2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
6 // Copyright (C) 2014 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.test;
27 import java.io.ByteArrayInputStream;
29 import java.io.FileInputStream;
30 import java.io.IOException;
31 import java.io.StringWriter;
32 import java.io.Writer;
34 import java.util.ArrayList;
35 import java.util.Date;
36 import java.util.HashSet;
37 import java.util.Iterator;
38 import java.util.List;
39 import java.util.Locale;
41 import java.util.SortedSet;
43 import org.forester.application.support_transfer;
44 import org.forester.archaeopteryx.AptxUtil;
45 import org.forester.archaeopteryx.TreePanelUtil;
46 import org.forester.archaeopteryx.webservices.WebserviceUtil;
47 import org.forester.development.DevelopmentTools;
48 import org.forester.evoinference.TestPhylogenyReconstruction;
49 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
50 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
51 import org.forester.go.TestGo;
52 import org.forester.io.parsers.FastaParser;
53 import org.forester.io.parsers.GeneralMsaParser;
54 import org.forester.io.parsers.HmmscanPerDomainTableParser;
55 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
56 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
57 import org.forester.io.parsers.nexus.NexusCharactersParser;
58 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
59 import org.forester.io.parsers.nhx.NHXParser;
60 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
61 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
62 import org.forester.io.parsers.tol.TolParser;
63 import org.forester.io.parsers.util.ParserUtils;
64 import org.forester.io.writers.PhylogenyWriter;
65 import org.forester.io.writers.SequenceWriter;
66 import org.forester.msa.BasicMsa;
67 import org.forester.msa.DeleteableMsa;
68 import org.forester.msa.Mafft;
69 import org.forester.msa.Msa;
70 import org.forester.msa.Msa.MSA_FORMAT;
71 import org.forester.msa.MsaInferrer;
72 import org.forester.msa.MsaMethods;
73 import org.forester.pccx.TestPccx;
74 import org.forester.phylogeny.Phylogeny;
75 import org.forester.phylogeny.PhylogenyBranch;
76 import org.forester.phylogeny.PhylogenyMethods;
77 import org.forester.phylogeny.PhylogenyNode;
78 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
79 import org.forester.phylogeny.data.Accession;
80 import org.forester.phylogeny.data.Accession.Source;
81 import org.forester.phylogeny.data.BinaryCharacters;
82 import org.forester.phylogeny.data.BranchWidth;
83 import org.forester.phylogeny.data.Confidence;
84 import org.forester.phylogeny.data.Distribution;
85 import org.forester.phylogeny.data.DomainArchitecture;
86 import org.forester.phylogeny.data.Event;
87 import org.forester.phylogeny.data.Identifier;
88 import org.forester.phylogeny.data.PhylogenyData;
89 import org.forester.phylogeny.data.PhylogenyDataUtil;
90 import org.forester.phylogeny.data.Polygon;
91 import org.forester.phylogeny.data.PropertiesMap;
92 import org.forester.phylogeny.data.Property;
93 import org.forester.phylogeny.data.Property.AppliesTo;
94 import org.forester.phylogeny.data.ProteinDomain;
95 import org.forester.phylogeny.data.Taxonomy;
96 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
97 import org.forester.phylogeny.factories.PhylogenyFactory;
98 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
99 import org.forester.protein.BasicDomain;
100 import org.forester.protein.BasicProtein;
101 import org.forester.protein.Domain;
102 import org.forester.protein.Protein;
103 import org.forester.protein.ProteinId;
104 import org.forester.rio.TestRIO;
105 import org.forester.sdi.SDI;
106 import org.forester.sdi.SDIR;
107 import org.forester.sdi.TestGSDI;
108 import org.forester.sequence.BasicSequence;
109 import org.forester.sequence.MolecularSequence;
110 import org.forester.species.BasicSpecies;
111 import org.forester.species.Species;
112 import org.forester.surfacing.TestSurfacing;
113 import org.forester.tools.ConfidenceAssessor;
114 import org.forester.tools.SupportCount;
115 import org.forester.tools.TreeSplitMatrix;
116 import org.forester.util.AsciiHistogram;
117 import org.forester.util.BasicDescriptiveStatistics;
118 import org.forester.util.BasicTable;
119 import org.forester.util.BasicTableParser;
120 import org.forester.util.DescriptiveStatistics;
121 import org.forester.util.ForesterConstants;
122 import org.forester.util.ForesterUtil;
123 import org.forester.util.GeneralTable;
124 import org.forester.util.SequenceAccessionTools;
125 import org.forester.ws.seqdb.SequenceDatabaseEntry;
126 import org.forester.ws.seqdb.SequenceDbWsTools;
127 import org.forester.ws.seqdb.UniProtTaxonomy;
128 import org.forester.ws.wabi.TxSearch;
129 import org.forester.ws.wabi.TxSearch.RANKS;
130 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
131 import org.forester.ws.wabi.TxSearch.TAX_RANK;
133 @SuppressWarnings( "unused")
134 public final class Test {
136 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
137 + ForesterUtil.getFileSeparator() + "resources"
138 + ForesterUtil.getFileSeparator();
139 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
140 + ForesterUtil.getFileSeparator() + "test_data"
141 + ForesterUtil.getFileSeparator();
142 private final static boolean PERFORM_DB_TESTS = true;
143 private static final boolean PERFORM_WEB_TREE_ACCESS = true;
144 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
145 + ForesterConstants.PHYLO_XML_VERSION + "/"
146 + ForesterConstants.PHYLO_XML_XSD;
147 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
148 + ForesterConstants.PHYLO_XML_VERSION + "/"
149 + ForesterConstants.PHYLO_XML_XSD;
150 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
151 private final static double ZERO_DIFF = 1.0E-9;
153 public static boolean isEqual( final double a, final double b ) {
154 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
157 public static void main( final String[] args ) {
158 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
159 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
161 Locale.setDefault( Locale.US );
162 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
165 System.out.print( "[Test if directory with files for testing exists/is readable: " );
166 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
171 System.out.println( "Testing aborted." );
174 System.out.print( "[Test if resources directory exists/is readable: " );
175 if ( testDir( PATH_TO_RESOURCES ) ) {
176 System.out.println( "OK.]" );
179 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
180 System.out.println( "Testing aborted." );
183 final long start_time = new Date().getTime();
184 System.out.print( "Basic node methods: " );
185 if ( Test.testBasicNodeMethods() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Protein id: " );
194 if ( !testProteinId() ) {
195 System.out.println( "failed." );
201 System.out.println( "OK." );
202 System.out.print( "Species: " );
203 if ( !testSpecies() ) {
204 System.out.println( "failed." );
210 System.out.println( "OK." );
211 System.out.print( "Basic domain: " );
212 if ( !testBasicDomain() ) {
213 System.out.println( "failed." );
219 System.out.println( "OK." );
220 System.out.print( "Basic protein: " );
221 if ( !testBasicProtein() ) {
222 System.out.println( "failed." );
228 System.out.println( "OK." );
229 System.out.print( "Sequence writer: " );
230 if ( testSequenceWriter() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "Sequence id parsing: " );
239 if ( testSequenceIdParsing() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "UniProtKB id extraction: " );
248 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "Sequence DB tools 1: " );
257 if ( testSequenceDbWsTools1() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "Hmmscan output parser: " );
266 if ( testHmmscanOutputParser() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "Overlap removal: " );
275 if ( !org.forester.test.Test.testOverlapRemoval() ) {
276 System.out.println( "failed." );
282 System.out.println( "OK." );
283 System.out.print( "Engulfing overlap removal: " );
284 if ( !Test.testEngulfingOverlapRemoval() ) {
285 System.out.println( "failed." );
291 System.out.println( "OK." );
292 System.out.print( "Taxonomy data extraction: " );
293 if ( Test.testExtractTaxonomyDataFromNodeName() ) {
294 System.out.println( "OK." );
298 System.out.println( "failed." );
301 System.out.print( "Taxonomy code extraction: " );
302 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "SN extraction: " );
311 if ( Test.testExtractSNFromNodeName() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "Taxonomy extraction (general): " );
320 if ( Test.testTaxonomyExtraction() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Uri for Aptx web sequence accession: " );
329 if ( Test.testCreateUriForSeqWeb() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "Basic node construction and parsing of NHX (node level): " );
338 if ( Test.testNHXNodeParsing() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "NHX parsing iterating: " );
347 if ( Test.testNHParsingIter() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "NH parsing: " );
356 if ( Test.testNHParsing() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "Conversion to NHX (node level): " );
365 if ( Test.testNHXconversion() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "NHX parsing: " );
374 if ( Test.testNHXParsing() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "NHX parsing with quotes: " );
383 if ( Test.testNHXParsingQuotes() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "NHX parsing (MrBayes): " );
392 if ( Test.testNHXParsingMB() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "Nexus characters parsing: " );
401 if ( Test.testNexusCharactersParsing() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Nexus tree parsing iterating: " );
410 if ( Test.testNexusTreeParsingIterating() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Nexus tree parsing: " );
419 if ( Test.testNexusTreeParsing() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Nexus tree parsing (translating): " );
428 if ( Test.testNexusTreeParsingTranslating() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Nexus matrix parsing: " );
437 if ( Test.testNexusMatrixParsing() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Basic phyloXML parsing: " );
446 if ( Test.testBasicPhyloXMLparsing() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Basic phyloXML parsing (validating against schema): " );
455 if ( testBasicPhyloXMLparsingValidating() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
464 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "phyloXML Distribution Element: " );
473 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "Tol XML parsing: " );
482 if ( Test.testBasicTolXMLparsing() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "Copying of node data: " );
491 if ( Test.testCopyOfNodeData() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Tree copy: " );
500 if ( Test.testTreeCopy() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "Basic tree methods: " );
509 if ( Test.testBasicTreeMethods() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "Tree methods: " );
518 if ( Test.testTreeMethods() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Postorder Iterator: " );
527 if ( Test.testPostOrderIterator() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Preorder Iterator: " );
536 if ( Test.testPreOrderIterator() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Levelorder Iterator: " );
545 if ( Test.testLevelOrderIterator() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Re-id methods: " );
554 if ( Test.testReIdMethods() ) {
555 System.out.println( "OK." );
559 System.out.println( "failed." );
562 System.out.print( "Methods on last external nodes: " );
563 if ( Test.testLastExternalNodeMethods() ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "Methods on external nodes: " );
572 if ( Test.testExternalNodeRelatedMethods() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "Deletion of external nodes: " );
581 if ( Test.testDeletionOfExternalNodes() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Subtree deletion: " );
590 if ( Test.testSubtreeDeletion() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Phylogeny branch: " );
599 if ( Test.testPhylogenyBranch() ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Rerooting: " );
608 if ( Test.testRerooting() ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "Mipoint rooting: " );
617 if ( Test.testMidpointrooting() ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Node removal: " );
626 if ( Test.testNodeRemoval() ) {
627 System.out.println( "OK." );
631 System.out.println( "failed." );
634 System.out.print( "Support count: " );
635 if ( Test.testSupportCount() ) {
636 System.out.println( "OK." );
640 System.out.println( "failed." );
643 System.out.print( "Support transfer: " );
644 if ( Test.testSupportTransfer() ) {
645 System.out.println( "OK." );
649 System.out.println( "failed." );
652 System.out.print( "Finding of LCA: " );
653 if ( Test.testGetLCA() ) {
654 System.out.println( "OK." );
658 System.out.println( "failed." );
661 System.out.print( "Finding of LCA 2: " );
662 if ( Test.testGetLCA2() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Calculation of distance between nodes: " );
671 if ( Test.testGetDistance() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 System.out.print( "Descriptive statistics: " );
680 if ( Test.testDescriptiveStatistics() ) {
681 System.out.println( "OK." );
685 System.out.println( "failed." );
688 System.out.print( "Data objects and methods: " );
689 if ( Test.testDataObjects() ) {
690 System.out.println( "OK." );
694 System.out.println( "failed." );
697 System.out.print( "Properties map: " );
698 if ( Test.testPropertiesMap() ) {
699 System.out.println( "OK." );
703 System.out.println( "failed." );
706 System.out.print( "SDIse: " );
707 if ( Test.testSDIse() ) {
708 System.out.println( "OK." );
712 System.out.println( "failed." );
715 System.out.print( "SDIunrooted: " );
716 if ( Test.testSDIunrooted() ) {
717 System.out.println( "OK." );
721 System.out.println( "failed." );
724 System.out.print( "GSDI: " );
725 if ( TestGSDI.test() ) {
726 System.out.println( "OK." );
730 System.out.println( "failed." );
733 System.out.print( "RIO: " );
734 if ( TestRIO.test() ) {
735 System.out.println( "OK." );
739 System.out.println( "failed." );
742 System.out.print( "Phylogeny reconstruction:" );
743 System.out.println();
744 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
745 System.out.println( "OK." );
749 System.out.println( "failed." );
752 System.out.print( "Analysis of domain architectures: " );
753 System.out.println();
754 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
755 System.out.println( "OK." );
759 System.out.println( "failed." );
762 System.out.print( "GO: " );
763 System.out.println();
764 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
765 System.out.println( "OK." );
769 System.out.println( "failed." );
772 System.out.print( "Modeling tools: " );
773 if ( TestPccx.test() ) {
774 System.out.println( "OK." );
778 System.out.println( "failed." );
781 System.out.print( "Split Matrix strict: " );
782 if ( Test.testSplitStrict() ) {
783 System.out.println( "OK." );
787 System.out.println( "failed." );
790 System.out.print( "Split Matrix: " );
791 if ( Test.testSplit() ) {
792 System.out.println( "OK." );
796 System.out.println( "failed." );
799 System.out.print( "Confidence Assessor: " );
800 if ( Test.testConfidenceAssessor() ) {
801 System.out.println( "OK." );
805 System.out.println( "failed." );
808 System.out.print( "Basic table: " );
809 if ( Test.testBasicTable() ) {
810 System.out.println( "OK." );
814 System.out.println( "failed." );
817 System.out.print( "General table: " );
818 if ( Test.testGeneralTable() ) {
819 System.out.println( "OK." );
823 System.out.println( "failed." );
826 System.out.print( "Amino acid sequence: " );
827 if ( Test.testAminoAcidSequence() ) {
828 System.out.println( "OK." );
832 System.out.println( "failed." );
835 System.out.print( "General MSA parser: " );
836 if ( Test.testGeneralMsaParser() ) {
837 System.out.println( "OK." );
841 System.out.println( "failed." );
844 System.out.print( "Fasta parser for msa: " );
845 if ( Test.testFastaParser() ) {
846 System.out.println( "OK." );
850 System.out.println( "failed." );
853 System.out.print( "Creation of balanced phylogeny: " );
854 if ( Test.testCreateBalancedPhylogeny() ) {
855 System.out.println( "OK." );
859 System.out.println( "failed." );
862 System.out.print( "Genbank accessor parsing: " );
863 if ( Test.testGenbankAccessorParsing() ) {
864 System.out.println( "OK." );
868 System.out.println( "failed." );
872 final String os = ForesterUtil.OS_NAME.toLowerCase();
873 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
874 path = "/usr/local/bin/mafft";
876 else if ( os.indexOf( "win" ) >= 0 ) {
877 path = "C:\\Program Files\\mafft-win\\mafft.bat";
881 if ( !MsaInferrer.isInstalled( path ) ) {
882 path = "/usr/bin/mafft";
884 if ( !MsaInferrer.isInstalled( path ) ) {
885 path = "/usr/local/bin/mafft";
888 if ( MsaInferrer.isInstalled( path ) ) {
889 System.out.print( "MAFFT (external program): " );
890 if ( Test.testMafft( path ) ) {
891 System.out.println( "OK." );
895 System.out.println( "failed [will not count towards failed tests]" );
898 System.out.print( "Next nodes with collapsed: " );
899 if ( Test.testNextNodeWithCollapsing() ) {
900 System.out.println( "OK." );
904 System.out.println( "failed." );
907 System.out.print( "Simple MSA quality: " );
908 if ( Test.testMsaQualityMethod() ) {
909 System.out.println( "OK." );
913 System.out.println( "failed." );
916 System.out.print( "Deleteable MSA: " );
917 if ( Test.testDeleteableMsa() ) {
918 System.out.println( "OK." );
922 System.out.println( "failed." );
925 System.out.print( "MSA entropy: " );
926 if ( Test.testMsaEntropy() ) {
927 System.out.println( "OK." );
931 System.out.println( "failed." );
934 if ( PERFORM_DB_TESTS ) {
935 System.out.print( "Uniprot Entry Retrieval: " );
936 if ( Test.testUniprotEntryRetrieval() ) {
937 System.out.println( "OK." );
941 System.out.println( "failed." );
944 System.out.print( "Ebi Entry Retrieval: " );
945 if ( Test.testEbiEntryRetrieval() ) {
946 System.out.println( "OK." );
950 System.out.println( "failed." );
953 System.out.print( "Sequence DB tools 2: " );
954 if ( testSequenceDbWsTools2() ) {
955 System.out.println( "OK." );
959 System.out.println( "failed." );
963 System.out.print( "Uniprot Taxonomy Search: " );
964 if ( Test.testUniprotTaxonomySearch() ) {
965 System.out.println( "OK." );
969 System.out.println( "failed." );
973 if ( PERFORM_WEB_TREE_ACCESS ) {
974 System.out.print( "NHX parsing from URL: " );
975 if ( Test.testNHXparsingFromURL() ) {
976 System.out.println( "OK." );
980 System.out.println( "failed." );
983 System.out.print( "NHX parsing from URL 2: " );
984 if ( Test.testNHXparsingFromURL2() ) {
985 System.out.println( "OK." );
989 System.out.println( "failed." );
992 System.out.print( "phyloXML parsing from URL: " );
993 if ( Test.testPhyloXMLparsingFromURL() ) {
994 System.out.println( "OK." );
998 System.out.println( "failed." );
1001 System.out.print( "TreeBase acccess: " );
1002 if ( Test.testTreeBaseReading() ) {
1003 System.out.println( "OK." );
1007 System.out.println( "failed." );
1011 System.out.print( "ToL access: " );
1012 if ( Test.testToLReading() ) {
1013 System.out.println( "OK." );
1017 System.out.println( "failed." );
1021 System.out.print( "TreeFam access: " );
1022 if ( Test.testTreeFamReading() ) {
1023 System.out.println( "OK." );
1027 System.out.println( "failed." );
1032 System.out.print( "Pfam tree access: " );
1033 if ( Test.testPfamTreeReading() ) {
1034 System.out.println( "OK." );
1038 System.out.println( "failed." );
1042 System.out.println();
1043 final Runtime rt = java.lang.Runtime.getRuntime();
1044 final long free_memory = rt.freeMemory() / 1000000;
1045 final long total_memory = rt.totalMemory() / 1000000;
1046 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1047 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1048 System.out.println();
1049 System.out.println( "Successful tests: " + succeeded );
1050 System.out.println( "Failed tests: " + failed );
1051 System.out.println();
1053 System.out.println( "OK." );
1056 System.out.println( "Not OK." );
1060 public static boolean testEngulfingOverlapRemoval() {
1062 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1063 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
1064 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
1065 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1066 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1067 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1068 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1069 final List<Boolean> covered = new ArrayList<Boolean>();
1070 covered.add( true ); // 0
1071 covered.add( false ); // 1
1072 covered.add( true ); // 2
1073 covered.add( false ); // 3
1074 covered.add( true ); // 4
1075 covered.add( true ); // 5
1076 covered.add( false ); // 6
1077 covered.add( true ); // 7
1078 covered.add( true ); // 8
1079 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
1082 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
1085 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
1088 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
1091 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
1094 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
1097 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
1100 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1101 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
1102 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
1103 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
1104 abc.addProteinDomain( a );
1105 abc.addProteinDomain( b );
1106 abc.addProteinDomain( c );
1107 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
1108 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
1109 if ( abc.getNumberOfProteinDomains() != 3 ) {
1112 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
1115 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
1118 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
1121 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
1124 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1125 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
1126 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
1127 final Protein def = new BasicProtein( "def", "nemve", 0 );
1128 def.addProteinDomain( d );
1129 def.addProteinDomain( e );
1130 def.addProteinDomain( f );
1131 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
1132 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
1133 if ( def.getNumberOfProteinDomains() != 3 ) {
1136 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
1139 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
1142 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
1145 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
1148 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
1152 catch ( final Exception e ) {
1153 e.printStackTrace( System.out );
1159 public static final boolean testNHXparsingFromURL2() {
1161 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1162 final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1166 TAXONOMY_EXTRACTION.NO,
1168 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1171 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1172 System.out.println( phys[ 0 ].toNewHampshire() );
1175 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1176 System.out.println( phys[ 1 ].toNewHampshire() );
1179 final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1183 TAXONOMY_EXTRACTION.NO,
1185 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1188 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1189 System.out.println( phys2[ 0 ].toNewHampshire() );
1192 if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1193 System.out.println( phys2[ 1 ].toNewHampshire() );
1196 final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1197 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1198 if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
1203 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1204 System.out.println( phys3[ 0 ].toNewHampshire() );
1207 final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1208 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1209 if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
1214 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1215 System.out.println( phys4[ 0 ].toNewHampshire() );
1219 catch ( final Exception e ) {
1220 e.printStackTrace();
1226 public static final boolean testNHXparsingFromURL() {
1228 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1229 final URL u = new URL( s );
1230 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1231 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1232 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1235 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1236 System.out.println( phys[ 0 ].toNewHampshire() );
1239 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1240 System.out.println( phys[ 1 ].toNewHampshire() );
1243 final URL u2 = new URL( s );
1244 final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
1245 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1248 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1249 System.out.println( phys2[ 0 ].toNewHampshire() );
1252 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1253 final NHXParser p = new NHXParser();
1254 final URL u3 = new URL( s );
1256 if ( !p.hasNext() ) {
1259 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1262 if ( !p.hasNext() ) {
1266 if ( !p.hasNext() ) {
1269 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1272 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1276 if ( !p.hasNext() ) {
1279 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1282 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1286 catch ( final Exception e ) {
1287 System.out.println( e.toString() );
1288 e.printStackTrace();
1294 public static boolean testOverlapRemoval() {
1296 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1297 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1298 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1299 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1300 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1301 final List<Boolean> covered = new ArrayList<Boolean>();
1302 covered.add( true ); // 0
1303 covered.add( false ); // 1
1304 covered.add( true ); // 2
1305 covered.add( false ); // 3
1306 covered.add( true ); // 4
1307 covered.add( true ); // 5
1308 covered.add( false ); // 6
1309 covered.add( true ); // 7
1310 covered.add( true ); // 8
1311 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1314 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1317 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1320 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1323 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1326 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1327 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1328 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1329 ab.addProteinDomain( a );
1330 ab.addProteinDomain( b );
1331 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1332 if ( ab.getNumberOfProteinDomains() != 2 ) {
1335 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1338 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1341 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1342 if ( ab.getNumberOfProteinDomains() != 2 ) {
1345 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1348 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1349 final Domain d = new BasicDomain( "d",
1356 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1357 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1358 cde.addProteinDomain( c );
1359 cde.addProteinDomain( d );
1360 cde.addProteinDomain( e );
1361 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1362 if ( cde.getNumberOfProteinDomains() != 3 ) {
1365 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1368 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1369 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1370 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1371 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1372 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1373 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1374 fghi.addProteinDomain( f );
1375 fghi.addProteinDomain( g );
1376 fghi.addProteinDomain( h );
1377 fghi.addProteinDomain( i );
1378 fghi.addProteinDomain( i );
1379 fghi.addProteinDomain( i );
1380 fghi.addProteinDomain( i2 );
