBase acccess: " );
962 if ( Test.testTreeBaseReading() ) {
963 System.out.println( "OK." );
967 System.out.println( "failed." );
971 System.out.print( "ToL access: " );
972 if ( Test.testToLReading() ) {
973 System.out.println( "OK." );
977 System.out.println( "failed." );
981 System.out.print( "TreeFam access: " );
982 if ( Test.testTreeFamReading() ) {
983 System.out.println( "OK." );
987 System.out.println( "failed." );
992 System.out.print( "Pfam tree access: " );
993 if ( Test.testPfamTreeReading() ) {
994 System.out.println( "OK." );
998 System.out.println( "failed." );
1002 System.out.println();
1003 final Runtime rt = java.lang.Runtime.getRuntime();
1004 final long free_memory = rt.freeMemory() / 1000000;
1005 final long total_memory = rt.totalMemory() / 1000000;
1006 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1007 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1008 System.out.println();
1009 System.out.println( "Successful tests: " + succeeded );
1010 System.out.println( "Failed tests: " + failed );
1011 System.out.println();
1013 System.out.println( "OK." );
1016 System.out.println( "Not OK." );
1020 public static boolean testEngulfingOverlapRemoval() {
1022 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1023 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
1024 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
1025 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1026 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1027 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1028 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1029 final List<Boolean> covered = new ArrayList<Boolean>();
1030 covered.add( true ); // 0
1031 covered.add( false ); // 1
1032 covered.add( true ); // 2
1033 covered.add( false ); // 3
1034 covered.add( true ); // 4
1035 covered.add( true ); // 5
1036 covered.add( false ); // 6
1037 covered.add( true ); // 7
1038 covered.add( true ); // 8
1039 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
1042 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
1045 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
1048 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
1051 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
1054 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
1057 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
1060 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1061 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
1062 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
1063 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
1064 abc.addProteinDomain( a );
1065 abc.addProteinDomain( b );
1066 abc.addProteinDomain( c );
1067 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
1068 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
1069 if ( abc.getNumberOfProteinDomains() != 3 ) {
1072 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
1075 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
1078 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
1081 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
1084 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1085 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
1086 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
1087 final Protein def = new BasicProtein( "def", "nemve", 0 );
1088 def.addProteinDomain( d );
1089 def.addProteinDomain( e );
1090 def.addProteinDomain( f );
1091 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
1092 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
1093 if ( def.getNumberOfProteinDomains() != 3 ) {
1096 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
1099 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
1102 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
1105 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
1108 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
1112 catch ( final Exception e ) {
1113 e.printStackTrace( System.out );
1119 public static final boolean testNHXparsingFromURL() {
1121 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1122 final URL u = new URL( s );
1123 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1124 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1125 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1128 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1129 System.out.println( phys[ 0 ].toNewHampshire() );
1132 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1133 System.out.println( phys[ 1 ].toNewHampshire() );
1136 final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
1137 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1140 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1141 System.out.println( phys2[ 0 ].toNewHampshire() );
1144 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1145 final NHXParser p = new NHXParser();
1146 final URL u2 = new URL( s );
1148 if ( !p.hasNext() ) {
1151 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1154 if ( !p.hasNext() ) {
1158 if ( !p.hasNext() ) {
1161 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1164 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1168 if ( !p.hasNext() ) {
1171 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1174 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1178 catch ( final Exception e ) {
1179 e.printStackTrace();
1184 public static boolean testOverlapRemoval() {
1186 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1187 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1188 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1189 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1190 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1191 final List<Boolean> covered = new ArrayList<Boolean>();
1192 covered.add( true ); // 0
1193 covered.add( false ); // 1
1194 covered.add( true ); // 2
1195 covered.add( false ); // 3
1196 covered.add( true ); // 4
1197 covered.add( true ); // 5
1198 covered.add( false ); // 6
1199 covered.add( true ); // 7
1200 covered.add( true ); // 8
1201 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1204 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1207 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1210 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1213 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1216 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1217 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1218 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1219 ab.addProteinDomain( a );
1220 ab.addProteinDomain( b );
1221 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1222 if ( ab.getNumberOfProteinDomains() != 2 ) {
1225 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1228 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1231 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1232 if ( ab.getNumberOfProteinDomains() != 2 ) {
1235 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1238 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1239 final Domain d = new BasicDomain( "d",
1246 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1247 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1248 cde.addProteinDomain( c );
1249 cde.addProteinDomain( d );
1250 cde.addProteinDomain( e );
1251 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1252 if ( cde.getNumberOfProteinDomains() != 3 ) {
1255 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1258 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1259 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1260 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1261 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1262 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1263 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1264 fghi.addProteinDomain( f );
1265 fghi.addProteinDomain( g );
1266 fghi.addProteinDomain( h );
1267 fghi.addProteinDomain( i );
1268 fghi.addProteinDomain( i );
1269 fghi.addProteinDomain( i );
1270 fghi.addProteinDomain( i2 );
1271 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1272 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1275 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1278 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1281 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1282 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1285 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1288 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1289 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1290 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1291 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1292 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1293 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1294 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1295 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1296 jklm.addProteinDomain( j );
1297 jklm.addProteinDomain( k );
1298 jklm.addProteinDomain( l );
1299 jklm.addProteinDomain( m );
1300 jklm.addProteinDomain( m0 );
1301 jklm.addProteinDomain( m1 );
1302 jklm.addProteinDomain( m2 );
1303 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1304 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1307 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1310 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1313 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1314 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1317 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1320 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1321 final Protein od = new BasicProtein( "od", "varanus", 0 );
1322 od.addProteinDomain( only );
1323 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1324 if ( od.getNumberOfProteinDomains() != 1 ) {
1327 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1331 catch ( final Exception e ) {
1332 e.printStackTrace( System.out );
1338 public static final boolean testPfamTreeReading() {
1340 final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
1341 final NHXParser parser = new NHXParser();
1342 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1343 parser.setReplaceUnderscores( false );
1344 parser.setGuessRootedness( true );
1345 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1346 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1347 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1350 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1354 catch ( final Exception e ) {
1355 e.printStackTrace();
1360 public static final boolean testPhyloXMLparsingFromURL() {
1362 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1363 final URL u = new URL( s );
1364 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1365 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1366 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1370 catch ( final Exception e ) {
1371 e.printStackTrace();
1376 public static final boolean testToLReading() {
1378 final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
1379 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1380 final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
1381 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1384 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
1387 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
1390 if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
1394 catch ( final Exception e ) {
1395 e.printStackTrace();
1400 public static final boolean testTreeBaseReading() {
1402 final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
1403 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1404 parser.setReplaceUnderscores( true );
1405 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1406 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1407 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1410 final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
1411 final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
1412 parser2.setReplaceUnderscores( true );
1413 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1414 final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
1415 if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
1419 catch ( final Exception e ) {
1420 e.printStackTrace();
1425 public static final boolean testTreeFamReading() {
1427 final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
1428 final NHXParser parser = new NHXParser();
1429 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
1430 parser.setReplaceUnderscores( false );
1431 parser.setGuessRootedness( true );
1432 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1433 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1434 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1437 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1441 catch ( final Exception e ) {
1442 e.printStackTrace();
1447 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1448 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1452 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1453 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1456 private static boolean testAminoAcidSequence() {
1458 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1459 if ( aa1.getLength() != 13 ) {
1462 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1465 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1468 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1471 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1472 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
1475 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1476 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1479 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1480 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1484 catch ( final Exception e ) {
1485 e.printStackTrace();
1491 private static boolean testBasicDomain() {
1493 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1494 if ( !pd.getDomainId().equals( "id" ) ) {
1497 if ( pd.getNumber() != 1 ) {
1500 if ( pd.getTotalCount() != 4 ) {
1503 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1506 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1507 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1508 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1509 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1510 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1511 if ( !a1.equals( a1 ) ) {
1514 if ( !a1.equals( a1_copy ) ) {
1517 if ( !a1.equals( a1_equal ) ) {
1520 if ( !a1.equals( a2 ) ) {
1523 if ( a1.equals( a3 ) ) {
1526 if ( a1.compareTo( a1 ) != 0 ) {
1529 if ( a1.compareTo( a1_copy ) != 0 ) {
1532 if ( a1.compareTo( a1_equal ) != 0 ) {
1535 if ( a1.compareTo( a2 ) != 0 ) {
1538 if ( a1.compareTo( a3 ) == 0 ) {
1542 catch ( final Exception e ) {
1543 e.printStackTrace( System.out );
1549 private static boolean testBasicNodeMethods() {
1551 if ( PhylogenyNode.getNodeCount() != 0 ) {
1554 final PhylogenyNode n1 = new PhylogenyNode();
1555 final PhylogenyNode n2 = PhylogenyNode
1556 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1557 final PhylogenyNode n3 = PhylogenyNode
1558 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1559 final PhylogenyNode n4 = PhylogenyNode
1560 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1561 if ( n1.isHasAssignedEvent() ) {
1564 if ( PhylogenyNode.getNodeCount() != 4 ) {
1567 if ( n3.getIndicator() != 0 ) {
1570 if ( n3.getNumberOfExternalNodes() != 1 ) {
1573 if ( !n3.isExternal() ) {
1576 if ( !n3.isRoot() ) {
1579 if ( !n4.getName().equals( "n4" ) ) {
1583 catch ( final Exception e ) {
1584 e.printStackTrace( System.out );
1590 private static boolean testBasicPhyloXMLparsing() {
1592 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1593 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1594 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1596 if ( xml_parser.getErrorCount() > 0 ) {
1597 System.out.println( xml_parser.getErrorMessages().toString() );
1600 if ( phylogenies_0.length != 4 ) {
1603 final Phylogeny t1 = phylogenies_0[ 0 ];
1604 final Phylogeny t2 = phylogenies_0[ 1 ];
1605 final Phylogeny t3 = phylogenies_0[ 2 ];
1606 final Phylogeny t4 = phylogenies_0[ 3 ];
1607 if ( t1.getNumberOfExternalNodes() != 1 ) {
1610 if ( !t1.isRooted() ) {
1613 if ( t1.isRerootable() ) {
1616 if ( !t1.getType().equals( "gene_tree" ) ) {
1619 if ( t2.getNumberOfExternalNodes() != 2 ) {
1622 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1625 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1628 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1631 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1634 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1637 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1640 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1641 .startsWith( "actgtgggggt" ) ) {
1644 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1645 .startsWith( "ctgtgatgcat" ) ) {
1648 if ( t3.getNumberOfExternalNodes() != 4 ) {
1651 if ( !t1.getName().equals( "t1" ) ) {
1654 if ( !t2.getName().equals( "t2" ) ) {
1657 if ( !t3.getName().equals( "t3" ) ) {
1660 if ( !t4.getName().equals( "t4" ) ) {
1663 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1666 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1669 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1672 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1673 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1676 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1679 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1682 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1685 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1686 .equals( "apoptosis" ) ) {
1689 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1690 .equals( "GO:0006915" ) ) {
1693 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1694 .equals( "UniProtKB" ) ) {
1697 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1698 .equals( "experimental" ) ) {
1701 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1702 .equals( "function" ) ) {
1705 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1706 .getValue() != 1 ) {
1709 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1710 .getType().equals( "ml" ) ) {
1713 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1714 .equals( "apoptosis" ) ) {
1717 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1718 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1721 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1722 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1725 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1726 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1729 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1730 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1733 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1734 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1737 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1738 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1741 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1742 .equals( "GO:0005829" ) ) {
1745 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1746 .equals( "intracellular organelle" ) ) {
1749 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1752 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1753 .equals( "UniProt link" ) ) ) {
1756 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1759 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1760 if ( x.size() != 4 ) {
1764 for( final Accession acc : x ) {
1766 if ( !acc.getSource().equals( "KEGG" ) ) {
1769 if ( !acc.getValue().equals( "hsa:596" ) ) {
1776 catch ( final Exception e ) {
1777 e.printStackTrace( System.out );
1783 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1785 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1786 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1787 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1788 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1791 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1793 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1795 if ( xml_parser.getErrorCount() > 0 ) {
1796 System.out.println( xml_parser.getErrorMessages().toString() );
1799 if ( phylogenies_0.length != 4 ) {
1802 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1803 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1804 if ( phylogenies_t1.length != 1 ) {
1807 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1808 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1811 if ( !t1_rt.isRooted() ) {
1814 if ( t1_rt.isRerootable() ) {
1817 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1820 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1821 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1822 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1823 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1826 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1829 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1832 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1835 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1836 .startsWith( "actgtgggggt" ) ) {
1839 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1840 .startsWith( "ctgtgatgcat" ) ) {
1843 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1844 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1845 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1846 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1847 if ( phylogenies_1.length != 1 ) {
1850 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1851 if ( !t3_rt.getName().equals( "t3" ) ) {
1854 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1857 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1860 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1863 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1866 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1867 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1870 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1873 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1876 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1877 .equals( "UniProtKB" ) ) {
1880 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1881 .equals( "apoptosis" ) ) {
1884 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1885 .equals( "GO:0006915" ) ) {
1888 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1889 .equals( "UniProtKB" ) ) {
1892 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1893 .equals( "experimental" ) ) {
1896 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1897 .equals( "function" ) ) {
1900 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1901 .getValue() != 1 ) {
1904 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1905 .getType().equals( "ml" ) ) {
1908 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1909 .equals( "apoptosis" ) ) {
1912 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1913 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1916 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1917 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1920 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1921 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1924 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1925 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1928 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1929 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1932 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1933 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1936 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1937 .equals( "GO:0005829" ) ) {
1940 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1941 .equals( "intracellular organelle" ) ) {
1944 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1947 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1948 .equals( "UniProt link" ) ) ) {
1951 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1954 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1957 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1958 .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." ) ) ) {
1961 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1964 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1967 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1970 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1973 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1974 .equals( "ncbi" ) ) {
1977 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1980 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1981 .getName().equals( "B" ) ) {
1984 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1985 .getFrom() != 21 ) {
1988 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1991 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1992 .getLength() != 24 ) {
1995 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1996 .getConfidence() != 2144 ) {
1999 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2000 .equals( "pfam" ) ) {
2003 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2006 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2009 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2012 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2015 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2016 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2019 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2022 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2025 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2028 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2031 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2034 if ( taxbb.getSynonyms().size() != 2 ) {
2037 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2040 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2043 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2046 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2049 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2052 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2053 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2056 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2059 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2062 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2065 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2068 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2071 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2074 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2078 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2081 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2082 .equalsIgnoreCase( "435" ) ) {
2085 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2088 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2089 .equalsIgnoreCase( "443.7" ) ) {
2092 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2095 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2098 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2099 .equalsIgnoreCase( "433" ) ) {
2102 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2103 .getCrossReferences();
2104 if ( x.size() != 4 ) {
2108 for( final Accession acc : x ) {
2110 if ( !acc.getSource().equals( "KEGG" ) ) {
2113 if ( !acc.getValue().equals( "hsa:596" ) ) {
2120 catch ( final Exception e ) {
2121 e.printStackTrace( System.out );
2127 private static boolean testBasicPhyloXMLparsingValidating() {
2129 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2130 PhyloXmlParser xml_parser = null;
2132 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2134 catch ( final Exception e ) {
2135 // Do nothing -- means were not running from jar.
2137 if ( xml_parser == null ) {
2138 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2139 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2140 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2143 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2146 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2148 if ( xml_parser.getErrorCount() > 0 ) {
2149 System.out.println( xml_parser.getErrorMessages().toString() );
2152 if ( phylogenies_0.length != 4 ) {
2155 final Phylogeny t1 = phylogenies_0[ 0 ];
2156 final Phylogeny t2 = phylogenies_0[ 1 ];
2157 final Phylogeny t3 = phylogenies_0[ 2 ];
2158 final Phylogeny t4 = phylogenies_0[ 3 ];
2159 if ( !t1.getName().equals( "t1" ) ) {
2162 if ( !t2.getName().equals( "t2" ) ) {
2165 if ( !t3.getName().equals( "t3" ) ) {
2168 if ( !t4.getName().equals( "t4" ) ) {
2171 if ( t1.getNumberOfExternalNodes() != 1 ) {
2174 if ( t2.getNumberOfExternalNodes() != 2 ) {
2177 if ( t3.getNumberOfExternalNodes() != 4 ) {
2180 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2181 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2182 if ( xml_parser.getErrorCount() > 0 ) {
2183 System.out.println( "errors:" );
2184 System.out.println( xml_parser.getErrorMessages().toString() );
2187 if ( phylogenies_1.length != 4 ) {
2190 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2192 if ( xml_parser.getErrorCount() > 0 ) {
2193 System.out.println( "errors:" );
2194 System.out.println( xml_parser.getErrorMessages().toString() );
2197 if ( phylogenies_2.length != 1 ) {
2200 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2203 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2205 if ( xml_parser.getErrorCount() > 0 ) {
2206 System.out.println( xml_parser.getErrorMessages().toString() );
2209 if ( phylogenies_3.length != 2 ) {
2212 final Phylogeny a = phylogenies_3[ 0 ];
2213 if ( !a.getName().equals( "tree 4" ) ) {
2216 if ( a.getNumberOfExternalNodes() != 3 ) {
2219 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2222 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2225 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2227 if ( xml_parser.getErrorCount() > 0 ) {
2228 System.out.println( xml_parser.getErrorMessages().toString() );
2231 if ( phylogenies_4.length != 1 ) {
2234 final Phylogeny s = phylogenies_4[ 0 ];
2235 if ( s.getNumberOfExternalNodes() != 6 ) {
2238 s.getNode( "first" );
2240 s.getNode( "\"<a'b&c'd\">\"" );
2241 s.getNode( "'''\"" );
2242 s.getNode( "\"\"\"" );
2243 s.getNode( "dick & doof" );
2245 catch ( final Exception e ) {
2246 e.printStackTrace( System.out );
2252 private static boolean testBasicProtein() {
2254 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2255 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2256 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2257 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2258 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2259 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2260 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2261 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2262 p0.addProteinDomain( y );
2263 p0.addProteinDomain( e );
2264 p0.addProteinDomain( b );
2265 p0.addProteinDomain( c );
2266 p0.addProteinDomain( d );
2267 p0.addProteinDomain( a );
2268 p0.addProteinDomain( x );
2269 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2272 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2276 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2277 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2278 aa0.addProteinDomain( a1 );
2279 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2282 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2286 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2287 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2288 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2289 aa1.addProteinDomain( a11 );
2290 aa1.addProteinDomain( a12 );
2291 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2294 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2297 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2298 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2301 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2304 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2307 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2308 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2311 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2314 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2317 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2320 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2321 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2324 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2327 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2330 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2333 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2334 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2337 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2340 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2343 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2347 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2348 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2349 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2350 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2351 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2352 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2353 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2354 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2355 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2356 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2357 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2358 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2359 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2360 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2361 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2362 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2363 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2364 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2365 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2366 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2367 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2368 p00.addProteinDomain( y0 );
2369 p00.addProteinDomain( e0 );
2370 p00.addProteinDomain( b0 );
2371 p00.addProteinDomain( c0 );
2372 p00.addProteinDomain( d0 );
2373 p00.addProteinDomain( a0 );
2374 p00.addProteinDomain( x0 );
2375 p00.addProteinDomain( y1 );
2376 p00.addProteinDomain( y2 );
2377 p00.addProteinDomain( y3 );
2378 p00.addProteinDomain( e1 );
2379 p00.addProteinDomain( e2 );
2380 p00.addProteinDomain( e3 );
2381 p00.addProteinDomain( e4 );
2382 p00.addProteinDomain( e5 );
2383 p00.addProteinDomain( z0 );
2384 p00.addProteinDomain( z1 );
2385 p00.addProteinDomain( z2 );
2386 p00.addProteinDomain( zz0 );
2387 p00.addProteinDomain( zz1 );
2388 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2391 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2394 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2397 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2400 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" ) ) {
2403 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2404 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2405 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2406 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2407 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2408 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2409 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2410 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2411 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2412 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2413 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2414 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2415 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2416 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2417 p.addProteinDomain( B15 );
2418 p.addProteinDomain( C50 );
2419 p.addProteinDomain( A60 );
2420 p.addProteinDomain( A30 );
2421 p.addProteinDomain( C70 );
2422 p.addProteinDomain( B35 );
2423 p.addProteinDomain( B40 );
2424 p.addProteinDomain( A0 );
2425 p.addProteinDomain( A10 );
2426 p.addProteinDomain( A20 );
2427 p.addProteinDomain( B25 );
2428 p.addProteinDomain( D80 );
2429 List<String> domains_ids = new ArrayList<String>();
2430 domains_ids.add( "A" );
2431 domains_ids.add( "B" );
2432 domains_ids.add( "C" );
2433 if ( !p.contains( domains_ids, false ) ) {
2436 if ( !p.contains( domains_ids, true ) ) {
2439 domains_ids.add( "X" );
2440 if ( p.contains( domains_ids, false ) ) {
2443 if ( p.contains( domains_ids, true ) ) {
2446 domains_ids = new ArrayList<String>();
2447 domains_ids.add( "A" );
2448 domains_ids.add( "C" );
2449 domains_ids.add( "D" );
2450 if ( !p.contains( domains_ids, false ) ) {
2453 if ( !p.contains( domains_ids, true ) ) {
2456 domains_ids = new ArrayList<String>();
2457 domains_ids.add( "A" );
2458 domains_ids.add( "D" );
2459 domains_ids.add( "C" );
2460 if ( !p.contains( domains_ids, false ) ) {
2463 if ( p.contains( domains_ids, true ) ) {
2466 domains_ids = new ArrayList<String>();
2467 domains_ids.add( "A" );
2468 domains_ids.add( "A" );
2469 domains_ids.add( "B" );
2470 if ( !p.contains( domains_ids, false ) ) {
2473 if ( !p.contains( domains_ids, true ) ) {
2476 domains_ids = new ArrayList<String>();
2477 domains_ids.add( "A" );
2478 domains_ids.add( "A" );
2479 domains_ids.add( "A" );
2480 domains_ids.add( "B" );
2481 domains_ids.add( "B" );
2482 if ( !p.contains( domains_ids, false ) ) {
2485 if ( !p.contains( domains_ids, true ) ) {
2488 domains_ids = new ArrayList<String>();
2489 domains_ids.add( "A" );
2490 domains_ids.add( "A" );
2491 domains_ids.add( "B" );
2492 domains_ids.add( "A" );
2493 domains_ids.add( "B" );
2494 domains_ids.add( "B" );
2495 domains_ids.add( "A" );
2496 domains_ids.add( "B" );
2497 domains_ids.add( "C" );
2498 domains_ids.add( "A" );
2499 domains_ids.add( "C" );
2500 domains_ids.add( "D" );
2501 if ( !p.contains( domains_ids, false ) ) {
2504 if ( p.contains( domains_ids, true ) ) {
2508 catch ( final Exception e ) {
2509 e.printStackTrace( System.out );
2515 private static boolean testBasicTable() {
2517 final BasicTable<String> t0 = new BasicTable<String>();
2518 if ( t0.getNumberOfColumns() != 0 ) {
2521 if ( t0.getNumberOfRows() != 0 ) {
2524 t0.setValue( 3, 2, "23" );
2525 t0.setValue( 10, 1, "error" );
2526 t0.setValue( 10, 1, "110" );
2527 t0.setValue( 9, 1, "19" );
2528 t0.setValue( 1, 10, "101" );
2529 t0.setValue( 10, 10, "1010" );
2530 t0.setValue( 100, 10, "10100" );
2531 t0.setValue( 0, 0, "00" );
2532 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2535 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2538 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2541 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2544 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2547 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2550 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2553 if ( t0.getNumberOfColumns() != 101 ) {
2556 if ( t0.getNumberOfRows() != 11 ) {
2559 if ( t0.getValueAsString( 49, 4 ) != null ) {
2562 final String l = ForesterUtil.getLineSeparator();
2563 final StringBuffer source = new StringBuffer();
2564 source.append( "" + l );
2565 source.append( "# 1 1 1 1 1 1 1 1" + l );
2566 source.append( " 00 01 02 03" + l );
2567 source.append( " 10 11 12 13 " + l );
2568 source.append( "20 21 22 23 " + l );
2569 source.append( " 30 31 32 33" + l );
2570 source.append( "40 41 42 43" + l );
2571 source.append( " # 1 1 1 1 1 " + l );
2572 source.append( "50 51 52 53 54" + l );
2573 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2574 if ( t1.getNumberOfColumns() != 5 ) {
2577 if ( t1.getNumberOfRows() != 6 ) {
2580 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2583 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2586 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2589 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2592 final StringBuffer source1 = new StringBuffer();
2593 source1.append( "" + l );
2594 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2595 source1.append( " 00; 01 ;02;03" + l );
2596 source1.append( " 10; 11; 12; 13 " + l );
2597 source1.append( "20; 21; 22; 23 " + l );
2598 source1.append( " 30; 31; 32; 33" + l );
2599 source1.append( "40;41;42;43" + l );
2600 source1.append( " # 1 1 1 1 1 " + l );
2601 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2602 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2603 if ( t2.getNumberOfColumns() != 5 ) {
2606 if ( t2.getNumberOfRows() != 6 ) {
2609 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2612 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2615 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2618 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2621 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2624 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2627 final StringBuffer source2 = new StringBuffer();
2628 source2.append( "" + l );
2629 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2630 source2.append( " 00; 01 ;02;03" + l );
2631 source2.append( " 10; 11; 12; 13 " + l );
2632 source2.append( "20; 21; 22; 23 " + l );
2633 source2.append( " " + l );
2634 source2.append( " 30; 31; 32; 33" + l );
2635 source2.append( "40;41;42;43" + l );
2636 source2.append( " comment: 1 1 1 1 1 " + l );
2637 source2.append( ";;;50 ; 52; 53;;54 " + l );
2638 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2644 if ( tl.size() != 2 ) {
2647 final BasicTable<String> t3 = tl.get( 0 );
2648 final BasicTable<String> t4 = tl.get( 1 );
2649 if ( t3.getNumberOfColumns() != 4 ) {
2652 if ( t3.getNumberOfRows() != 3 ) {
2655 if ( t4.getNumberOfColumns() != 4 ) {
2658 if ( t4.getNumberOfRows() != 3 ) {
2661 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2664 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2668 catch ( final Exception e ) {
2669 e.printStackTrace( System.out );
2675 private static boolean testBasicTolXMLparsing() {
2677 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2678 final TolParser parser = new TolParser();
2679 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2680 if ( parser.getErrorCount() > 0 ) {
2681 System.out.println( parser.getErrorMessages().toString() );
2684 if ( phylogenies_0.length != 1 ) {
2687 final Phylogeny t1 = phylogenies_0[ 0 ];
2688 if ( t1.getNumberOfExternalNodes() != 5 ) {
2691 if ( !t1.isRooted() ) {
2694 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2697 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2700 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2703 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2706 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2707 if ( parser.getErrorCount() > 0 ) {
2708 System.out.println( parser.getErrorMessages().toString() );
2711 if ( phylogenies_1.length != 1 ) {
2714 final Phylogeny t2 = phylogenies_1[ 0 ];
2715 if ( t2.getNumberOfExternalNodes() != 664 ) {
2718 if ( !t2.isRooted() ) {
2721 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2724 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2727 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2730 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2733 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2736 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2737 .equals( "Aquifex" ) ) {
2740 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2741 if ( parser.getErrorCount() > 0 ) {
2742 System.out.println( parser.getErrorMessages().toString() );
2745 if ( phylogenies_2.length != 1 ) {
2748 final Phylogeny t3 = phylogenies_2[ 0 ];
2749 if ( t3.getNumberOfExternalNodes() != 184 ) {
2752 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2755 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2758 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2761 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2762 if ( parser.getErrorCount() > 0 ) {
2763 System.out.println( parser.getErrorMessages().toString() );
2766 if ( phylogenies_3.length != 1 ) {
2769 final Phylogeny t4 = phylogenies_3[ 0 ];
2770 if ( t4.getNumberOfExternalNodes() != 1 ) {
2773 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2776 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2779 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2782 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2783 if ( parser.getErrorCount() > 0 ) {
2784 System.out.println( parser.getErrorMessages().toString() );
2787 if ( phylogenies_4.length != 1 ) {
2790 final Phylogeny t5 = phylogenies_4[ 0 ];
2791 if ( t5.getNumberOfExternalNodes() != 13 ) {
2794 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2797 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2800 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2804 catch ( final Exception e ) {
2805 e.printStackTrace( System.out );
2811 private static boolean testBasicTreeMethods() {
2813 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2814 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2815 if ( t2.getNumberOfExternalNodes() != 4 ) {
2818 if ( t2.getHeight() != 8.5 ) {
2821 if ( !t2.isCompletelyBinary() ) {
2824 if ( t2.isEmpty() ) {
2827 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2828 if ( t3.getNumberOfExternalNodes() != 5 ) {
2831 if ( t3.getHeight() != 11 ) {
2834 if ( t3.isCompletelyBinary() ) {
2837 final PhylogenyNode n = t3.getNode( "ABC" );
2838 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 ];
2839 if ( t4.getNumberOfExternalNodes() != 9 ) {
2842 if ( t4.getHeight() != 11 ) {
2845 if ( t4.isCompletelyBinary() ) {
2848 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)" );
2849 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2850 if ( t5.getNumberOfExternalNodes() != 8 ) {
2853 if ( t5.getHeight() != 15 ) {
2856 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)" );
2857 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2858 if ( t6.getHeight() != 15 ) {
2861 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)" );
2862 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2863 if ( t7.getHeight() != 15 ) {
2866 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)" );
2867 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2868 if ( t8.getNumberOfExternalNodes() != 10 ) {
2871 if ( t8.getHeight() != 15 ) {
2874 final char[] a9 = new char[] { 'a' };
2875 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2876 if ( t9.getHeight() != 0 ) {
2879 final char[] a10 = new char[] { 'a', ':', '6' };
2880 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2881 if ( t10.getHeight() != 6 ) {
2885 catch ( final Exception e ) {
2886 e.printStackTrace( System.out );
2892 private static boolean testConfidenceAssessor() {
2894 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2895 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2896 final Phylogeny[] ev0 = factory
2897 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2899 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2900 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2903 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2906 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2907 final Phylogeny[] ev1 = factory
2908 .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)));",
2910 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2911 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2914 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2917 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2918 final Phylogeny[] ev_b = factory
2919 .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",
2921 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2922 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2925 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2929 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2930 final Phylogeny[] ev1x = factory
2931 .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)));",
2933 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2934 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2937 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2940 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2941 final Phylogeny[] ev_bx = factory
2942 .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",
2944 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2945 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2948 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2952 final Phylogeny[] t2 = factory
2953 .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);",
2955 final Phylogeny[] ev2 = factory
2956 .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);",
2958 for( final Phylogeny target : t2 ) {
2959 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2962 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2963 new NHXParser() )[ 0 ];
2964 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2965 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2966 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2969 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2972 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2976 catch ( final Exception e ) {
2977 e.printStackTrace();
2983 private static boolean testCopyOfNodeData() {
2985 final PhylogenyNode n1 = PhylogenyNode
2986 .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]" );
2987 final PhylogenyNode n2 = n1.copyNodeData();
2988 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2992 catch ( final Exception e ) {
2993 e.printStackTrace();
2999 private static boolean testCreateBalancedPhylogeny() {
3001 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3002 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3005 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3008 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3009 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3012 if ( p1.getNumberOfExternalNodes() != 100 ) {
3016 catch ( final Exception e ) {
3017 e.printStackTrace();
3023 private static boolean testCreateUriForSeqWeb() {
3025 final PhylogenyNode n = new PhylogenyNode();
3026 n.setName( "tr|B3RJ64" );
3027 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3030 n.setName( "B0LM41_HUMAN" );
3031 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3034 n.setName( "NP_001025424" );
3035 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3038 n.setName( "_NM_001030253-" );
3039 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3042 n.setName( "XM_002122186" );
3043 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3046 n.setName( "dgh_AAA34956_gdg" );
3047 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3050 n.setName( "AAA34956" );
3051 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3054 n.setName( "GI:394892" );
3055 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3056 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3059 n.setName( "gi_394892" );
3060 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3061 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3064 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3065 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3066 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3069 n.setName( "P12345" );
3070 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3071 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3074 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3075 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3076 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3080 catch ( final Exception e ) {
3081 e.printStackTrace( System.out );
3087 private static boolean testDataObjects() {
3089 final Confidence s0 = new Confidence();
3090 final Confidence s1 = new Confidence();
3091 if ( !s0.isEqual( s1 ) ) {
3094 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3095 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3096 if ( s2.isEqual( s1 ) ) {
3099 if ( !s2.isEqual( s3 ) ) {
3102 final Confidence s4 = ( Confidence ) s3.copy();
3103 if ( !s4.isEqual( s3 ) ) {
3110 final Taxonomy t1 = new Taxonomy();
3111 final Taxonomy t2 = new Taxonomy();
3112 final Taxonomy t3 = new Taxonomy();
3113 final Taxonomy t4 = new Taxonomy();
3114 final Taxonomy t5 = new Taxonomy();
3115 t1.setIdentifier( new Identifier( "ecoli" ) );
3116 t1.setTaxonomyCode( "ECOLI" );
3117 t1.setScientificName( "E. coli" );
3118 t1.setCommonName( "coli" );
3119 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3120 if ( !t1.isEqual( t0 ) ) {
3123 t2.setIdentifier( new Identifier( "ecoli" ) );
3124 t2.setTaxonomyCode( "OTHER" );
3125 t2.setScientificName( "what" );
3126 t2.setCommonName( "something" );
3127 if ( !t1.isEqual( t2 ) ) {
3130 t2.setIdentifier( new Identifier( "nemve" ) );
3131 if ( t1.isEqual( t2 ) ) {
3134 t1.setIdentifier( null );
3135 t3.setTaxonomyCode( "ECOLI" );
3136 t3.setScientificName( "what" );
3137 t3.setCommonName( "something" );
3138 if ( !t1.isEqual( t3 ) ) {
3141 t1.setIdentifier( null );
3142 t1.setTaxonomyCode( "" );
3143 t4.setScientificName( "E. ColI" );
3144 t4.setCommonName( "something" );
3145 if ( !t1.isEqual( t4 ) ) {
3148 t4.setScientificName( "B. subtilis" );
3149 t4.setCommonName( "something" );
3150 if ( t1.isEqual( t4 ) ) {
3153 t1.setIdentifier( null );
3154 t1.setTaxonomyCode( "" );
3155 t1.setScientificName( "" );
3156 t5.setCommonName( "COLI" );
3157 if ( !t1.isEqual( t5 ) ) {
3160 t5.setCommonName( "vibrio" );
3161 if ( t1.isEqual( t5 ) ) {
3166 final Identifier id0 = new Identifier( "123", "pfam" );
3167 final Identifier id1 = ( Identifier ) id0.copy();
3168 if ( !id1.isEqual( id1 ) ) {
3171 if ( !id1.isEqual( id0 ) ) {
3174 if ( !id0.isEqual( id1 ) ) {
3181 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3182 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3183 if ( !pd1.isEqual( pd1 ) ) {
3186 if ( !pd1.isEqual( pd0 ) ) {
3191 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3192 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3193 if ( !pd3.isEqual( pd3 ) ) {
3196 if ( !pd2.isEqual( pd3 ) ) {
3199 if ( !pd0.isEqual( pd3 ) ) {
3204 // DomainArchitecture
3205 // ------------------
3206 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3207 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3208 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3209 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3210 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3211 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3216 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3217 if ( ds0.getNumberOfDomains() != 4 ) {
3220 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3221 if ( !ds0.isEqual( ds0 ) ) {
3224 if ( !ds0.isEqual( ds1 ) ) {
3227 if ( ds1.getNumberOfDomains() != 4 ) {
3230 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3235 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3236 if ( ds0.isEqual( ds2 ) ) {
3242 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3243 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3244 System.out.println( ds3.toNHX() );
3247 if ( ds3.getNumberOfDomains() != 3 ) {
3252 final Event e1 = new Event( Event.EventType.fusion );
3253 if ( e1.isDuplication() ) {
3256 if ( !e1.isFusion() ) {
3259 if ( !e1.asText().toString().equals( "fusion" ) ) {
3262 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3265 final Event e11 = new Event( Event.EventType.fusion );
3266 if ( !e11.isEqual( e1 ) ) {
3269 if ( !e11.toNHX().toString().equals( "" ) ) {
3272 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3273 if ( e2.isDuplication() ) {
3276 if ( !e2.isSpeciationOrDuplication() ) {
3279 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3282 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3285 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3288 if ( e11.isEqual( e2 ) ) {
3291 final Event e2c = ( Event ) e2.copy();
3292 if ( !e2c.isEqual( e2 ) ) {
3295 Event e3 = new Event( 1, 2, 3 );
3296 if ( e3.isDuplication() ) {
3299 if ( e3.isSpeciation() ) {
3302 if ( e3.isGeneLoss() ) {
3305 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3308 final Event e3c = ( Event ) e3.copy();
3309 final Event e3cc = ( Event ) e3c.copy();
3310 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3314 if ( !e3c.isEqual( e3cc ) ) {
3317 Event e4 = new Event( 1, 2, 3 );
3318 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3321 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3324 final Event e4c = ( Event ) e4.copy();
3326 final Event e4cc = ( Event ) e4c.copy();
3327 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3330 if ( !e4c.isEqual( e4cc ) ) {
3333 final Event e5 = new Event();
3334 if ( !e5.isUnassigned() ) {
3337 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3340 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3343 final Event e6 = new Event( 1, 0, 0 );
3344 if ( !e6.asText().toString().equals( "duplication" ) ) {
3347 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3350 final Event e7 = new Event( 0, 1, 0 );
3351 if ( !e7.asText().toString().equals( "speciation" ) ) {
3354 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3357 final Event e8 = new Event( 0, 0, 1 );
3358 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3361 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3365 catch ( final Exception e ) {
3366 e.printStackTrace( System.out );
3372 private static boolean testDeletionOfExternalNodes() {
3374 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3375 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3376 final PhylogenyWriter w = new PhylogenyWriter();
3377 if ( t0.isEmpty() ) {
3380 if ( t0.getNumberOfExternalNodes() != 1 ) {
3383 t0.deleteSubtree( t0.getNode( "A" ), false );
3384 if ( t0.getNumberOfExternalNodes() != 0 ) {
3387 if ( !t0.isEmpty() ) {
3390 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3391 if ( t1.getNumberOfExternalNodes() != 2 ) {
3394 t1.deleteSubtree( t1.getNode( "A" ), false );
3395 if ( t1.getNumberOfExternalNodes() != 1 ) {
3398 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3401 t1.deleteSubtree( t1.getNode( "B" ), false );
3402 if ( t1.getNumberOfExternalNodes() != 1 ) {
3405 t1.deleteSubtree( t1.getNode( "r" ), false );
3406 if ( !t1.isEmpty() ) {
3409 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3410 if ( t2.getNumberOfExternalNodes() != 3 ) {
3413 t2.deleteSubtree( t2.getNode( "B" ), false );
3414 if ( t2.getNumberOfExternalNodes() != 2 ) {
3417 t2.toNewHampshireX();
3418 PhylogenyNode n = t2.getNode( "A" );
3419 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3422 t2.deleteSubtree( t2.getNode( "A" ), false );
3423 if ( t2.getNumberOfExternalNodes() != 2 ) {
3426 t2.deleteSubtree( t2.getNode( "C" ), true );
3427 if ( t2.getNumberOfExternalNodes() != 1 ) {
3430 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3431 if ( t3.getNumberOfExternalNodes() != 4 ) {
3434 t3.deleteSubtree( t3.getNode( "B" ), true );
3435 if ( t3.getNumberOfExternalNodes() != 3 ) {
3438 n = t3.getNode( "A" );
3439 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3442 n = n.getNextExternalNode();
3443 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3446 t3.deleteSubtree( t3.getNode( "A" ), true );
3447 if ( t3.getNumberOfExternalNodes() != 2 ) {
3450 n = t3.getNode( "C" );
3451 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3454 t3.deleteSubtree( t3.getNode( "C" ), true );
3455 if ( t3.getNumberOfExternalNodes() != 1 ) {
3458 t3.deleteSubtree( t3.getNode( "D" ), true );
3459 if ( t3.getNumberOfExternalNodes() != 0 ) {
3462 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3463 if ( t4.getNumberOfExternalNodes() != 6 ) {
3466 t4.deleteSubtree( t4.getNode( "B2" ), true );
3467 if ( t4.getNumberOfExternalNodes() != 5 ) {
3470 String s = w.toNewHampshire( t4, true ).toString();
3471 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3474 t4.deleteSubtree( t4.getNode( "B11" ), true );
3475 if ( t4.getNumberOfExternalNodes() != 4 ) {
3478 t4.deleteSubtree( t4.getNode( "C" ), true );
3479 if ( t4.getNumberOfExternalNodes() != 3 ) {
3482 n = t4.getNode( "A" );
3483 n = n.getNextExternalNode();
3484 if ( !n.getName().equals( "B12" ) ) {
3487 n = n.getNextExternalNode();
3488 if ( !n.getName().equals( "D" ) ) {
3491 s = w.toNewHampshire( t4, true ).toString();
3492 if ( !s.equals( "((A,B12),D);" ) ) {
3495 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3496 t5.deleteSubtree( t5.getNode( "A" ), true );
3497 if ( t5.getNumberOfExternalNodes() != 5 ) {
3500 s = w.toNewHampshire( t5, true ).toString();
3501 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3504 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3505 t6.deleteSubtree( t6.getNode( "B11" ), true );
3506 if ( t6.getNumberOfExternalNodes() != 5 ) {
3509 s = w.toNewHampshire( t6, false ).toString();
3510 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3513 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3514 t7.deleteSubtree( t7.getNode( "B12" ), true );
3515 if ( t7.getNumberOfExternalNodes() != 5 ) {
3518 s = w.toNewHampshire( t7, true ).toString();
3519 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3522 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3523 t8.deleteSubtree( t8.getNode( "B2" ), true );
3524 if ( t8.getNumberOfExternalNodes() != 5 ) {
3527 s = w.toNewHampshire( t8, false ).toString();
3528 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3531 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3532 t9.deleteSubtree( t9.getNode( "C" ), true );
3533 if ( t9.getNumberOfExternalNodes() != 5 ) {
3536 s = w.toNewHampshire( t9, true ).toString();
3537 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3540 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3541 t10.deleteSubtree( t10.getNode( "D" ), true );
3542 if ( t10.getNumberOfExternalNodes() != 5 ) {
3545 s = w.toNewHampshire( t10, true ).toString();
3546 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3549 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3550 t11.deleteSubtree( t11.getNode( "A" ), true );
3551 if ( t11.getNumberOfExternalNodes() != 2 ) {
3554 s = w.toNewHampshire( t11, true ).toString();
3555 if ( !s.equals( "(B,C);" ) ) {
3558 t11.deleteSubtree( t11.getNode( "C" ), true );
3559 if ( t11.getNumberOfExternalNodes() != 1 ) {
3562 s = w.toNewHampshire( t11, false ).toString();
3563 if ( !s.equals( "B;" ) ) {
3566 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3567 t12.deleteSubtree( t12.getNode( "B2" ), true );
3568 if ( t12.getNumberOfExternalNodes() != 8 ) {
3571 s = w.toNewHampshire( t12, true ).toString();
3572 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3575 t12.deleteSubtree( t12.getNode( "B3" ), true );
3576 if ( t12.getNumberOfExternalNodes() != 7 ) {
3579 s = w.toNewHampshire( t12, true ).toString();
3580 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3583 t12.deleteSubtree( t12.getNode( "C3" ), true );
3584 if ( t12.getNumberOfExternalNodes() != 6 ) {
3587 s = w.toNewHampshire( t12, true ).toString();
3588 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3591 t12.deleteSubtree( t12.getNode( "A1" ), true );
3592 if ( t12.getNumberOfExternalNodes() != 5 ) {
3595 s = w.toNewHampshire( t12, true ).toString();
3596 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3599 t12.deleteSubtree( t12.getNode( "B1" ), true );
3600 if ( t12.getNumberOfExternalNodes() != 4 ) {
3603 s = w.toNewHampshire( t12, true ).toString();
3604 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3607 t12.deleteSubtree( t12.getNode( "A3" ), true );
3608 if ( t12.getNumberOfExternalNodes() != 3 ) {
3611 s = w.toNewHampshire( t12, true ).toString();
3612 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3615 t12.deleteSubtree( t12.getNode( "A2" ), true );
3616 if ( t12.getNumberOfExternalNodes() != 2 ) {
3619 s = w.toNewHampshire( t12, true ).toString();
3620 if ( !s.equals( "(C1,C2);" ) ) {
3623 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3624 t13.deleteSubtree( t13.getNode( "D" ), true );
3625 if ( t13.getNumberOfExternalNodes() != 4 ) {
3628 s = w.toNewHampshire( t13, true ).toString();
3629 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3632 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3633 t14.deleteSubtree( t14.getNode( "E" ), true );
3634 if ( t14.getNumberOfExternalNodes() != 5 ) {
3637 s = w.toNewHampshire( t14, true ).toString();
3638 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3641 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3642 t15.deleteSubtree( t15.getNode( "B2" ), true );
3643 if ( t15.getNumberOfExternalNodes() != 11 ) {
3646 t15.deleteSubtree( t15.getNode( "B1" ), true );
3647 if ( t15.getNumberOfExternalNodes() != 10 ) {
3650 t15.deleteSubtree( t15.getNode( "B3" ), true );
3651 if ( t15.getNumberOfExternalNodes() != 9 ) {
3654 t15.deleteSubtree( t15.getNode( "B4" ), true );
3655 if ( t15.getNumberOfExternalNodes() != 8 ) {
3658 t15.deleteSubtree( t15.getNode( "A1" ), true );
3659 if ( t15.getNumberOfExternalNodes() != 7 ) {
3662 t15.deleteSubtree( t15.getNode( "C4" ), true );
3663 if ( t15.getNumberOfExternalNodes() != 6 ) {
3667 catch ( final Exception e ) {
3668 e.printStackTrace( System.out );
3674 private static boolean testDescriptiveStatistics() {
3676 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3677 dss1.addValue( 82 );
3678 dss1.addValue( 78 );
3679 dss1.addValue( 70 );
3680 dss1.addValue( 58 );
3681 dss1.addValue( 42 );
3682 if ( dss1.getN() != 5 ) {
3685 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3688 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3691 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3694 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3697 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3700 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3703 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3706 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3709 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3712 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3715 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3718 dss1.addValue( 123 );
3719 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3722 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3725 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3728 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3729 dss2.addValue( -1.85 );
3730 dss2.addValue( 57.5 );
3731 dss2.addValue( 92.78 );
3732 dss2.addValue( 57.78 );
3733 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3736 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3739 final double[] a = dss2.getDataAsDoubleArray();
3740 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3743 dss2.addValue( -100 );
3744 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3747 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3750 final double[] ds = new double[ 14 ];
3765 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3766 if ( bins.length != 4 ) {
3769 if ( bins[ 0 ] != 2 ) {
3772 if ( bins[ 1 ] != 3 ) {