1381 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1382 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1385 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1388 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1391 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1392 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1395 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1398 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1399 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1400 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1401 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1402 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1403 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1404 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1405 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1406 jklm.addProteinDomain( j );
1407 jklm.addProteinDomain( k );
1408 jklm.addProteinDomain( l );
1409 jklm.addProteinDomain( m );
1410 jklm.addProteinDomain( m0 );
1411 jklm.addProteinDomain( m1 );
1412 jklm.addProteinDomain( m2 );
1413 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1414 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1417 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1420 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1423 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1424 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1427 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1430 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1431 final Protein od = new BasicProtein( "od", "varanus", 0 );
1432 od.addProteinDomain( only );
1433 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1434 if ( od.getNumberOfProteinDomains() != 1 ) {
1437 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1441 catch ( final Exception e ) {
1442 e.printStackTrace( System.out );
1448 public static final boolean testPfamTreeReading() {
1450 final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
1451 final NHXParser parser = new NHXParser();
1452 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1453 parser.setReplaceUnderscores( false );
1454 parser.setGuessRootedness( true );
1455 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1456 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1457 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1460 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1464 catch ( final Exception e ) {
1465 e.printStackTrace();
1470 public static final boolean testPhyloXMLparsingFromURL() {
1472 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1473 final URL u = new URL( s );
1474 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1475 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1476 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1480 catch ( final Exception e ) {
1481 e.printStackTrace();
1486 public static final boolean testToLReading() {
1488 final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
1489 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1490 final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
1491 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1494 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
1497 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
1500 if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
1504 catch ( final Exception e ) {
1505 e.printStackTrace();
1510 public static final boolean testTreeBaseReading() {
1512 final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
1513 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1514 parser.setReplaceUnderscores( true );
1515 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1516 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1517 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1520 final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
1521 final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
1522 parser2.setReplaceUnderscores( true );
1523 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1524 final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
1525 if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
1529 catch ( final Exception e ) {
1530 e.printStackTrace();
1535 public static final boolean testTreeFamReading() {
1537 final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
1538 final NHXParser parser = new NHXParser();
1539 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
1540 parser.setReplaceUnderscores( false );
1541 parser.setGuessRootedness( true );
1542 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1543 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1544 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1547 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1551 catch ( final Exception e ) {
1552 e.printStackTrace();
1557 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1558 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1562 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1563 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1566 private static boolean testAminoAcidSequence() {
1568 final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1569 if ( aa1.getLength() != 13 ) {
1572 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1575 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1578 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1581 final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1582 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
1585 final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1586 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1589 final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1590 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1594 catch ( final Exception e ) {
1595 e.printStackTrace();
1601 private static boolean testBasicDomain() {
1603 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1604 if ( !pd.getDomainId().equals( "id" ) ) {
1607 if ( pd.getNumber() != 1 ) {
1610 if ( pd.getTotalCount() != 4 ) {
1613 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1616 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1617 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1618 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1619 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1620 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1621 if ( !a1.equals( a1 ) ) {
1624 if ( !a1.equals( a1_copy ) ) {
1627 if ( !a1.equals( a1_equal ) ) {
1630 if ( !a1.equals( a2 ) ) {
1633 if ( a1.equals( a3 ) ) {
1636 if ( a1.compareTo( a1 ) != 0 ) {
1639 if ( a1.compareTo( a1_copy ) != 0 ) {
1642 if ( a1.compareTo( a1_equal ) != 0 ) {
1645 if ( a1.compareTo( a2 ) != 0 ) {
1648 if ( a1.compareTo( a3 ) == 0 ) {
1652 catch ( final Exception e ) {
1653 e.printStackTrace( System.out );
1659 private static boolean testBasicNodeMethods() {
1661 if ( PhylogenyNode.getNodeCount() != 0 ) {
1664 final PhylogenyNode n1 = new PhylogenyNode();
1665 final PhylogenyNode n2 = PhylogenyNode
1666 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1667 final PhylogenyNode n3 = PhylogenyNode
1668 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1669 final PhylogenyNode n4 = PhylogenyNode
1670 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1671 if ( n1.isHasAssignedEvent() ) {
1674 if ( PhylogenyNode.getNodeCount() != 4 ) {
1677 if ( n3.getIndicator() != 0 ) {
1680 if ( n3.getNumberOfExternalNodes() != 1 ) {
1683 if ( !n3.isExternal() ) {
1686 if ( !n3.isRoot() ) {
1689 if ( !n4.getName().equals( "n4" ) ) {
1693 catch ( final Exception e ) {
1694 e.printStackTrace( System.out );
1700 private static boolean testBasicPhyloXMLparsing() {
1702 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1703 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1704 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1706 if ( xml_parser.getErrorCount() > 0 ) {
1707 System.out.println( xml_parser.getErrorMessages().toString() );
1710 if ( phylogenies_0.length != 4 ) {
1713 final Phylogeny t1 = phylogenies_0[ 0 ];
1714 final Phylogeny t2 = phylogenies_0[ 1 ];
1715 final Phylogeny t3 = phylogenies_0[ 2 ];
1716 final Phylogeny t4 = phylogenies_0[ 3 ];
1717 if ( t1.getNumberOfExternalNodes() != 1 ) {
1720 if ( !t1.isRooted() ) {
1723 if ( t1.isRerootable() ) {
1726 if ( !t1.getType().equals( "gene_tree" ) ) {
1729 if ( t2.getNumberOfExternalNodes() != 2 ) {
1732 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1735 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1738 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1741 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1744 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1747 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1750 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1751 .startsWith( "actgtgggggt" ) ) {
1754 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1755 .startsWith( "ctgtgatgcat" ) ) {
1758 if ( t3.getNumberOfExternalNodes() != 4 ) {
1761 if ( !t1.getName().equals( "t1" ) ) {
1764 if ( !t2.getName().equals( "t2" ) ) {
1767 if ( !t3.getName().equals( "t3" ) ) {
1770 if ( !t4.getName().equals( "t4" ) ) {
1773 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1776 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1779 if ( !t3.getNode( "root node" ).isDuplication() ) {
1782 if ( !t3.getNode( "node a" ).isDuplication() ) {
1785 if ( t3.getNode( "node a" ).isSpeciation() ) {
1788 if ( t3.getNode( "node bc" ).isDuplication() ) {
1791 if ( !t3.getNode( "node bc" ).isSpeciation() ) {
1794 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1797 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1798 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1801 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1804 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1807 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1810 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1811 .equals( "apoptosis" ) ) {
1814 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1815 .equals( "GO:0006915" ) ) {
1818 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1819 .equals( "UniProtKB" ) ) {
1822 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1823 .equals( "experimental" ) ) {
1826 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1827 .equals( "function" ) ) {
1830 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1831 .getValue() != 1 ) {
1834 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1835 .getType().equals( "ml" ) ) {
1838 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1839 .equals( "apoptosis" ) ) {
1842 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1843 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1846 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1847 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1850 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1851 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1854 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1855 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1858 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1859 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1862 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1863 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1866 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1867 .equals( "GO:0005829" ) ) {
1870 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1871 .equals( "intracellular organelle" ) ) {
1874 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1877 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1878 .equals( "UniProt link" ) ) ) {
1881 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1884 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1885 if ( x.size() != 4 ) {
1889 for( final Accession acc : x ) {
1891 if ( !acc.getSource().equals( "KEGG" ) ) {
1894 if ( !acc.getValue().equals( "hsa:596" ) ) {
1901 catch ( final Exception e ) {
1902 e.printStackTrace( System.out );
1908 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1910 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1911 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1912 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1913 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1916 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1918 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1920 if ( xml_parser.getErrorCount() > 0 ) {
1921 System.out.println( xml_parser.getErrorMessages().toString() );
1924 if ( phylogenies_0.length != 4 ) {
1927 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1928 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1929 if ( phylogenies_t1.length != 1 ) {
1932 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1933 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1936 if ( !t1_rt.isRooted() ) {
1939 if ( t1_rt.isRerootable() ) {
1942 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1945 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1946 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1947 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1948 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1951 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1954 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1957 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1960 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1961 .startsWith( "actgtgggggt" ) ) {
1964 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1965 .startsWith( "ctgtgatgcat" ) ) {
1968 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1969 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1970 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1971 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1972 if ( phylogenies_1.length != 1 ) {
1975 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1976 if ( !t3_rt.getName().equals( "t3" ) ) {
1979 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1982 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1985 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1988 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1991 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1992 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1995 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1998 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
2001 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
2002 .equals( "UniProtKB" ) ) {
2005 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2006 .equals( "apoptosis" ) ) {
2009 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
2010 .equals( "GO:0006915" ) ) {
2013 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
2014 .equals( "UniProtKB" ) ) {
2017 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
2018 .equals( "experimental" ) ) {
2021 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
2022 .equals( "function" ) ) {
2025 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2026 .getValue() != 1 ) {
2029 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2030 .getType().equals( "ml" ) ) {
2033 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2034 .equals( "apoptosis" ) ) {
2037 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2038 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
2041 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2042 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
2045 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2046 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
2049 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2050 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
2053 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2054 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
2057 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2058 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
2061 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
2062 .equals( "GO:0005829" ) ) {
2065 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
2066 .equals( "intracellular organelle" ) ) {
2069 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
2072 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
2073 .equals( "UniProt link" ) ) ) {
2076 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
2079 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
2082 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
2083 .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." ) ) ) {
2086 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
2089 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
2092 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
2095 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
2098 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
2099 .equals( "ncbi" ) ) {
2102 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
2105 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2106 .getName().equals( "B" ) ) {
2109 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2110 .getFrom() != 21 ) {
2113 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
2116 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2117 .getLength() != 24 ) {
2120 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2121 .getConfidence() != 0 ) {
2124 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2125 .equals( "pfam" ) ) {
2128 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2131 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2134 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2137 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2140 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2141 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2144 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2147 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2150 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2153 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2156 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2159 if ( taxbb.getSynonyms().size() != 2 ) {
2162 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2165 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2168 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2171 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2174 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2177 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2178 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2181 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2184 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2187 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2190 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2193 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2196 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2199 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2202 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2205 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2206 .equalsIgnoreCase( "435" ) ) {
2209 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2212 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2213 .equalsIgnoreCase( "443.7" ) ) {
2216 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2219 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2222 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2223 .equalsIgnoreCase( "433" ) ) {
2226 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2227 .getCrossReferences();
2228 if ( x.size() != 4 ) {
2232 for( final Accession acc : x ) {
2234 if ( !acc.getSource().equals( "KEGG" ) ) {
2237 if ( !acc.getValue().equals( "hsa:596" ) ) {
2244 catch ( final Exception e ) {
2245 e.printStackTrace( System.out );
2251 private static boolean testBasicPhyloXMLparsingValidating() {
2253 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2254 PhyloXmlParser xml_parser = null;
2256 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2258 catch ( final Exception e ) {
2259 // Do nothing -- means were not running from jar.
2261 if ( xml_parser == null ) {
2262 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2263 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2264 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2267 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2270 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2272 if ( xml_parser.getErrorCount() > 0 ) {
2273 System.out.println( xml_parser.getErrorMessages().toString() );
2276 if ( phylogenies_0.length != 4 ) {
2279 final Phylogeny t1 = phylogenies_0[ 0 ];
2280 final Phylogeny t2 = phylogenies_0[ 1 ];
2281 final Phylogeny t3 = phylogenies_0[ 2 ];
2282 final Phylogeny t4 = phylogenies_0[ 3 ];
2283 if ( !t1.getName().equals( "t1" ) ) {
2286 if ( !t2.getName().equals( "t2" ) ) {
2289 if ( !t3.getName().equals( "t3" ) ) {
2292 if ( !t4.getName().equals( "t4" ) ) {
2295 if ( t1.getNumberOfExternalNodes() != 1 ) {
2298 if ( t2.getNumberOfExternalNodes() != 2 ) {
2301 if ( t3.getNumberOfExternalNodes() != 4 ) {
2304 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2305 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2306 if ( xml_parser.getErrorCount() > 0 ) {
2307 System.out.println( "errors:" );
2308 System.out.println( xml_parser.getErrorMessages().toString() );
2311 if ( phylogenies_1.length != 4 ) {
2314 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2316 if ( xml_parser.getErrorCount() > 0 ) {
2317 System.out.println( "errors:" );
2318 System.out.println( xml_parser.getErrorMessages().toString() );
2321 if ( phylogenies_2.length != 1 ) {
2324 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2327 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2329 if ( xml_parser.getErrorCount() > 0 ) {
2330 System.out.println( xml_parser.getErrorMessages().toString() );
2333 if ( phylogenies_3.length != 2 ) {
2336 final Phylogeny a = phylogenies_3[ 0 ];
2337 if ( !a.getName().equals( "tree 4" ) ) {
2340 if ( a.getNumberOfExternalNodes() != 3 ) {
2343 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2346 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2349 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2351 if ( xml_parser.getErrorCount() > 0 ) {
2352 System.out.println( xml_parser.getErrorMessages().toString() );
2355 if ( phylogenies_4.length != 1 ) {
2358 final Phylogeny s = phylogenies_4[ 0 ];
2359 if ( s.getNumberOfExternalNodes() != 6 ) {
2362 s.getNode( "first" );
2364 s.getNode( "\"<a'b&c'd\">\"" );
2365 s.getNode( "'''\"" );
2366 s.getNode( "\"\"\"" );
2367 s.getNode( "dick & doof" );
2369 catch ( final Exception e ) {
2370 e.printStackTrace( System.out );
2376 private static boolean testBasicProtein() {
2378 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2379 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2380 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2381 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2382 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2383 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2384 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2385 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2386 p0.addProteinDomain( y );
2387 p0.addProteinDomain( e );
2388 p0.addProteinDomain( b );
2389 p0.addProteinDomain( c );
2390 p0.addProteinDomain( d );
2391 p0.addProteinDomain( a );
2392 p0.addProteinDomain( x );
2393 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2396 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2400 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2401 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2402 aa0.addProteinDomain( a1 );
2403 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2406 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2410 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2411 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2412 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2413 aa1.addProteinDomain( a11 );
2414 aa1.addProteinDomain( a12 );
2415 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2418 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2421 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2422 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2425 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2428 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2431 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2432 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2435 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2438 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2441 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2444 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2445 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2448 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2451 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2454 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2457 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2458 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2461 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2464 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2467 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2471 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2472 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2473 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2474 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2475 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2476 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2477 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2478 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2479 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2480 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2481 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2482 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2483 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2484 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2485 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2486 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2487 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2488 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2489 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2490 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2491 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2492 p00.addProteinDomain( y0 );
2493 p00.addProteinDomain( e0 );
2494 p00.addProteinDomain( b0 );
2495 p00.addProteinDomain( c0 );
2496 p00.addProteinDomain( d0 );
2497 p00.addProteinDomain( a0 );
2498 p00.addProteinDomain( x0 );
2499 p00.addProteinDomain( y1 );
2500 p00.addProteinDomain( y2 );
2501 p00.addProteinDomain( y3 );
2502 p00.addProteinDomain( e1 );
2503 p00.addProteinDomain( e2 );
2504 p00.addProteinDomain( e3 );
2505 p00.addProteinDomain( e4 );
2506 p00.addProteinDomain( e5 );
2507 p00.addProteinDomain( z0 );
2508 p00.addProteinDomain( z1 );
2509 p00.addProteinDomain( z2 );
2510 p00.addProteinDomain( zz0 );
2511 p00.addProteinDomain( zz1 );
2512 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2515 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2518 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2521 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2524 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" ) ) {
2527 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2528 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2529 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2530 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2531 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2532 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2533 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2534 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2535 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2536 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2537 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2538 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2539 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2540 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2541 p.addProteinDomain( B15 );
2542 p.addProteinDomain( C50 );
2543 p.addProteinDomain( A60 );
2544 p.addProteinDomain( A30 );
2545 p.addProteinDomain( C70 );
2546 p.addProteinDomain( B35 );
2547 p.addProteinDomain( B40 );
2548 p.addProteinDomain( A0 );
2549 p.addProteinDomain( A10 );
2550 p.addProteinDomain( A20 );
2551 p.addProteinDomain( B25 );
2552 p.addProteinDomain( D80 );
2553 List<String> domains_ids = new ArrayList<String>();
2554 domains_ids.add( "A" );
2555 domains_ids.add( "B" );
2556 domains_ids.add( "C" );
2557 if ( !p.contains( domains_ids, false ) ) {
2560 if ( !p.contains( domains_ids, true ) ) {
2563 domains_ids.add( "X" );
2564 if ( p.contains( domains_ids, false ) ) {
2567 if ( p.contains( domains_ids, true ) ) {
2570 domains_ids = new ArrayList<String>();
2571 domains_ids.add( "A" );
2572 domains_ids.add( "C" );
2573 domains_ids.add( "D" );
2574 if ( !p.contains( domains_ids, false ) ) {
2577 if ( !p.contains( domains_ids, true ) ) {
2580 domains_ids = new ArrayList<String>();
2581 domains_ids.add( "A" );
2582 domains_ids.add( "D" );
2583 domains_ids.add( "C" );
2584 if ( !p.contains( domains_ids, false ) ) {
2587 if ( p.contains( domains_ids, true ) ) {
2590 domains_ids = new ArrayList<String>();
2591 domains_ids.add( "A" );
2592 domains_ids.add( "A" );
2593 domains_ids.add( "B" );
2594 if ( !p.contains( domains_ids, false ) ) {
2597 if ( !p.contains( domains_ids, true ) ) {
2600 domains_ids = new ArrayList<String>();
2601 domains_ids.add( "A" );
2602 domains_ids.add( "A" );
2603 domains_ids.add( "A" );
2604 domains_ids.add( "B" );
2605 domains_ids.add( "B" );
2606 if ( !p.contains( domains_ids, false ) ) {
2609 if ( !p.contains( domains_ids, true ) ) {
2612 domains_ids = new ArrayList<String>();
2613 domains_ids.add( "A" );
2614 domains_ids.add( "A" );
2615 domains_ids.add( "B" );
2616 domains_ids.add( "A" );
2617 domains_ids.add( "B" );
2618 domains_ids.add( "B" );
2619 domains_ids.add( "A" );
2620 domains_ids.add( "B" );
2621 domains_ids.add( "C" );
2622 domains_ids.add( "A" );
2623 domains_ids.add( "C" );
2624 domains_ids.add( "D" );
2625 if ( !p.contains( domains_ids, false ) ) {
2628 if ( p.contains( domains_ids, true ) ) {
2632 catch ( final Exception e ) {
2633 e.printStackTrace( System.out );
2639 private static boolean testBasicTable() {
2641 final BasicTable<String> t0 = new BasicTable<String>();
2642 if ( t0.getNumberOfColumns() != 0 ) {
2645 if ( t0.getNumberOfRows() != 0 ) {
2648 t0.setValue( 3, 2, "23" );
2649 t0.setValue( 10, 1, "error" );
2650 t0.setValue( 10, 1, "110" );
2651 t0.setValue( 9, 1, "19" );
2652 t0.setValue( 1, 10, "101" );
2653 t0.setValue( 10, 10, "1010" );
2654 t0.setValue( 100, 10, "10100" );
2655 t0.setValue( 0, 0, "00" );
2656 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2659 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2662 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2665 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2668 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2671 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2674 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2677 if ( t0.getNumberOfColumns() != 101 ) {
2680 if ( t0.getNumberOfRows() != 11 ) {
2683 if ( t0.getValueAsString( 49, 4 ) != null ) {
2686 final String l = ForesterUtil.getLineSeparator();
2687 final StringBuffer source = new StringBuffer();
2688 source.append( "" + l );
2689 source.append( "# 1 1 1 1 1 1 1 1" + l );
2690 source.append( " 00 01 02 03" + l );
2691 source.append( " 10 11 12 13 " + l );
2692 source.append( "20 21 22 23 " + l );
2693 source.append( " 30 31 32 33" + l );
2694 source.append( "40 41 42 43" + l );
2695 source.append( " # 1 1 1 1 1 " + l );
2696 source.append( "50 51 52 53 54" + l );
2697 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2698 if ( t1.getNumberOfColumns() != 5 ) {
2701 if ( t1.getNumberOfRows() != 6 ) {
2704 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2707 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2710 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2713 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2716 final StringBuffer source1 = new StringBuffer();
2717 source1.append( "" + l );
2718 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2719 source1.append( " 00; 01 ;02;03" + l );
2720 source1.append( " 10; 11; 12; 13 " + l );
2721 source1.append( "20; 21; 22; 23 " + l );
2722 source1.append( " 30; 31; 32; 33" + l );
2723 source1.append( "40;41;42;43" + l );
2724 source1.append( " # 1 1 1 1 1 " + l );
2725 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2726 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2727 if ( t2.getNumberOfColumns() != 5 ) {
2730 if ( t2.getNumberOfRows() != 6 ) {
2733 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2736 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2739 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2742 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2745 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2748 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2751 final StringBuffer source2 = new StringBuffer();
2752 source2.append( "" + l );
2753 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2754 source2.append( " 00; 01 ;02;03" + l );
2755 source2.append( " 10; 11; 12; 13 " + l );
2756 source2.append( "20; 21; 22; 23 " + l );
2757 source2.append( " " + l );
2758 source2.append( " 30; 31; 32; 33" + l );
2759 source2.append( "40;41;42;43" + l );
2760 source2.append( " comment: 1 1 1 1 1 " + l );
2761 source2.append( ";;;50 ; 52; 53;;54 " + l );
2762 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2768 if ( tl.size() != 2 ) {
2771 final BasicTable<String> t3 = tl.get( 0 );
2772 final BasicTable<String> t4 = tl.get( 1 );
2773 if ( t3.getNumberOfColumns() != 4 ) {
2776 if ( t3.getNumberOfRows() != 3 ) {
2779 if ( t4.getNumberOfColumns() != 4 ) {
2782 if ( t4.getNumberOfRows() != 3 ) {
2785 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2788 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2792 catch ( final Exception e ) {
2793 e.printStackTrace( System.out );
2799 private static boolean testBasicTolXMLparsing() {
2801 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2802 final TolParser parser = new TolParser();
2803 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2804 if ( parser.getErrorCount() > 0 ) {
2805 System.out.println( parser.getErrorMessages().toString() );
2808 if ( phylogenies_0.length != 1 ) {
2811 final Phylogeny t1 = phylogenies_0[ 0 ];
2812 if ( t1.getNumberOfExternalNodes() != 5 ) {
2815 if ( !t1.isRooted() ) {
2818 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2821 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2824 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2827 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2830 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2831 if ( parser.getErrorCount() > 0 ) {
2832 System.out.println( parser.getErrorMessages().toString() );
2835 if ( phylogenies_1.length != 1 ) {
2838 final Phylogeny t2 = phylogenies_1[ 0 ];
2839 if ( t2.getNumberOfExternalNodes() != 664 ) {
2842 if ( !t2.isRooted() ) {
2845 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2848 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2851 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2854 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2857 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2860 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2861 .equals( "Aquifex" ) ) {
2864 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2865 if ( parser.getErrorCount() > 0 ) {
2866 System.out.println( parser.getErrorMessages().toString() );
2869 if ( phylogenies_2.length != 1 ) {
2872 final Phylogeny t3 = phylogenies_2[ 0 ];
2873 if ( t3.getNumberOfExternalNodes() != 184 ) {
2876 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2879 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2882 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2885 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2886 if ( parser.getErrorCount() > 0 ) {
2887 System.out.println( parser.getErrorMessages().toString() );
2890 if ( phylogenies_3.length != 1 ) {
2893 final Phylogeny t4 = phylogenies_3[ 0 ];
2894 if ( t4.getNumberOfExternalNodes() != 1 ) {
2897 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2900 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2903 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2906 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2907 if ( parser.getErrorCount() > 0 ) {
2908 System.out.println( parser.getErrorMessages().toString() );
2911 if ( phylogenies_4.length != 1 ) {
2914 final Phylogeny t5 = phylogenies_4[ 0 ];
2915 if ( t5.getNumberOfExternalNodes() != 13 ) {
2918 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2921 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2924 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2928 catch ( final Exception e ) {
2929 e.printStackTrace( System.out );
2935 private static boolean testBasicTreeMethods() {
2937 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2938 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2939 if ( t2.getNumberOfExternalNodes() != 4 ) {
2942 if ( t2.getHeight() != 8.5 ) {
2945 if ( !t2.isCompletelyBinary() ) {
2948 if ( t2.isEmpty() ) {
2951 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2952 if ( t3.getNumberOfExternalNodes() != 5 ) {
2955 if ( t3.getHeight() != 11 ) {
2958 if ( t3.isCompletelyBinary() ) {
2961 final PhylogenyNode n = t3.getNode( "ABC" );
2962 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 ];
2963 if ( t4.getNumberOfExternalNodes() != 9 ) {
2966 if ( t4.getHeight() != 11 ) {
2969 if ( t4.isCompletelyBinary() ) {
2972 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)" );
2973 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2974 if ( t5.getNumberOfExternalNodes() != 8 ) {
2977 if ( t5.getHeight() != 15 ) {
2980 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)" );
2981 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2982 if ( t6.getHeight() != 15 ) {
2985 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)" );
2986 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2987 if ( t7.getHeight() != 15 ) {
2990 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)" );
2991 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2992 if ( t8.getNumberOfExternalNodes() != 10 ) {
2995 if ( t8.getHeight() != 15 ) {
2998 final char[] a9 = new char[] { 'a' };
2999 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
3000 if ( t9.getHeight() != 0 ) {
3003 final char[] a10 = new char[] { 'a', ':', '6' };
3004 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
3005 if ( t10.getHeight() != 6 ) {
3009 catch ( final Exception e ) {
3010 e.printStackTrace( System.out );
3016 private static boolean testConfidenceAssessor() {
3018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3019 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3020 final Phylogeny[] ev0 = factory
3021 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
3023 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
3024 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3027 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3030 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3031 final Phylogeny[] ev1 = factory
3032 .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)));",
3034 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
3035 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
3038 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3041 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3042 final Phylogeny[] ev_b = factory
3043 .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",
3045 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
3046 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
3049 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3053 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3054 final Phylogeny[] ev1x = factory
3055 .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)));",
3057 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
3058 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3061 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3064 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3065 final Phylogeny[] ev_bx = factory
3066 .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",
3068 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
3069 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3072 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3075 final Phylogeny[] t2 = factory
3076 .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);",
3078 final Phylogeny[] ev2 = factory
3079 .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);",
3081 for( final Phylogeny target : t2 ) {
3082 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
3084 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
3085 new NHXParser() )[ 0 ];
3086 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
3087 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
3088 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3091 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
3094 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3098 catch ( final Exception e ) {
3099 e.printStackTrace();
3105 private static boolean testCopyOfNodeData() {
3107 final PhylogenyNode n1 = PhylogenyNode
3108 .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]" );
3109 final PhylogenyNode n2 = n1.copyNodeData();
3110 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
3114 catch ( final Exception e ) {
3115 e.printStackTrace();
3121 private static boolean testCreateBalancedPhylogeny() {
3123 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3124 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3127 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3130 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3131 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3134 if ( p1.getNumberOfExternalNodes() != 100 ) {
3138 catch ( final Exception e ) {
3139 e.printStackTrace();
3145 private static boolean testCreateUriForSeqWeb() {
3147 final PhylogenyNode n = new PhylogenyNode();
3148 n.setName( "tr|B3RJ64" );
3149 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3152 n.setName( "B0LM41_HUMAN" );
3153 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3156 n.setName( "NP_001025424" );
3157 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3160 n.setName( "_NM_001030253-" );
3161 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3164 n.setName( "XM_002122186" );
3165 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3168 n.setName( "dgh_AAA34956_gdg" );
3169 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3172 n.setName( "AAA34956" );
3173 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3176 n.setName( "GI:394892" );
3177 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3178 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3181 n.setName( "gi_394892" );
3182 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3183 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3186 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3187 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3188 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3191 n.setName( "P12345" );
3192 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3193 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3196 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3197 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3198 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3202 catch ( final Exception e ) {
3203 e.printStackTrace( System.out );
3209 private static boolean testDataObjects() {
3211 final Confidence s0 = new Confidence();
3212 final Confidence s1 = new Confidence();
3213 if ( !s0.isEqual( s1 ) ) {
3216 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3217 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3218 if ( s2.isEqual( s1 ) ) {
3221 if ( !s2.isEqual( s3 ) ) {
3224 final Confidence s4 = ( Confidence ) s3.copy();
3225 if ( !s4.isEqual( s3 ) ) {
3232 final Taxonomy t1 = new Taxonomy();
3233 final Taxonomy t2 = new Taxonomy();
3234 final Taxonomy t3 = new Taxonomy();
3235 final Taxonomy t4 = new Taxonomy();
3236 final Taxonomy t5 = new Taxonomy();
3237 t1.setIdentifier( new Identifier( "ecoli" ) );
3238 t1.setTaxonomyCode( "ECOLI" );
3239 t1.setScientificName( "E. coli" );
3240 t1.setCommonName( "coli" );
3241 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3242 if ( !t1.isEqual( t0 ) ) {
3245 t2.setIdentifier( new Identifier( "ecoli" ) );
3246 t2.setTaxonomyCode( "OTHER" );
3247 t2.setScientificName( "what" );
3248 t2.setCommonName( "something" );
3249 if ( !t1.isEqual( t2 ) ) {
3252 t2.setIdentifier( new Identifier( "nemve" ) );
3253 if ( t1.isEqual( t2 ) ) {
3256 t1.setIdentifier( null );
3257 t3.setTaxonomyCode( "ECOLI" );
3258 t3.setScientificName( "what" );
3259 t3.setCommonName( "something" );
3260 if ( !t1.isEqual( t3 ) ) {
3263 t1.setIdentifier( null );
3264 t1.setTaxonomyCode( "" );
3265 t4.setScientificName( "E. ColI" );
3266 t4.setCommonName( "something" );
3267 if ( !t1.isEqual( t4 ) ) {
3270 t4.setScientificName( "B. subtilis" );
3271 t4.setCommonName( "something" );
3272 if ( t1.isEqual( t4 ) ) {
3275 t1.setIdentifier( null );
3276 t1.setTaxonomyCode( "" );
3277 t1.setScientificName( "" );
3278 t5.setCommonName( "COLI" );
3279 if ( !t1.isEqual( t5 ) ) {
3282 t5.setCommonName( "vibrio" );
3283 if ( t1.isEqual( t5 ) ) {
3288 final Identifier id0 = new Identifier( "123", "pfam" );
3289 final Identifier id1 = ( Identifier ) id0.copy();
3290 if ( !id1.isEqual( id1 ) ) {
3293 if ( !id1.isEqual( id0 ) ) {
3296 if ( !id0.isEqual( id1 ) ) {
3303 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3304 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3305 if ( !pd1.isEqual( pd1 ) ) {
3308 if ( !pd1.isEqual( pd0 ) ) {
3313 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3314 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3315 if ( !pd3.isEqual( pd3 ) ) {
3318 if ( !pd2.isEqual( pd3 ) ) {
3321 if ( !pd0.isEqual( pd3 ) ) {
3326 // DomainArchitecture
3327 // ------------------
3328 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3329 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3330 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3331 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3332 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3333 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3338 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3339 if ( ds0.getNumberOfDomains() != 4 ) {
3342 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3343 if ( !ds0.isEqual( ds0 ) ) {
3346 if ( !ds0.isEqual( ds1 ) ) {
3349 if ( ds1.getNumberOfDomains() != 4 ) {
3352 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3357 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3358 if ( ds0.isEqual( ds2 ) ) {
3364 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3365 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3366 System.out.println( ds3.toNHX() );
3369 if ( ds3.getNumberOfDomains() != 3 ) {
3374 final Event e1 = new Event( Event.EventType.fusion );
3375 if ( e1.isDuplication() ) {
3378 if ( !e1.isFusion() ) {
3381 if ( !e1.asText().toString().equals( "fusion" ) ) {
3384 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3387 final Event e11 = new Event( Event.EventType.fusion );
3388 if ( !e11.isEqual( e1 ) ) {
3391 if ( !e11.toNHX().toString().equals( "" ) ) {
3394 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3395 if ( e2.isDuplication() ) {
3398 if ( !e2.isSpeciationOrDuplication() ) {
3401 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3404 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3407 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3410 if ( e11.isEqual( e2 ) ) {
3413 final Event e2c = ( Event ) e2.copy();
3414 if ( !e2c.isEqual( e2 ) ) {
3417 Event e3 = new Event( 1, 2, 3 );
3418 if ( e3.isDuplication() ) {
3421 if ( e3.isSpeciation() ) {
3424 if ( e3.isGeneLoss() ) {
3427 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3430 final Event e3c = ( Event ) e3.copy();
3431 final Event e3cc = ( Event ) e3c.copy();
3432 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3436 if ( !e3c.isEqual( e3cc ) ) {
3439 Event e4 = new Event( 1, 2, 3 );
3440 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3443 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3446 final Event e4c = ( Event ) e4.copy();
3448 final Event e4cc = ( Event ) e4c.copy();
3449 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3452 if ( !e4c.isEqual( e4cc ) ) {
3455 final Event e5 = new Event();
3456 if ( !e5.isUnassigned() ) {
3459 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3462 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3465 final Event e6 = new Event( 1, 0, 0 );
3466 if ( !e6.asText().toString().equals( "duplication" ) ) {
3469 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3472 final Event e7 = new Event( 0, 1, 0 );
3473 if ( !e7.asText().toString().equals( "speciation" ) ) {
3476 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3479 final Event e8 = new Event( 0, 0, 1 );
3480 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3483 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3487 catch ( final Exception e ) {
3488 e.printStackTrace( System.out );
3494 private static boolean testDeletionOfExternalNodes() {
3496 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3497 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3498 final PhylogenyWriter w = new PhylogenyWriter();
3499 if ( t0.isEmpty() ) {
3502 if ( t0.getNumberOfExternalNodes() != 1 ) {
3505 t0.deleteSubtree( t0.getNode( "A" ), false );
3506 if ( t0.getNumberOfExternalNodes() != 0 ) {
3509 if ( !t0.isEmpty() ) {
3512 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3513 if ( t1.getNumberOfExternalNodes() != 2 ) {
3516 t1.deleteSubtree( t1.getNode( "A" ), false );
3517 if ( t1.getNumberOfExternalNodes() != 1 ) {
3520 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3523 t1.deleteSubtree( t1.getNode( "B" ), false );
3524 if ( t1.getNumberOfExternalNodes() != 1 ) {
3527 t1.deleteSubtree( t1.getNode( "r" ), false );
3528 if ( !t1.isEmpty() ) {
3531 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3532 if ( t2.getNumberOfExternalNodes() != 3 ) {
3535 t2.deleteSubtree( t2.getNode( "B" ), false );
3536 if ( t2.getNumberOfExternalNodes() != 2 ) {
3539 t2.toNewHampshireX();
3540 PhylogenyNode n = t2.getNode( "A" );
3541 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3544 t2.deleteSubtree( t2.getNode( "A" ), false );
3545 if ( t2.getNumberOfExternalNodes() != 2 ) {
3548 t2.deleteSubtree( t2.getNode( "C" ), true );
3549 if ( t2.getNumberOfExternalNodes() != 1 ) {
3552 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3553 if ( t3.getNumberOfExternalNodes() != 4 ) {
3556 t3.deleteSubtree( t3.getNode( "B" ), true );
3557 if ( t3.getNumberOfExternalNodes() != 3 ) {
3560 n = t3.getNode( "A" );
3561 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3564 n = n.getNextExternalNode();
3565 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3568 t3.deleteSubtree( t3.getNode( "A" ), true );
3569 if ( t3.getNumberOfExternalNodes() != 2 ) {
3572 n = t3.getNode( "C" );
3573 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3576 t3.deleteSubtree( t3.getNode( "C" ), true );
3577 if ( t3.getNumberOfExternalNodes() != 1 ) {
3580 t3.deleteSubtree( t3.getNode( "D" ), true );
3581 if ( t3.getNumberOfExternalNodes() != 0 ) {
3584 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3585 if ( t4.getNumberOfExternalNodes() != 6 ) {
3588 t4.deleteSubtree( t4.getNode( "B2" ), true );
3589 if ( t4.getNumberOfExternalNodes() != 5 ) {
3592 String s = w.toNewHampshire( t4, true ).toString();
3593 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3596 t4.deleteSubtree( t4.getNode( "B11" ), true );
3597 if ( t4.getNumberOfExternalNodes() != 4 ) {
3600 t4.deleteSubtree( t4.getNode( "C" ), true );
3601 if ( t4.getNumberOfExternalNodes() != 3 ) {
3604 n = t4.getNode( "A" );
3605 n = n.getNextExternalNode();
3606 if ( !n.getName().equals( "B12" ) ) {
3609 n = n.getNextExternalNode();
3610 if ( !n.getName().equals( "D" ) ) {
3613 s = w.toNewHampshire( t4, true ).toString();
3614 if ( !s.equals( "((A,B12),D);" ) ) {
3617 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3618 t5.deleteSubtree( t5.getNode( "A" ), true );
3619 if ( t5.getNumberOfExternalNodes() != 5 ) {
3622 s = w.toNewHampshire( t5, true ).toString();
3623 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3626 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3627 t6.deleteSubtree( t6.getNode( "B11" ), true );
3628 if ( t6.getNumberOfExternalNodes() != 5 ) {
3631 s = w.toNewHampshire( t6, false ).toString();
3632 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3635 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3636 t7.deleteSubtree( t7.getNode( "B12" ), true );
3637 if ( t7.getNumberOfExternalNodes() != 5 ) {
3640 s = w.toNewHampshire( t7, true ).toString();
3641 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3644 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3645 t8.deleteSubtree( t8.getNode( "B2" ), true );
3646 if ( t8.getNumberOfExternalNodes() != 5 ) {
3649 s = w.toNewHampshire( t8, false ).toString();
3650 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3653 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3654 t9.deleteSubtree( t9.getNode( "C" ), true );
3655 if ( t9.getNumberOfExternalNodes() != 5 ) {
3658 s = w.toNewHampshire( t9, true ).toString();
3659 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3662 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3663 t10.deleteSubtree( t10.getNode( "D" ), true );
3664 if ( t10.getNumberOfExternalNodes() != 5 ) {
3667 s = w.toNewHampshire( t10, true ).toString();
3668 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3671 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3672 t11.deleteSubtree( t11.getNode( "A" ), true );
3673 if ( t11.getNumberOfExternalNodes() != 2 ) {
3676 s = w.toNewHampshire( t11, true ).toString();
3677 if ( !s.equals( "(B,C);" ) ) {
3680 t11.deleteSubtree( t11.getNode( "C" ), true );
3681 if ( t11.getNumberOfExternalNodes() != 1 ) {
3684 s = w.toNewHampshire( t11, false ).toString();
3685 if ( !s.equals( "B;" ) ) {
3688 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3689 t12.deleteSubtree( t12.getNode( "B2" ), true );
3690 if ( t12.getNumberOfExternalNodes() != 8 ) {
3693 s = w.toNewHampshire( t12, true ).toString();
3694 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3697 t12.deleteSubtree( t12.getNode( "B3" ), true );
3698 if ( t12.getNumberOfExternalNodes() != 7 ) {
3701 s = w.toNewHampshire( t12, true ).toString();
3702 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3705 t12.deleteSubtree( t12.getNode( "C3" ), true );
3706 if ( t12.getNumberOfExternalNodes() != 6 ) {
3709 s = w.toNewHampshire( t12, true ).toString();
3710 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3713 t12.deleteSubtree( t12.getNode( "A1" ), true );
3714 if ( t12.getNumberOfExternalNodes() != 5 ) {
3717 s = w.toNewHampshire( t12, true ).toString();
3718 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3721 t12.deleteSubtree( t12.getNode( "B1" ), true );
3722 if ( t12.getNumberOfExternalNodes() != 4 ) {
3725 s = w.toNewHampshire( t12, true ).toString();
3726 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3729 t12.deleteSubtree( t12.getNode( "A3" ), true );
3730 if ( t12.getNumberOfExternalNodes() != 3 ) {
3733 s = w.toNewHampshire( t12, true ).toString();
3734 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3737 t12.deleteSubtree( t12.getNode( "A2" ), true );
3738 if ( t12.getNumberOfExternalNodes() != 2 ) {
3741 s = w.toNewHampshire( t12, true ).toString();
3742 if ( !s.equals( "(C1,C2);" ) ) {
3745 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3746 t13.deleteSubtree( t13.getNode( "D" ), true );
3747 if ( t13.getNumberOfExternalNodes() != 4 ) {
3750 s = w.toNewHampshire( t13, true ).toString();
3751 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3754 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3755 t14.deleteSubtree( t14.getNode( "E" ), true );
3756 if ( t14.getNumberOfExternalNodes() != 5 ) {
3759 s = w.toNewHampshire( t14, true ).toString();
3760 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3763 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3764 t15.deleteSubtree( t15.getNode( "B2" ), true );
3765 if ( t15.getNumberOfExternalNodes() != 11 ) {
3768 t15.deleteSubtree( t15.getNode( "B1" ), true );
3769 if ( t15.getNumberOfExternalNodes() != 10 ) {
3772 t15.deleteSubtree( t15.getNode( "B3" ), true );
3773 if ( t15.getNumberOfExternalNodes() != 9 ) {
3776 t15.deleteSubtree( t15.getNode( "B4" ), true );
3777 if ( t15.getNumberOfExternalNodes() != 8 ) {
3780 t15.deleteSubtree( t15.getNode( "A1" ), true );
3781 if ( t15.getNumberOfExternalNodes() != 7 ) {
3784 t15.deleteSubtree( t15.getNode( "C4" ), true );
3785 if ( t15.getNumberOfExternalNodes() != 6 ) {
3789 catch ( final Exception e ) {
3790 e.printStackTrace( System.out );
3796 private static boolean testDescriptiveStatistics() {
3798 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3799 dss1.addValue( 82 );
3800 dss1.addValue( 78 );
3801 dss1.addValue( 70 );
3802 dss1.addValue( 58 );
3803 dss1.addValue( 42 );
3804 if ( dss1.getN() != 5 ) {
3807 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3810 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3813 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3816 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3819 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3822 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3825 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3828 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3831 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3834 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3837 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3840 dss1.addValue( 123 );
3841 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3844 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3847 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3850 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3851 dss2.addValue( -1.85 );
3852 dss2.addValue( 57.5 );
3853 dss2.addValue( 92.78 );
3854 dss2.addValue( 57.78 );
3855 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3858 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3861 final double[] a = dss2.getDataAsDoubleArray();