3775 if ( bins[ 2 ] != 4 ) {
3778 if ( bins[ 3 ] != 5 ) {
3781 final double[] ds1 = new double[ 9 ];
3791 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3792 if ( bins1.length != 4 ) {
3795 if ( bins1[ 0 ] != 2 ) {
3798 if ( bins1[ 1 ] != 3 ) {
3801 if ( bins1[ 2 ] != 0 ) {
3804 if ( bins1[ 3 ] != 4 ) {
3807 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3808 if ( bins1_1.length != 3 ) {
3811 if ( bins1_1[ 0 ] != 3 ) {
3814 if ( bins1_1[ 1 ] != 2 ) {
3817 if ( bins1_1[ 2 ] != 4 ) {
3820 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3821 if ( bins1_2.length != 3 ) {
3824 if ( bins1_2[ 0 ] != 2 ) {
3827 if ( bins1_2[ 1 ] != 2 ) {
3830 if ( bins1_2[ 2 ] != 2 ) {
3833 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3847 dss3.addValue( 10 );
3848 dss3.addValue( 10 );
3849 dss3.addValue( 10 );
3850 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3851 histo.toStringBuffer( 10, '=', 40, 5 );
3852 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3854 catch ( final Exception e ) {
3855 e.printStackTrace( System.out );
3861 private static boolean testDir( final String file ) {
3863 final File f = new File( file );
3864 if ( !f.exists() ) {
3867 if ( !f.isDirectory() ) {
3870 if ( !f.canRead() ) {
3874 catch ( final Exception e ) {
3880 private static boolean testEbiEntryRetrieval() {
3882 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3883 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3884 System.out.println( entry.getAccession() );
3887 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
3888 System.out.println( entry.getTaxonomyScientificName() );
3891 if ( !entry.getSequenceName()
3892 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
3893 System.out.println( entry.getSequenceName() );
3896 // if ( !entry.getSequenceSymbol().equals( "" ) ) {
3897 // System.out.println( entry.getSequenceSymbol() );
3900 if ( !entry.getGeneName().equals( "treX-like" ) ) {
3901 System.out.println( entry.getGeneName() );
3904 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
3905 System.out.println( entry.getTaxonomyIdentifier() );
3908 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
3909 System.out.println( entry.getAnnotations().first().getRefValue() );
3912 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
3913 System.out.println( entry.getAnnotations().first().getRefSource() );
3916 if ( entry.getCrossReferences().size() != 5 ) {
3920 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
3921 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
3924 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
3925 System.out.println( entry1.getTaxonomyScientificName() );
3928 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
3929 System.out.println( entry1.getSequenceName() );
3932 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
3933 System.out.println( entry1.getTaxonomyIdentifier() );
3936 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
3937 System.out.println( entry1.getGeneName() );
3940 if ( entry1.getCrossReferences().size() != 6 ) {
3944 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
3945 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
3948 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
3949 System.out.println( entry2.getTaxonomyScientificName() );
3952 if ( !entry2.getSequenceName()
3953 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
3954 System.out.println( entry2.getSequenceName() );
3957 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
3958 System.out.println( entry2.getTaxonomyIdentifier() );
3961 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
3962 System.out.println( entry2.getGeneName() );
3965 if ( entry2.getCrossReferences().size() != 3 ) {
3969 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
3970 if ( !entry3.getAccession().equals( "HM043801" ) ) {
3973 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
3974 System.out.println( entry3.getTaxonomyScientificName() );
3977 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
3978 System.out.println( entry3.getSequenceName() );
3981 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
3982 System.out.println( entry3.getTaxonomyIdentifier() );
3985 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
3986 System.out.println( entry3.getSequenceSymbol() );
3989 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
3992 if ( entry3.getCrossReferences().size() != 8 ) {
3997 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
3998 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4001 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4002 System.out.println( entry4.getTaxonomyScientificName() );
4005 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4006 System.out.println( entry4.getSequenceName() );
4009 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4010 System.out.println( entry4.getTaxonomyIdentifier() );
4013 if ( !entry4.getGeneName().equals( "ras" ) ) {
4014 System.out.println( entry4.getGeneName() );
4017 // if ( !entry4.getChromosome().equals( "ras" ) ) {
4018 // System.out.println( entry4.getChromosome() );
4021 // if ( !entry4.getMap().equals( "ras" ) ) {
4022 // System.out.println( entry4.getMap() );
4028 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
4029 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
4032 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4033 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4036 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4037 System.out.println( entry5.getTaxonomyScientificName() );
4040 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4041 System.out.println( entry5.getSequenceName() );
4044 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4045 System.out.println( entry5.getTaxonomyIdentifier() );
4049 catch ( final IOException e ) {
4050 System.out.println();
4051 System.out.println( "the following might be due to absence internet connection:" );
4052 e.printStackTrace( System.out );
4055 catch ( final Exception e ) {
4056 e.printStackTrace();
4062 private static boolean testExternalNodeRelatedMethods() {
4064 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4065 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4066 PhylogenyNode n = t1.getNode( "A" );
4067 n = n.getNextExternalNode();
4068 if ( !n.getName().equals( "B" ) ) {
4071 n = n.getNextExternalNode();
4072 if ( !n.getName().equals( "C" ) ) {
4075 n = n.getNextExternalNode();
4076 if ( !n.getName().equals( "D" ) ) {
4079 n = t1.getNode( "B" );
4080 while ( !n.isLastExternalNode() ) {
4081 n = n.getNextExternalNode();
4083 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4084 n = t2.getNode( "A" );
4085 n = n.getNextExternalNode();
4086 if ( !n.getName().equals( "B" ) ) {
4089 n = n.getNextExternalNode();
4090 if ( !n.getName().equals( "C" ) ) {
4093 n = n.getNextExternalNode();
4094 if ( !n.getName().equals( "D" ) ) {
4097 n = t2.getNode( "B" );
4098 while ( !n.isLastExternalNode() ) {
4099 n = n.getNextExternalNode();
4101 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4102 n = t3.getNode( "A" );
4103 n = n.getNextExternalNode();
4104 if ( !n.getName().equals( "B" ) ) {
4107 n = n.getNextExternalNode();
4108 if ( !n.getName().equals( "C" ) ) {
4111 n = n.getNextExternalNode();
4112 if ( !n.getName().equals( "D" ) ) {
4115 n = n.getNextExternalNode();
4116 if ( !n.getName().equals( "E" ) ) {
4119 n = n.getNextExternalNode();
4120 if ( !n.getName().equals( "F" ) ) {
4123 n = n.getNextExternalNode();
4124 if ( !n.getName().equals( "G" ) ) {
4127 n = n.getNextExternalNode();
4128 if ( !n.getName().equals( "H" ) ) {
4131 n = t3.getNode( "B" );
4132 while ( !n.isLastExternalNode() ) {
4133 n = n.getNextExternalNode();
4135 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4136 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4137 final PhylogenyNode node = iter.next();
4139 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4140 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4141 final PhylogenyNode node = iter.next();
4143 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4144 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4145 if ( !iter.next().getName().equals( "A" ) ) {
4148 if ( !iter.next().getName().equals( "B" ) ) {
4151 if ( !iter.next().getName().equals( "C" ) ) {
4154 if ( !iter.next().getName().equals( "D" ) ) {
4157 if ( !iter.next().getName().equals( "E" ) ) {
4160 if ( !iter.next().getName().equals( "F" ) ) {
4163 if ( iter.hasNext() ) {
4167 catch ( final Exception e ) {
4168 e.printStackTrace( System.out );
4174 private static boolean testExtractSNFromNodeName() {
4176 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4179 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4182 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4185 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4186 .equals( "Mus musculus musculus" ) ) {
4189 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4190 .equals( "Mus musculus musculus" ) ) {
4193 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4194 .equals( "Mus musculus musculus" ) ) {
4197 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4198 .equals( "Mus musculus musculus" ) ) {
4201 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4204 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4205 .equals( "Mus musculus musculus" ) ) {
4208 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4209 .equals( "Mus musculus musculus" ) ) {
4212 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4215 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4218 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4221 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4224 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4225 .equals( "Mus musculus musculus" ) ) {
4228 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4231 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4234 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4237 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4240 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4243 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4246 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4249 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4252 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4253 .equals( "Mus musculus" ) ) {
4256 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4257 .equals( "Mus musculus" ) ) {
4260 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4263 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4264 .equals( "Mus musculus musculus" ) ) {
4267 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4268 .equals( "Mus musculus musculus" ) ) {
4271 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4272 .equals( "Mus musculus musculus" ) ) {
4275 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4278 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4279 .equals( "Pilostyles mexicana" ) ) {
4282 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4283 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4286 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4287 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4290 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4291 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4294 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4295 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4298 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4299 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4302 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4303 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4306 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
4307 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4310 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
4311 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4314 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
4315 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4318 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4319 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4322 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4323 .equals( "Escherichia coli (strain K12)" ) ) {
4326 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4327 .equals( "Escherichia coli (strain K12)" ) ) {
4330 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4331 .equals( "Escherichia coli (str. K12)" ) ) {
4334 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4335 .equals( "Escherichia coli (str. K12)" ) ) {
4338 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4339 .equals( "Escherichia coli (str. K12)" ) ) {
4342 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4343 .equals( "Escherichia coli (var. K12)" ) ) {
4346 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4347 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4350 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4351 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4355 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4356 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4359 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4360 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4364 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4365 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4368 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4369 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4372 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4373 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4376 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4379 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4382 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4385 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4386 .equals( "Macrocera sp." ) ) {
4389 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4392 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4393 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4396 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
4397 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4400 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
4401 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4404 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
4405 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4409 catch ( final Exception e ) {
4410 e.printStackTrace( System.out );
4416 private static boolean testExtractTaxonomyCodeFromNodeName() {
4418 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4421 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4422 .equals( "SOYBN" ) ) {
4425 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4426 .equals( "ARATH" ) ) {
4429 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4430 .equals( "ARATH" ) ) {
4433 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4436 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4439 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4442 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4443 .equals( "SOYBN" ) ) {
4446 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4447 .equals( "SOYBN" ) ) {
4450 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4451 .equals( "SOYBN" ) ) {
4454 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4455 .equals( "SOYBN" ) ) {
4458 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4459 .equals( "SOYBN" ) ) {
4462 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4463 .equals( "SOYBN" ) ) {
4466 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4467 .equals( "SOYBN" ) ) {
4470 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4471 .equals( "SOYBN" ) ) {
4474 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4477 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4478 .equals( "SOYBN" ) ) {
4481 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4482 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4485 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4486 .equals( "9YX45" ) ) {
4489 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4490 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4491 .equals( "MOUSE" ) ) {
4494 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4495 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4496 .equals( "MOUSE" ) ) {
4499 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4500 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4501 .equals( "MOUSE" ) ) {
4504 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4505 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4508 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4509 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4512 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4513 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4516 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4517 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4520 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4521 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4524 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4525 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4528 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4529 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4532 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4533 .equals( "RAT" ) ) {
4536 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4537 .equals( "PIG" ) ) {
4541 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4542 .equals( "MOUSE" ) ) {
4545 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4546 .equals( "MOUSE" ) ) {
4549 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4553 catch ( final Exception e ) {
4554 e.printStackTrace( System.out );
4560 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4562 PhylogenyNode n = new PhylogenyNode();
4563 n.setName( "tr|B3RJ64" );
4564 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4567 n.setName( "tr.B3RJ64" );
4568 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4571 n.setName( "tr=B3RJ64" );
4572 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4575 n.setName( "tr-B3RJ64" );
4576 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4579 n.setName( "tr/B3RJ64" );
4580 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4583 n.setName( "tr\\B3RJ64" );
4584 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4587 n.setName( "tr_B3RJ64" );
4588 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4591 n.setName( " tr|B3RJ64 " );
4592 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4595 n.setName( "-tr|B3RJ64-" );
4596 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4599 n.setName( "-tr=B3RJ64-" );
4600 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4603 n.setName( "_tr=B3RJ64_" );
4604 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4607 n.setName( " tr_tr|B3RJ64_sp|123 " );
4608 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4611 n.setName( "B3RJ64" );
4612 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4615 n.setName( "sp|B3RJ64" );
4616 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4619 n.setName( "sp|B3RJ64C" );
4620 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4623 n.setName( "sp B3RJ64" );
4624 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4627 n.setName( "sp|B3RJ6X" );
4628 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4631 n.setName( "sp|B3RJ6" );
4632 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4635 n.setName( "K1PYK7_CRAGI" );
4636 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4639 n.setName( "K1PYK7_PEA" );
4640 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4643 n.setName( "K1PYK7_RAT" );
4644 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4647 n.setName( "K1PYK7_PIG" );
4648 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4651 n.setName( "~K1PYK7_PIG~" );
4652 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4655 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4656 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4659 n.setName( "K1PYKX_CRAGI" );
4660 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4663 n.setName( "XXXXX_CRAGI" );
4664 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4667 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4668 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4671 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4672 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4675 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4676 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4679 n = new PhylogenyNode();
4680 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4681 seq.setSymbol( "K1PYK7_CRAGI" );
4682 n.getNodeData().addSequence( seq );
4683 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4686 seq.setSymbol( "tr|B3RJ64" );
4687 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4690 n = new PhylogenyNode();
4691 seq = new org.forester.phylogeny.data.Sequence();
4692 seq.setName( "K1PYK7_CRAGI" );
4693 n.getNodeData().addSequence( seq );
4694 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4697 seq.setName( "tr|B3RJ64" );
4698 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4701 n = new PhylogenyNode();
4702 seq = new org.forester.phylogeny.data.Sequence();
4703 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4704 n.getNodeData().addSequence( seq );
4705 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4708 n = new PhylogenyNode();
4709 seq = new org.forester.phylogeny.data.Sequence();
4710 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4711 n.getNodeData().addSequence( seq );
4712 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4716 n = new PhylogenyNode();
4717 n.setName( "ACP19736" );
4718 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4721 n = new PhylogenyNode();
4722 n.setName( "|ACP19736|" );
4723 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4727 catch ( final Exception e ) {
4728 e.printStackTrace( System.out );
4734 private static boolean testFastaParser() {
4736 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4739 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4742 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4743 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4746 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4749 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4752 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
4755 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4758 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4762 catch ( final Exception e ) {
4763 e.printStackTrace();
4769 private static boolean testGenbankAccessorParsing() {
4770 //The format for GenBank Accession numbers are:
4771 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4772 //Protein: 3 letters + 5 numerals
4773 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4774 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4777 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4780 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4783 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4786 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4789 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4792 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4795 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4798 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4801 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4804 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4807 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4810 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4813 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4819 private static boolean testGeneralMsaParser() {
4821 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4822 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4823 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4824 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4825 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4826 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4827 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4828 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4829 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4832 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4835 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4838 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4841 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4844 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4847 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4850 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4853 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4856 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4859 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4862 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4865 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
4866 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4869 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4872 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4875 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
4876 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
4879 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
4882 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
4885 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
4886 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4889 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4892 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4896 catch ( final Exception e ) {
4897 e.printStackTrace();
4903 private static boolean testGeneralTable() {
4905 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
4906 t0.setValue( 3, 2, "23" );
4907 t0.setValue( 10, 1, "error" );
4908 t0.setValue( 10, 1, "110" );
4909 t0.setValue( 9, 1, "19" );
4910 t0.setValue( 1, 10, "101" );
4911 t0.setValue( 10, 10, "1010" );
4912 t0.setValue( 100, 10, "10100" );
4913 t0.setValue( 0, 0, "00" );
4914 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
4917 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
4920 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
4923 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
4926 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
4929 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
4932 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
4935 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
4938 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
4941 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
4942 t1.setValue( "3", "2", "23" );
4943 t1.setValue( "10", "1", "error" );
4944 t1.setValue( "10", "1", "110" );
4945 t1.setValue( "9", "1", "19" );
4946 t1.setValue( "1", "10", "101" );
4947 t1.setValue( "10", "10", "1010" );
4948 t1.setValue( "100", "10", "10100" );
4949 t1.setValue( "0", "0", "00" );
4950 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
4951 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
4954 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
4957 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
4960 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
4963 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
4966 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
4969 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
4972 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
4975 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
4978 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
4982 catch ( final Exception e ) {
4983 e.printStackTrace( System.out );
4989 private static boolean testGetDistance() {
4991 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4992 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",
4993 new NHXParser() )[ 0 ];
4994 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
4997 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5000 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5003 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5006 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5009 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5012 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5015 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5018 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5021 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5024 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5027 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5030 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5033 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5036 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5039 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5042 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5045 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5048 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5051 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5054 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5057 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5060 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5063 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5066 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5069 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5072 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5075 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5078 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5081 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5084 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5087 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",
5088 new NHXParser() )[ 0 ];
5089 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5092 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5095 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5098 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5101 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5104 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5107 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5110 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5113 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5116 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5119 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5123 catch ( final Exception e ) {
5124 e.printStackTrace( System.out );
5130 private static boolean testGetLCA() {
5132 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5133 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5134 new NHXParser() )[ 0 ];
5135 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5136 if ( !A.getName().equals( "A" ) ) {
5139 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5140 if ( !gh.getName().equals( "gh" ) ) {
5143 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5144 if ( !ab.getName().equals( "ab" ) ) {
5147 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5148 if ( !ab2.getName().equals( "ab" ) ) {
5151 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5152 if ( !gh2.getName().equals( "gh" ) ) {
5155 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5156 if ( !gh3.getName().equals( "gh" ) ) {
5159 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5160 if ( !abc.getName().equals( "abc" ) ) {
5163 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5164 if ( !abc2.getName().equals( "abc" ) ) {
5167 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5168 if ( !abcd.getName().equals( "abcd" ) ) {
5171 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5172 if ( !abcd2.getName().equals( "abcd" ) ) {
5175 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5176 if ( !abcdef.getName().equals( "abcdef" ) ) {
5179 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5180 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5183 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5184 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5187 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5188 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5191 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5192 if ( !abcde.getName().equals( "abcde" ) ) {
5195 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5196 if ( !abcde2.getName().equals( "abcde" ) ) {
5199 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5200 if ( !r.getName().equals( "abcdefgh" ) ) {
5203 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5204 if ( !r2.getName().equals( "abcdefgh" ) ) {
5207 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5208 if ( !r3.getName().equals( "abcdefgh" ) ) {
5211 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5212 if ( !abcde3.getName().equals( "abcde" ) ) {
5215 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5216 if ( !abcde4.getName().equals( "abcde" ) ) {
5219 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5220 if ( !ab3.getName().equals( "ab" ) ) {
5223 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5224 if ( !ab4.getName().equals( "ab" ) ) {
5227 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5228 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5229 if ( !cd.getName().equals( "cd" ) ) {
5232 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5233 if ( !cd2.getName().equals( "cd" ) ) {
5236 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5237 if ( !cde.getName().equals( "cde" ) ) {
5240 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5241 if ( !cde2.getName().equals( "cde" ) ) {