3862 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3865 dss2.addValue( -100 );
3866 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3869 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3872 final double[] ds = new double[ 14 ];
3887 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3888 if ( bins.length != 4 ) {
3891 if ( bins[ 0 ] != 2 ) {
3894 if ( bins[ 1 ] != 3 ) {
3897 if ( bins[ 2 ] != 4 ) {
3900 if ( bins[ 3 ] != 5 ) {
3903 final double[] ds1 = new double[ 9 ];
3913 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3914 if ( bins1.length != 4 ) {
3917 if ( bins1[ 0 ] != 2 ) {
3920 if ( bins1[ 1 ] != 3 ) {
3923 if ( bins1[ 2 ] != 0 ) {
3926 if ( bins1[ 3 ] != 4 ) {
3929 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3930 if ( bins1_1.length != 3 ) {
3933 if ( bins1_1[ 0 ] != 3 ) {
3936 if ( bins1_1[ 1 ] != 2 ) {
3939 if ( bins1_1[ 2 ] != 4 ) {
3942 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3943 if ( bins1_2.length != 3 ) {
3946 if ( bins1_2[ 0 ] != 2 ) {
3949 if ( bins1_2[ 1 ] != 2 ) {
3952 if ( bins1_2[ 2 ] != 2 ) {
3955 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3969 dss3.addValue( 10 );
3970 dss3.addValue( 10 );
3971 dss3.addValue( 10 );
3972 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3973 histo.toStringBuffer( 10, '=', 40, 5 );
3974 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3976 catch ( final Exception e ) {
3977 e.printStackTrace( System.out );
3983 private static boolean testDir( final String file ) {
3985 final File f = new File( file );
3986 if ( !f.exists() ) {
3989 if ( !f.isDirectory() ) {
3992 if ( !f.canRead() ) {
3996 catch ( final Exception e ) {
4002 private static boolean testEbiEntryRetrieval() {
4004 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
4005 if ( !entry.getAccession().equals( "AAK41263" ) ) {
4006 System.out.println( entry.getAccession() );
4009 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
4010 System.out.println( entry.getTaxonomyScientificName() );
4013 if ( !entry.getSequenceName()
4014 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
4015 System.out.println( entry.getSequenceName() );
4018 if ( !entry.getGeneName().equals( "treX-like" ) ) {
4019 System.out.println( entry.getGeneName() );
4022 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
4023 System.out.println( entry.getTaxonomyIdentifier() );
4026 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
4027 System.out.println( entry.getAnnotations().first().getRefValue() );
4030 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
4031 System.out.println( entry.getAnnotations().first().getRefSource() );
4034 if ( entry.getCrossReferences().size() < 1 ) {
4037 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
4038 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
4041 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
4042 System.out.println( entry1.getTaxonomyScientificName() );
4045 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
4046 System.out.println( entry1.getSequenceName() );
4049 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
4050 System.out.println( entry1.getTaxonomyIdentifier() );
4053 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
4054 System.out.println( entry1.getGeneName() );
4057 if ( entry1.getCrossReferences().size() < 1 ) {
4060 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
4061 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
4064 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4065 System.out.println( entry2.getTaxonomyScientificName() );
4068 if ( !entry2.getSequenceName()
4069 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
4070 System.out.println( entry2.getSequenceName() );
4073 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
4074 System.out.println( entry2.getTaxonomyIdentifier() );
4077 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
4078 System.out.println( entry2.getGeneName() );
4081 if ( entry2.getCrossReferences().size() < 1 ) {
4084 if ( !entry2.getChromosome().equals( "20" ) ) {
4087 if ( !entry2.getMap().equals( "20q11.22" ) ) {
4090 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
4091 if ( !entry3.getAccession().equals( "HM043801" ) ) {
4094 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
4095 System.out.println( entry3.getTaxonomyScientificName() );
4098 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
4099 System.out.println( entry3.getSequenceName() );
4102 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
4103 System.out.println( entry3.getTaxonomyIdentifier() );
4106 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
4107 System.out.println( entry3.getSequenceSymbol() );
4110 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
4113 if ( entry3.getCrossReferences().size() < 1 ) {
4116 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
4117 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4120 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4121 System.out.println( entry4.getTaxonomyScientificName() );
4124 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4125 System.out.println( entry4.getSequenceName() );
4128 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4129 System.out.println( entry4.getTaxonomyIdentifier() );
4132 if ( !entry4.getGeneName().equals( "ras" ) ) {
4133 System.out.println( entry4.getGeneName() );
4136 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4137 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4140 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4141 System.out.println( entry5.getTaxonomyScientificName() );
4144 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4145 System.out.println( entry5.getSequenceName() );
4148 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4149 System.out.println( entry5.getTaxonomyIdentifier() );
4152 final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" );
4153 if ( !entry6.getAccession().equals( "M30539" ) ) {
4156 if ( !entry6.getGeneName().equals( "ras" ) ) {
4159 if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) {
4162 if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) {
4165 if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4168 if ( entry6.getCrossReferences().size() < 1 ) {
4172 catch ( final IOException e ) {
4173 System.out.println();
4174 System.out.println( "the following might be due to absence internet connection:" );
4175 e.printStackTrace( System.out );
4178 catch ( final Exception e ) {
4179 e.printStackTrace();
4185 private static boolean testExternalNodeRelatedMethods() {
4187 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4188 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4189 PhylogenyNode n = t1.getNode( "A" );
4190 n = n.getNextExternalNode();
4191 if ( !n.getName().equals( "B" ) ) {
4194 n = n.getNextExternalNode();
4195 if ( !n.getName().equals( "C" ) ) {
4198 n = n.getNextExternalNode();
4199 if ( !n.getName().equals( "D" ) ) {
4202 n = t1.getNode( "B" );
4203 while ( !n.isLastExternalNode() ) {
4204 n = n.getNextExternalNode();
4206 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4207 n = t2.getNode( "A" );
4208 n = n.getNextExternalNode();
4209 if ( !n.getName().equals( "B" ) ) {
4212 n = n.getNextExternalNode();
4213 if ( !n.getName().equals( "C" ) ) {
4216 n = n.getNextExternalNode();
4217 if ( !n.getName().equals( "D" ) ) {
4220 n = t2.getNode( "B" );
4221 while ( !n.isLastExternalNode() ) {
4222 n = n.getNextExternalNode();
4224 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4225 n = t3.getNode( "A" );
4226 n = n.getNextExternalNode();
4227 if ( !n.getName().equals( "B" ) ) {
4230 n = n.getNextExternalNode();
4231 if ( !n.getName().equals( "C" ) ) {
4234 n = n.getNextExternalNode();
4235 if ( !n.getName().equals( "D" ) ) {
4238 n = n.getNextExternalNode();
4239 if ( !n.getName().equals( "E" ) ) {
4242 n = n.getNextExternalNode();
4243 if ( !n.getName().equals( "F" ) ) {
4246 n = n.getNextExternalNode();
4247 if ( !n.getName().equals( "G" ) ) {
4250 n = n.getNextExternalNode();
4251 if ( !n.getName().equals( "H" ) ) {
4254 n = t3.getNode( "B" );
4255 while ( !n.isLastExternalNode() ) {
4256 n = n.getNextExternalNode();
4258 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4259 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4260 final PhylogenyNode node = iter.next();
4262 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4263 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4264 final PhylogenyNode node = iter.next();
4266 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4267 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4268 if ( !iter.next().getName().equals( "A" ) ) {
4271 if ( !iter.next().getName().equals( "B" ) ) {
4274 if ( !iter.next().getName().equals( "C" ) ) {
4277 if ( !iter.next().getName().equals( "D" ) ) {
4280 if ( !iter.next().getName().equals( "E" ) ) {
4283 if ( !iter.next().getName().equals( "F" ) ) {
4286 if ( iter.hasNext() ) {
4290 catch ( final Exception e ) {
4291 e.printStackTrace( System.out );
4297 private static boolean testExtractSNFromNodeName() {
4299 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4302 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4305 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4308 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4309 .equals( "Mus musculus musculus" ) ) {
4312 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4313 .equals( "Mus musculus musculus" ) ) {
4316 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4317 .equals( "Mus musculus musculus" ) ) {
4320 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4321 .equals( "Mus musculus musculus" ) ) {
4324 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4327 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4328 .equals( "Mus musculus musculus" ) ) {
4331 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4332 .equals( "Mus musculus musculus" ) ) {
4335 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4338 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4341 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4344 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4347 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4348 .equals( "Mus musculus musculus" ) ) {
4351 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4354 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4357 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4360 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4363 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4366 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4369 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4372 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4375 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4376 .equals( "Mus musculus" ) ) {
4379 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4380 .equals( "Mus musculus" ) ) {
4383 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4386 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4387 .equals( "Mus musculus musculus" ) ) {
4390 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4391 .equals( "Mus musculus musculus" ) ) {
4394 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4395 .equals( "Mus musculus musculus" ) ) {
4398 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4401 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4402 .equals( "Pilostyles mexicana" ) ) {
4405 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4406 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4409 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4410 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4413 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4414 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4417 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4418 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4421 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4422 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4425 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4426 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4429 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
4430 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4433 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
4434 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4437 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
4438 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4441 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4442 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4445 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4446 .equals( "Escherichia coli (strain K12)" ) ) {
4449 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4450 .equals( "Escherichia coli (strain K12)" ) ) {
4453 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4454 .equals( "Escherichia coli (str. K12)" ) ) {
4457 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4458 .equals( "Escherichia coli (str. K12)" ) ) {
4461 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4462 .equals( "Escherichia coli (str. K12)" ) ) {
4465 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4466 .equals( "Escherichia coli (var. K12)" ) ) {
4469 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4470 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4473 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4474 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4478 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4479 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4482 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4483 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4487 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4488 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4491 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4492 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4495 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4496 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4499 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4502 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4505 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4508 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4509 .equals( "Macrocera sp." ) ) {
4512 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4515 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4516 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4519 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
4520 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4523 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
4524 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4527 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
4528 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4532 catch ( final Exception e ) {
4533 e.printStackTrace( System.out );
4539 private static boolean testExtractTaxonomyDataFromNodeName() {
4541 PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
4542 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4545 n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
4546 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4549 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
4550 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4553 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" );
4554 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4557 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" );
4558 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4561 n = new PhylogenyNode( "HNRPR_HUMAN" );
4562 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4565 n = new PhylogenyNode( "HNRPR_HUMAN_X" );
4566 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4570 catch ( final Exception e ) {
4571 e.printStackTrace( System.out );
4577 private static boolean testExtractTaxonomyCodeFromNodeName() {
4579 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4582 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4583 .equals( "SOYBN" ) ) {
4586 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4587 .equals( "ARATH" ) ) {
4590 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4591 .equals( "ARATH" ) ) {
4594 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4597 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4600 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4603 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4604 .equals( "SOYBN" ) ) {
4607 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4608 .equals( "SOYBN" ) ) {
4611 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4612 .equals( "SOYBN" ) ) {
4615 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4616 .equals( "SOYBN" ) ) {
4619 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4620 .equals( "SOYBN" ) ) {
4623 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4624 .equals( "SOYBN" ) ) {
4627 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4628 .equals( "SOYBN" ) ) {
4631 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4632 .equals( "SOYBN" ) ) {
4635 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4638 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4639 .equals( "SOYBN" ) ) {
4642 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4643 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4646 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4647 .equals( "9YX45" ) ) {
4650 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4651 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4652 .equals( "MOUSE" ) ) {
4655 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4656 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4657 .equals( "MOUSE" ) ) {
4660 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4661 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4662 .equals( "MOUSE" ) ) {
4665 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4666 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4669 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4670 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4673 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4674 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4677 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4678 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4681 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4682 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4685 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4686 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4689 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4690 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4693 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4694 .equals( "RAT" ) ) {
4697 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4698 .equals( "PIG" ) ) {
4702 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4703 .equals( "MOUSE" ) ) {
4706 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4707 .equals( "MOUSE" ) ) {
4710 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4714 catch ( final Exception e ) {
4715 e.printStackTrace( System.out );
4721 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4723 PhylogenyNode n = new PhylogenyNode();
4724 n.setName( "tr|B3RJ64" );
4725 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4728 n.setName( "tr.B3RJ64" );
4729 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4732 n.setName( "tr=B3RJ64" );
4733 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4736 n.setName( "tr-B3RJ64" );
4737 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4740 n.setName( "tr/B3RJ64" );
4741 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4744 n.setName( "tr\\B3RJ64" );
4745 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4748 n.setName( "tr_B3RJ64" );
4749 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4752 n.setName( " tr|B3RJ64 " );
4753 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4756 n.setName( "-tr|B3RJ64-" );
4757 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4760 n.setName( "-tr=B3RJ64-" );
4761 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4764 n.setName( "_tr=B3RJ64_" );
4765 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4768 n.setName( " tr_tr|B3RJ64_sp|123 " );
4769 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4772 n.setName( "B3RJ64" );
4773 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4776 n.setName( "sp|B3RJ64" );
4777 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4780 n.setName( "sp|B3RJ64C" );
4781 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4784 n.setName( "sp B3RJ64" );
4785 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4788 n.setName( "sp|B3RJ6X" );
4789 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4792 n.setName( "sp|B3RJ6" );
4793 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4796 n.setName( "K1PYK7_CRAGI" );
4797 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4800 n.setName( "K1PYK7_PEA" );
4801 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4804 n.setName( "K1PYK7_RAT" );
4805 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4808 n.setName( "K1PYK7_PIG" );
4809 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4812 n.setName( "~K1PYK7_PIG~" );
4813 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4816 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4817 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4820 n.setName( "K1PYKX_CRAGI" );
4821 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4824 n.setName( "XXXXX_CRAGI" );
4825 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4828 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4829 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4832 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4833 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4836 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4837 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4840 n = new PhylogenyNode();
4841 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4842 seq.setSymbol( "K1PYK7_CRAGI" );
4843 n.getNodeData().addSequence( seq );
4844 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4847 seq.setSymbol( "tr|B3RJ64" );
4848 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4851 n = new PhylogenyNode();
4852 seq = new org.forester.phylogeny.data.Sequence();
4853 seq.setName( "K1PYK7_CRAGI" );
4854 n.getNodeData().addSequence( seq );
4855 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4858 seq.setName( "tr|B3RJ64" );
4859 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4862 n = new PhylogenyNode();
4863 seq = new org.forester.phylogeny.data.Sequence();
4864 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4865 n.getNodeData().addSequence( seq );
4866 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4869 n = new PhylogenyNode();
4870 seq = new org.forester.phylogeny.data.Sequence();
4871 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4872 n.getNodeData().addSequence( seq );
4873 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4877 n = new PhylogenyNode();
4878 n.setName( "ACP19736" );
4879 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4882 n = new PhylogenyNode();
4883 n.setName( "|ACP19736|" );
4884 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4888 catch ( final Exception e ) {
4889 e.printStackTrace( System.out );
4895 private static boolean testFastaParser() {
4897 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4900 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4903 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4904 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4907 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4910 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4913 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
4916 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4919 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4923 catch ( final Exception e ) {
4924 e.printStackTrace();
4930 private static boolean testGenbankAccessorParsing() {
4931 //The format for GenBank Accession numbers are:
4932 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4933 //Protein: 3 letters + 5 numerals
4934 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4935 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4938 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4941 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4944 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4947 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4950 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4953 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4956 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4959 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4962 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4965 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4968 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4971 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4974 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4980 private static boolean testGeneralMsaParser() {
4982 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4983 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4984 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4985 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4986 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4987 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4988 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4989 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4990 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4993 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4996 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4999 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5002 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
5005 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
5008 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
5011 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5014 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
5017 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
5020 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
5023 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5026 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
5027 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5030 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5033 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5036 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
5037 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
5040 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
5043 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
5046 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
5047 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5050 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5053 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5057 catch ( final Exception e ) {
5058 e.printStackTrace();
5064 private static boolean testGeneralTable() {
5066 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
5067 t0.setValue( 3, 2, "23" );
5068 t0.setValue( 10, 1, "error" );
5069 t0.setValue( 10, 1, "110" );
5070 t0.setValue( 9, 1, "19" );
5071 t0.setValue( 1, 10, "101" );
5072 t0.setValue( 10, 10, "1010" );
5073 t0.setValue( 100, 10, "10100" );
5074 t0.setValue( 0, 0, "00" );
5075 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
5078 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
5081 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
5084 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
5087 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
5090 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
5093 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
5096 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
5099 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
5102 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
5103 t1.setValue( "3", "2", "23" );
5104 t1.setValue( "10", "1", "error" );
5105 t1.setValue( "10", "1", "110" );
5106 t1.setValue( "9", "1", "19" );
5107 t1.setValue( "1", "10", "101" );
5108 t1.setValue( "10", "10", "1010" );
5109 t1.setValue( "100", "10", "10100" );
5110 t1.setValue( "0", "0", "00" );
5111 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
5112 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
5115 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
5118 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
5121 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
5124 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
5127 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
5130 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
5133 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
5136 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
5139 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
5143 catch ( final Exception e ) {
5144 e.printStackTrace( System.out );
5150 private static boolean testGetDistance() {
5152 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5153 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",