5244 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5245 if ( !cdef.getName().equals( "cdef" ) ) {
5248 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5249 if ( !cdef2.getName().equals( "cdef" ) ) {
5252 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5253 if ( !cdef3.getName().equals( "cdef" ) ) {
5256 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5257 if ( !rt.getName().equals( "r" ) ) {
5260 final Phylogeny p3 = factory
5261 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5262 new NHXParser() )[ 0 ];
5263 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5264 if ( !bc_3.getName().equals( "bc" ) ) {
5267 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5268 if ( !ac_3.getName().equals( "abc" ) ) {
5271 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5272 if ( !ad_3.getName().equals( "abcde" ) ) {
5275 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5276 if ( !af_3.getName().equals( "abcdef" ) ) {
5279 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5280 if ( !ag_3.getName().equals( "" ) ) {
5283 if ( !ag_3.isRoot() ) {
5286 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5287 if ( !al_3.getName().equals( "" ) ) {
5290 if ( !al_3.isRoot() ) {
5293 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5294 if ( !kl_3.getName().equals( "" ) ) {
5297 if ( !kl_3.isRoot() ) {
5300 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5301 if ( !fl_3.getName().equals( "" ) ) {
5304 if ( !fl_3.isRoot() ) {
5307 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5308 if ( !gk_3.getName().equals( "ghijk" ) ) {
5311 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5312 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5313 if ( !r_4.getName().equals( "r" ) ) {
5316 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5317 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5318 if ( !r_5.getName().equals( "root" ) ) {
5321 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5322 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), 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 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5328 if ( !r_7.getName().equals( "rott" ) ) {
5332 catch ( final Exception e ) {
5333 e.printStackTrace( System.out );
5339 private static boolean testGetLCA2() {
5341 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5342 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5343 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5344 PhylogenyMethods.preOrderReId( p_a );
5345 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5346 p_a.getNode( "a" ) );
5347 if ( !p_a_1.getName().equals( "a" ) ) {
5350 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5351 PhylogenyMethods.preOrderReId( p_b );
5352 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5353 p_b.getNode( "a" ) );
5354 if ( !p_b_1.getName().equals( "b" ) ) {
5357 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5358 p_b.getNode( "b" ) );
5359 if ( !p_b_2.getName().equals( "b" ) ) {
5362 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5363 PhylogenyMethods.preOrderReId( p_c );
5364 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5365 p_c.getNode( "a" ) );
5366 if ( !p_c_1.getName().equals( "b" ) ) {
5369 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5370 p_c.getNode( "c" ) );
5371 if ( !p_c_2.getName().equals( "c" ) ) {
5372 System.out.println( p_c_2.getName() );
5376 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5377 p_c.getNode( "b" ) );
5378 if ( !p_c_3.getName().equals( "b" ) ) {
5381 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5382 p_c.getNode( "a" ) );
5383 if ( !p_c_4.getName().equals( "c" ) ) {
5386 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5387 new NHXParser() )[ 0 ];
5388 PhylogenyMethods.preOrderReId( p1 );
5389 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5390 p1.getNode( "A" ) );
5391 if ( !A.getName().equals( "A" ) ) {
5394 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5395 p1.getNode( "gh" ) );
5396 if ( !gh.getName().equals( "gh" ) ) {
5399 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5400 p1.getNode( "B" ) );
5401 if ( !ab.getName().equals( "ab" ) ) {
5404 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5405 p1.getNode( "A" ) );
5406 if ( !ab2.getName().equals( "ab" ) ) {
5409 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5410 p1.getNode( "G" ) );
5411 if ( !gh2.getName().equals( "gh" ) ) {
5414 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5415 p1.getNode( "H" ) );
5416 if ( !gh3.getName().equals( "gh" ) ) {
5419 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5420 p1.getNode( "A" ) );
5421 if ( !abc.getName().equals( "abc" ) ) {
5424 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5425 p1.getNode( "C" ) );
5426 if ( !abc2.getName().equals( "abc" ) ) {
5429 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5430 p1.getNode( "D" ) );
5431 if ( !abcd.getName().equals( "abcd" ) ) {
5434 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5435 p1.getNode( "A" ) );
5436 if ( !abcd2.getName().equals( "abcd" ) ) {
5439 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5440 p1.getNode( "F" ) );
5441 if ( !abcdef.getName().equals( "abcdef" ) ) {
5444 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5445 p1.getNode( "A" ) );
5446 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5449 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5450 p1.getNode( "F" ) );
5451 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5454 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5455 p1.getNode( "ab" ) );
5456 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5459 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5460 p1.getNode( "E" ) );
5461 if ( !abcde.getName().equals( "abcde" ) ) {
5464 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5465 p1.getNode( "A" ) );
5466 if ( !abcde2.getName().equals( "abcde" ) ) {
5469 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5470 p1.getNode( "abcdefgh" ) );
5471 if ( !r.getName().equals( "abcdefgh" ) ) {
5474 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5475 p1.getNode( "H" ) );
5476 if ( !r2.getName().equals( "abcdefgh" ) ) {
5479 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5480 p1.getNode( "A" ) );
5481 if ( !r3.getName().equals( "abcdefgh" ) ) {
5484 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5485 p1.getNode( "abcde" ) );
5486 if ( !abcde3.getName().equals( "abcde" ) ) {
5489 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5490 p1.getNode( "E" ) );
5491 if ( !abcde4.getName().equals( "abcde" ) ) {
5494 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5495 p1.getNode( "B" ) );
5496 if ( !ab3.getName().equals( "ab" ) ) {
5499 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5500 p1.getNode( "ab" ) );
5501 if ( !ab4.getName().equals( "ab" ) ) {
5504 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5505 PhylogenyMethods.preOrderReId( p2 );
5506 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5507 p2.getNode( "d" ) );
5508 if ( !cd.getName().equals( "cd" ) ) {
5511 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5512 p2.getNode( "c" ) );
5513 if ( !cd2.getName().equals( "cd" ) ) {
5516 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5517 p2.getNode( "e" ) );
5518 if ( !cde.getName().equals( "cde" ) ) {
5521 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5522 p2.getNode( "c" ) );
5523 if ( !cde2.getName().equals( "cde" ) ) {
5526 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5527 p2.getNode( "f" ) );
5528 if ( !cdef.getName().equals( "cdef" ) ) {
5531 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5532 p2.getNode( "f" ) );
5533 if ( !cdef2.getName().equals( "cdef" ) ) {
5536 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5537 p2.getNode( "d" ) );
5538 if ( !cdef3.getName().equals( "cdef" ) ) {
5541 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5542 p2.getNode( "a" ) );
5543 if ( !rt.getName().equals( "r" ) ) {
5546 final Phylogeny p3 = factory
5547 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5548 new NHXParser() )[ 0 ];
5549 PhylogenyMethods.preOrderReId( p3 );
5550 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5551 p3.getNode( "c" ) );
5552 if ( !bc_3.getName().equals( "bc" ) ) {
5555 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5556 p3.getNode( "c" ) );
5557 if ( !ac_3.getName().equals( "abc" ) ) {
5560 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5561 p3.getNode( "d" ) );
5562 if ( !ad_3.getName().equals( "abcde" ) ) {
5565 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5566 p3.getNode( "f" ) );
5567 if ( !af_3.getName().equals( "abcdef" ) ) {
5570 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5571 p3.getNode( "g" ) );
5572 if ( !ag_3.getName().equals( "" ) ) {
5575 if ( !ag_3.isRoot() ) {
5578 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5579 p3.getNode( "l" ) );
5580 if ( !al_3.getName().equals( "" ) ) {
5583 if ( !al_3.isRoot() ) {
5586 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5587 p3.getNode( "l" ) );
5588 if ( !kl_3.getName().equals( "" ) ) {
5591 if ( !kl_3.isRoot() ) {
5594 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5595 p3.getNode( "l" ) );
5596 if ( !fl_3.getName().equals( "" ) ) {
5599 if ( !fl_3.isRoot() ) {
5602 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5603 p3.getNode( "k" ) );
5604 if ( !gk_3.getName().equals( "ghijk" ) ) {
5607 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5608 PhylogenyMethods.preOrderReId( p4 );
5609 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5610 p4.getNode( "c" ) );
5611 if ( !r_4.getName().equals( "r" ) ) {
5614 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5615 PhylogenyMethods.preOrderReId( p5 );
5616 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5617 p5.getNode( "c" ) );
5618 if ( !r_5.getName().equals( "root" ) ) {
5621 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5622 PhylogenyMethods.preOrderReId( p6 );
5623 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5624 p6.getNode( "a" ) );
5625 if ( !r_6.getName().equals( "rot" ) ) {
5628 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5629 PhylogenyMethods.preOrderReId( p7 );
5630 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5631 p7.getNode( "e" ) );
5632 if ( !r_7.getName().equals( "rott" ) ) {
5635 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5636 p7.getNode( "a" ) );
5637 if ( !r_71.getName().equals( "rott" ) ) {
5640 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5641 p7.getNode( "rott" ) );
5642 if ( !r_72.getName().equals( "rott" ) ) {
5645 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5646 p7.getNode( "a" ) );
5647 if ( !r_73.getName().equals( "rott" ) ) {
5650 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5651 p7.getNode( "rott" ) );
5652 if ( !r_74.getName().equals( "rott" ) ) {
5655 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5656 p7.getNode( "e" ) );
5657 if ( !r_75.getName().equals( "e" ) ) {
5661 catch ( final Exception e ) {
5662 e.printStackTrace( System.out );
5668 private static boolean testHmmscanOutputParser() {
5669 final String test_dir = Test.PATH_TO_TEST_DATA;
5671 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5672 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5674 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5675 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5676 final List<Protein> proteins = parser2.parse();
5677 if ( parser2.getProteinsEncountered() != 4 ) {
5680 if ( proteins.size() != 4 ) {
5683 if ( parser2.getDomainsEncountered() != 69 ) {
5686 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5689 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5692 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5695 final Protein p1 = proteins.get( 0 );
5696 if ( p1.getNumberOfProteinDomains() != 15 ) {
5699 if ( p1.getLength() != 850 ) {
5702 final Protein p2 = proteins.get( 1 );
5703 if ( p2.getNumberOfProteinDomains() != 51 ) {
5706 if ( p2.getLength() != 1291 ) {
5709 final Protein p3 = proteins.get( 2 );
5710 if ( p3.getNumberOfProteinDomains() != 2 ) {
5713 final Protein p4 = proteins.get( 3 );
5714 if ( p4.getNumberOfProteinDomains() != 1 ) {
5717 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5720 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5723 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5726 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5729 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5732 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5735 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5739 catch ( final Exception e ) {
5740 e.printStackTrace( System.out );
5746 private static boolean testLastExternalNodeMethods() {
5748 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5749 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5750 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5751 final PhylogenyNode n1 = t0.getNode( "A" );
5752 if ( n1.isLastExternalNode() ) {
5755 final PhylogenyNode n2 = t0.getNode( "B" );
5756 if ( n2.isLastExternalNode() ) {
5759 final PhylogenyNode n3 = t0.getNode( "C" );
5760 if ( n3.isLastExternalNode() ) {
5763 final PhylogenyNode n4 = t0.getNode( "D" );
5764 if ( !n4.isLastExternalNode() ) {
5768 catch ( final Exception e ) {
5769 e.printStackTrace( System.out );
5775 private static boolean testLevelOrderIterator() {
5777 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5778 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5779 PhylogenyNodeIterator it0;
5780 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5783 for( it0.reset(); it0.hasNext(); ) {
5786 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5787 if ( !it.next().getName().equals( "r" ) ) {
5790 if ( !it.next().getName().equals( "ab" ) ) {
5793 if ( !it.next().getName().equals( "cd" ) ) {
5796 if ( !it.next().getName().equals( "A" ) ) {
5799 if ( !it.next().getName().equals( "B" ) ) {
5802 if ( !it.next().getName().equals( "C" ) ) {
5805 if ( !it.next().getName().equals( "D" ) ) {
5808 if ( it.hasNext() ) {
5811 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",
5812 new NHXParser() )[ 0 ];
5813 PhylogenyNodeIterator it2;
5814 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5817 for( it2.reset(); it2.hasNext(); ) {
5820 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5821 if ( !it3.next().getName().equals( "r" ) ) {
5824 if ( !it3.next().getName().equals( "abc" ) ) {
5827 if ( !it3.next().getName().equals( "defg" ) ) {
5830 if ( !it3.next().getName().equals( "A" ) ) {
5833 if ( !it3.next().getName().equals( "B" ) ) {
5836 if ( !it3.next().getName().equals( "C" ) ) {
5839 if ( !it3.next().getName().equals( "D" ) ) {
5842 if ( !it3.next().getName().equals( "E" ) ) {
5845 if ( !it3.next().getName().equals( "F" ) ) {
5848 if ( !it3.next().getName().equals( "G" ) ) {
5851 if ( !it3.next().getName().equals( "1" ) ) {
5854 if ( !it3.next().getName().equals( "2" ) ) {
5857 if ( !it3.next().getName().equals( "3" ) ) {
5860 if ( !it3.next().getName().equals( "4" ) ) {
5863 if ( !it3.next().getName().equals( "5" ) ) {
5866 if ( !it3.next().getName().equals( "6" ) ) {
5869 if ( !it3.next().getName().equals( "f1" ) ) {
5872 if ( !it3.next().getName().equals( "f2" ) ) {
5875 if ( !it3.next().getName().equals( "f3" ) ) {
5878 if ( !it3.next().getName().equals( "a" ) ) {
5881 if ( !it3.next().getName().equals( "b" ) ) {
5884 if ( !it3.next().getName().equals( "f21" ) ) {
5887 if ( !it3.next().getName().equals( "X" ) ) {
5890 if ( !it3.next().getName().equals( "Y" ) ) {
5893 if ( !it3.next().getName().equals( "Z" ) ) {
5896 if ( it3.hasNext() ) {
5899 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
5900 PhylogenyNodeIterator it4;
5901 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
5904 for( it4.reset(); it4.hasNext(); ) {
5907 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
5908 if ( !it5.next().getName().equals( "r" ) ) {
5911 if ( !it5.next().getName().equals( "A" ) ) {
5914 if ( !it5.next().getName().equals( "B" ) ) {
5917 if ( !it5.next().getName().equals( "C" ) ) {
5920 if ( !it5.next().getName().equals( "D" ) ) {
5923 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
5924 PhylogenyNodeIterator it6;
5925 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
5928 for( it6.reset(); it6.hasNext(); ) {
5931 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
5932 if ( !it7.next().getName().equals( "A" ) ) {
5935 if ( it.hasNext() ) {
5939 catch ( final Exception e ) {
5940 e.printStackTrace( System.out );
5946 private static boolean testMafft( final String path ) {
5948 final List<String> opts = new ArrayList<String>();
5949 opts.add( "--maxiterate" );
5951 opts.add( "--localpair" );
5952 opts.add( "--quiet" );
5954 final MsaInferrer mafft = Mafft.createInstance( path );
5955 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
5956 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
5959 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
5963 catch ( final Exception e ) {
5964 e.printStackTrace( System.out );
5970 private static boolean testMidpointrooting() {
5972 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5973 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
5974 PhylogenyMethods.midpointRoot( t0 );
5975 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
5978 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
5981 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
5985 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",
5986 new NHXParser() )[ 0 ];
5987 if ( !t1.isRooted() ) {
5990 PhylogenyMethods.midpointRoot( t1 );
5991 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5994 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5997 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6000 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6003 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6006 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6009 t1.reRoot( t1.getNode( "A" ) );
6010 PhylogenyMethods.midpointRoot( t1 );
6011 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6014 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6017 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6020 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6023 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6027 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6031 catch ( final Exception e ) {
6032 e.printStackTrace( System.out );
6038 private static boolean testMsaQualityMethod() {
6040 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6041 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6042 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6043 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6044 final List<Sequence> l = new ArrayList<Sequence>();
6049 final Msa msa = BasicMsa.createInstance( l );
6050 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6053 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6056 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6059 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6062 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6065 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6068 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6072 catch ( final Exception e ) {
6073 e.printStackTrace( System.out );
6079 private static boolean testNextNodeWithCollapsing() {
6081 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6083 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6084 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6085 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6086 t0.getNode( "cd" ).setCollapse( true );
6087 t0.getNode( "cde" ).setCollapse( true );
6088 n = t0.getFirstExternalNode();
6089 while ( n != null ) {
6091 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6093 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6096 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6099 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6102 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6105 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6108 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6112 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6113 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6114 t1.getNode( "ab" ).setCollapse( true );
6115 t1.getNode( "cd" ).setCollapse( true );
6116 t1.getNode( "cde" ).setCollapse( true );
6117 n = t1.getNode( "ab" );
6118 ext = new ArrayList<PhylogenyNode>();
6119 while ( n != null ) {
6121 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6123 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6126 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6129 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6132 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6135 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6141 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6142 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6143 t2.getNode( "ab" ).setCollapse( true );
6144 t2.getNode( "cd" ).setCollapse( true );
6145 t2.getNode( "cde" ).setCollapse( true );
6146 t2.getNode( "c" ).setCollapse( true );
6147 t2.getNode( "d" ).setCollapse( true );
6148 t2.getNode( "e" ).setCollapse( true );
6149 t2.getNode( "gh" ).setCollapse( true );
6150 n = t2.getNode( "ab" );
6151 ext = new ArrayList<PhylogenyNode>();
6152 while ( n != null ) {
6154 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6156 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6159 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6162 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6165 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6171 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6172 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6173 t3.getNode( "ab" ).setCollapse( true );
6174 t3.getNode( "cd" ).setCollapse( true );
6175 t3.getNode( "cde" ).setCollapse( true );
6176 t3.getNode( "c" ).setCollapse( true );
6177 t3.getNode( "d" ).setCollapse( true );
6178 t3.getNode( "e" ).setCollapse( true );
6179 t3.getNode( "gh" ).setCollapse( true );
6180 t3.getNode( "fgh" ).setCollapse( true );
6181 n = t3.getNode( "ab" );
6182 ext = new ArrayList<PhylogenyNode>();
6183 while ( n != null ) {
6185 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6187 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6190 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6193 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6199 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6200 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6201 t4.getNode( "ab" ).setCollapse( true );
6202 t4.getNode( "cd" ).setCollapse( true );
6203 t4.getNode( "cde" ).setCollapse( true );
6204 t4.getNode( "c" ).setCollapse( true );
6205 t4.getNode( "d" ).setCollapse( true );
6206 t4.getNode( "e" ).setCollapse( true );
6207 t4.getNode( "gh" ).setCollapse( true );
6208 t4.getNode( "fgh" ).setCollapse( true );
6209 t4.getNode( "abcdefgh" ).setCollapse( true );
6210 n = t4.getNode( "abcdefgh" );
6211 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6216 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6217 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6219 n = t5.getFirstExternalNode();
6220 while ( n != null ) {
6222 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6224 if ( ext.size() != 8 ) {
6227 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6230 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6233 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6236 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6239 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6242 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6245 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6248 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6253 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6254 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6256 t6.getNode( "ab" ).setCollapse( true );
6257 n = t6.getNode( "ab" );
6258 while ( n != null ) {
6260 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6262 if ( ext.size() != 7 ) {
6265 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6268 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6271 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6274 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6277 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6280 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6283 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6288 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6289 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6291 t7.getNode( "cd" ).setCollapse( true );
6292 n = t7.getNode( "a" );
6293 while ( n != null ) {
6295 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6297 if ( ext.size() != 7 ) {
6300 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6303 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6306 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6309 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6312 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6315 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6318 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6323 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6324 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6326 t8.getNode( "cd" ).setCollapse( true );
6327 t8.getNode( "c" ).setCollapse( true );
6328 t8.getNode( "d" ).setCollapse( true );
6329 n = t8.getNode( "a" );
6330 while ( n != null ) {
6332 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6334 if ( ext.size() != 7 ) {
6337 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6340 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6343 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6344 System.out.println( "2 fail" );
6347 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6350 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6353 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6356 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6361 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6362 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6364 t9.getNode( "gh" ).setCollapse( true );
6365 n = t9.getNode( "a" );
6366 while ( n != null ) {
6368 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6370 if ( ext.size() != 7 ) {
6373 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6376 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6379 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6382 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6385 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6388 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6391 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6396 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6397 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6399 t10.getNode( "gh" ).setCollapse( true );
6400 t10.getNode( "g" ).setCollapse( true );
6401 t10.getNode( "h" ).setCollapse( true );
6402 n = t10.getNode( "a" );
6403 while ( n != null ) {
6405 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6407 if ( ext.size() != 7 ) {
6410 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6413 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6416 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6419 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6422 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6425 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6428 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6433 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6434 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6436 t11.getNode( "gh" ).setCollapse( true );
6437 t11.getNode( "fgh" ).setCollapse( true );
6438 n = t11.getNode( "a" );
6439 while ( n != null ) {
6441 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6443 if ( ext.size() != 6 ) {
6446 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6449 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6452 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6455 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6458 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6461 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6466 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6467 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6469 t12.getNode( "gh" ).setCollapse( true );
6470 t12.getNode( "fgh" ).setCollapse( true );
6471 t12.getNode( "g" ).setCollapse( true );
6472 t12.getNode( "h" ).setCollapse( true );
6473 t12.getNode( "f" ).setCollapse( true );
6474 n = t12.getNode( "a" );
6475 while ( n != null ) {
6477 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6479 if ( ext.size() != 6 ) {
6482 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6485 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6488 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6491 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6494 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6497 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6502 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6503 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6505 t13.getNode( "ab" ).setCollapse( true );
6506 t13.getNode( "b" ).setCollapse( true );
6507 t13.getNode( "fgh" ).setCollapse( true );
6508 t13.getNode( "gh" ).setCollapse( true );
6509 n = t13.getNode( "ab" );
6510 while ( n != null ) {
6512 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6514 if ( ext.size() != 5 ) {
6517 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6520 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6523 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6526 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6529 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6534 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6535 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6537 t14.getNode( "ab" ).setCollapse( true );
6538 t14.getNode( "a" ).setCollapse( true );
6539 t14.getNode( "fgh" ).setCollapse( true );
6540 t14.getNode( "gh" ).setCollapse( true );
6541 n = t14.getNode( "ab" );
6542 while ( n != null ) {
6544 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6546 if ( ext.size() != 5 ) {
6549 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6552 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6555 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6558 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6561 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6566 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" );
6567 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6569 t15.getNode( "ab" ).setCollapse( true );
6570 t15.getNode( "a" ).setCollapse( true );
6571 t15.getNode( "fgh" ).setCollapse( true );
6572 t15.getNode( "gh" ).setCollapse( true );
6573 n = t15.getNode( "ab" );
6574 while ( n != null ) {
6576 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6578 if ( ext.size() != 6 ) {
6581 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6584 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6587 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6590 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6593 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6596 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6601 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" );
6602 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6604 t16.getNode( "ab" ).setCollapse( true );
6605 t16.getNode( "a" ).setCollapse( true );
6606 t16.getNode( "fgh" ).setCollapse( true );
6607 t16.getNode( "gh" ).setCollapse( true );
6608 t16.getNode( "cd" ).setCollapse( true );
6609 t16.getNode( "cde" ).setCollapse( true );
6610 t16.getNode( "d" ).setCollapse( true );
6611 t16.getNode( "x" ).setCollapse( true );
6612 n = t16.getNode( "ab" );
6613 while ( n != null ) {
6615 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6617 if ( ext.size() != 4 ) {
6620 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6623 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6626 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6629 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6633 catch ( final Exception e ) {
6634 e.printStackTrace( System.out );
6640 private static boolean testNexusCharactersParsing() {
6642 final NexusCharactersParser parser = new NexusCharactersParser();
6643 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6645 String[] labels = parser.getCharStateLabels();
6646 if ( labels.length != 7 ) {
6649 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6652 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6655 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6658 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6661 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6664 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6667 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6670 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6672 labels = parser.getCharStateLabels();
6673 if ( labels.length != 7 ) {
6676 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6679 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6682 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6685 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6688 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6691 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6694 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6698 catch ( final Exception e ) {