5154 new NHXParser() )[ 0 ];
5155 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
5158 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5161 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5164 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5167 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5170 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5173 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5176 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5179 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5182 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5185 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5188 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5191 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5194 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5197 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5200 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5203 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5206 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5209 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5212 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5215 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5218 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5221 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5224 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5227 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5230 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5233 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5236 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5239 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5242 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5245 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5248 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",
5249 new NHXParser() )[ 0 ];
5250 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5253 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5256 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5259 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5262 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5265 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5268 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5271 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5274 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5277 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5280 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5284 catch ( final Exception e ) {
5285 e.printStackTrace( System.out );
5291 private static boolean testGetLCA() {
5293 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5294 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5295 new NHXParser() )[ 0 ];
5296 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5297 if ( !A.getName().equals( "A" ) ) {
5300 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5301 if ( !gh.getName().equals( "gh" ) ) {
5304 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5305 if ( !ab.getName().equals( "ab" ) ) {
5308 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5309 if ( !ab2.getName().equals( "ab" ) ) {
5312 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5313 if ( !gh2.getName().equals( "gh" ) ) {
5316 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5317 if ( !gh3.getName().equals( "gh" ) ) {
5320 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5321 if ( !abc.getName().equals( "abc" ) ) {
5324 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5325 if ( !abc2.getName().equals( "abc" ) ) {
5328 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5329 if ( !abcd.getName().equals( "abcd" ) ) {
5332 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5333 if ( !abcd2.getName().equals( "abcd" ) ) {
5336 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5337 if ( !abcdef.getName().equals( "abcdef" ) ) {
5340 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5341 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5344 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5345 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5348 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5349 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5352 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5353 if ( !abcde.getName().equals( "abcde" ) ) {
5356 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5357 if ( !abcde2.getName().equals( "abcde" ) ) {
5360 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5361 if ( !r.getName().equals( "abcdefgh" ) ) {
5364 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5365 if ( !r2.getName().equals( "abcdefgh" ) ) {
5368 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5369 if ( !r3.getName().equals( "abcdefgh" ) ) {
5372 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5373 if ( !abcde3.getName().equals( "abcde" ) ) {
5376 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5377 if ( !abcde4.getName().equals( "abcde" ) ) {
5380 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5381 if ( !ab3.getName().equals( "ab" ) ) {
5384 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5385 if ( !ab4.getName().equals( "ab" ) ) {
5388 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5389 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5390 if ( !cd.getName().equals( "cd" ) ) {
5393 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5394 if ( !cd2.getName().equals( "cd" ) ) {
5397 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5398 if ( !cde.getName().equals( "cde" ) ) {
5401 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5402 if ( !cde2.getName().equals( "cde" ) ) {
5405 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5406 if ( !cdef.getName().equals( "cdef" ) ) {
5409 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5410 if ( !cdef2.getName().equals( "cdef" ) ) {
5413 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5414 if ( !cdef3.getName().equals( "cdef" ) ) {
5417 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5418 if ( !rt.getName().equals( "r" ) ) {
5421 final Phylogeny p3 = factory
5422 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5423 new NHXParser() )[ 0 ];
5424 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5425 if ( !bc_3.getName().equals( "bc" ) ) {
5428 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5429 if ( !ac_3.getName().equals( "abc" ) ) {
5432 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5433 if ( !ad_3.getName().equals( "abcde" ) ) {
5436 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5437 if ( !af_3.getName().equals( "abcdef" ) ) {
5440 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5441 if ( !ag_3.getName().equals( "" ) ) {
5444 if ( !ag_3.isRoot() ) {
5447 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5448 if ( !al_3.getName().equals( "" ) ) {
5451 if ( !al_3.isRoot() ) {
5454 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5455 if ( !kl_3.getName().equals( "" ) ) {
5458 if ( !kl_3.isRoot() ) {
5461 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5462 if ( !fl_3.getName().equals( "" ) ) {
5465 if ( !fl_3.isRoot() ) {
5468 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5469 if ( !gk_3.getName().equals( "ghijk" ) ) {
5472 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5473 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5474 if ( !r_4.getName().equals( "r" ) ) {
5477 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5478 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5479 if ( !r_5.getName().equals( "root" ) ) {
5482 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5483 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5484 if ( !r_6.getName().equals( "rot" ) ) {
5487 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5488 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5489 if ( !r_7.getName().equals( "rott" ) ) {
5493 catch ( final Exception e ) {
5494 e.printStackTrace( System.out );
5500 private static boolean testGetLCA2() {
5502 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5503 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5504 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5505 PhylogenyMethods.preOrderReId( p_a );
5506 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5507 p_a.getNode( "a" ) );
5508 if ( !p_a_1.getName().equals( "a" ) ) {
5511 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5512 PhylogenyMethods.preOrderReId( p_b );
5513 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5514 p_b.getNode( "a" ) );
5515 if ( !p_b_1.getName().equals( "b" ) ) {
5518 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5519 p_b.getNode( "b" ) );
5520 if ( !p_b_2.getName().equals( "b" ) ) {
5523 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5524 PhylogenyMethods.preOrderReId( p_c );
5525 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5526 p_c.getNode( "a" ) );
5527 if ( !p_c_1.getName().equals( "b" ) ) {
5530 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5531 p_c.getNode( "c" ) );
5532 if ( !p_c_2.getName().equals( "c" ) ) {
5533 System.out.println( p_c_2.getName() );
5537 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5538 p_c.getNode( "b" ) );
5539 if ( !p_c_3.getName().equals( "b" ) ) {
5542 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5543 p_c.getNode( "a" ) );
5544 if ( !p_c_4.getName().equals( "c" ) ) {
5547 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5548 new NHXParser() )[ 0 ];
5549 PhylogenyMethods.preOrderReId( p1 );
5550 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5551 p1.getNode( "A" ) );
5552 if ( !A.getName().equals( "A" ) ) {
5555 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5556 p1.getNode( "gh" ) );
5557 if ( !gh.getName().equals( "gh" ) ) {
5560 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5561 p1.getNode( "B" ) );
5562 if ( !ab.getName().equals( "ab" ) ) {
5565 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5566 p1.getNode( "A" ) );
5567 if ( !ab2.getName().equals( "ab" ) ) {
5570 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5571 p1.getNode( "G" ) );
5572 if ( !gh2.getName().equals( "gh" ) ) {
5575 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5576 p1.getNode( "H" ) );
5577 if ( !gh3.getName().equals( "gh" ) ) {
5580 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5581 p1.getNode( "A" ) );
5582 if ( !abc.getName().equals( "abc" ) ) {
5585 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5586 p1.getNode( "C" ) );
5587 if ( !abc2.getName().equals( "abc" ) ) {
5590 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5591 p1.getNode( "D" ) );
5592 if ( !abcd.getName().equals( "abcd" ) ) {
5595 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5596 p1.getNode( "A" ) );
5597 if ( !abcd2.getName().equals( "abcd" ) ) {
5600 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5601 p1.getNode( "F" ) );
5602 if ( !abcdef.getName().equals( "abcdef" ) ) {
5605 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5606 p1.getNode( "A" ) );
5607 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5610 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5611 p1.getNode( "F" ) );
5612 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5615 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5616 p1.getNode( "ab" ) );
5617 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5620 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5621 p1.getNode( "E" ) );
5622 if ( !abcde.getName().equals( "abcde" ) ) {
5625 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5626 p1.getNode( "A" ) );
5627 if ( !abcde2.getName().equals( "abcde" ) ) {
5630 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5631 p1.getNode( "abcdefgh" ) );
5632 if ( !r.getName().equals( "abcdefgh" ) ) {
5635 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5636 p1.getNode( "H" ) );
5637 if ( !r2.getName().equals( "abcdefgh" ) ) {
5640 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5641 p1.getNode( "A" ) );
5642 if ( !r3.getName().equals( "abcdefgh" ) ) {
5645 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5646 p1.getNode( "abcde" ) );
5647 if ( !abcde3.getName().equals( "abcde" ) ) {
5650 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5651 p1.getNode( "E" ) );
5652 if ( !abcde4.getName().equals( "abcde" ) ) {
5655 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5656 p1.getNode( "B" ) );
5657 if ( !ab3.getName().equals( "ab" ) ) {
5660 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5661 p1.getNode( "ab" ) );
5662 if ( !ab4.getName().equals( "ab" ) ) {
5665 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5666 PhylogenyMethods.preOrderReId( p2 );
5667 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5668 p2.getNode( "d" ) );
5669 if ( !cd.getName().equals( "cd" ) ) {
5672 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5673 p2.getNode( "c" ) );
5674 if ( !cd2.getName().equals( "cd" ) ) {
5677 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5678 p2.getNode( "e" ) );
5679 if ( !cde.getName().equals( "cde" ) ) {
5682 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5683 p2.getNode( "c" ) );
5684 if ( !cde2.getName().equals( "cde" ) ) {
5687 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5688 p2.getNode( "f" ) );
5689 if ( !cdef.getName().equals( "cdef" ) ) {
5692 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5693 p2.getNode( "f" ) );
5694 if ( !cdef2.getName().equals( "cdef" ) ) {
5697 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5698 p2.getNode( "d" ) );
5699 if ( !cdef3.getName().equals( "cdef" ) ) {
5702 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5703 p2.getNode( "a" ) );
5704 if ( !rt.getName().equals( "r" ) ) {
5707 final Phylogeny p3 = factory
5708 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5709 new NHXParser() )[ 0 ];
5710 PhylogenyMethods.preOrderReId( p3 );
5711 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5712 p3.getNode( "c" ) );
5713 if ( !bc_3.getName().equals( "bc" ) ) {
5716 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5717 p3.getNode( "c" ) );
5718 if ( !ac_3.getName().equals( "abc" ) ) {
5721 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5722 p3.getNode( "d" ) );
5723 if ( !ad_3.getName().equals( "abcde" ) ) {
5726 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5727 p3.getNode( "f" ) );
5728 if ( !af_3.getName().equals( "abcdef" ) ) {
5731 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5732 p3.getNode( "g" ) );
5733 if ( !ag_3.getName().equals( "" ) ) {
5736 if ( !ag_3.isRoot() ) {
5739 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5740 p3.getNode( "l" ) );
5741 if ( !al_3.getName().equals( "" ) ) {
5744 if ( !al_3.isRoot() ) {
5747 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5748 p3.getNode( "l" ) );
5749 if ( !kl_3.getName().equals( "" ) ) {
5752 if ( !kl_3.isRoot() ) {
5755 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5756 p3.getNode( "l" ) );
5757 if ( !fl_3.getName().equals( "" ) ) {
5760 if ( !fl_3.isRoot() ) {
5763 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5764 p3.getNode( "k" ) );
5765 if ( !gk_3.getName().equals( "ghijk" ) ) {
5768 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5769 PhylogenyMethods.preOrderReId( p4 );
5770 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5771 p4.getNode( "c" ) );
5772 if ( !r_4.getName().equals( "r" ) ) {
5775 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5776 PhylogenyMethods.preOrderReId( p5 );
5777 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5778 p5.getNode( "c" ) );
5779 if ( !r_5.getName().equals( "root" ) ) {
5782 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5783 PhylogenyMethods.preOrderReId( p6 );
5784 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5785 p6.getNode( "a" ) );
5786 if ( !r_6.getName().equals( "rot" ) ) {
5789 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5790 PhylogenyMethods.preOrderReId( p7 );
5791 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5792 p7.getNode( "e" ) );
5793 if ( !r_7.getName().equals( "rott" ) ) {
5796 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5797 p7.getNode( "a" ) );
5798 if ( !r_71.getName().equals( "rott" ) ) {
5801 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5802 p7.getNode( "rott" ) );
5803 if ( !r_72.getName().equals( "rott" ) ) {
5806 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5807 p7.getNode( "a" ) );
5808 if ( !r_73.getName().equals( "rott" ) ) {
5811 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5812 p7.getNode( "rott" ) );
5813 if ( !r_74.getName().equals( "rott" ) ) {
5816 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5817 p7.getNode( "e" ) );
5818 if ( !r_75.getName().equals( "e" ) ) {
5822 catch ( final Exception e ) {
5823 e.printStackTrace( System.out );
5829 private static boolean testHmmscanOutputParser() {
5830 final String test_dir = Test.PATH_TO_TEST_DATA;
5832 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5833 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5835 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5836 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5837 final List<Protein> proteins = parser2.parse();
5838 if ( parser2.getProteinsEncountered() != 4 ) {
5841 if ( proteins.size() != 4 ) {
5844 if ( parser2.getDomainsEncountered() != 69 ) {
5847 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5850 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5853 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5856 final Protein p1 = proteins.get( 0 );
5857 if ( p1.getNumberOfProteinDomains() != 15 ) {
5860 if ( p1.getLength() != 850 ) {
5863 final Protein p2 = proteins.get( 1 );
5864 if ( p2.getNumberOfProteinDomains() != 51 ) {
5867 if ( p2.getLength() != 1291 ) {
5870 final Protein p3 = proteins.get( 2 );
5871 if ( p3.getNumberOfProteinDomains() != 2 ) {
5874 final Protein p4 = proteins.get( 3 );
5875 if ( p4.getNumberOfProteinDomains() != 1 ) {
5878 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5881 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5884 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5887 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5890 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5893 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5896 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5900 catch ( final Exception e ) {
5901 e.printStackTrace( System.out );
5907 private static boolean testLastExternalNodeMethods() {
5909 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5910 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5911 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5912 final PhylogenyNode n1 = t0.getNode( "A" );
5913 if ( n1.isLastExternalNode() ) {
5916 final PhylogenyNode n2 = t0.getNode( "B" );
5917 if ( n2.isLastExternalNode() ) {
5920 final PhylogenyNode n3 = t0.getNode( "C" );
5921 if ( n3.isLastExternalNode() ) {
5924 final PhylogenyNode n4 = t0.getNode( "D" );
5925 if ( !n4.isLastExternalNode() ) {
5929 catch ( final Exception e ) {
5930 e.printStackTrace( System.out );
5936 private static boolean testLevelOrderIterator() {
5938 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5939 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5940 PhylogenyNodeIterator it0;
5941 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5944 for( it0.reset(); it0.hasNext(); ) {
5947 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5948 if ( !it.next().getName().equals( "r" ) ) {
5951 if ( !it.next().getName().equals( "ab" ) ) {
5954 if ( !it.next().getName().equals( "cd" ) ) {
5957 if ( !it.next().getName().equals( "A" ) ) {
5960 if ( !it.next().getName().equals( "B" ) ) {
5963 if ( !it.next().getName().equals( "C" ) ) {
5966 if ( !it.next().getName().equals( "D" ) ) {
5969 if ( it.hasNext() ) {
5972 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",
5973 new NHXParser() )[ 0 ];
5974 PhylogenyNodeIterator it2;
5975 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5978 for( it2.reset(); it2.hasNext(); ) {
5981 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5982 if ( !it3.next().getName().equals( "r" ) ) {
5985 if ( !it3.next().getName().equals( "abc" ) ) {
5988 if ( !it3.next().getName().equals( "defg" ) ) {
5991 if ( !it3.next().getName().equals( "A" ) ) {
5994 if ( !it3.next().getName().equals( "B" ) ) {
5997 if ( !it3.next().getName().equals( "C" ) ) {
6000 if ( !it3.next().getName().equals( "D" ) ) {
6003 if ( !it3.next().getName().equals( "E" ) ) {
6006 if ( !it3.next().getName().equals( "F" ) ) {
6009 if ( !it3.next().getName().equals( "G" ) ) {
6012 if ( !it3.next().getName().equals( "1" ) ) {
6015 if ( !it3.next().getName().equals( "2" ) ) {
6018 if ( !it3.next().getName().equals( "3" ) ) {
6021 if ( !it3.next().getName().equals( "4" ) ) {
6024 if ( !it3.next().getName().equals( "5" ) ) {
6027 if ( !it3.next().getName().equals( "6" ) ) {
6030 if ( !it3.next().getName().equals( "f1" ) ) {
6033 if ( !it3.next().getName().equals( "f2" ) ) {
6036 if ( !it3.next().getName().equals( "f3" ) ) {
6039 if ( !it3.next().getName().equals( "a" ) ) {
6042 if ( !it3.next().getName().equals( "b" ) ) {
6045 if ( !it3.next().getName().equals( "f21" ) ) {
6048 if ( !it3.next().getName().equals( "X" ) ) {
6051 if ( !it3.next().getName().equals( "Y" ) ) {
6054 if ( !it3.next().getName().equals( "Z" ) ) {
6057 if ( it3.hasNext() ) {
6060 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
6061 PhylogenyNodeIterator it4;
6062 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
6065 for( it4.reset(); it4.hasNext(); ) {
6068 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
6069 if ( !it5.next().getName().equals( "r" ) ) {
6072 if ( !it5.next().getName().equals( "A" ) ) {
6075 if ( !it5.next().getName().equals( "B" ) ) {
6078 if ( !it5.next().getName().equals( "C" ) ) {
6081 if ( !it5.next().getName().equals( "D" ) ) {
6084 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
6085 PhylogenyNodeIterator it6;
6086 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
6089 for( it6.reset(); it6.hasNext(); ) {
6092 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
6093 if ( !it7.next().getName().equals( "A" ) ) {
6096 if ( it.hasNext() ) {
6100 catch ( final Exception e ) {
6101 e.printStackTrace( System.out );
6107 private static boolean testMafft( final String path ) {
6109 final List<String> opts = new ArrayList<String>();
6110 opts.add( "--maxiterate" );
6112 opts.add( "--localpair" );
6113 opts.add( "--quiet" );
6115 final MsaInferrer mafft = Mafft.createInstance( path );
6116 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
6117 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
6120 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
6124 catch ( final Exception e ) {
6125 e.printStackTrace( System.out );
6131 private static boolean testMidpointrooting() {
6133 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6134 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
6135 PhylogenyMethods.midpointRoot( t0 );
6136 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
6139 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
6142 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
6146 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",
6147 new NHXParser() )[ 0 ];
6148 if ( !t1.isRooted() ) {
6151 PhylogenyMethods.midpointRoot( t1 );
6152 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6155 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6158 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6161 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6164 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6167 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6170 t1.reRoot( t1.getNode( "A" ) );
6171 PhylogenyMethods.midpointRoot( t1 );
6172 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6175 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6178 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6181 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6184 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6188 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6192 catch ( final Exception e ) {
6193 e.printStackTrace( System.out );
6199 private static boolean testMsaQualityMethod() {
6201 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6202 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6203 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6204 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6205 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6210 final Msa msa = BasicMsa.createInstance( l );
6211 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6214 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6217 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6220 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6223 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6226 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6229 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6233 catch ( final Exception e ) {
6234 e.printStackTrace( System.out );
6240 private static boolean testMsaEntropy() {
6242 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
6243 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
6244 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
6245 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
6246 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6251 final Msa msa = BasicMsa.createInstance( l );
6252 //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
6254 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
6255 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
6256 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
6257 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
6258 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
6259 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
6260 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
6261 // System.out.println();
6262 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
6263 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
6264 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
6265 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
6266 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
6267 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
6268 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
6269 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6270 l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
6271 l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
6272 l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
6273 l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
6274 l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
6275 l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
6276 l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
6277 l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
6278 l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
6279 l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
6280 l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
6281 l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
6282 l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
6283 l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
6284 l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
6285 l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
6286 l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
6287 l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
6288 l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
6289 l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
6290 l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
6291 l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
6292 final Msa msa2 = BasicMsa.createInstance( l2 );
6293 // System.out.println();
6294 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
6295 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
6296 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
6298 catch ( final Exception e ) {
6299 e.printStackTrace( System.out );
6305 private static boolean testDeleteableMsa() {
6307 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
6308 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
6309 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
6310 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
6311 final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
6312 final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
6313 final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
6320 final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
6321 dmsa0.deleteRow( "b", false );
6322 if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
6325 dmsa0.deleteRow( "e", false );
6326 dmsa0.deleteRow( "a", false );
6327 dmsa0.deleteRow( "f", false );
6328 if ( dmsa0.getLength() != 4 ) {
6331 if ( dmsa0.getNumberOfSequences() != 2 ) {
6334 if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
6337 if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
6340 if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
6343 if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
6346 if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
6349 dmsa0.deleteRow( "c", false );