6699 e.printStackTrace( System.out );
6705 private static boolean testNexusMatrixParsing() {
6707 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
6708 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
6710 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
6711 if ( m.getNumberOfCharacters() != 9 ) {
6714 if ( m.getNumberOfIdentifiers() != 5 ) {
6717 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
6720 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
6723 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
6726 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
6729 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
6732 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
6735 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
6738 // if ( labels.length != 7 ) {
6741 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6744 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6747 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6750 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6753 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6756 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6759 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6762 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6764 // labels = parser.getCharStateLabels();
6765 // if ( labels.length != 7 ) {
6768 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6771 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6774 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6777 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6780 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6783 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6786 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6790 catch ( final Exception e ) {
6791 e.printStackTrace( System.out );
6797 private static boolean testNexusTreeParsing() {
6799 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6800 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6801 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
6802 if ( phylogenies.length != 1 ) {
6805 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
6808 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6812 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
6813 if ( phylogenies.length != 1 ) {
6816 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6819 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
6823 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
6824 if ( phylogenies.length != 1 ) {
6827 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6830 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6833 if ( phylogenies[ 0 ].isRooted() ) {
6837 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
6838 if ( phylogenies.length != 18 ) {
6841 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6844 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
6847 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
6850 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
6853 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
6856 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
6859 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
6862 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
6865 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
6868 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
6871 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
6874 if ( phylogenies[ 8 ].isRooted() ) {
6877 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
6880 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
6883 if ( !phylogenies[ 9 ].isRooted() ) {
6886 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
6889 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
6892 if ( !phylogenies[ 10 ].isRooted() ) {
6895 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
6898 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
6901 if ( phylogenies[ 11 ].isRooted() ) {
6904 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
6907 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
6910 if ( !phylogenies[ 12 ].isRooted() ) {
6913 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
6916 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
6919 if ( !phylogenies[ 13 ].isRooted() ) {
6922 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
6925 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
6928 if ( !phylogenies[ 14 ].isRooted() ) {
6931 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
6934 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
6937 if ( phylogenies[ 15 ].isRooted() ) {
6940 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
6943 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
6946 if ( !phylogenies[ 16 ].isRooted() ) {
6949 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
6952 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
6955 if ( phylogenies[ 17 ].isRooted() ) {
6958 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
6961 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
6963 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
6964 if ( phylogenies.length != 9 ) {
6967 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
6968 .getDistanceToParent() ) ) {
6971 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
6972 .getDistanceToParent() ) ) {
6975 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
6978 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
6981 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
6984 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
6987 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
6991 catch ( final Exception e ) {
6992 e.printStackTrace( System.out );
6998 private static boolean testNexusTreeParsingIterating() {
7000 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7001 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7002 if ( !p.hasNext() ) {
7005 Phylogeny phy = p.next();
7006 if ( phy == null ) {
7009 if ( phy.getNumberOfExternalNodes() != 25 ) {
7012 if ( !phy.getName().equals( "" ) ) {
7015 if ( p.hasNext() ) {
7019 if ( phy != null ) {
7024 if ( !p.hasNext() ) {
7028 if ( phy == null ) {
7031 if ( phy.getNumberOfExternalNodes() != 25 ) {
7034 if ( !phy.getName().equals( "" ) ) {
7037 if ( p.hasNext() ) {
7041 if ( phy != null ) {
7045 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7046 if ( !p.hasNext() ) {
7050 if ( phy == null ) {
7053 if ( phy.getNumberOfExternalNodes() != 10 ) {
7056 if ( !phy.getName().equals( "name" ) ) {
7059 if ( p.hasNext() ) {
7063 if ( phy != null ) {
7068 if ( !p.hasNext() ) {
7072 if ( phy == null ) {
7075 if ( phy.getNumberOfExternalNodes() != 10 ) {
7078 if ( !phy.getName().equals( "name" ) ) {
7081 if ( p.hasNext() ) {
7085 if ( phy != null ) {
7089 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7090 if ( !p.hasNext() ) {
7094 if ( phy == null ) {
7097 if ( phy.getNumberOfExternalNodes() != 3 ) {
7100 if ( !phy.getName().equals( "" ) ) {
7103 if ( phy.isRooted() ) {
7106 if ( p.hasNext() ) {
7110 if ( phy != null ) {
7115 if ( !p.hasNext() ) {
7119 if ( phy == null ) {
7122 if ( phy.getNumberOfExternalNodes() != 3 ) {
7125 if ( !phy.getName().equals( "" ) ) {
7128 if ( p.hasNext() ) {
7132 if ( phy != null ) {
7136 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7137 if ( !p.hasNext() ) {
7142 if ( phy == null ) {
7145 if ( phy.getNumberOfExternalNodes() != 10 ) {
7148 if ( !phy.getName().equals( "tree 0" ) ) {
7152 if ( !p.hasNext() ) {
7156 if ( phy == null ) {
7159 if ( phy.getNumberOfExternalNodes() != 10 ) {
7162 if ( !phy.getName().equals( "tree 1" ) ) {
7166 if ( !p.hasNext() ) {
7170 if ( phy == null ) {
7173 if ( phy.getNumberOfExternalNodes() != 3 ) {
7174 System.out.println( phy.toString() );
7177 if ( !phy.getName().equals( "" ) ) {
7180 if ( phy.isRooted() ) {
7184 if ( !p.hasNext() ) {
7188 if ( phy == null ) {
7191 if ( phy.getNumberOfExternalNodes() != 4 ) {
7194 if ( !phy.getName().equals( "" ) ) {
7197 if ( !phy.isRooted() ) {
7201 if ( !p.hasNext() ) {
7205 if ( phy == null ) {
7208 if ( phy.getNumberOfExternalNodes() != 5 ) {
7209 System.out.println( phy.getNumberOfExternalNodes() );
7212 if ( !phy.getName().equals( "" ) ) {
7215 if ( !phy.isRooted() ) {
7219 if ( !p.hasNext() ) {
7223 if ( phy == null ) {
7226 if ( phy.getNumberOfExternalNodes() != 3 ) {
7229 if ( !phy.getName().equals( "" ) ) {
7232 if ( phy.isRooted() ) {
7236 if ( !p.hasNext() ) {
7240 if ( phy == null ) {
7243 if ( phy.getNumberOfExternalNodes() != 2 ) {
7246 if ( !phy.getName().equals( "" ) ) {
7249 if ( !phy.isRooted() ) {
7253 if ( !p.hasNext() ) {
7257 if ( phy.getNumberOfExternalNodes() != 3 ) {
7260 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7263 if ( !phy.isRooted() ) {
7267 if ( !p.hasNext() ) {
7271 if ( phy.getNumberOfExternalNodes() != 3 ) {
7274 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7277 if ( !phy.getName().equals( "tree 8" ) ) {
7281 if ( !p.hasNext() ) {
7285 if ( phy.getNumberOfExternalNodes() != 3 ) {
7288 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7291 if ( !phy.getName().equals( "tree 9" ) ) {
7295 if ( !p.hasNext() ) {
7299 if ( phy.getNumberOfExternalNodes() != 3 ) {
7302 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7305 if ( !phy.getName().equals( "tree 10" ) ) {
7308 if ( !phy.isRooted() ) {
7312 if ( !p.hasNext() ) {
7316 if ( phy.getNumberOfExternalNodes() != 3 ) {
7319 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7322 if ( !phy.getName().equals( "tree 11" ) ) {
7325 if ( phy.isRooted() ) {
7329 if ( !p.hasNext() ) {
7333 if ( phy.getNumberOfExternalNodes() != 3 ) {
7336 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7339 if ( !phy.getName().equals( "tree 12" ) ) {
7342 if ( !phy.isRooted() ) {
7346 if ( !p.hasNext() ) {
7350 if ( phy.getNumberOfExternalNodes() != 3 ) {
7353 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7356 if ( !phy.getName().equals( "tree 13" ) ) {
7359 if ( !phy.isRooted() ) {
7363 if ( !p.hasNext() ) {
7367 if ( phy.getNumberOfExternalNodes() != 10 ) {
7368 System.out.println( phy.getNumberOfExternalNodes() );
7373 .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;" ) ) {
7374 System.out.println( phy.toNewHampshire() );
7377 if ( !phy.getName().equals( "tree 14" ) ) {
7380 if ( !phy.isRooted() ) {
7384 if ( !p.hasNext() ) {
7388 if ( phy.getNumberOfExternalNodes() != 10 ) {
7389 System.out.println( phy.getNumberOfExternalNodes() );
7394 .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;" ) ) {
7395 System.out.println( phy.toNewHampshire() );
7398 if ( !phy.getName().equals( "tree 15" ) ) {
7401 if ( phy.isRooted() ) {
7405 if ( !p.hasNext() ) {
7409 if ( phy.getNumberOfExternalNodes() != 10 ) {
7410 System.out.println( phy.getNumberOfExternalNodes() );
7415 .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;" ) ) {
7416 System.out.println( phy.toNewHampshire() );
7419 if ( !phy.getName().equals( "tree 16" ) ) {
7422 if ( !phy.isRooted() ) {
7426 if ( !p.hasNext() ) {
7430 if ( phy.getNumberOfExternalNodes() != 10 ) {
7431 System.out.println( phy.getNumberOfExternalNodes() );
7436 .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;" ) ) {
7437 System.out.println( phy.toNewHampshire() );
7440 if ( !phy.getName().equals( "tree 17" ) ) {
7443 if ( phy.isRooted() ) {
7447 if ( p.hasNext() ) {
7451 if ( phy != null ) {
7456 if ( !p.hasNext() ) {
7460 if ( phy == null ) {
7463 if ( phy.getNumberOfExternalNodes() != 10 ) {
7466 if ( !phy.getName().equals( "tree 0" ) ) {
7470 if ( !p.hasNext() ) {
7474 if ( phy == null ) {
7477 if ( phy.getNumberOfExternalNodes() != 10 ) {
7480 if ( !phy.getName().equals( "tree 1" ) ) {
7484 if ( !p.hasNext() ) {
7488 if ( phy == null ) {
7491 if ( phy.getNumberOfExternalNodes() != 3 ) {
7494 if ( !phy.getName().equals( "" ) ) {
7497 if ( phy.isRooted() ) {
7501 if ( !p.hasNext() ) {
7505 if ( phy == null ) {
7508 if ( phy.getNumberOfExternalNodes() != 4 ) {
7511 if ( !phy.getName().equals( "" ) ) {
7514 if ( !phy.isRooted() ) {
7518 if ( !p.hasNext() ) {
7522 if ( phy == null ) {
7525 if ( phy.getNumberOfExternalNodes() != 5 ) {
7526 System.out.println( phy.getNumberOfExternalNodes() );
7529 if ( !phy.getName().equals( "" ) ) {
7532 if ( !phy.isRooted() ) {
7536 if ( !p.hasNext() ) {
7540 if ( phy == null ) {
7543 if ( phy.getNumberOfExternalNodes() != 3 ) {
7546 if ( !phy.getName().equals( "" ) ) {
7549 if ( phy.isRooted() ) {
7553 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7554 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7556 if ( !p2.hasNext() ) {
7560 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7563 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7567 if ( !p2.hasNext() ) {
7572 if ( !p2.hasNext() ) {
7577 if ( !p2.hasNext() ) {
7582 if ( !p2.hasNext() ) {
7587 if ( !p2.hasNext() ) {
7592 if ( !p2.hasNext() ) {
7597 if ( !p2.hasNext() ) {
7602 if ( !p2.hasNext() ) {
7606 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7609 if ( p2.hasNext() ) {
7613 if ( phy != null ) {
7618 if ( !p2.hasNext() ) {
7622 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7625 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7629 catch ( final Exception e ) {
7630 e.printStackTrace( System.out );
7636 private static boolean testNexusTreeParsingTranslating() {
7638 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7639 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7640 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7641 if ( phylogenies.length != 1 ) {
7644 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7647 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7650 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7653 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7656 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7657 .equals( "Aranaeus" ) ) {
7661 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7662 if ( phylogenies.length != 3 ) {
7665 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7668 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7671 if ( phylogenies[ 0 ].isRooted() ) {
7674 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7677 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7680 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7681 .equals( "Aranaeus" ) ) {
7684 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7687 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7690 if ( phylogenies[ 1 ].isRooted() ) {
7693 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7696 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7699 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7700 .equals( "Aranaeus" ) ) {
7703 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7706 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7709 if ( !phylogenies[ 2 ].isRooted() ) {
7712 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7715 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7718 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7719 .equals( "Aranaeus" ) ) {
7723 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
7724 if ( phylogenies.length != 3 ) {
7727 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7730 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7733 if ( phylogenies[ 0 ].isRooted() ) {
7736 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7739 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7742 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7743 .equals( "Aranaeus" ) ) {
7746 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7749 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7752 if ( phylogenies[ 1 ].isRooted() ) {
7755 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7758 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7761 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7762 .equals( "Aranaeus" ) ) {
7765 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7768 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7771 if ( !phylogenies[ 2 ].isRooted() ) {
7774 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7777 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7780 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7781 .equals( "Aranaeus" ) ) {
7784 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
7785 if ( phylogenies.length != 3 ) {
7788 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
7793 catch ( final Exception e ) {
7794 e.printStackTrace( System.out );
7800 private static boolean testNHParsing() {
7802 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7803 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
7804 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
7807 final NHXParser nhxp = new NHXParser();
7808 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
7809 nhxp.setReplaceUnderscores( true );
7810 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
7811 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
7814 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
7817 final Phylogeny p1b = factory
7818 .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 ",
7819 new NHXParser() )[ 0 ];
7820 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
7823 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
7826 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
7827 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
7828 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
7829 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
7830 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
7831 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
7832 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
7833 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
7834 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
7835 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
7836 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
7837 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
7838 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
7840 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
7843 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
7846 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
7849 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
7852 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
7853 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
7854 final String p16_S = "((A,B),C)";
7855 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
7856 if ( p16.length != 1 ) {
7859 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
7862 final String p17_S = "(C,(A,B))";
7863 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
7864 if ( p17.length != 1 ) {
7867 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
7870 final String p18_S = "((A,B),(C,D))";
7871 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
7872 if ( p18.length != 1 ) {
7875 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
7878 final String p19_S = "(((A,B),C),D)";
7879 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
7880 if ( p19.length != 1 ) {
7883 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
7886 final String p20_S = "(A,(B,(C,D)))";
7887 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
7888 if ( p20.length != 1 ) {
7891 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
7894 final String p21_S = "(A,(B,(C,(D,E))))";
7895 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
7896 if ( p21.length != 1 ) {
7899 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
7902 final String p22_S = "((((A,B),C),D),E)";
7903 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
7904 if ( p22.length != 1 ) {
7907 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
7910 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7911 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
7912 if ( p23.length != 1 ) {
7913 System.out.println( "xl=" + p23.length );
7917 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
7920 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7921 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
7922 if ( p24.length != 1 ) {
7925 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
7928 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7929 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7930 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
7931 if ( p241.length != 2 ) {
7934 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
7937 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
7940 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
7941 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
7942 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
7943 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
7944 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
7945 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
7946 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
7947 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
7948 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
7949 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
7952 final String p26_S = "(A,B)ab";
7953 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
7954 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
7957 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7958 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
7959 if ( p27s.length != 1 ) {
7960 System.out.println( "xxl=" + p27s.length );
7964 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7965 System.out.println( p27s[ 0 ].toNewHampshireX() );
7969 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
7971 if ( p27.length != 1 ) {
7972 System.out.println( "yl=" + p27.length );
7976 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7977 System.out.println( p27[ 0 ].toNewHampshireX() );
7981 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7982 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7983 final String p28_S3 = "(A,B)ab";
7984 final String p28_S4 = "((((A,B),C),D),;E;)";
7985 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
7987 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
7990 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
7993 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
7996 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
7999 if ( p28.length != 4 ) {
8002 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";
8003 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8004 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8007 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";
8008 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8009 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8012 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8013 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8014 if ( ( p32.length != 0 ) ) {
8017 final String p33_S = "A";
8018 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8019 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8022 final String p34_S = "B;";
8023 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8024 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8027 final String p35_S = "B:0.2";
8028 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8029 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8032 final String p36_S = "(A)";
8033 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8034 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8037 final String p37_S = "((A))";
8038 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8039 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8042 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8043 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8044 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8047 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8048 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8049 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8052 final String p40_S = "(A,B,C)";
8053 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8054 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8057 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8058 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8059 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8062 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8063 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8064 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8067 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)";
8068 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8069 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8072 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)))";
8073 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8074 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8077 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8078 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8079 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8082 final String p46_S = "";
8083 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8084 if ( p46.length != 0 ) {
8087 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8088 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8091 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8092 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8095 final Phylogeny p49 = factory
8096 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8097 new NHXParser() )[ 0 ];
8098 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8101 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8102 if ( p50.getNode( "A" ) == null ) {
8105 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8106 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8109 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8112 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8113 .equals( "((A,B)88:2.0,C);" ) ) {
8116 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8117 if ( p51.getNode( "A(A" ) == null ) {
8120 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8121 if ( p52.getNode( "A(A" ) == null ) {
8124 final Phylogeny p53 = factory
8125 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8126 new NHXParser() )[ 0 ];
8127 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8130 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8131 if ( p54.getNode( "A" ) == null ) {
8134 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8137 final Phylogeny p55 = factory
8138 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
8139 new NHXParser() )[ 0 ];
8142 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,lcl|HPV66_L1.1x:0.0798012);" ) ) {
8143 System.out.println( p55.toNewHampshire() );
8146 final Phylogeny p56 = factory
8147 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
8148 new NHXParser() )[ 0 ];
8151 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8152 System.out.println( p56.toNewHampshire() );
8155 final Phylogeny p57 = factory
8156 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
8157 new NHXParser() )[ 0 ];
8160 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8161 System.out.println( p56.toNewHampshire() );
8164 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8165 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8166 if ( !p58.toNewHampshire().equals( s58 ) ) {
8167 System.out.println( p58.toNewHampshire() );
8170 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8171 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8172 if ( !p59.toNewHampshire().equals( s59 ) ) {
8173 System.out.println( p59.toNewHampshire() );
8176 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8177 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8178 if ( !p60.toNewHampshire().equals( s60 ) ) {
8179 System.out.println( p60.toNewHampshire() );
8182 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8183 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8184 if ( !p61.toNewHampshire()
8185 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8186 System.out.println( p61.toNewHampshire() );
8190 catch ( final Exception e ) {
8191 e.printStackTrace( System.out );
8197 private static boolean testNHParsingIter() {
8199 final String p0_str = "(A,B);";
8200 final NHXParser p = new NHXParser();
8201 p.setSource( p0_str );
8202 if ( !p.hasNext() ) {
8205 final Phylogeny p0 = p.next();
8206 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8207 System.out.println( p0.toNewHampshire() );
8210 if ( p.hasNext() ) {
8213 if ( p.next() != null ) {
8217 final String p00_str = "(A,B)root;";
8218 p.setSource( p00_str );
8219 final Phylogeny p00 = p.next();
8220 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8221 System.out.println( p00.toNewHampshire() );
8225 final String p000_str = "A;";
8226 p.setSource( p000_str );
8227 final Phylogeny p000 = p.next();
8228 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8229 System.out.println( p000.toNewHampshire() );
8233 final String p0000_str = "A";
8234 p.setSource( p0000_str );
8235 final Phylogeny p0000 = p.next();
8236 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8237 System.out.println( p0000.toNewHampshire() );
8241 p.setSource( "(A)" );
8242 final Phylogeny p00000 = p.next();
8243 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8244 System.out.println( p00000.toNewHampshire() );
8248 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8249 p.setSource( p1_str );
8250 if ( !p.hasNext() ) {
8253 final Phylogeny p1_0 = p.next();
8254 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8255 System.out.println( p1_0.toNewHampshire() );
8258 if ( !p.hasNext() ) {
8261 final Phylogeny p1_1 = p.next();
8262 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8263 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8266 if ( !p.hasNext() ) {
8269 final Phylogeny p1_2 = p.next();
8270 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8271 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8274 if ( !p.hasNext() ) {
8277 final Phylogeny p1_3 = p.next();
8278 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8279 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8282 if ( p.hasNext() ) {
8285 if ( p.next() != null ) {
8289 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8290 p.setSource( p2_str );
8291 if ( !p.hasNext() ) {
8294 Phylogeny p2_0 = p.next();
8295 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8296 System.out.println( p2_0.toNewHampshire() );
8299 if ( !p.hasNext() ) {
8302 Phylogeny p2_1 = p.next();
8303 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8304 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8307 if ( !p.hasNext() ) {
8310 Phylogeny p2_2 = p.next();
8311 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8312 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8315 if ( !p.hasNext() ) {
8318 Phylogeny p2_3 = p.next();
8319 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8320 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8323 if ( !p.hasNext() ) {
8326 Phylogeny p2_4 = p.next();
8327 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8328 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8331 if ( p.hasNext() ) {
8334 if ( p.next() != null ) {
8339 if ( !p.hasNext() ) {
8343 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8344 System.out.println( p2_0.toNewHampshire() );
8347 if ( !p.hasNext() ) {
8351 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8352 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8355 if ( !p.hasNext() ) {
8359 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8360 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8363 if ( !p.hasNext() ) {
8367 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8368 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8371 if ( !p.hasNext() ) {
8375 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8376 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8379 if ( p.hasNext() ) {
8382 if ( p.next() != null ) {
8386 final String p3_str = "((A,B),C)abc";
8387 p.setSource( p3_str );
8388 if ( !p.hasNext() ) {
8391 final Phylogeny p3_0 = p.next();
8392 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8395 if ( p.hasNext() ) {
8398 if ( p.next() != null ) {
8402 final String p4_str = "((A,B)ab,C)abc";
8403 p.setSource( p4_str );
8404 if ( !p.hasNext() ) {
8407 final Phylogeny p4_0 = p.next();
8408 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8411 if ( p.hasNext() ) {
8414 if ( p.next() != null ) {
8418 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8419 p.setSource( p5_str );
8420 if ( !p.hasNext() ) {
8423 final Phylogeny p5_0 = p.next();
8424 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8427 if ( p.hasNext() ) {
8430 if ( p.next() != null ) {
8434 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8435 p.setSource( p6_str );
8436 if ( !p.hasNext() ) {
8439 Phylogeny p6_0 = p.next();
8440 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8443 if ( p.hasNext() ) {
8446 if ( p.next() != null ) {
8450 if ( !p.hasNext() ) {
8454 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8457 if ( p.hasNext() ) {
8460 if ( p.next() != null ) {
8464 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8465 p.setSource( p7_str );
8466 if ( !p.hasNext() ) {
8469 Phylogeny p7_0 = p.next();
8470 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8473 if ( p.hasNext() ) {
8476 if ( p.next() != null ) {
8480 if ( !p.hasNext() ) {
8484 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8487 if ( p.hasNext() ) {
8490 if ( p.next() != null ) {