6350 dmsa0.deleteRow( "d", false );
6351 if ( dmsa0.getNumberOfSequences() != 0 ) {
6355 final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
6356 final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
6357 final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
6358 final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
6359 final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
6360 final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
6361 final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
6368 final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
6369 dmsa1.deleteGapOnlyColumns();
6370 dmsa1.deleteRow( "a", false );
6371 dmsa1.deleteRow( "f", false );
6372 dmsa1.deleteRow( "d", false );
6373 dmsa1.deleteGapOnlyColumns();
6374 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
6377 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
6380 if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
6383 dmsa1.deleteRow( "c", false );
6384 dmsa1.deleteGapOnlyColumns();
6385 final Writer w0 = new StringWriter();
6386 dmsa1.write( w0, MSA_FORMAT.FASTA );
6387 final Writer w1 = new StringWriter();
6388 dmsa1.write( w1, MSA_FORMAT.PHYLIP );
6389 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
6392 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
6395 final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
6396 final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
6397 final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
6398 final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
6399 final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
6400 final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
6401 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6408 final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
6409 dmsa2.deleteGapColumns( 0.5 );
6410 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
6413 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
6416 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
6419 dmsa2.deleteGapColumns( 0.2 );
6420 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
6423 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
6426 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
6429 dmsa2.deleteGapColumns( 0 );
6430 dmsa2.deleteRow( "a", false );
6431 dmsa2.deleteRow( "b", false );
6432 dmsa2.deleteRow( "f", false );
6433 dmsa2.deleteRow( "e", false );
6434 dmsa2.setIdentifier( 0, "new_c" );
6435 dmsa2.setIdentifier( 1, "new_d" );
6436 dmsa2.setResidueAt( 0, 0, 'x' );
6437 final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
6438 if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
6441 final Writer w = new StringWriter();
6442 dmsa2.write( w, MSA_FORMAT.PHYLIP );
6443 final String phylip = w.toString();
6444 if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
6445 System.out.println( phylip );
6448 final Writer w2 = new StringWriter();
6449 dmsa2.write( w2, MSA_FORMAT.FASTA );
6450 final String fasta = w2.toString();
6451 if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
6452 System.out.println( fasta );
6456 catch ( final Exception e ) {
6457 e.printStackTrace( System.out );
6463 private static boolean testNextNodeWithCollapsing() {
6465 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6467 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6468 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6469 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6470 t0.getNode( "cd" ).setCollapse( true );
6471 t0.getNode( "cde" ).setCollapse( true );
6472 n = t0.getFirstExternalNode();
6473 while ( n != null ) {
6475 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6477 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6480 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6483 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6486 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6489 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6492 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6496 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6497 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6498 t1.getNode( "ab" ).setCollapse( true );
6499 t1.getNode( "cd" ).setCollapse( true );
6500 t1.getNode( "cde" ).setCollapse( true );
6501 n = t1.getNode( "ab" );
6502 ext = new ArrayList<PhylogenyNode>();
6503 while ( n != null ) {
6505 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6507 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6510 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6513 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6516 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6519 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6523 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6524 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6525 t2.getNode( "ab" ).setCollapse( true );
6526 t2.getNode( "cd" ).setCollapse( true );
6527 t2.getNode( "cde" ).setCollapse( true );
6528 t2.getNode( "c" ).setCollapse( true );
6529 t2.getNode( "d" ).setCollapse( true );
6530 t2.getNode( "e" ).setCollapse( true );
6531 t2.getNode( "gh" ).setCollapse( true );
6532 n = t2.getNode( "ab" );
6533 ext = new ArrayList<PhylogenyNode>();
6534 while ( n != null ) {
6536 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6538 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6541 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6544 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6547 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6551 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6552 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6553 t3.getNode( "ab" ).setCollapse( true );
6554 t3.getNode( "cd" ).setCollapse( true );
6555 t3.getNode( "cde" ).setCollapse( true );
6556 t3.getNode( "c" ).setCollapse( true );
6557 t3.getNode( "d" ).setCollapse( true );
6558 t3.getNode( "e" ).setCollapse( true );
6559 t3.getNode( "gh" ).setCollapse( true );
6560 t3.getNode( "fgh" ).setCollapse( true );
6561 n = t3.getNode( "ab" );
6562 ext = new ArrayList<PhylogenyNode>();
6563 while ( n != null ) {
6565 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6567 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6570 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6573 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6577 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6578 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6579 t4.getNode( "ab" ).setCollapse( true );
6580 t4.getNode( "cd" ).setCollapse( true );
6581 t4.getNode( "cde" ).setCollapse( true );
6582 t4.getNode( "c" ).setCollapse( true );
6583 t4.getNode( "d" ).setCollapse( true );
6584 t4.getNode( "e" ).setCollapse( true );
6585 t4.getNode( "gh" ).setCollapse( true );
6586 t4.getNode( "fgh" ).setCollapse( true );
6587 t4.getNode( "abcdefgh" ).setCollapse( true );
6588 n = t4.getNode( "abcdefgh" );
6589 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6592 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6593 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6595 n = t5.getFirstExternalNode();
6596 while ( n != null ) {
6598 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6600 if ( ext.size() != 8 ) {
6603 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6606 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6609 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6612 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6615 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6618 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6621 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6624 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6627 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6628 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6630 t6.getNode( "ab" ).setCollapse( true );
6631 n = t6.getNode( "ab" );
6632 while ( n != null ) {
6634 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6636 if ( ext.size() != 7 ) {
6639 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6642 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6645 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6648 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6651 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6654 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6657 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6660 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6661 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6663 t7.getNode( "cd" ).setCollapse( true );
6664 n = t7.getNode( "a" );
6665 while ( n != null ) {
6667 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6669 if ( ext.size() != 7 ) {
6672 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6675 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6678 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6681 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6684 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6687 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6690 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6693 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6694 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6696 t8.getNode( "cd" ).setCollapse( true );
6697 t8.getNode( "c" ).setCollapse( true );
6698 t8.getNode( "d" ).setCollapse( true );
6699 n = t8.getNode( "a" );
6700 while ( n != null ) {
6702 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6704 if ( ext.size() != 7 ) {
6707 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6710 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6713 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6714 System.out.println( "2 fail" );
6717 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6720 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6723 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6726 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6729 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6730 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6732 t9.getNode( "gh" ).setCollapse( true );
6733 n = t9.getNode( "a" );
6734 while ( n != null ) {
6736 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6738 if ( ext.size() != 7 ) {
6741 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6744 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6747 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6750 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6753 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6756 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6759 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6762 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6763 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6765 t10.getNode( "gh" ).setCollapse( true );
6766 t10.getNode( "g" ).setCollapse( true );
6767 t10.getNode( "h" ).setCollapse( true );
6768 n = t10.getNode( "a" );
6769 while ( n != null ) {
6771 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6773 if ( ext.size() != 7 ) {
6776 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6779 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6782 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6785 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6788 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6791 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6794 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6797 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6798 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6800 t11.getNode( "gh" ).setCollapse( true );
6801 t11.getNode( "fgh" ).setCollapse( true );
6802 n = t11.getNode( "a" );
6803 while ( n != null ) {
6805 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6807 if ( ext.size() != 6 ) {
6810 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6813 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6816 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6819 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6822 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6825 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6828 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6829 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6831 t12.getNode( "gh" ).setCollapse( true );
6832 t12.getNode( "fgh" ).setCollapse( true );
6833 t12.getNode( "g" ).setCollapse( true );
6834 t12.getNode( "h" ).setCollapse( true );
6835 t12.getNode( "f" ).setCollapse( true );
6836 n = t12.getNode( "a" );
6837 while ( n != null ) {
6839 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6841 if ( ext.size() != 6 ) {
6844 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6847 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6850 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6853 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6856 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6859 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6862 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6863 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6865 t13.getNode( "ab" ).setCollapse( true );
6866 t13.getNode( "b" ).setCollapse( true );
6867 t13.getNode( "fgh" ).setCollapse( true );
6868 t13.getNode( "gh" ).setCollapse( true );
6869 n = t13.getNode( "ab" );
6870 while ( n != null ) {
6872 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6874 if ( ext.size() != 5 ) {
6877 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6880 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6883 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6886 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6889 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6892 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6893 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6895 t14.getNode( "ab" ).setCollapse( true );
6896 t14.getNode( "a" ).setCollapse( true );
6897 t14.getNode( "fgh" ).setCollapse( true );
6898 t14.getNode( "gh" ).setCollapse( true );
6899 n = t14.getNode( "ab" );
6900 while ( n != null ) {
6902 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6904 if ( ext.size() != 5 ) {
6907 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6910 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6913 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6916 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6919 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6922 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" );
6923 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6925 t15.getNode( "ab" ).setCollapse( true );
6926 t15.getNode( "a" ).setCollapse( true );
6927 t15.getNode( "fgh" ).setCollapse( true );
6928 t15.getNode( "gh" ).setCollapse( true );
6929 n = t15.getNode( "ab" );
6930 while ( n != null ) {
6932 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6934 if ( ext.size() != 6 ) {
6937 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6940 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6943 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6946 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6949 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6952 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6957 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" );
6958 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6960 t16.getNode( "ab" ).setCollapse( true );
6961 t16.getNode( "a" ).setCollapse( true );
6962 t16.getNode( "fgh" ).setCollapse( true );
6963 t16.getNode( "gh" ).setCollapse( true );
6964 t16.getNode( "cd" ).setCollapse( true );
6965 t16.getNode( "cde" ).setCollapse( true );
6966 t16.getNode( "d" ).setCollapse( true );
6967 t16.getNode( "x" ).setCollapse( true );
6968 n = t16.getNode( "ab" );
6969 while ( n != null ) {
6971 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6973 if ( ext.size() != 4 ) {
6976 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6979 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6982 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6985 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6989 catch ( final Exception e ) {
6990 e.printStackTrace( System.out );
6996 private static boolean testNexusCharactersParsing() {
6998 final NexusCharactersParser parser = new NexusCharactersParser();
6999 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
7001 String[] labels = parser.getCharStateLabels();
7002 if ( labels.length != 7 ) {
7005 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7008 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7011 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7014 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7017 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7020 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7023 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7026 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7028 labels = parser.getCharStateLabels();
7029 if ( labels.length != 7 ) {
7032 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7035 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7038 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7041 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7044 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7047 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7050 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7054 catch ( final Exception e ) {
7055 e.printStackTrace( System.out );
7061 private static boolean testNexusMatrixParsing() {
7063 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
7064 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
7066 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
7067 if ( m.getNumberOfCharacters() != 9 ) {
7070 if ( m.getNumberOfIdentifiers() != 5 ) {
7073 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
7076 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
7079 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
7082 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
7085 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
7088 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
7091 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
7094 // if ( labels.length != 7 ) {
7097 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7100 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7103 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7106 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7109 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7112 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7115 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7118 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7120 // labels = parser.getCharStateLabels();
7121 // if ( labels.length != 7 ) {
7124 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7127 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7130 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7133 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7136 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7139 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7142 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7146 catch ( final Exception e ) {
7147 e.printStackTrace( System.out );
7153 private static boolean testNexusTreeParsing() {
7155 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7156 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7157 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
7158 if ( phylogenies.length != 1 ) {
7161 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
7164 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7168 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
7169 if ( phylogenies.length != 1 ) {
7172 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7175 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
7179 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
7180 if ( phylogenies.length != 1 ) {
7183 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7186 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7189 if ( phylogenies[ 0 ].isRooted() ) {
7193 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
7194 if ( phylogenies.length != 18 ) {
7197 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7200 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
7203 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
7206 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
7209 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7212 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
7215 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
7218 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
7221 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
7224 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
7227 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
7230 if ( phylogenies[ 8 ].isRooted() ) {
7233 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
7236 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
7239 if ( !phylogenies[ 9 ].isRooted() ) {
7242 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
7245 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
7248 if ( !phylogenies[ 10 ].isRooted() ) {
7251 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
7254 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
7257 if ( phylogenies[ 11 ].isRooted() ) {
7260 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
7263 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
7266 if ( !phylogenies[ 12 ].isRooted() ) {
7269 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
7272 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
7275 if ( !phylogenies[ 13 ].isRooted() ) {
7278 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
7281 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
7284 if ( !phylogenies[ 14 ].isRooted() ) {
7287 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
7290 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
7293 if ( phylogenies[ 15 ].isRooted() ) {
7296 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
7299 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
7302 if ( !phylogenies[ 16 ].isRooted() ) {
7305 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
7308 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
7311 if ( phylogenies[ 17 ].isRooted() ) {
7314 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
7317 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7319 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
7320 if ( phylogenies.length != 9 ) {
7323 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
7324 .getDistanceToParent() ) ) {
7327 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
7328 .getDistanceToParent() ) ) {
7331 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
7334 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7337 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7340 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7343 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7347 catch ( final Exception e ) {
7348 e.printStackTrace( System.out );
7354 private static boolean testNexusTreeParsingIterating() {
7356 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7357 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7358 if ( !p.hasNext() ) {
7361 Phylogeny phy = p.next();
7362 if ( phy == null ) {
7365 if ( phy.getNumberOfExternalNodes() != 25 ) {
7368 if ( !phy.getName().equals( "" ) ) {
7371 if ( p.hasNext() ) {
7375 if ( phy != null ) {
7379 if ( !p.hasNext() ) {
7383 if ( phy == null ) {
7386 if ( phy.getNumberOfExternalNodes() != 25 ) {
7389 if ( !phy.getName().equals( "" ) ) {
7392 if ( p.hasNext() ) {
7396 if ( phy != null ) {
7399 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7400 if ( !p.hasNext() ) {
7404 if ( phy == null ) {
7407 if ( phy.getNumberOfExternalNodes() != 10 ) {
7410 if ( !phy.getName().equals( "name" ) ) {
7413 if ( p.hasNext() ) {
7417 if ( phy != null ) {
7421 if ( !p.hasNext() ) {
7425 if ( phy == null ) {
7428 if ( phy.getNumberOfExternalNodes() != 10 ) {
7431 if ( !phy.getName().equals( "name" ) ) {
7434 if ( p.hasNext() ) {
7438 if ( phy != null ) {
7441 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7442 if ( !p.hasNext() ) {
7446 if ( phy == null ) {
7449 if ( phy.getNumberOfExternalNodes() != 3 ) {
7452 if ( !phy.getName().equals( "" ) ) {
7455 if ( phy.isRooted() ) {
7458 if ( p.hasNext() ) {
7462 if ( phy != null ) {
7467 if ( !p.hasNext() ) {
7471 if ( phy == null ) {
7474 if ( phy.getNumberOfExternalNodes() != 3 ) {
7477 if ( !phy.getName().equals( "" ) ) {
7480 if ( p.hasNext() ) {
7484 if ( phy != null ) {
7488 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7489 if ( !p.hasNext() ) {
7494 if ( phy == null ) {
7497 if ( phy.getNumberOfExternalNodes() != 10 ) {
7500 if ( !phy.getName().equals( "tree 0" ) ) {
7504 if ( !p.hasNext() ) {
7508 if ( phy == null ) {
7511 if ( phy.getNumberOfExternalNodes() != 10 ) {
7514 if ( !phy.getName().equals( "tree 1" ) ) {
7518 if ( !p.hasNext() ) {
7522 if ( phy == null ) {
7525 if ( phy.getNumberOfExternalNodes() != 3 ) {
7526 System.out.println( phy.toString() );
7529 if ( !phy.getName().equals( "" ) ) {
7532 if ( phy.isRooted() ) {
7536 if ( !p.hasNext() ) {
7540 if ( phy == null ) {
7543 if ( phy.getNumberOfExternalNodes() != 4 ) {
7546 if ( !phy.getName().equals( "" ) ) {
7549 if ( !phy.isRooted() ) {
7553 if ( !p.hasNext() ) {
7557 if ( phy == null ) {
7560 if ( phy.getNumberOfExternalNodes() != 5 ) {
7561 System.out.println( phy.getNumberOfExternalNodes() );
7564 if ( !phy.getName().equals( "" ) ) {
7567 if ( !phy.isRooted() ) {
7571 if ( !p.hasNext() ) {
7575 if ( phy == null ) {
7578 if ( phy.getNumberOfExternalNodes() != 3 ) {
7581 if ( !phy.getName().equals( "" ) ) {
7584 if ( phy.isRooted() ) {
7588 if ( !p.hasNext() ) {
7592 if ( phy == null ) {
7595 if ( phy.getNumberOfExternalNodes() != 2 ) {
7598 if ( !phy.getName().equals( "" ) ) {
7601 if ( !phy.isRooted() ) {
7605 if ( !p.hasNext() ) {
7609 if ( phy.getNumberOfExternalNodes() != 3 ) {
7612 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7615 if ( !phy.isRooted() ) {
7619 if ( !p.hasNext() ) {
7623 if ( phy.getNumberOfExternalNodes() != 3 ) {
7626 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7629 if ( !phy.getName().equals( "tree 8" ) ) {
7633 if ( !p.hasNext() ) {
7637 if ( phy.getNumberOfExternalNodes() != 3 ) {
7640 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7643 if ( !phy.getName().equals( "tree 9" ) ) {
7647 if ( !p.hasNext() ) {
7651 if ( phy.getNumberOfExternalNodes() != 3 ) {
7654 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7657 if ( !phy.getName().equals( "tree 10" ) ) {
7660 if ( !phy.isRooted() ) {
7664 if ( !p.hasNext() ) {
7668 if ( phy.getNumberOfExternalNodes() != 3 ) {
7671 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7674 if ( !phy.getName().equals( "tree 11" ) ) {
7677 if ( phy.isRooted() ) {
7681 if ( !p.hasNext() ) {
7685 if ( phy.getNumberOfExternalNodes() != 3 ) {
7688 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7691 if ( !phy.getName().equals( "tree 12" ) ) {
7694 if ( !phy.isRooted() ) {
7698 if ( !p.hasNext() ) {
7702 if ( phy.getNumberOfExternalNodes() != 3 ) {
7705 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7708 if ( !phy.getName().equals( "tree 13" ) ) {
7711 if ( !phy.isRooted() ) {
7715 if ( !p.hasNext() ) {
7719 if ( phy.getNumberOfExternalNodes() != 10 ) {
7720 System.out.println( phy.getNumberOfExternalNodes() );
7725 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7726 System.out.println( phy.toNewHampshire() );
7729 if ( !phy.getName().equals( "tree 14" ) ) {
7732 if ( !phy.isRooted() ) {
7736 if ( !p.hasNext() ) {
7740 if ( phy.getNumberOfExternalNodes() != 10 ) {
7741 System.out.println( phy.getNumberOfExternalNodes() );
7746 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7747 System.out.println( phy.toNewHampshire() );
7750 if ( !phy.getName().equals( "tree 15" ) ) {
7753 if ( phy.isRooted() ) {
7757 if ( !p.hasNext() ) {
7761 if ( phy.getNumberOfExternalNodes() != 10 ) {
7762 System.out.println( phy.getNumberOfExternalNodes() );
7767 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
7768 System.out.println( phy.toNewHampshire() );
7771 if ( !phy.getName().equals( "tree 16" ) ) {
7774 if ( !phy.isRooted() ) {
7778 if ( !p.hasNext() ) {
7782 if ( phy.getNumberOfExternalNodes() != 10 ) {
7783 System.out.println( phy.getNumberOfExternalNodes() );
7788 .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;" ) ) {
7789 System.out.println( phy.toNewHampshire() );
7792 if ( !phy.getName().equals( "tree 17" ) ) {
7795 if ( phy.isRooted() ) {
7799 if ( p.hasNext() ) {
7803 if ( phy != null ) {
7808 if ( !p.hasNext() ) {
7812 if ( phy == null ) {
7815 if ( phy.getNumberOfExternalNodes() != 10 ) {
7818 if ( !phy.getName().equals( "tree 0" ) ) {
7822 if ( !p.hasNext() ) {
7826 if ( phy == null ) {
7829 if ( phy.getNumberOfExternalNodes() != 10 ) {
7832 if ( !phy.getName().equals( "tree 1" ) ) {
7836 if ( !p.hasNext() ) {
7840 if ( phy == null ) {
7843 if ( phy.getNumberOfExternalNodes() != 3 ) {
7846 if ( !phy.getName().equals( "" ) ) {
7849 if ( phy.isRooted() ) {
7853 if ( !p.hasNext() ) {
7857 if ( phy == null ) {
7860 if ( phy.getNumberOfExternalNodes() != 4 ) {
7863 if ( !phy.getName().equals( "" ) ) {
7866 if ( !phy.isRooted() ) {
7870 if ( !p.hasNext() ) {
7874 if ( phy == null ) {
7877 if ( phy.getNumberOfExternalNodes() != 5 ) {
7878 System.out.println( phy.getNumberOfExternalNodes() );
7881 if ( !phy.getName().equals( "" ) ) {
7884 if ( !phy.isRooted() ) {
7888 if ( !p.hasNext() ) {
7892 if ( phy == null ) {
7895 if ( phy.getNumberOfExternalNodes() != 3 ) {
7898 if ( !phy.getName().equals( "" ) ) {
7901 if ( phy.isRooted() ) {
7905 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7906 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7908 if ( !p2.hasNext() ) {
7912 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7915 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7919 if ( !p2.hasNext() ) {
7924 if ( !p2.hasNext() ) {
7929 if ( !p2.hasNext() ) {
7934 if ( !p2.hasNext() ) {
7939 if ( !p2.hasNext() ) {
7944 if ( !p2.hasNext() ) {
7949 if ( !p2.hasNext() ) {
7954 if ( !p2.hasNext() ) {
7958 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7961 if ( p2.hasNext() ) {
7965 if ( phy != null ) {
7970 if ( !p2.hasNext() ) {
7974 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7977 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7981 catch ( final Exception e ) {
7982 e.printStackTrace( System.out );
7988 private static boolean testNexusTreeParsingTranslating() {
7990 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7991 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7992 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7993 if ( phylogenies.length != 1 ) {
7996 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7999 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8002 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8005 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8008 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8009 .equals( "Aranaeus" ) ) {
8013 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
8014 if ( phylogenies.length != 3 ) {
8017 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8020 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8023 if ( phylogenies[ 0 ].isRooted() ) {
8026 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8029 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8032 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8033 .equals( "Aranaeus" ) ) {
8036 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8039 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8042 if ( phylogenies[ 1 ].isRooted() ) {
8045 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8048 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8051 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8052 .equals( "Aranaeus" ) ) {
8055 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8058 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8061 if ( !phylogenies[ 2 ].isRooted() ) {
8064 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8067 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8070 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8071 .equals( "Aranaeus" ) ) {
8075 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
8076 if ( phylogenies.length != 3 ) {
8079 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8082 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8085 if ( phylogenies[ 0 ].isRooted() ) {
8088 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8091 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8094 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8095 .equals( "Aranaeus" ) ) {
8098 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8101 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8104 if ( phylogenies[ 1 ].isRooted() ) {
8107 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8110 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8113 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8114 .equals( "Aranaeus" ) ) {
8117 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8120 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8123 if ( !phylogenies[ 2 ].isRooted() ) {
8126 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8129 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8132 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8133 .equals( "Aranaeus" ) ) {
8136 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
8137 if ( phylogenies.length != 3 ) {
8140 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
8145 catch ( final Exception e ) {
8146 e.printStackTrace( System.out );
8152 private static boolean testNHParsing() {
8154 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8155 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
8156 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
8159 final NHXParser nhxp = new NHXParser();
8160 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
8161 nhxp.setReplaceUnderscores( true );
8162 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
8163 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
8166 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
8169 final Phylogeny p1b = factory
8170 .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 ",
8171 new NHXParser() )[ 0 ];
8172 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
8175 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
8178 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
8179 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
8180 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
8181 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
8182 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
8183 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
8184 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
8185 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
8186 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
8187 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
8188 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
8189 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
8190 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
8192 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
8195 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
8198 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
8201 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
8204 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
8205 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
8206 final String p16_S = "((A,B),C)";
8207 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
8208 if ( p16.length != 1 ) {
8211 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
8214 final String p17_S = "(C,(A,B))";
8215 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
8216 if ( p17.length != 1 ) {
8219 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
8222 final String p18_S = "((A,B),(C,D))";
8223 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
8224 if ( p18.length != 1 ) {
8227 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
8230 final String p19_S = "(((A,B),C),D)";
8231 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
8232 if ( p19.length != 1 ) {
8235 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
8238 final String p20_S = "(A,(B,(C,D)))";
8239 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
8240 if ( p20.length != 1 ) {
8243 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
8246 final String p21_S = "(A,(B,(C,(D,E))))";
8247 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
8248 if ( p21.length != 1 ) {
8251 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
8254 final String p22_S = "((((A,B),C),D),E)";
8255 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
8256 if ( p22.length != 1 ) {
8259 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
8262 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8263 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
8264 if ( p23.length != 1 ) {
8265 System.out.println( "xl=" + p23.length );
8269 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
8272 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8273 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
8274 if ( p24.length != 1 ) {
8277 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
8280 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8281 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8282 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
8283 if ( p241.length != 2 ) {
8286 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
8289 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
8292 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
8293 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
8294 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
8295 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
8296 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
8297 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
8298 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
8299 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
8300 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
8301 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
8304 final String p26_S = "(A,B)ab";
8305 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
8306 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
8309 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8310 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
8311 if ( p27s.length != 1 ) {
8312 System.out.println( "xxl=" + p27s.length );
8316 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8317 System.out.println( p27s[ 0 ].toNewHampshireX() );
8321 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
8323 if ( p27.length != 1 ) {
8324 System.out.println( "yl=" + p27.length );
8328 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8329 System.out.println( p27[ 0 ].toNewHampshireX() );
8333 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8334 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8335 final String p28_S3 = "(A,B)ab";
8336 final String p28_S4 = "((((A,B),C),D),;E;)";
8337 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
8339 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
8342 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
8345 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
8348 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
8351 if ( p28.length != 4 ) {
8354 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";
8355 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8356 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8359 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";
8360 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8361 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8364 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8365 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8366 if ( ( p32.length != 0 ) ) {
8369 final String p33_S = "A";
8370 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8371 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8374 final String p34_S = "B;";
8375 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8376 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8379 final String p35_S = "B:0.2";
8380 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8381 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8384 final String p36_S = "(A)";
8385 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8386 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8389 final String p37_S = "((A))";
8390 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8391 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8394 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8395 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8396 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8399 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8400 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8401 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8404 final String p40_S = "(A,B,C)";
8405 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8406 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8409 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8410 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8411 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8414 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8415 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8416 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8419 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)";
8420 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8421 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8424 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)))";
8425 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8426 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8429 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8430 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8431 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8434 final String p46_S = "";
8435 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8436 if ( p46.length != 0 ) {
8439 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8440 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8443 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8444 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8447 final Phylogeny p49 = factory
8448 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8449 new NHXParser() )[ 0 ];
8450 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8453 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8454 if ( p50.getNode( "A" ) == null ) {
8457 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8458 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8461 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8464 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8465 .equals( "((A,B)88:2.0,C);" ) ) {
8468 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8469 if ( p51.getNode( "A(A" ) == null ) {
8472 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8473 if ( p52.getNode( "A(A" ) == null ) {
8476 final Phylogeny p53 = factory
8477 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8478 new NHXParser() )[ 0 ];
8479 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8482 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8483 if ( p54.getNode( "A" ) == null ) {
8486 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8489 final Phylogeny p55 = factory
8490 .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);" ),
8491 new NHXParser() )[ 0 ];
8494 .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);" ) ) {
8495 System.out.println( p55.toNewHampshire() );
8498 final Phylogeny p56 = factory
8499 .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);" ),
8500 new NHXParser() )[ 0 ];
8503 .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);" ) ) {
8504 System.out.println( p56.toNewHampshire() );
8507 final Phylogeny p57 = factory
8508 .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);" ),
8509 new NHXParser() )[ 0 ];
8512 .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);" ) ) {
8513 System.out.println( p56.toNewHampshire() );
8516 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8517 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8518 if ( !p58.toNewHampshire().equals( s58 ) ) {
8519 System.out.println( p58.toNewHampshire() );
8522 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8523 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8524 if ( !p59.toNewHampshire().equals( s59 ) ) {
8525 System.out.println( p59.toNewHampshire() );
8528 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8529 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8530 if ( !p60.toNewHampshire().equals( s60 ) ) {
8531 System.out.println( p60.toNewHampshire() );
8534 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8535 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8536 if ( !p61.toNewHampshire()
8537 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8538 System.out.println( p61.toNewHampshire() );
8542 catch ( final Exception e ) {
8543 e.printStackTrace( System.out );
8549 private static boolean testNHParsingIter() {
8551 final String p0_str = "(A,B);";
8552 final NHXParser p = new NHXParser();
8553 p.setSource( p0_str );
8554 if ( !p.hasNext() ) {
8557 final Phylogeny p0 = p.next();
8558 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8559 System.out.println( p0.toNewHampshire() );
8562 if ( p.hasNext() ) {
8565 if ( p.next() != null ) {
8569 final String p00_str = "(A,B)root;";
8570 p.setSource( p00_str );
8571 final Phylogeny p00 = p.next();
8572 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8573 System.out.println( p00.toNewHampshire() );
8577 final String p000_str = "A;";
8578 p.setSource( p000_str );
8579 final Phylogeny p000 = p.next();
8580 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8581 System.out.println( p000.toNewHampshire() );
8585 final String p0000_str = "A";
8586 p.setSource( p0000_str );
8587 final Phylogeny p0000 = p.next();
8588 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8589 System.out.println( p0000.toNewHampshire() );
8593 p.setSource( "(A)" );
8594 final Phylogeny p00000 = p.next();
8595 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8596 System.out.println( p00000.toNewHampshire() );
8600 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8601 p.setSource( p1_str );
8602 if ( !p.hasNext() ) {
8605 final Phylogeny p1_0 = p.next();
8606 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8607 System.out.println( p1_0.toNewHampshire() );
8610 if ( !p.hasNext() ) {
8613 final Phylogeny p1_1 = p.next();
8614 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8615 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8618 if ( !p.hasNext() ) {
8621 final Phylogeny p1_2 = p.next();
8622 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8623 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8626 if ( !p.hasNext() ) {
8629 final Phylogeny p1_3 = p.next();
8630 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8631 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8634 if ( p.hasNext() ) {
8637 if ( p.next() != null ) {
8641 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8642 p.setSource( p2_str );
8643 if ( !p.hasNext() ) {
8646 Phylogeny p2_0 = p.next();
8647 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8648 System.out.println( p2_0.toNewHampshire() );
8651 if ( !p.hasNext() ) {
8654 Phylogeny p2_1 = p.next();
8655 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8656 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8659 if ( !p.hasNext() ) {
8662 Phylogeny p2_2 = p.next();
8663 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8664 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8667 if ( !p.hasNext() ) {
8670 Phylogeny p2_3 = p.next();
8671 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8672 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8675 if ( !p.hasNext() ) {
8678 Phylogeny p2_4 = p.next();
8679 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8680 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8683 if ( p.hasNext() ) {
8686 if ( p.next() != null ) {
8691 if ( !p.hasNext() ) {
8695 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8696 System.out.println( p2_0.toNewHampshire() );
8699 if ( !p.hasNext() ) {
8703 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8704 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8707 if ( !p.hasNext() ) {
8711 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8712 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8715 if ( !p.hasNext() ) {
8719 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8720 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8723 if ( !p.hasNext() ) {
8727 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8728 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8731 if ( p.hasNext() ) {
8734 if ( p.next() != null ) {
8738 final String p3_str = "((A,B),C)abc";
8739 p.setSource( p3_str );
8740 if ( !p.hasNext() ) {
8743 final Phylogeny p3_0 = p.next();
8744 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8747 if ( p.hasNext() ) {
8750 if ( p.next() != null ) {
8754 final String p4_str = "((A,B)ab,C)abc";
8755 p.setSource( p4_str );
8756 if ( !p.hasNext() ) {
8759 final Phylogeny p4_0 = p.next();
8760 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8763 if ( p.hasNext() ) {
8766 if ( p.next() != null ) {
8770 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8771 p.setSource( p5_str );
8772 if ( !p.hasNext() ) {
8775 final Phylogeny p5_0 = p.next();
8776 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8779 if ( p.hasNext() ) {
8782 if ( p.next() != null ) {
8786 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8787 p.setSource( p6_str );
8788 if ( !p.hasNext() ) {
8791 Phylogeny p6_0 = p.next();
8792 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8795 if ( p.hasNext() ) {
8798 if ( p.next() != null ) {
8802 if ( !p.hasNext() ) {
8806 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8809 if ( p.hasNext() ) {
8812 if ( p.next() != null ) {
8816 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8817 p.setSource( p7_str );
8818 if ( !p.hasNext() ) {
8821 Phylogeny p7_0 = p.next();
8822 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8825 if ( p.hasNext() ) {
8828 if ( p.next() != null ) {
8832 if ( !p.hasNext() ) {
8836 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8839 if ( p.hasNext() ) {
8842 if ( p.next() != null ) {
8846 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8847 p.setSource( p8_str );
8848 if ( !p.hasNext() ) {
8851 Phylogeny p8_0 = p.next();
8852 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8855 if ( !p.hasNext() ) {
8858 if ( !p.hasNext() ) {
8861 Phylogeny p8_1 = p.next();
8862 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8865 if ( p.hasNext() ) {
8868 if ( p.next() != null ) {
8872 if ( !p.hasNext() ) {
8876 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8879 if ( !p.hasNext() ) {
8883 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8886 if ( p.hasNext() ) {
8889 if ( p.next() != null ) {
8895 if ( p.hasNext() ) {
8899 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8900 if ( !p.hasNext() ) {
8903 Phylogeny p_27 = p.next();
8904 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8905 System.out.println( p_27.toNewHampshireX() );
8909 if ( p.hasNext() ) {
8912 if ( p.next() != null ) {
8916 if ( !p.hasNext() ) {
8920 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8921 System.out.println( p_27.toNewHampshireX() );
8925 if ( p.hasNext() ) {
8928 if ( p.next() != null ) {
8932 final String p30_str = "(A,B);(C,D)";
8933 final NHXParser p30 = new NHXParser();
8934 p30.setSource( p30_str );
8935 if ( !p30.hasNext() ) {
8938 Phylogeny phy30 = p30.next();
8939 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8940 System.out.println( phy30.toNewHampshire() );
8943 if ( !p30.hasNext() ) {
8946 Phylogeny phy301 = p30.next();
8947 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8948 System.out.println( phy301.toNewHampshire() );
8951 if ( p30.hasNext() ) {
8954 if ( p30.hasNext() ) {
8957 if ( p30.next() != null ) {
8960 if ( p30.next() != null ) {
8964 if ( !p30.hasNext() ) {
8968 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8969 System.out.println( phy30.toNewHampshire() );
8972 if ( !p30.hasNext() ) {
8975 phy301 = p30.next();
8976 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8977 System.out.println( phy301.toNewHampshire() );
8980 if ( p30.hasNext() ) {
8983 if ( p30.hasNext() ) {
8986 if ( p30.next() != null ) {
8989 if ( p30.next() != null ) {
8993 catch ( final Exception e ) {
8994 e.printStackTrace( System.out );
9000 private static boolean testNHXconversion() {
9002 final PhylogenyNode n1 = new PhylogenyNode();
9003 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9004 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9005 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9006 final PhylogenyNode n5 = PhylogenyNode
9007 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
9008 final PhylogenyNode n6 = PhylogenyNode
9009 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
9010 if ( !n1.toNewHampshireX().equals( "" ) ) {
9013 if ( !n2.toNewHampshireX().equals( "" ) ) {
9016 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
9019 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
9022 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
9025 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
9026 System.out.println( n6.toNewHampshireX() );
9029 final PhylogenyNode n7 = new PhylogenyNode();
9030 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
9031 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
9032 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
9033 System.out.println( n7
9034 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
9038 catch ( final Exception e ) {
9039 e.printStackTrace( System.out );
9045 private static boolean testNHXNodeParsing() {
9047 final PhylogenyNode n1 = new PhylogenyNode();
9048 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9049 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9050 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9051 final PhylogenyNode n5 = PhylogenyNode
9052 .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]" );
9053 if ( !n3.getName().equals( "n3" ) ) {
9056 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9059 if ( n3.isDuplication() ) {
9062 if ( n3.isHasAssignedEvent() ) {
9065 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
9068 if ( !n4.getName().equals( "n4" ) ) {
9071 if ( n4.getDistanceToParent() != 0.01 ) {
9074 if ( !n5.getName().equals( "n5" ) ) {
9077 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
9080 if ( n5.getDistanceToParent() != 0.1 ) {
9083 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
9086 if ( !n5.isDuplication() ) {
9089 if ( !n5.isHasAssignedEvent() ) {
9092 final PhylogenyNode n8 = PhylogenyNode
9093 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
9094 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9095 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9098 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
9101 final PhylogenyNode n9 = PhylogenyNode
9102 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
9103 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9104 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
9107 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
9110 final PhylogenyNode n10 = PhylogenyNode
9111 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9112 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
9115 final PhylogenyNode n20 = PhylogenyNode
9116 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9117 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9120 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
9123 final PhylogenyNode n20x = PhylogenyNode
9124 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9125 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
9128 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
9131 final PhylogenyNode n20xx = PhylogenyNode
9132 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9133 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
9136 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
9139 final PhylogenyNode n20xxx = PhylogenyNode
9140 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9141 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
9144 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
9147 final PhylogenyNode n20xxxx = PhylogenyNode
9148 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9149 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
9152 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
9155 final PhylogenyNode n21 = PhylogenyNode
9156 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9157 if ( !n21.getName().equals( "N21_PIG" ) ) {
9160 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
9163 final PhylogenyNode n21x = PhylogenyNode
9164 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9165 if ( !n21x.getName().equals( "n21_PIG" ) ) {
9168 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
9171 final PhylogenyNode n22 = PhylogenyNode
9172 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9173 if ( !n22.getName().equals( "n22/PIG" ) ) {
9176 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
9179 final PhylogenyNode n23 = PhylogenyNode
9180 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9181 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
9184 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
9187 final PhylogenyNode a = PhylogenyNode
9188 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9189 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9192 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
9195 final PhylogenyNode c1 = PhylogenyNode
9196 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
9197 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9198 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
9201 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
9204 final PhylogenyNode c2 = PhylogenyNode
9205 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