8494 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8495 p.setSource( p8_str );
8496 if ( !p.hasNext() ) {
8499 Phylogeny p8_0 = p.next();
8500 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8503 if ( !p.hasNext() ) {
8506 if ( !p.hasNext() ) {
8509 Phylogeny p8_1 = p.next();
8510 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8513 if ( p.hasNext() ) {
8516 if ( p.next() != null ) {
8520 if ( !p.hasNext() ) {
8524 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8527 if ( !p.hasNext() ) {
8531 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8534 if ( p.hasNext() ) {
8537 if ( p.next() != null ) {
8543 if ( p.hasNext() ) {
8547 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8548 if ( !p.hasNext() ) {
8551 Phylogeny p_27 = p.next();
8552 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8553 System.out.println( p_27.toNewHampshireX() );
8557 if ( p.hasNext() ) {
8560 if ( p.next() != null ) {
8564 if ( !p.hasNext() ) {
8568 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8569 System.out.println( p_27.toNewHampshireX() );
8573 if ( p.hasNext() ) {
8576 if ( p.next() != null ) {
8580 final String p30_str = "(A,B);(C,D)";
8581 final NHXParser p30 = new NHXParser();
8582 p30.setSource( p30_str );
8583 if ( !p30.hasNext() ) {
8586 Phylogeny phy30 = p30.next();
8587 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8588 System.out.println( phy30.toNewHampshire() );
8591 if ( !p30.hasNext() ) {
8594 Phylogeny phy301 = p30.next();
8595 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8596 System.out.println( phy301.toNewHampshire() );
8599 if ( p30.hasNext() ) {
8602 if ( p30.hasNext() ) {
8605 if ( p30.next() != null ) {
8608 if ( p30.next() != null ) {
8612 if ( !p30.hasNext() ) {
8616 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8617 System.out.println( phy30.toNewHampshire() );
8620 if ( !p30.hasNext() ) {
8623 phy301 = p30.next();
8624 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8625 System.out.println( phy301.toNewHampshire() );
8628 if ( p30.hasNext() ) {
8631 if ( p30.hasNext() ) {
8634 if ( p30.next() != null ) {
8637 if ( p30.next() != null ) {
8641 catch ( final Exception e ) {
8642 e.printStackTrace( System.out );
8648 private static boolean testNHXconversion() {
8650 final PhylogenyNode n1 = new PhylogenyNode();
8651 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8652 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8653 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8654 final PhylogenyNode n5 = PhylogenyNode
8655 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8656 final PhylogenyNode n6 = PhylogenyNode
8657 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8658 if ( !n1.toNewHampshireX().equals( "" ) ) {
8661 if ( !n2.toNewHampshireX().equals( "" ) ) {
8664 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8667 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
8670 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
8673 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
8674 System.out.println( n6.toNewHampshireX() );
8677 final PhylogenyNode n7 = new PhylogenyNode();
8678 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
8679 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8680 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
8681 System.out.println( n7
8682 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
8686 catch ( final Exception e ) {
8687 e.printStackTrace( System.out );
8693 private static boolean testNHXNodeParsing() {
8695 final PhylogenyNode n1 = new PhylogenyNode();
8696 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8697 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8698 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8699 final PhylogenyNode n5 = PhylogenyNode
8700 .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]" );
8701 if ( !n3.getName().equals( "n3" ) ) {
8704 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8707 if ( n3.isDuplication() ) {
8710 if ( n3.isHasAssignedEvent() ) {
8713 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
8716 if ( !n4.getName().equals( "n4" ) ) {
8719 if ( n4.getDistanceToParent() != 0.01 ) {
8722 if ( !n5.getName().equals( "n5" ) ) {
8725 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
8728 if ( n5.getDistanceToParent() != 0.1 ) {
8731 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
8734 if ( !n5.isDuplication() ) {
8737 if ( !n5.isHasAssignedEvent() ) {
8740 final PhylogenyNode n8 = PhylogenyNode
8741 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
8742 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8743 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8746 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
8749 final PhylogenyNode n9 = PhylogenyNode
8750 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
8751 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8752 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
8755 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
8758 final PhylogenyNode n10 = PhylogenyNode
8759 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8760 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
8763 final PhylogenyNode n20 = PhylogenyNode
8764 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8765 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8768 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
8771 final PhylogenyNode n20x = PhylogenyNode
8772 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8773 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
8776 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
8779 final PhylogenyNode n20xx = PhylogenyNode
8780 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8781 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
8784 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
8787 final PhylogenyNode n20xxx = PhylogenyNode
8788 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8789 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
8792 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
8795 final PhylogenyNode n20xxxx = PhylogenyNode
8796 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8797 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
8800 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
8803 final PhylogenyNode n21 = PhylogenyNode
8804 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8805 if ( !n21.getName().equals( "N21_PIG" ) ) {
8808 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
8811 final PhylogenyNode n21x = PhylogenyNode
8812 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8813 if ( !n21x.getName().equals( "n21_PIG" ) ) {
8816 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
8819 final PhylogenyNode n22 = PhylogenyNode
8820 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8821 if ( !n22.getName().equals( "n22/PIG" ) ) {
8824 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
8827 final PhylogenyNode n23 = PhylogenyNode
8828 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8829 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
8832 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
8835 final PhylogenyNode a = PhylogenyNode
8836 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8837 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8840 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
8843 final PhylogenyNode c1 = PhylogenyNode
8844 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
8845 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8846 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
8849 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
8852 final PhylogenyNode c2 = PhylogenyNode
8853 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
8854 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8855 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
8858 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
8861 final PhylogenyNode e3 = PhylogenyNode
8862 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8863 if ( !e3.getName().equals( "n10_RAT~" ) ) {
8866 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
8869 final PhylogenyNode n11 = PhylogenyNode
8870 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
8871 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8872 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
8875 if ( n11.getDistanceToParent() != 0.4 ) {
8878 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
8881 final PhylogenyNode n12 = PhylogenyNode
8882 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
8883 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8884 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
8887 if ( n12.getDistanceToParent() != 0.4 ) {
8890 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
8893 final PhylogenyNode o = PhylogenyNode
8894 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8895 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
8898 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
8901 if ( n1.getName().compareTo( "" ) != 0 ) {
8904 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8907 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8910 if ( n2.getName().compareTo( "" ) != 0 ) {
8913 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8916 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8919 final PhylogenyNode n00 = PhylogenyNode
8920 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
8921 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
8924 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
8927 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
8928 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
8931 final PhylogenyNode n13 = PhylogenyNode
8932 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8933 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
8936 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
8939 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8942 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8945 final PhylogenyNode n14 = PhylogenyNode
8946 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8947 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
8950 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
8953 final PhylogenyNode n15 = PhylogenyNode
8954 .createInstanceFromNhxString( "something_wicked[123]",
8955 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8956 if ( !n15.getName().equals( "something_wicked" ) ) {
8959 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
8962 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
8965 final PhylogenyNode n16 = PhylogenyNode
8966 .createInstanceFromNhxString( "something_wicked2[9]",
8967 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8968 if ( !n16.getName().equals( "something_wicked2" ) ) {
8971 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
8974 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
8977 final PhylogenyNode n17 = PhylogenyNode
8978 .createInstanceFromNhxString( "something_wicked3[a]",
8979 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8980 if ( !n17.getName().equals( "something_wicked3" ) ) {
8983 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
8986 final PhylogenyNode n18 = PhylogenyNode
8987 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8988 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
8991 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
8994 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
8997 final PhylogenyNode n19 = PhylogenyNode
8998 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8999 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9002 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9005 final PhylogenyNode n30 = PhylogenyNode
9006 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9007 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9008 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9011 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9014 final PhylogenyNode n31 = PhylogenyNode
9015 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9016 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9017 if ( n31.getNodeData().isHasTaxonomy() ) {
9020 final PhylogenyNode n32 = PhylogenyNode
9021 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9022 if ( n32.getNodeData().isHasTaxonomy() ) {
9025 final PhylogenyNode n40 = PhylogenyNode
9026 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9027 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9030 final PhylogenyNode n41 = PhylogenyNode
9031 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9032 if ( n41.getNodeData().isHasTaxonomy() ) {
9035 final PhylogenyNode n42 = PhylogenyNode
9036 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9037 if ( n42.getNodeData().isHasTaxonomy() ) {
9040 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9041 NHXParser.TAXONOMY_EXTRACTION.NO );
9042 if ( n43.getNodeData().isHasTaxonomy() ) {
9045 final PhylogenyNode n44 = PhylogenyNode
9046 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9047 if ( n44.getNodeData().isHasTaxonomy() ) {
9051 catch ( final Exception e ) {
9052 e.printStackTrace( System.out );
9058 private static boolean testNHXParsing() {
9060 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9061 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9062 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9065 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]";
9066 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9067 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9070 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]";
9071 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9072 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9075 final Phylogeny[] p3 = factory
9076 .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]",
9078 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9081 final Phylogeny[] p4 = factory
9082 .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(]",
9084 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9087 final Phylogeny[] p5 = factory
9088 .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(((]",
9090 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9093 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)";
9094 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)";
9095 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9096 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9099 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)))";
9100 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)))";
9101 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9102 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9105 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]) ))[,,, ])))))))";
9106 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9107 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9108 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9111 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9112 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9115 final Phylogeny p10 = factory
9116 .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]",
9117 new NHXParser() )[ 0 ];
9118 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9121 final Phylogeny p11 = factory
9122 .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]",
9123 new NHXParser() )[ 0 ];
9124 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9128 catch ( final Exception e ) {
9129 e.printStackTrace( System.out );
9135 private static boolean testNHXParsingMB() {
9137 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9138 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9139 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9140 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9141 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9142 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9143 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9144 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9145 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9146 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9147 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9150 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9153 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9154 0.1100000000000000e+00 ) ) {
9157 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9160 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9163 final Phylogeny p2 = factory
9164 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9165 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9166 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9167 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9168 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9169 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9170 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9171 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9172 + "7.369400000000000e-02}])",
9173 new NHXParser() )[ 0 ];
9174 if ( p2.getNode( "1" ) == null ) {
9177 if ( p2.getNode( "2" ) == null ) {
9181 catch ( final Exception e ) {
9182 e.printStackTrace( System.out );
9189 private static boolean testNHXParsingQuotes() {
9191 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9192 final NHXParser p = new NHXParser();
9193 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9194 if ( phylogenies_0.length != 5 ) {
9197 final Phylogeny phy = phylogenies_0[ 4 ];
9198 if ( phy.getNumberOfExternalNodes() != 7 ) {
9201 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9204 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9207 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9208 .getScientificName().equals( "hsapiens" ) ) {
9211 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9214 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9217 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9220 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9223 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9226 final NHXParser p1p = new NHXParser();
9227 p1p.setIgnoreQuotes( true );
9228 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9229 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9232 final NHXParser p2p = new NHXParser();
9233 p1p.setIgnoreQuotes( false );
9234 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9235 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9238 final NHXParser p3p = new NHXParser();
9239 p3p.setIgnoreQuotes( false );
9240 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9241 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9244 final NHXParser p4p = new NHXParser();
9245 p4p.setIgnoreQuotes( false );
9246 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9247 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9250 final Phylogeny p10 = factory
9251 .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]",
9252 new NHXParser() )[ 0 ];
9253 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]";
9254 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9257 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9258 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9261 final Phylogeny p12 = factory
9262 .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]",
9263 new NHXParser() )[ 0 ];
9264 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]";
9265 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9268 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9269 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9272 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;";
9273 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9276 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9277 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9281 catch ( final Exception e ) {
9282 e.printStackTrace( System.out );
9288 private static boolean testNodeRemoval() {
9290 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9291 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9292 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9293 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9296 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9297 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9298 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9301 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9302 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9303 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9307 catch ( final Exception e ) {
9308 e.printStackTrace( System.out );
9314 private static boolean testPhylogenyBranch() {
9316 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9317 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9318 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9319 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9320 if ( !a1b1.equals( a1b1 ) ) {
9323 if ( !a1b1.equals( b1a1 ) ) {
9326 if ( !b1a1.equals( a1b1 ) ) {
9329 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9330 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9331 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9332 if ( a1_b1.equals( b1_a1 ) ) {
9335 if ( a1_b1.equals( a1_b1_ ) ) {
9338 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9339 if ( !a1_b1.equals( b1_a1_ ) ) {
9342 if ( a1_b1_.equals( b1_a1_ ) ) {
9345 if ( !a1_b1_.equals( b1_a1 ) ) {
9349 catch ( final Exception e ) {
9350 e.printStackTrace( System.out );
9356 private static boolean testPhyloXMLparsingOfDistributionElement() {
9358 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9359 PhyloXmlParser xml_parser = null;
9361 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9363 catch ( final Exception e ) {
9364 // Do nothing -- means were not running from jar.
9366 if ( xml_parser == null ) {
9367 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9368 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9369 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9372 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9375 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9377 if ( xml_parser.getErrorCount() > 0 ) {
9378 System.out.println( xml_parser.getErrorMessages().toString() );
9381 if ( phylogenies_0.length != 1 ) {
9384 final Phylogeny t1 = phylogenies_0[ 0 ];
9385 PhylogenyNode n = null;
9386 Distribution d = null;
9387 n = t1.getNode( "root node" );
9388 if ( !n.getNodeData().isHasDistribution() ) {
9391 if ( n.getNodeData().getDistributions().size() != 1 ) {
9394 d = n.getNodeData().getDistribution();
9395 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9398 if ( d.getPoints().size() != 1 ) {
9401 if ( d.getPolygons() != null ) {
9404 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9407 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9410 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9413 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9416 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9419 n = t1.getNode( "node a" );
9420 if ( !n.getNodeData().isHasDistribution() ) {
9423 if ( n.getNodeData().getDistributions().size() != 2 ) {
9426 d = n.getNodeData().getDistribution( 1 );
9427 if ( !d.getDesc().equals( "San Diego" ) ) {
9430 if ( d.getPoints().size() != 1 ) {
9433 if ( d.getPolygons() != null ) {
9436 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9439 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9442 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9445 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9448 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9451 n = t1.getNode( "node bb" );
9452 if ( !n.getNodeData().isHasDistribution() ) {
9455 if ( n.getNodeData().getDistributions().size() != 1 ) {
9458 d = n.getNodeData().getDistribution( 0 );
9459 if ( d.getPoints().size() != 3 ) {
9462 if ( d.getPolygons().size() != 2 ) {
9465 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9468 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9471 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9474 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9477 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9480 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9483 Polygon p = d.getPolygons().get( 0 );
9484 if ( p.getPoints().size() != 3 ) {
9487 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9490 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9493 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9496 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9499 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9502 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9505 p = d.getPolygons().get( 1 );
9506 if ( p.getPoints().size() != 3 ) {
9509 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9512 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9515 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9519 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9520 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9521 if ( rt.length != 1 ) {
9524 final Phylogeny t1_rt = rt[ 0 ];
9525 n = t1_rt.getNode( "root node" );
9526 if ( !n.getNodeData().isHasDistribution() ) {
9529 if ( n.getNodeData().getDistributions().size() != 1 ) {
9532 d = n.getNodeData().getDistribution();
9533 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9536 if ( d.getPoints().size() != 1 ) {
9539 if ( d.getPolygons() != null ) {
9542 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9545 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9548 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9551 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9554 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9557 n = t1_rt.getNode( "node a" );
9558 if ( !n.getNodeData().isHasDistribution() ) {
9561 if ( n.getNodeData().getDistributions().size() != 2 ) {
9564 d = n.getNodeData().getDistribution( 1 );
9565 if ( !d.getDesc().equals( "San Diego" ) ) {
9568 if ( d.getPoints().size() != 1 ) {
9571 if ( d.getPolygons() != null ) {
9574 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9577 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9580 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9583 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9586 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9589 n = t1_rt.getNode( "node bb" );
9590 if ( !n.getNodeData().isHasDistribution() ) {
9593 if ( n.getNodeData().getDistributions().size() != 1 ) {
9596 d = n.getNodeData().getDistribution( 0 );
9597 if ( d.getPoints().size() != 3 ) {
9600 if ( d.getPolygons().size() != 2 ) {
9603 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9606 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9609 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9612 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9615 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9618 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9621 p = d.getPolygons().get( 0 );
9622 if ( p.getPoints().size() != 3 ) {
9625 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9628 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9631 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9634 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9637 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9640 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9643 p = d.getPolygons().get( 1 );
9644 if ( p.getPoints().size() != 3 ) {
9647 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9650 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9653 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9657 catch ( final Exception e ) {
9658 e.printStackTrace( System.out );
9664 private static boolean testPostOrderIterator() {
9666 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9667 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9668 PhylogenyNodeIterator it0;
9669 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
9672 for( it0.reset(); it0.hasNext(); ) {
9675 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
9676 final PhylogenyNodeIterator it = t1.iteratorPostorder();
9677 if ( !it.next().getName().equals( "A" ) ) {
9680 if ( !it.next().getName().equals( "B" ) ) {
9683 if ( !it.next().getName().equals( "ab" ) ) {
9686 if ( !it.next().getName().equals( "C" ) ) {
9689 if ( !it.next().getName().equals( "D" ) ) {
9692 if ( !it.next().getName().equals( "cd" ) ) {
9695 if ( !it.next().getName().equals( "abcd" ) ) {
9698 if ( !it.next().getName().equals( "E" ) ) {
9701 if ( !it.next().getName().equals( "F" ) ) {
9704 if ( !it.next().getName().equals( "ef" ) ) {
9707 if ( !it.next().getName().equals( "G" ) ) {
9710 if ( !it.next().getName().equals( "H" ) ) {
9713 if ( !it.next().getName().equals( "gh" ) ) {
9716 if ( !it.next().getName().equals( "efgh" ) ) {
9719 if ( !it.next().getName().equals( "r" ) ) {
9722 if ( it.hasNext() ) {
9726 catch ( final Exception e ) {
9727 e.printStackTrace( System.out );
9733 private static boolean testPreOrderIterator() {
9735 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9736 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9737 PhylogenyNodeIterator it0;
9738 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
9741 for( it0.reset(); it0.hasNext(); ) {
9744 PhylogenyNodeIterator it = t0.iteratorPreorder();
9745 if ( !it.next().getName().equals( "r" ) ) {
9748 if ( !it.next().getName().equals( "ab" ) ) {
9751 if ( !it.next().getName().equals( "A" ) ) {
9754 if ( !it.next().getName().equals( "B" ) ) {
9757 if ( !it.next().getName().equals( "cd" ) ) {
9760 if ( !it.next().getName().equals( "C" ) ) {
9763 if ( !it.next().getName().equals( "D" ) ) {
9766 if ( it.hasNext() ) {
9769 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
9770 it = t1.iteratorPreorder();
9771 if ( !it.next().getName().equals( "r" ) ) {
9774 if ( !it.next().getName().equals( "abcd" ) ) {
9777 if ( !it.next().getName().equals( "ab" ) ) {
9780 if ( !it.next().getName().equals( "A" ) ) {
9783 if ( !it.next().getName().equals( "B" ) ) {
9786 if ( !it.next().getName().equals( "cd" ) ) {
9789 if ( !it.next().getName().equals( "C" ) ) {
9792 if ( !it.next().getName().equals( "D" ) ) {
9795 if ( !it.next().getName().equals( "efgh" ) ) {
9798 if ( !it.next().getName().equals( "ef" ) ) {
9801 if ( !it.next().getName().equals( "E" ) ) {
9804 if ( !it.next().getName().equals( "F" ) ) {
9807 if ( !it.next().getName().equals( "gh" ) ) {
9810 if ( !it.next().getName().equals( "G" ) ) {
9813 if ( !it.next().getName().equals( "H" ) ) {
9816 if ( it.hasNext() ) {
9820 catch ( final Exception e ) {
9821 e.printStackTrace( System.out );
9827 private static boolean testPropertiesMap() {
9829 final PropertiesMap pm = new PropertiesMap();
9830 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9831 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9832 final Property p2 = new Property( "something:else",
9834 "improbable:research",
9837 pm.addProperty( p0 );
9838 pm.addProperty( p1 );
9839 pm.addProperty( p2 );
9840 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
9843 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
9846 if ( pm.getProperties().size() != 3 ) {
9849 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
9852 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9855 if ( pm.getProperties().size() != 3 ) {
9858 pm.removeProperty( "dimensions:diameter" );
9859 if ( pm.getProperties().size() != 2 ) {
9862 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
9865 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9869 catch ( final Exception e ) {
9870 e.printStackTrace( System.out );
9876 private static boolean testProteinId() {
9878 final ProteinId id1 = new ProteinId( "a" );
9879 final ProteinId id2 = new ProteinId( "a" );
9880 final ProteinId id3 = new ProteinId( "A" );
9881 final ProteinId id4 = new ProteinId( "b" );
9882 if ( !id1.equals( id1 ) ) {
9885 if ( id1.getId().equals( "x" ) ) {
9888 if ( id1.getId().equals( null ) ) {
9891 if ( !id1.equals( id2 ) ) {
9894 if ( id1.equals( id3 ) ) {
9897 if ( id1.hashCode() != id1.hashCode() ) {
9900 if ( id1.hashCode() != id2.hashCode() ) {
9903 if ( id1.hashCode() == id3.hashCode() ) {
9906 if ( id1.compareTo( id1 ) != 0 ) {
9909 if ( id1.compareTo( id2 ) != 0 ) {
9912 if ( id1.compareTo( id3 ) != 0 ) {
9915 if ( id1.compareTo( id4 ) >= 0 ) {
9918 if ( id4.compareTo( id1 ) <= 0 ) {
9921 if ( !id4.getId().equals( "b" ) ) {
9924 final ProteinId id5 = new ProteinId( " C " );
9925 if ( !id5.getId().equals( "C" ) ) {
9928 if ( id5.equals( id1 ) ) {
9932 catch ( final Exception e ) {
9933 e.printStackTrace( System.out );
9939 private static boolean testReIdMethods() {
9941 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9942 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
9943 final long count = PhylogenyNode.getNodeCount();
9945 if ( p.getNode( "r" ).getId() != count ) {
9948 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
9951 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
9954 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
9957 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
9960 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
9963 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
9966 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
9969 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
9972 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
9975 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
9978 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
9981 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
9984 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
9987 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
9991 catch ( final Exception e ) {
9992 e.printStackTrace( System.out );
9998 private static boolean testRerooting() {
10000 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10001 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",
10002 new NHXParser() )[ 0 ];
10003 if ( !t1.isRooted() ) {
10006 t1.reRoot( t1.getNode( "D" ) );
10007 t1.reRoot( t1.getNode( "CD" ) );
10008 t1.reRoot( t1.getNode( "A" ) );
10009 t1.reRoot( t1.getNode( "B" ) );
10010 t1.reRoot( t1.getNode( "AB" ) );
10011 t1.reRoot( t1.getNode( "D" ) );
10012 t1.reRoot( t1.getNode( "C" ) );
10013 t1.reRoot( t1.getNode( "CD" ) );
10014 t1.reRoot( t1.getNode( "A" ) );
10015 t1.reRoot( t1.getNode( "B" ) );
10016 t1.reRoot( t1.getNode( "AB" ) );
10017 t1.reRoot( t1.getNode( "D" ) );
10018 t1.reRoot( t1.getNode( "D" ) );
10019 t1.reRoot( t1.getNode( "C" ) );
10020 t1.reRoot( t1.getNode( "A" ) );
10021 t1.reRoot( t1.getNode( "B" ) );
10022 t1.reRoot( t1.getNode( "AB" ) );
10023 t1.reRoot( t1.getNode( "C" ) );
10024 t1.reRoot( t1.getNode( "D" ) );
10025 t1.reRoot( t1.getNode( "CD" ) );
10026 t1.reRoot( t1.getNode( "D" ) );
10027 t1.reRoot( t1.getNode( "A" ) );
10028 t1.reRoot( t1.getNode( "B" ) );
10029 t1.reRoot( t1.getNode( "AB" ) );
10030 t1.reRoot( t1.getNode( "C" ) );
10031 t1.reRoot( t1.getNode( "D" ) );
10032 t1.reRoot( t1.getNode( "CD" ) );
10033 t1.reRoot( t1.getNode( "D" ) );
10034 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10037 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10040 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10043 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10046 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10049 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10052 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",
10053 new NHXParser() )[ 0 ];
10054 t2.reRoot( t2.getNode( "A" ) );
10055 t2.reRoot( t2.getNode( "D" ) );
10056 t2.reRoot( t2.getNode( "ABC" ) );
10057 t2.reRoot( t2.getNode( "A" ) );
10058 t2.reRoot( t2.getNode( "B" ) );
10059 t2.reRoot( t2.getNode( "D" ) );
10060 t2.reRoot( t2.getNode( "C" ) );
10061 t2.reRoot( t2.getNode( "ABC" ) );
10062 t2.reRoot( t2.getNode( "A" ) );
10063 t2.reRoot( t2.getNode( "B" ) );
10064 t2.reRoot( t2.getNode( "AB" ) );
10065 t2.reRoot( t2.getNode( "AB" ) );
10066 t2.reRoot( t2.getNode( "D" ) );
10067 t2.reRoot( t2.getNode( "C" ) );
10068 t2.reRoot( t2.getNode( "B" ) );
10069 t2.reRoot( t2.getNode( "AB" ) );
10070 t2.reRoot( t2.getNode( "D" ) );
10071 t2.reRoot( t2.getNode( "D" ) );
10072 t2.reRoot( t2.getNode( "ABC" ) );
10073 t2.reRoot( t2.getNode( "A" ) );
10074 t2.reRoot( t2.getNode( "B" ) );
10075 t2.reRoot( t2.getNode( "AB" ) );
10076 t2.reRoot( t2.getNode( "D" ) );
10077 t2.reRoot( t2.getNode( "C" ) );
10078 t2.reRoot( t2.getNode( "ABC" ) );
10079 t2.reRoot( t2.getNode( "A" ) );
10080 t2.reRoot( t2.getNode( "B" ) );
10081 t2.reRoot( t2.getNode( "AB" ) );
10082 t2.reRoot( t2.getNode( "D" ) );
10083 t2.reRoot( t2.getNode( "D" ) );
10084 t2.reRoot( t2.getNode( "C" ) );
10085 t2.reRoot( t2.getNode( "A" ) );
10086 t2.reRoot( t2.getNode( "B" ) );
10087 t2.reRoot( t2.getNode( "AB" ) );
10088 t2.reRoot( t2.getNode( "C" ) );
10089 t2.reRoot( t2.getNode( "D" ) );
10090 t2.reRoot( t2.getNode( "ABC" ) );
10091 t2.reRoot( t2.getNode( "D" ) );
10092 t2.reRoot( t2.getNode( "A" ) );
10093 t2.reRoot( t2.getNode( "B" ) );
10094 t2.reRoot( t2.getNode( "AB" ) );
10095 t2.reRoot( t2.getNode( "C" ) );
10096 t2.reRoot( t2.getNode( "D" ) );
10097 t2.reRoot( t2.getNode( "ABC" ) );
10098 t2.reRoot( t2.getNode( "D" ) );
10099 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10102 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10105 t2.reRoot( t2.getNode( "ABC" ) );
10106 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10109 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10112 t2.reRoot( t2.getNode( "AB" ) );
10113 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10116 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10119 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10122 t2.reRoot( t2.getNode( "AB" ) );
10123 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10126 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10129 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10132 t2.reRoot( t2.getNode( "D" ) );
10133 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10136 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10139 t2.reRoot( t2.getNode( "ABC" ) );
10140 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10143 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10146 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10147 new NHXParser() )[ 0 ];
10148 t3.reRoot( t3.getNode( "B" ) );
10149 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10152 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10155 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10158 t3.reRoot( t3.getNode( "B" ) );
10159 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10162 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10165 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10168 t3.reRoot( t3.getRoot() );
10169 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10172 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10175 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10179 catch ( final Exception e ) {
10180 e.printStackTrace( System.out );
10186 private static boolean testSDIse() {
10188 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10189 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10190 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10191 gene1.setRooted( true );
10192 species1.setRooted( true );
10193 final SDI sdi = new SDI( gene1, species1 );
10194 if ( !gene1.getRoot().isDuplication() ) {
10197 final Phylogeny species2 = factory
10198 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10199 new NHXParser() )[ 0 ];
10200 final Phylogeny gene2 = factory
10201 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10202 new NHXParser() )[ 0 ];
10203 species2.setRooted( true );
10204 gene2.setRooted( true );
10205 final SDI sdi2 = new SDI( gene2, species2 );
10206 if ( sdi2.getDuplicationsSum() != 0 ) {
10209 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10212 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10215 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10218 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10221 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10224 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10227 final Phylogeny species3 = factory
10228 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10229 new NHXParser() )[ 0 ];
10230 final Phylogeny gene3 = factory
10231 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10232 new NHXParser() )[ 0 ];
10233 species3.setRooted( true );
10234 gene3.setRooted( true );
10235 final SDI sdi3 = new SDI( gene3, species3 );
10236 if ( sdi3.getDuplicationsSum() != 1 ) {
10239 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10242 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10245 final Phylogeny species4 = factory
10246 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10247 new NHXParser() )[ 0 ];
10248 final Phylogeny gene4 = factory
10249 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10250 new NHXParser() )[ 0 ];
10251 species4.setRooted( true );
10252 gene4.setRooted( true );
10253 final SDI sdi4 = new SDI( gene4, species4 );
10254 if ( sdi4.getDuplicationsSum() != 1 ) {
10257 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10260 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10263 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10266 if ( species4.getNumberOfExternalNodes() != 6 ) {
10269 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10272 final Phylogeny species5 = factory
10273 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10274 new NHXParser() )[ 0 ];
10275 final Phylogeny gene5 = factory
10276 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10277 new NHXParser() )[ 0 ];
10278 species5.setRooted( true );
10279 gene5.setRooted( true );
10280 final SDI sdi5 = new SDI( gene5, species5 );
10281 if ( sdi5.getDuplicationsSum() != 2 ) {
10284 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10287 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10290 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10293 if ( species5.getNumberOfExternalNodes() != 6 ) {
10296 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10299 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10300 // Conjecture for Comparing Molecular Phylogenies"
10301 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10302 final Phylogeny species6 = factory
10303 .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,"
10304 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10305 new NHXParser() )[ 0 ];
10306 final Phylogeny gene6 = factory
10307 .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,"
10308 + "((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,"
10309 + "(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;",
10310 new NHXParser() )[ 0 ];
10311 species6.setRooted( true );
10312 gene6.setRooted( true );
10313 final SDI sdi6 = new SDI( gene6, species6 );
10314 if ( sdi6.getDuplicationsSum() != 3 ) {
10317 if ( !gene6.getNode( "r" ).isDuplication() ) {
10320 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10323 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10326 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10329 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10332 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10335 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10338 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10341 sdi6.computeMappingCostL();
10342 if ( sdi6.computeMappingCostL() != 17 ) {
10345 if ( species6.getNumberOfExternalNodes() != 9 ) {
10348 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10351 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10352 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10353 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10354 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10355 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10356 species7.setRooted( true );
10357 final Phylogeny gene7_1 = Test
10358 .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])" );
10359 gene7_1.setRooted( true );
10360 final SDI sdi7 = new SDI( gene7_1, species7 );
10361 if ( sdi7.getDuplicationsSum() != 0 ) {
10364 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10367 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10370 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10373 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10376 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10379 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10382 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10385 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10388 final Phylogeny gene7_2 = Test
10389 .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])" );
10390 gene7_2.setRooted( true );
10391 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10392 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10395 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10398 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10401 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10404 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10407 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10410 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10413 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10416 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10419 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10423 catch ( final Exception e ) {
10429 private static boolean testSDIunrooted() {
10431 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10432 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10433 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10434 final Iterator<PhylogenyBranch> iter = l.iterator();
10435 PhylogenyBranch br = iter.next();
10436 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10439 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10443 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10446 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10450 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10453 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10457 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10460 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10464 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10467 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10471 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10474 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10478 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10481 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10485 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10488 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10492 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10495 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10499 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10502 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10506 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10509 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10513 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10516 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10520 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10523 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10527 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10530 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10534 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10537 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10540 if ( iter.hasNext() ) {
10543 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10544 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10545 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10547 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10550 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10554 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10557 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10561 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10564 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10567 if ( iter1.hasNext() ) {
10570 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10571 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10572 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10574 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10577 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10581 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10584 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10588 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10591 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10594 if ( iter2.hasNext() ) {
10597 final Phylogeny species0 = factory
10598 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10599 new NHXParser() )[ 0 ];
10600 final Phylogeny gene1 = factory
10601 .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])",
10602 new NHXParser() )[ 0 ];
10603 species0.setRooted( true );
10604 gene1.setRooted( true );
10605 final SDIR sdi_unrooted = new SDIR();
10606 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10607 if ( sdi_unrooted.getCount() != 1 ) {
10610 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10613 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10616 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10619 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10622 final Phylogeny gene2 = factory
10623 .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])",
10624 new NHXParser() )[ 0 ];
10625 gene2.setRooted( true );
10626 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10627 if ( sdi_unrooted.getCount() != 1 ) {
10630 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10633 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10636 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10639 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10642 final Phylogeny species6 = factory
10643 .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,"
10644 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10645 new NHXParser() )[ 0 ];
10646 final Phylogeny gene6 = factory
10647 .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],"
10648 + "(((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],"
10649 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10650 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10651 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10652 new NHXParser() )[ 0 ];
10653 species6.setRooted( true );
10654 gene6.setRooted( true );
10655 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10656 if ( sdi_unrooted.getCount() != 1 ) {
10659 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10662 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10665 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10668 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10671 if ( !p6[ 0 ].getRoot().isDuplication() ) {
10674 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10677 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10680 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
10683 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10686 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
10689 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
10692 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10696 final Phylogeny species7 = factory
10697 .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,"
10698 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10699 new NHXParser() )[ 0 ];
10700 final Phylogeny gene7 = factory
10701 .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],"
10702 + "(((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],"
10703 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10704 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10705 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10706 new NHXParser() )[ 0 ];
10707 species7.setRooted( true );
10708 gene7.setRooted( true );
10709 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
10710 if ( sdi_unrooted.getCount() != 1 ) {
10713 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10716 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10719 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10722 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
10725 if ( !p7[ 0 ].getRoot().isDuplication() ) {
10728 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10731 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10734 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
10737 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10740 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
10743 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
10746 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10750 final Phylogeny species8 = factory
10751 .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,"
10752 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10753 new NHXParser() )[ 0 ];
10754 final Phylogeny gene8 = factory
10755 .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],"
10756 + "(((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],"
10757 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10758 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10759 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10760 new NHXParser() )[ 0 ];
10761 species8.setRooted( true );
10762 gene8.setRooted( true );
10763 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
10764 if ( sdi_unrooted.getCount() != 1 ) {
10767 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10770 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10773 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10776 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10779 if ( !p8[ 0 ].getRoot().isDuplication() ) {
10782 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10785 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10788 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
10791 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10794 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
10797 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
10800 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10805 catch ( final Exception e ) {
10806 e.printStackTrace( System.out );
10812 private static boolean testSequenceDbWsTools1() {
10814 final PhylogenyNode n = new PhylogenyNode();
10815 n.setName( "NP_001025424" );
10816 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
10817 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10818 || !acc.getValue().equals( "NP_001025424" ) ) {
10821 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
10822 acc = SequenceDbWsTools.obtainSeqAccession( n );
10823 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10824 || !acc.getValue().equals( "NP_001025424" ) ) {
10827 n.setName( "NP_001025424.1" );
10828 acc = SequenceDbWsTools.obtainSeqAccession( n );
10829 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10830 || !acc.getValue().equals( "NP_001025424" ) ) {
10833 n.setName( "NM_001030253" );
10834 acc = SequenceDbWsTools.obtainSeqAccession( n );
10835 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
10836 || !acc.getValue().equals( "NM_001030253" ) ) {
10839 n.setName( "BCL2_HUMAN" );
10840 acc = SequenceDbWsTools.obtainSeqAccession( n );
10841 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10842 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
10843 System.out.println( acc.toString() );
10846 n.setName( "P10415" );
10847 acc = SequenceDbWsTools.obtainSeqAccession( n );
10848 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10849 || !acc.getValue().equals( "P10415" ) ) {
10850 System.out.println( acc.toString() );
10853 n.setName( " P10415 " );
10854 acc = SequenceDbWsTools.obtainSeqAccession( n );
10855 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10856 || !acc.getValue().equals( "P10415" ) ) {
10857 System.out.println( acc.toString() );
10860 n.setName( "_P10415|" );
10861 acc = SequenceDbWsTools.obtainSeqAccession( n );
10862 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
10863 || !acc.getValue().equals( "P10415" ) ) {
10864 System.out.println( acc.toString() );
10867 n.setName( "AY695820" );
10868 acc = SequenceDbWsTools.obtainSeqAccession( n );
10869 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10870 || !acc.getValue().equals( "AY695820" ) ) {
10871 System.out.println( acc.toString() );
10874 n.setName( "_AY695820_" );
10875 acc = SequenceDbWsTools.obtainSeqAccession( n );
10876 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10877 || !acc.getValue().equals( "AY695820" ) ) {
10878 System.out.println( acc.toString() );
10881 n.setName( "AAA59452" );
10882 acc = SequenceDbWsTools.obtainSeqAccession( n );
10883 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10884 || !acc.getValue().equals( "AAA59452" ) ) {
10885 System.out.println( acc.toString() );
10888 n.setName( "_AAA59452_" );
10889 acc = SequenceDbWsTools.obtainSeqAccession( n );
10890 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10891 || !acc.getValue().equals( "AAA59452" ) ) {
10892 System.out.println( acc.toString() );
10895 n.setName( "AAA59452.1" );
10896 acc = SequenceDbWsTools.obtainSeqAccession( n );
10897 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10898 || !acc.getValue().equals( "AAA59452.1" ) ) {
10899 System.out.println( acc.toString() );
10902 n.setName( "_AAA59452.1_" );
10903 acc = SequenceDbWsTools.obtainSeqAccession( n );
10904 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10905 || !acc.getValue().equals( "AAA59452.1" ) ) {
10906 System.out.println( acc.toString() );
10909 n.setName( "GI:94894583" );
10910 acc = SequenceDbWsTools.obtainSeqAccession( n );
10911 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
10912 || !acc.getValue().equals( "94894583" ) ) {
10913 System.out.println( acc.toString() );
10916 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
10917 acc = SequenceDbWsTools.obtainSeqAccession( n );
10918 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
10919 || !acc.getValue().equals( "71845847" ) ) {
10920 System.out.println( acc.toString() );
10923 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
10924 acc = SequenceDbWsTools.obtainSeqAccession( n );
10925 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
10926 || !acc.getValue().equals( "AAZ45343.1" ) ) {
10927 System.out.println( acc.toString() );
10931 catch ( final Exception e ) {
10937 private static boolean testSequenceDbWsTools2() {
10939 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
10940 SequenceDbWsTools.obtainSeqInformation( n1 );
10941 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
10944 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
10947 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10950 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
10953 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
10954 SequenceDbWsTools.obtainSeqInformation( n2 );
10955 if ( !n2.getNodeData().getSequence().getName()
10956 .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
10959 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
10962 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10965 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
10968 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
10969 SequenceDbWsTools.obtainSeqInformation( n3 );
10970 if ( !n3.getNodeData().getSequence().getName()
10971 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
10974 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
10977 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
10980 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
10984 catch ( final IOException e ) {
10985 System.out.println();
10986 System.out.println( "the following might be due to absence internet connection:" );
10987 e.printStackTrace( System.out );
10990 catch ( final Exception e ) {
10991 e.printStackTrace();
10997 private static boolean testSequenceIdParsing() {
10999 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11000 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11001 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11002 if ( id != null ) {
11003 System.out.println( "value =" + id.getValue() );
11004 System.out.println( "provider=" + id.getSource() );
11009 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11010 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11011 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11012 if ( id != null ) {
11013 System.out.println( "value =" + id.getValue() );
11014 System.out.println( "provider=" + id.getSource() );
11019 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11020 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11021 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11022 if ( id != null ) {
11023 System.out.println( "value =" + id.getValue() );
11024 System.out.println( "provider=" + id.getSource() );
11029 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11030 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11031 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11032 if ( id != null ) {
11033 System.out.println( "value =" + id.getValue() );
11034 System.out.println( "provider=" + id.getSource() );
11039 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11040 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11041 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11042 if ( id != null ) {
11043 System.out.println( "value =" + id.getValue() );
11044 System.out.println( "provider=" + id.getSource() );
11049 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11050 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11051 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11052 if ( id != null ) {
11053 System.out.println( "value =" + id.getValue() );
11054 System.out.println( "provider=" + id.getSource() );
11059 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11060 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11061 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11062 if ( id != null ) {
11063 System.out.println( "value =" + id.getValue() );
11064 System.out.println( "provider=" + id.getSource() );
11069 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11070 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11071 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11072 if ( id != null ) {
11073 System.out.println( "value =" + id.getValue() );
11074 System.out.println( "provider=" + id.getSource() );
11079 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11080 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11081 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11082 if ( id != null ) {
11083 System.out.println( "value =" + id.getValue() );
11084 System.out.println( "provider=" + id.getSource() );
11089 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11090 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11091 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11092 if ( id != null ) {
11093 System.out.println( "value =" + id.getValue() );
11094 System.out.println( "provider=" + id.getSource() );
11098 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11099 if ( id != null ) {
11100 System.out.println( "value =" + id.getValue() );
11101 System.out.println( "provider=" + id.getSource() );
11105 catch ( final Exception e ) {
11106 e.printStackTrace( System.out );
11112 private static boolean testSequenceWriter() {
11114 final String n = ForesterUtil.LINE_SEPARATOR;
11115 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11118 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11121 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11124 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11127 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11128 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11131 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11132 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11136 catch ( final Exception e ) {
11137 e.printStackTrace();
11143 private static boolean testSpecies() {
11145 final Species s1 = new BasicSpecies( "a" );
11146 final Species s2 = new BasicSpecies( "a" );
11147 final Species s3 = new BasicSpecies( "A" );
11148 final Species s4 = new BasicSpecies( "b" );
11149 if ( !s1.equals( s1 ) ) {
11152 if ( s1.getSpeciesId().equals( "x" ) ) {
11155 if ( s1.getSpeciesId().equals( null ) ) {
11158 if ( !s1.equals( s2 ) ) {
11161 if ( s1.equals( s3 ) ) {
11164 if ( s1.hashCode() != s1.hashCode() ) {
11167 if ( s1.hashCode() != s2.hashCode() ) {
11170 if ( s1.hashCode() == s3.hashCode() ) {
11173 if ( s1.compareTo( s1 ) != 0 ) {
11176 if ( s1.compareTo( s2 ) != 0 ) {
11179 if ( s1.compareTo( s3 ) != 0 ) {
11182 if ( s1.compareTo( s4 ) >= 0 ) {
11185 if ( s4.compareTo( s1 ) <= 0 ) {
11188 if ( !s4.getSpeciesId().equals( "b" ) ) {
11191 final Species s5 = new BasicSpecies( " C " );
11192 if ( !s5.getSpeciesId().equals( "C" ) ) {
11195 if ( s5.equals( s1 ) ) {
11199 catch ( final Exception e ) {
11200 e.printStackTrace( System.out );
11206 private static boolean testSplit() {
11208 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11209 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11210 //Archaeopteryx.createApplication( p0 );
11211 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11212 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11213 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11214 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11215 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11216 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11217 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11218 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11219 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11220 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11221 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11222 // System.out.println( s0.toString() );
11224 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11225 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11227 if ( s0.match( query_nodes ) ) {
11230 query_nodes = new HashSet<PhylogenyNode>();
11231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11232 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11233 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11234 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11238 if ( !s0.match( query_nodes ) ) {
11242 query_nodes = new HashSet<PhylogenyNode>();
11243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11246 if ( !s0.match( query_nodes ) ) {
11250 query_nodes = new HashSet<PhylogenyNode>();
11251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11255 if ( !s0.match( query_nodes ) ) {
11259 query_nodes = new HashSet<PhylogenyNode>();
11260 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11261 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11264 if ( !s0.match( query_nodes ) ) {
11268 query_nodes = new HashSet<PhylogenyNode>();
11269 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11272 if ( !s0.match( query_nodes ) ) {
11276 query_nodes = new HashSet<PhylogenyNode>();
11277 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11279 if ( !s0.match( query_nodes ) ) {
11283 query_nodes = new HashSet<PhylogenyNode>();
11284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11289 if ( !s0.match( query_nodes ) ) {
11293 query_nodes = new HashSet<PhylogenyNode>();
11294 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11297 if ( !s0.match( query_nodes ) ) {
11301 query_nodes = new HashSet<PhylogenyNode>();
11302 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11303 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11305 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11306 if ( !s0.match( query_nodes ) ) {
11310 query_nodes = new HashSet<PhylogenyNode>();
11311 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11312 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11313 if ( s0.match( query_nodes ) ) {
11317 query_nodes = new HashSet<PhylogenyNode>();
11318 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11319 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11322 if ( s0.match( query_nodes ) ) {
11326 query_nodes = new HashSet<PhylogenyNode>();
11327 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11328 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11329 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11330 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
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( "B" ) );
11339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11340 if ( s0.match( query_nodes ) ) {
11344 query_nodes = new HashSet<PhylogenyNode>();
11345 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11346 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11347 if ( s0.match( query_nodes ) ) {
11351 query_nodes = new HashSet<PhylogenyNode>();
11352 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11353 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11354 if ( s0.match( query_nodes ) ) {
11358 query_nodes = new HashSet<PhylogenyNode>();
11359 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11360 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11361 if ( s0.match( query_nodes ) ) {
11365 query_nodes = new HashSet<PhylogenyNode>();
11366 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11367 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11368 if ( s0.match( query_nodes ) ) {
11372 query_nodes = new HashSet<PhylogenyNode>();
11373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11375 if ( s0.match( query_nodes ) ) {
11379 query_nodes = new HashSet<PhylogenyNode>();
11380 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11382 if ( s0.match( query_nodes ) ) {
11386 query_nodes = new HashSet<PhylogenyNode>();
11387 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11388 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11389 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11390 if ( s0.match( query_nodes ) ) {
11394 query_nodes = new HashSet<PhylogenyNode>();
11395 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11396 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11397 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11398 if ( s0.match( query_nodes ) ) {
11402 query_nodes = new HashSet<PhylogenyNode>();
11403 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11404 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11405 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11406 if ( s0.match( query_nodes ) ) {
11410 query_nodes = new HashSet<PhylogenyNode>();
11411 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11412 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11413 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11415 if ( s0.match( query_nodes ) ) {
11419 // query_nodes = new HashSet<PhylogenyNode>();
11420 // query_nodes.add( new PhylogenyNode( "X" ) );
11421 // query_nodes.add( new PhylogenyNode( "Y" ) );
11422 // query_nodes.add( new PhylogenyNode( "A" ) );
11423 // query_nodes.add( new PhylogenyNode( "B" ) );
11424 // query_nodes.add( new PhylogenyNode( "C" ) );
11425 // query_nodes.add( new PhylogenyNode( "D" ) );
11426 // query_nodes.add( new PhylogenyNode( "E" ) );
11427 // query_nodes.add( new PhylogenyNode( "F" ) );
11428 // query_nodes.add( new PhylogenyNode( "G" ) );
11429 // if ( !s0.match( query_nodes ) ) {
11432 // query_nodes = new HashSet<PhylogenyNode>();
11433 // query_nodes.add( new PhylogenyNode( "X" ) );
11434 // query_nodes.add( new PhylogenyNode( "Y" ) );
11435 // query_nodes.add( new PhylogenyNode( "A" ) );
11436 // query_nodes.add( new PhylogenyNode( "B" ) );
11437 // query_nodes.add( new PhylogenyNode( "C" ) );
11438 // if ( !s0.match( query_nodes ) ) {
11442 // query_nodes = new HashSet<PhylogenyNode>();
11443 // query_nodes.add( new PhylogenyNode( "X" ) );
11444 // query_nodes.add( new PhylogenyNode( "Y" ) );
11445 // query_nodes.add( new PhylogenyNode( "D" ) );
11446 // query_nodes.add( new PhylogenyNode( "E" ) );
11447 // query_nodes.add( new PhylogenyNode( "F" ) );
11448 // query_nodes.add( new PhylogenyNode( "G" ) );
11449 // if ( !s0.match( query_nodes ) ) {
11453 // query_nodes = new HashSet<PhylogenyNode>();
11454 // query_nodes.add( new PhylogenyNode( "X" ) );
11455 // query_nodes.add( new PhylogenyNode( "Y" ) );
11456 // query_nodes.add( new PhylogenyNode( "A" ) );
11457 // query_nodes.add( new PhylogenyNode( "B" ) );
11458 // query_nodes.add( new PhylogenyNode( "C" ) );
11459 // query_nodes.add( new PhylogenyNode( "D" ) );
11460 // if ( !s0.match( query_nodes ) ) {
11464 // query_nodes = new HashSet<PhylogenyNode>();
11465 // query_nodes.add( new PhylogenyNode( "X" ) );
11466 // query_nodes.add( new PhylogenyNode( "Y" ) );
11467 // query_nodes.add( new PhylogenyNode( "E" ) );
11468 // query_nodes.add( new PhylogenyNode( "F" ) );
11469 // query_nodes.add( new PhylogenyNode( "G" ) );
11470 // if ( !s0.match( query_nodes ) ) {
11474 // query_nodes = new HashSet<PhylogenyNode>();
11475 // query_nodes.add( new PhylogenyNode( "X" ) );
11476 // query_nodes.add( new PhylogenyNode( "Y" ) );
11477 // query_nodes.add( new PhylogenyNode( "F" ) );
11478 // query_nodes.add( new PhylogenyNode( "G" ) );
11479 // if ( !s0.match( query_nodes ) ) {
11483 query_nodes = new HashSet<PhylogenyNode>();
11484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11486 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11487 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11488 if ( s0.match( query_nodes ) ) {
11492 query_nodes = new HashSet<PhylogenyNode>();
11493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11494 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11495 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11496 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11497 if ( s0.match( query_nodes ) ) {
11500 ///////////////////////////
11502 query_nodes = new HashSet<PhylogenyNode>();
11503 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11504 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11505 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11506 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11507 if ( s0.match( query_nodes ) ) {
11511 query_nodes = new HashSet<PhylogenyNode>();
11512 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11514 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11515 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11516 if ( s0.match( query_nodes ) ) {
11520 query_nodes = new HashSet<PhylogenyNode>();
11521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11523 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11525 if ( s0.match( query_nodes ) ) {
11529 query_nodes = new HashSet<PhylogenyNode>();
11530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11534 if ( s0.match( query_nodes ) ) {
11538 query_nodes = new HashSet<PhylogenyNode>();
11539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11540 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11541 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11542 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11543 if ( s0.match( query_nodes ) ) {
11547 query_nodes = new HashSet<PhylogenyNode>();
11548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11551 if ( s0.match( query_nodes ) ) {
11555 query_nodes = new HashSet<PhylogenyNode>();
11556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11560 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11561 if ( s0.match( query_nodes ) ) {
11565 query_nodes = new HashSet<PhylogenyNode>();
11566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11569 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11571 if ( s0.match( query_nodes ) ) {
11575 query_nodes = new HashSet<PhylogenyNode>();
11576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11581 if ( s0.match( query_nodes ) ) {
11585 query_nodes = new HashSet<PhylogenyNode>();
11586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11592 if ( s0.match( query_nodes ) ) {
11596 catch ( final Exception e ) {
11597 e.printStackTrace();
11603 private static boolean testSplitStrict() {
11605 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11606 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11607 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11608 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11609 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11610 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11611 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11612 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11613 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11614 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11615 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11616 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11619 if ( s0.match( query_nodes ) ) {
11622 query_nodes = new HashSet<PhylogenyNode>();
11623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11630 if ( !s0.match( query_nodes ) ) {
11634 query_nodes = new HashSet<PhylogenyNode>();
11635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11638 if ( !s0.match( query_nodes ) ) {
11642 query_nodes = new HashSet<PhylogenyNode>();
11643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11647 if ( !s0.match( query_nodes ) ) {
11651 query_nodes = new HashSet<PhylogenyNode>();
11652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11656 if ( !s0.match( query_nodes ) ) {
11660 query_nodes = new HashSet<PhylogenyNode>();
11661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11664 if ( !s0.match( query_nodes ) ) {
11668 query_nodes = new HashSet<PhylogenyNode>();
11669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11671 if ( !s0.match( query_nodes ) ) {
11675 query_nodes = new HashSet<PhylogenyNode>();
11676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11681 if ( !s0.match( query_nodes ) ) {
11685 query_nodes = new HashSet<PhylogenyNode>();
11686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11689 if ( !s0.match( query_nodes ) ) {
11693 query_nodes = new HashSet<PhylogenyNode>();
11694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11698 if ( !s0.match( query_nodes ) ) {
11702 query_nodes = new HashSet<PhylogenyNode>();
11703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11705 if ( s0.match( query_nodes ) ) {
11709 query_nodes = new HashSet<PhylogenyNode>();
11710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11714 if ( s0.match( query_nodes ) ) {
11718 query_nodes = new HashSet<PhylogenyNode>();
11719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11724 if ( s0.match( query_nodes ) ) {
11728 query_nodes = new HashSet<PhylogenyNode>();
11729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11732 if ( s0.match( query_nodes ) ) {
11736 query_nodes = new HashSet<PhylogenyNode>();
11737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11739 if ( s0.match( query_nodes ) ) {
11743 query_nodes = new HashSet<PhylogenyNode>();
11744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11745 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11746 if ( s0.match( query_nodes ) ) {
11750 query_nodes = new HashSet<PhylogenyNode>();
11751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11753 if ( s0.match( query_nodes ) ) {
11757 query_nodes = new HashSet<PhylogenyNode>();
11758 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11759 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11760 if ( s0.match( query_nodes ) ) {
11764 query_nodes = new HashSet<PhylogenyNode>();
11765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11767 if ( s0.match( query_nodes ) ) {
11771 query_nodes = new HashSet<PhylogenyNode>();
11772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11774 if ( s0.match( query_nodes ) ) {
11778 query_nodes = new HashSet<PhylogenyNode>();
11779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11780 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11781 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11782 if ( s0.match( query_nodes ) ) {
11786 query_nodes = new HashSet<PhylogenyNode>();
11787 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11788 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11790 if ( s0.match( query_nodes ) ) {
11794 query_nodes = new HashSet<PhylogenyNode>();
11795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11798 if ( s0.match( query_nodes ) ) {
11802 query_nodes = new HashSet<PhylogenyNode>();
11803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11807 if ( s0.match( query_nodes ) ) {
11811 catch ( final Exception e ) {
11812 e.printStackTrace();
11818 private static boolean testSubtreeDeletion() {
11820 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11821 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
11822 t1.deleteSubtree( t1.getNode( "A" ), false );
11823 if ( t1.getNumberOfExternalNodes() != 5 ) {
11826 t1.toNewHampshireX();
11827 t1.deleteSubtree( t1.getNode( "E" ), false );
11828 if ( t1.getNumberOfExternalNodes() != 4 ) {
11831 t1.toNewHampshireX();
11832 t1.deleteSubtree( t1.getNode( "F" ), false );
11833 if ( t1.getNumberOfExternalNodes() != 3 ) {
11836 t1.toNewHampshireX();
11837 t1.deleteSubtree( t1.getNode( "D" ), false );
11838 t1.toNewHampshireX();
11839 if ( t1.getNumberOfExternalNodes() != 3 ) {
11842 t1.deleteSubtree( t1.getNode( "def" ), false );
11843 t1.toNewHampshireX();
11844 if ( t1.getNumberOfExternalNodes() != 2 ) {
11847 t1.deleteSubtree( t1.getNode( "B" ), false );
11848 t1.toNewHampshireX();
11849 if ( t1.getNumberOfExternalNodes() != 1 ) {
11852 t1.deleteSubtree( t1.getNode( "C" ), false );
11853 t1.toNewHampshireX();
11854 if ( t1.getNumberOfExternalNodes() != 1 ) {
11857 t1.deleteSubtree( t1.getNode( "abc" ), false );
11858 t1.toNewHampshireX();
11859 if ( t1.getNumberOfExternalNodes() != 1 ) {
11862 t1.deleteSubtree( t1.getNode( "r" ), false );
11863 if ( t1.getNumberOfExternalNodes() != 0 ) {
11866 if ( !t1.isEmpty() ) {
11869 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
11870 t2.deleteSubtree( t2.getNode( "A" ), false );
11871 t2.toNewHampshireX();
11872 if ( t2.getNumberOfExternalNodes() != 5 ) {
11875 t2.deleteSubtree( t2.getNode( "abc" ), false );
11876 t2.toNewHampshireX();
11877 if ( t2.getNumberOfExternalNodes() != 3 ) {
11880 t2.deleteSubtree( t2.getNode( "def" ), false );
11881 t2.toNewHampshireX();
11882 if ( t2.getNumberOfExternalNodes() != 1 ) {
11886 catch ( final Exception e ) {
11887 e.printStackTrace( System.out );
11893 private static boolean testSupportCount() {
11895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11896 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
11897 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
11898 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
11899 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
11900 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
11901 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
11903 SupportCount.count( t0_1, phylogenies_1, true, false );
11904 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
11905 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
11906 + "(((((A,B),C),D),E),((F,G),X))"
11907 + "(((((A,Y),B),C),D),((F,G),E))"
11908 + "(((((A,B),C),D),E),(F,G))"
11909 + "(((((A,B),C),D),E),(F,G))"
11910 + "(((((A,B),C),D),E),(F,G))"
11911 + "(((((A,B),C),D),E),(F,G),Z)"
11912 + "(((((A,B),C),D),E),(F,G))"
11913 + "((((((A,B),C),D),E),F),G)"
11914 + "(((((X,Y),F,G),E),((A,B),C)),D)",
11916 SupportCount.count( t0_2, phylogenies_2, true, false );
11917 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
11918 while ( it.hasNext() ) {
11919 final PhylogenyNode n = it.next();
11920 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
11924 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
11925 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
11926 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
11927 SupportCount.count( t0_3, phylogenies_3, true, false );
11928 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
11929 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
11932 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
11935 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
11938 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
11941 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
11944 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
11947 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
11950 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
11953 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
11956 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
11959 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11960 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
11961 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
11962 SupportCount.count( t0_4, phylogenies_4, true, false );
11963 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
11964 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
11967 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
11970 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
11973 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
11976 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
11979 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
11982 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
11985 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
11988 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
11991 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
11994 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11995 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11996 double d = SupportCount.compare( b1, a, true, true, true );
11997 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12000 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12001 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12002 d = SupportCount.compare( b2, a, true, true, true );
12003 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12006 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12007 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12008 d = SupportCount.compare( b3, a, true, true, true );
12009 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12012 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12013 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12014 d = SupportCount.compare( b4, a, true, true, false );
12015 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12019 catch ( final Exception e ) {
12020 e.printStackTrace( System.out );
12026 private static boolean testSupportTransfer() {
12028 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12029 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)",
12030 new NHXParser() )[ 0 ];
12031 final Phylogeny p2 = factory
12032 .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 ];
12033 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12036 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12039 support_transfer.moveBranchLengthsToBootstrap( p1 );
12040 support_transfer.transferSupportValues( p1, p2 );
12041 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12044 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12047 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12050 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12053 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12056 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12059 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12062 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12066 catch ( final Exception e ) {
12067 e.printStackTrace( System.out );
12073 private static boolean testTaxonomyExtraction() {
12075 final PhylogenyNode n0 = PhylogenyNode
12076 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12077 if ( n0.getNodeData().isHasTaxonomy() ) {
12080 final PhylogenyNode n1 = PhylogenyNode
12081 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12082 if ( n1.getNodeData().isHasTaxonomy() ) {
12083 System.out.println( n1.toString() );
12086 final PhylogenyNode n2x = PhylogenyNode
12087 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12088 if ( n2x.getNodeData().isHasTaxonomy() ) {
12091 final PhylogenyNode n3 = PhylogenyNode
12092 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12093 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12094 System.out.println( n3.toString() );
12097 final PhylogenyNode n4 = PhylogenyNode
12098 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12099 if ( n4.getNodeData().isHasTaxonomy() ) {
12100 System.out.println( n4.toString() );
12103 final PhylogenyNode n5 = PhylogenyNode
12104 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12105 if ( n5.getNodeData().isHasTaxonomy() ) {
12106 System.out.println( n5.toString() );
12109 final PhylogenyNode n6 = PhylogenyNode
12110 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12111 if ( n6.getNodeData().isHasTaxonomy() ) {
12112 System.out.println( n6.toString() );
12115 final PhylogenyNode n7 = PhylogenyNode
12116 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12117 if ( n7.getNodeData().isHasTaxonomy() ) {
12118 System.out.println( n7.toString() );
12121 final PhylogenyNode n8 = PhylogenyNode
12122 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12123 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12124 System.out.println( n8.toString() );
12127 final PhylogenyNode n9 = PhylogenyNode
12128 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12129 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12130 System.out.println( n9.toString() );
12133 final PhylogenyNode n10x = PhylogenyNode
12134 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12135 if ( n10x.getNodeData().isHasTaxonomy() ) {
12136 System.out.println( n10x.toString() );
12139 final PhylogenyNode n10xx = PhylogenyNode
12140 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12141 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12142 System.out.println( n10xx.toString() );
12145 final PhylogenyNode n10 = PhylogenyNode
12146 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12147 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12148 System.out.println( n10.toString() );
12151 final PhylogenyNode n11 = PhylogenyNode
12152 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12153 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12154 System.out.println( n11.toString() );
12157 final PhylogenyNode n12 = PhylogenyNode
12158 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12159 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12160 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12161 System.out.println( n12.toString() );
12164 final PhylogenyNode n13 = PhylogenyNode
12165 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12166 if ( n13.getNodeData().isHasTaxonomy() ) {
12167 System.out.println( n13.toString() );
12170 final PhylogenyNode n14 = PhylogenyNode
12171 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12172 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12173 System.out.println( n14.toString() );
12176 final PhylogenyNode n15 = PhylogenyNode
12177 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12178 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12179 System.out.println( n15.toString() );
12182 final PhylogenyNode n16 = PhylogenyNode
12183 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12184 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12185 System.out.println( n16.toString() );
12188 final PhylogenyNode n17 = PhylogenyNode
12189 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12190 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12191 System.out.println( n17.toString() );
12195 final PhylogenyNode n18 = PhylogenyNode
12196 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12197 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12198 System.out.println( n18.toString() );
12201 final PhylogenyNode n19 = PhylogenyNode
12202 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12203 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12204 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12205 System.out.println( n19.toString() );
12208 final PhylogenyNode n20 = PhylogenyNode
12209 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12210 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12211 System.out.println( n20.toString() );
12214 final PhylogenyNode n21 = PhylogenyNode
12215 .createInstanceFromNhxString( "Mus musculus musculus K392",
12216 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12217 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12218 System.out.println( n21.toString() );
12222 catch ( final Exception e ) {
12223 e.printStackTrace( System.out );
12229 private static boolean testTreeCopy() {
12231 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12232 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12233 final Phylogeny t1 = t0.copy();
12234 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12237 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12240 t0.deleteSubtree( t0.getNode( "c" ), true );
12241 t0.deleteSubtree( t0.getNode( "a" ), true );
12242 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12243 t0.getNode( "b" ).setName( "Bee" );
12244 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12247 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12250 t0.deleteSubtree( t0.getNode( "e" ), true );
12251 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12252 t0.deleteSubtree( t0.getNode( "d" ), true );
12253 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12257 catch ( final Exception e ) {
12258 e.printStackTrace();
12264 private static boolean testTreeMethods() {
12266 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12267 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12268 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12269 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12270 System.out.println( t0.toNewHampshireX() );
12273 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12274 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12275 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12278 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12281 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12285 catch ( final Exception e ) {
12286 e.printStackTrace( System.out );
12292 private static boolean testUniprotEntryRetrieval() {
12294 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
12295 if ( !entry.getAccession().equals( "P12345" ) ) {
12298 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12301 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12304 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12307 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12310 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12314 catch ( final IOException e ) {
12315 System.out.println();
12316 System.out.println( "the following might be due to absence internet connection:" );
12317 e.printStackTrace( System.out );
12320 catch ( final Exception e ) {
12326 private static boolean testUniprotTaxonomySearch() {
12328 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12330 if ( results.size() != 1 ) {
12333 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12336 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12339 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12342 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12345 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12349 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12350 if ( results.size() != 1 ) {
12353 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12356 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12359 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12362 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12365 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12369 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12370 if ( results.size() != 1 ) {
12373 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12376 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12379 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12382 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12385 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12389 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12390 if ( results.size() != 1 ) {
12393 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12396 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12399 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12402 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12405 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12408 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12411 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12414 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12415 .equals( "Nematostella vectensis" ) ) {
12416 System.out.println( results.get( 0 ).getLineage() );
12421 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12422 if ( results.size() != 1 ) {
12425 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12428 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12431 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12434 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12437 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12440 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12441 .equals( "Xenopus tropicalis" ) ) {
12442 System.out.println( results.get( 0 ).getLineage() );
12447 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12448 if ( results.size() != 1 ) {
12451 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12454 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12457 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12460 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12463 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12466 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12467 .equals( "Xenopus tropicalis" ) ) {
12468 System.out.println( results.get( 0 ).getLineage() );
12473 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12474 if ( results.size() != 1 ) {
12477 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12480 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12483 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12486 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12489 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12492 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12493 .equals( "Xenopus tropicalis" ) ) {
12494 System.out.println( results.get( 0 ).getLineage() );
12498 catch ( final IOException e ) {
12499 System.out.println();
12500 System.out.println( "the following might be due to absence internet connection:" );
12501 e.printStackTrace( System.out );
12504 catch ( final Exception e ) {
12510 private static boolean testWabiTxSearch() {
12512 String result = "";
12513 result = TxSearch.searchSimple( "nematostella" );
12514 result = TxSearch.getTxId( "nematostella" );
12515 if ( !result.equals( "45350" ) ) {
12518 result = TxSearch.getTxName( "45350" );
12519 if ( !result.equals( "Nematostella" ) ) {
12522 result = TxSearch.getTxId( "nematostella vectensis" );
12523 if ( !result.equals( "45351" ) ) {
12526 result = TxSearch.getTxName( "45351" );
12527 if ( !result.equals( "Nematostella vectensis" ) ) {
12530 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12531 if ( !result.equals( "536089" ) ) {
12534 result = TxSearch.getTxName( "536089" );
12535 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12538 final List<String> queries = new ArrayList<String>();
12539 queries.add( "Campylobacter coli" );
12540 queries.add( "Escherichia coli" );
12541 queries.add( "Arabidopsis" );
12542 queries.add( "Trichoplax" );
12543 queries.add( "Samanea saman" );
12544 queries.add( "Kluyveromyces marxianus" );
12545 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12546 queries.add( "Bornavirus parrot/PDD/2008" );
12547 final List<RANKS> ranks = new ArrayList<RANKS>();
12548 ranks.add( RANKS.SUPERKINGDOM );
12549 ranks.add( RANKS.KINGDOM );
12550 ranks.add( RANKS.FAMILY );
12551 ranks.add( RANKS.GENUS );
12552 ranks.add( RANKS.TRIBE );
12553 result = TxSearch.searchLineage( queries, ranks );
12554 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12555 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12557 catch ( final Exception e ) {
12558 System.out.println();
12559 System.out.println( "the following might be due to absence internet connection:" );
12560 e.printStackTrace( System.out );