9206 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9207 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
9210 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
9213 final PhylogenyNode e3 = PhylogenyNode
9214 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9215 if ( !e3.getName().equals( "n10_RAT~" ) ) {
9218 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
9221 final PhylogenyNode n11 = PhylogenyNode
9222 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
9223 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9224 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
9227 if ( n11.getDistanceToParent() != 0.4 ) {
9230 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
9233 final PhylogenyNode n12 = PhylogenyNode
9234 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
9235 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9236 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
9239 if ( n12.getDistanceToParent() != 0.4 ) {
9242 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
9245 final PhylogenyNode o = PhylogenyNode
9246 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9247 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
9250 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
9253 if ( n1.getName().compareTo( "" ) != 0 ) {
9256 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9259 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9262 if ( n2.getName().compareTo( "" ) != 0 ) {
9265 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9268 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9271 final PhylogenyNode n00 = PhylogenyNode
9272 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
9273 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
9276 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
9279 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
9280 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
9283 final PhylogenyNode n13 = PhylogenyNode
9284 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9285 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
9288 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
9291 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9294 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9297 final PhylogenyNode n14 = PhylogenyNode
9298 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9299 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
9302 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
9305 final PhylogenyNode n15 = PhylogenyNode
9306 .createInstanceFromNhxString( "something_wicked[123]",
9307 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9308 if ( !n15.getName().equals( "something_wicked" ) ) {
9311 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
9314 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
9317 final PhylogenyNode n16 = PhylogenyNode
9318 .createInstanceFromNhxString( "something_wicked2[9]",
9319 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9320 if ( !n16.getName().equals( "something_wicked2" ) ) {
9323 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
9326 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
9329 final PhylogenyNode n17 = PhylogenyNode
9330 .createInstanceFromNhxString( "something_wicked3[a]",
9331 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9332 if ( !n17.getName().equals( "something_wicked3" ) ) {
9335 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
9338 final PhylogenyNode n18 = PhylogenyNode
9339 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9340 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
9343 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
9346 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
9349 final PhylogenyNode n19 = PhylogenyNode
9350 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9351 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9354 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9357 final PhylogenyNode n30 = PhylogenyNode
9358 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9359 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9360 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9363 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9366 final PhylogenyNode n31 = PhylogenyNode
9367 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9368 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9369 if ( n31.getNodeData().isHasTaxonomy() ) {
9372 final PhylogenyNode n32 = PhylogenyNode
9373 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9374 if ( n32.getNodeData().isHasTaxonomy() ) {
9377 final PhylogenyNode n40 = PhylogenyNode
9378 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9379 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9382 final PhylogenyNode n41 = PhylogenyNode
9383 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9384 if ( n41.getNodeData().isHasTaxonomy() ) {
9387 final PhylogenyNode n42 = PhylogenyNode
9388 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9389 if ( n42.getNodeData().isHasTaxonomy() ) {
9392 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9393 NHXParser.TAXONOMY_EXTRACTION.NO );
9394 if ( n43.getNodeData().isHasTaxonomy() ) {
9397 final PhylogenyNode n44 = PhylogenyNode
9398 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9399 if ( n44.getNodeData().isHasTaxonomy() ) {
9403 catch ( final Exception e ) {
9404 e.printStackTrace( System.out );
9410 private static boolean testNHXParsing() {
9412 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9413 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9414 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9417 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]";
9418 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9419 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9422 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]";
9423 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9424 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9427 final Phylogeny[] p3 = factory
9428 .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]",
9430 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9433 final Phylogeny[] p4 = factory
9434 .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(]",
9436 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9439 final Phylogeny[] p5 = factory
9440 .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(((]",
9442 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9445 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)";
9446 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)";
9447 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9448 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9451 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)))";
9452 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)))";
9453 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9454 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9457 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]) ))[,,, ])))))))";
9458 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9459 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9460 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9463 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9464 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9467 final Phylogeny p10 = factory
9468 .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]",
9469 new NHXParser() )[ 0 ];
9470 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9473 final Phylogeny p11 = factory
9474 .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]",
9475 new NHXParser() )[ 0 ];
9476 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9479 final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
9480 new NHXParser() )[ 0 ];
9481 if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9485 catch ( final Exception e ) {
9486 e.printStackTrace( System.out );
9492 private static boolean testNHXParsingMB() {
9494 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9495 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9496 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9497 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9498 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9499 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9500 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9501 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9502 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9503 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9504 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9507 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9510 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9511 0.1100000000000000e+00 ) ) {
9514 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9517 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9520 final Phylogeny p2 = factory
9521 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9522 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9523 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9524 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9525 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9526 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9527 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9528 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9529 + "7.369400000000000e-02}])",
9530 new NHXParser() )[ 0 ];
9531 if ( p2.getNode( "1" ) == null ) {
9534 if ( p2.getNode( "2" ) == null ) {
9538 catch ( final Exception e ) {
9539 e.printStackTrace( System.out );
9546 private static boolean testNHXParsingQuotes() {
9548 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9549 final NHXParser p = new NHXParser();
9550 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9551 if ( phylogenies_0.length != 5 ) {
9554 final Phylogeny phy = phylogenies_0[ 4 ];
9555 if ( phy.getNumberOfExternalNodes() != 7 ) {
9558 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9561 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9564 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9565 .getScientificName().equals( "hsapiens" ) ) {
9568 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9571 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9574 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9577 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9580 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9583 final NHXParser p1p = new NHXParser();
9584 p1p.setIgnoreQuotes( true );
9585 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9586 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9589 final NHXParser p2p = new NHXParser();
9590 p1p.setIgnoreQuotes( false );
9591 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9592 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9595 final NHXParser p3p = new NHXParser();
9596 p3p.setIgnoreQuotes( false );
9597 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9598 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9601 final NHXParser p4p = new NHXParser();
9602 p4p.setIgnoreQuotes( false );
9603 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9604 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9607 final Phylogeny p10 = factory
9608 .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]",
9609 new NHXParser() )[ 0 ];
9610 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]";
9611 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9614 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9615 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9618 final Phylogeny p12 = factory
9619 .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]",
9620 new NHXParser() )[ 0 ];
9621 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]";
9622 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9625 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9626 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9629 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;";
9630 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9633 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9634 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9638 catch ( final Exception e ) {
9639 e.printStackTrace( System.out );
9645 private static boolean testNodeRemoval() {
9647 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9648 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9649 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9650 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9653 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9654 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9655 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9658 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9659 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9660 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9664 catch ( final Exception e ) {
9665 e.printStackTrace( System.out );
9671 private static boolean testPhylogenyBranch() {
9673 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9674 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9675 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9676 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9677 if ( !a1b1.equals( a1b1 ) ) {
9680 if ( !a1b1.equals( b1a1 ) ) {
9683 if ( !b1a1.equals( a1b1 ) ) {
9686 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9687 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9688 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9689 if ( a1_b1.equals( b1_a1 ) ) {
9692 if ( a1_b1.equals( a1_b1_ ) ) {
9695 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9696 if ( !a1_b1.equals( b1_a1_ ) ) {
9699 if ( a1_b1_.equals( b1_a1_ ) ) {
9702 if ( !a1_b1_.equals( b1_a1 ) ) {
9706 catch ( final Exception e ) {
9707 e.printStackTrace( System.out );
9713 private static boolean testPhyloXMLparsingOfDistributionElement() {
9715 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9716 PhyloXmlParser xml_parser = null;
9718 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9720 catch ( final Exception e ) {
9721 // Do nothing -- means were not running from jar.
9723 if ( xml_parser == null ) {
9724 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9725 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9726 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9729 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9732 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9734 if ( xml_parser.getErrorCount() > 0 ) {
9735 System.out.println( xml_parser.getErrorMessages().toString() );
9738 if ( phylogenies_0.length != 1 ) {
9741 final Phylogeny t1 = phylogenies_0[ 0 ];
9742 PhylogenyNode n = null;
9743 Distribution d = null;
9744 n = t1.getNode( "root node" );
9745 if ( !n.getNodeData().isHasDistribution() ) {
9748 if ( n.getNodeData().getDistributions().size() != 1 ) {
9751 d = n.getNodeData().getDistribution();
9752 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9755 if ( d.getPoints().size() != 1 ) {
9758 if ( d.getPolygons() != null ) {
9761 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9764 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9767 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9770 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9773 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9776 n = t1.getNode( "node a" );
9777 if ( !n.getNodeData().isHasDistribution() ) {
9780 if ( n.getNodeData().getDistributions().size() != 2 ) {
9783 d = n.getNodeData().getDistribution( 1 );
9784 if ( !d.getDesc().equals( "San Diego" ) ) {
9787 if ( d.getPoints().size() != 1 ) {
9790 if ( d.getPolygons() != null ) {
9793 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9796 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9799 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9802 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9805 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9808 n = t1.getNode( "node bb" );
9809 if ( !n.getNodeData().isHasDistribution() ) {
9812 if ( n.getNodeData().getDistributions().size() != 1 ) {
9815 d = n.getNodeData().getDistribution( 0 );
9816 if ( d.getPoints().size() != 3 ) {
9819 if ( d.getPolygons().size() != 2 ) {
9822 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9825 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9828 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9831 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9834 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9837 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9840 Polygon p = d.getPolygons().get( 0 );
9841 if ( p.getPoints().size() != 3 ) {
9844 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9847 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9850 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9853 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9856 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9859 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9862 p = d.getPolygons().get( 1 );
9863 if ( p.getPoints().size() != 3 ) {
9866 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9869 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9872 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9876 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9877 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9878 if ( rt.length != 1 ) {
9881 final Phylogeny t1_rt = rt[ 0 ];
9882 n = t1_rt.getNode( "root node" );
9883 if ( !n.getNodeData().isHasDistribution() ) {
9886 if ( n.getNodeData().getDistributions().size() != 1 ) {
9889 d = n.getNodeData().getDistribution();
9890 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9893 if ( d.getPoints().size() != 1 ) {
9896 if ( d.getPolygons() != null ) {
9899 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9902 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9905 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9908 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9911 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9914 n = t1_rt.getNode( "node a" );
9915 if ( !n.getNodeData().isHasDistribution() ) {
9918 if ( n.getNodeData().getDistributions().size() != 2 ) {
9921 d = n.getNodeData().getDistribution( 1 );
9922 if ( !d.getDesc().equals( "San Diego" ) ) {
9925 if ( d.getPoints().size() != 1 ) {
9928 if ( d.getPolygons() != null ) {
9931 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9934 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9937 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9940 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9943 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9946 n = t1_rt.getNode( "node bb" );
9947 if ( !n.getNodeData().isHasDistribution() ) {
9950 if ( n.getNodeData().getDistributions().size() != 1 ) {
9953 d = n.getNodeData().getDistribution( 0 );
9954 if ( d.getPoints().size() != 3 ) {
9957 if ( d.getPolygons().size() != 2 ) {
9960 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9963 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9966 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9969 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9972 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9975 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9978 p = d.getPolygons().get( 0 );
9979 if ( p.getPoints().size() != 3 ) {
9982 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9985 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9988 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9991 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9994 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9997 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
10000 p = d.getPolygons().get( 1 );
10001 if ( p.getPoints().size() != 3 ) {
10004 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
10007 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
10010 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
10014 catch ( final Exception e ) {
10015 e.printStackTrace( System.out );
10021 private static boolean testPostOrderIterator() {
10023 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10024 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10025 PhylogenyNodeIterator it0;
10026 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
10029 for( it0.reset(); it0.hasNext(); ) {
10032 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10033 final PhylogenyNodeIterator it = t1.iteratorPostorder();
10034 if ( !it.next().getName().equals( "A" ) ) {
10037 if ( !it.next().getName().equals( "B" ) ) {
10040 if ( !it.next().getName().equals( "ab" ) ) {
10043 if ( !it.next().getName().equals( "C" ) ) {
10046 if ( !it.next().getName().equals( "D" ) ) {
10049 if ( !it.next().getName().equals( "cd" ) ) {
10052 if ( !it.next().getName().equals( "abcd" ) ) {
10055 if ( !it.next().getName().equals( "E" ) ) {
10058 if ( !it.next().getName().equals( "F" ) ) {
10061 if ( !it.next().getName().equals( "ef" ) ) {
10064 if ( !it.next().getName().equals( "G" ) ) {
10067 if ( !it.next().getName().equals( "H" ) ) {
10070 if ( !it.next().getName().equals( "gh" ) ) {
10073 if ( !it.next().getName().equals( "efgh" ) ) {
10076 if ( !it.next().getName().equals( "r" ) ) {
10079 if ( it.hasNext() ) {
10083 catch ( final Exception e ) {
10084 e.printStackTrace( System.out );
10090 private static boolean testPreOrderIterator() {
10092 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10093 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10094 PhylogenyNodeIterator it0;
10095 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
10098 for( it0.reset(); it0.hasNext(); ) {
10101 PhylogenyNodeIterator it = t0.iteratorPreorder();
10102 if ( !it.next().getName().equals( "r" ) ) {
10105 if ( !it.next().getName().equals( "ab" ) ) {
10108 if ( !it.next().getName().equals( "A" ) ) {
10111 if ( !it.next().getName().equals( "B" ) ) {
10114 if ( !it.next().getName().equals( "cd" ) ) {
10117 if ( !it.next().getName().equals( "C" ) ) {
10120 if ( !it.next().getName().equals( "D" ) ) {
10123 if ( it.hasNext() ) {
10126 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10127 it = t1.iteratorPreorder();
10128 if ( !it.next().getName().equals( "r" ) ) {
10131 if ( !it.next().getName().equals( "abcd" ) ) {
10134 if ( !it.next().getName().equals( "ab" ) ) {
10137 if ( !it.next().getName().equals( "A" ) ) {
10140 if ( !it.next().getName().equals( "B" ) ) {
10143 if ( !it.next().getName().equals( "cd" ) ) {
10146 if ( !it.next().getName().equals( "C" ) ) {
10149 if ( !it.next().getName().equals( "D" ) ) {
10152 if ( !it.next().getName().equals( "efgh" ) ) {
10155 if ( !it.next().getName().equals( "ef" ) ) {
10158 if ( !it.next().getName().equals( "E" ) ) {
10161 if ( !it.next().getName().equals( "F" ) ) {
10164 if ( !it.next().getName().equals( "gh" ) ) {
10167 if ( !it.next().getName().equals( "G" ) ) {
10170 if ( !it.next().getName().equals( "H" ) ) {
10173 if ( it.hasNext() ) {
10177 catch ( final Exception e ) {
10178 e.printStackTrace( System.out );
10184 private static boolean testPropertiesMap() {
10186 final PropertiesMap pm = new PropertiesMap();
10187 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10188 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10189 final Property p2 = new Property( "something:else",
10191 "improbable:research",
10194 pm.addProperty( p0 );
10195 pm.addProperty( p1 );
10196 pm.addProperty( p2 );
10197 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
10200 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
10203 if ( pm.getProperties().size() != 3 ) {
10206 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
10209 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10212 if ( pm.getProperties().size() != 3 ) {
10215 pm.removeProperty( "dimensions:diameter" );
10216 if ( pm.getProperties().size() != 2 ) {
10219 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
10222 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10226 catch ( final Exception e ) {
10227 e.printStackTrace( System.out );
10233 private static boolean testProteinId() {
10235 final ProteinId id1 = new ProteinId( "a" );
10236 final ProteinId id2 = new ProteinId( "a" );
10237 final ProteinId id3 = new ProteinId( "A" );
10238 final ProteinId id4 = new ProteinId( "b" );
10239 if ( !id1.equals( id1 ) ) {
10242 if ( id1.getId().equals( "x" ) ) {
10245 if ( id1.getId().equals( null ) ) {
10248 if ( !id1.equals( id2 ) ) {
10251 if ( id1.equals( id3 ) ) {
10254 if ( id1.hashCode() != id1.hashCode() ) {
10257 if ( id1.hashCode() != id2.hashCode() ) {
10260 if ( id1.hashCode() == id3.hashCode() ) {
10263 if ( id1.compareTo( id1 ) != 0 ) {
10266 if ( id1.compareTo( id2 ) != 0 ) {
10269 if ( id1.compareTo( id3 ) != 0 ) {
10272 if ( id1.compareTo( id4 ) >= 0 ) {
10275 if ( id4.compareTo( id1 ) <= 0 ) {
10278 if ( !id4.getId().equals( "b" ) ) {
10281 final ProteinId id5 = new ProteinId( " C " );
10282 if ( !id5.getId().equals( "C" ) ) {
10285 if ( id5.equals( id1 ) ) {
10289 catch ( final Exception e ) {
10290 e.printStackTrace( System.out );
10296 private static boolean testReIdMethods() {
10298 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10299 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
10300 final long count = PhylogenyNode.getNodeCount();
10301 p.levelOrderReID();
10302 if ( p.getNode( "r" ).getId() != count ) {
10305 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
10308 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
10311 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
10314 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
10317 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
10320 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
10323 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
10326 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
10329 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
10332 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
10335 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
10338 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
10341 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
10344 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
10348 catch ( final Exception e ) {
10349 e.printStackTrace( System.out );
10355 private static boolean testRerooting() {
10357 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10358 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",
10359 new NHXParser() )[ 0 ];
10360 if ( !t1.isRooted() ) {
10363 t1.reRoot( t1.getNode( "D" ) );
10364 t1.reRoot( t1.getNode( "CD" ) );
10365 t1.reRoot( t1.getNode( "A" ) );
10366 t1.reRoot( t1.getNode( "B" ) );
10367 t1.reRoot( t1.getNode( "AB" ) );
10368 t1.reRoot( t1.getNode( "D" ) );
10369 t1.reRoot( t1.getNode( "C" ) );
10370 t1.reRoot( t1.getNode( "CD" ) );
10371 t1.reRoot( t1.getNode( "A" ) );
10372 t1.reRoot( t1.getNode( "B" ) );
10373 t1.reRoot( t1.getNode( "AB" ) );
10374 t1.reRoot( t1.getNode( "D" ) );
10375 t1.reRoot( t1.getNode( "D" ) );
10376 t1.reRoot( t1.getNode( "C" ) );
10377 t1.reRoot( t1.getNode( "A" ) );
10378 t1.reRoot( t1.getNode( "B" ) );
10379 t1.reRoot( t1.getNode( "AB" ) );
10380 t1.reRoot( t1.getNode( "C" ) );
10381 t1.reRoot( t1.getNode( "D" ) );
10382 t1.reRoot( t1.getNode( "CD" ) );
10383 t1.reRoot( t1.getNode( "D" ) );
10384 t1.reRoot( t1.getNode( "A" ) );
10385 t1.reRoot( t1.getNode( "B" ) );
10386 t1.reRoot( t1.getNode( "AB" ) );
10387 t1.reRoot( t1.getNode( "C" ) );
10388 t1.reRoot( t1.getNode( "D" ) );
10389 t1.reRoot( t1.getNode( "CD" ) );
10390 t1.reRoot( t1.getNode( "D" ) );
10391 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10394 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10397 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10400 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10403 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10406 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10409 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",
10410 new NHXParser() )[ 0 ];
10411 t2.reRoot( t2.getNode( "A" ) );
10412 t2.reRoot( t2.getNode( "D" ) );
10413 t2.reRoot( t2.getNode( "ABC" ) );
10414 t2.reRoot( t2.getNode( "A" ) );
10415 t2.reRoot( t2.getNode( "B" ) );
10416 t2.reRoot( t2.getNode( "D" ) );
10417 t2.reRoot( t2.getNode( "C" ) );
10418 t2.reRoot( t2.getNode( "ABC" ) );
10419 t2.reRoot( t2.getNode( "A" ) );
10420 t2.reRoot( t2.getNode( "B" ) );
10421 t2.reRoot( t2.getNode( "AB" ) );
10422 t2.reRoot( t2.getNode( "AB" ) );
10423 t2.reRoot( t2.getNode( "D" ) );
10424 t2.reRoot( t2.getNode( "C" ) );
10425 t2.reRoot( t2.getNode( "B" ) );
10426 t2.reRoot( t2.getNode( "AB" ) );
10427 t2.reRoot( t2.getNode( "D" ) );
10428 t2.reRoot( t2.getNode( "D" ) );
10429 t2.reRoot( t2.getNode( "ABC" ) );
10430 t2.reRoot( t2.getNode( "A" ) );
10431 t2.reRoot( t2.getNode( "B" ) );
10432 t2.reRoot( t2.getNode( "AB" ) );
10433 t2.reRoot( t2.getNode( "D" ) );
10434 t2.reRoot( t2.getNode( "C" ) );
10435 t2.reRoot( t2.getNode( "ABC" ) );
10436 t2.reRoot( t2.getNode( "A" ) );
10437 t2.reRoot( t2.getNode( "B" ) );
10438 t2.reRoot( t2.getNode( "AB" ) );
10439 t2.reRoot( t2.getNode( "D" ) );
10440 t2.reRoot( t2.getNode( "D" ) );
10441 t2.reRoot( t2.getNode( "C" ) );
10442 t2.reRoot( t2.getNode( "A" ) );
10443 t2.reRoot( t2.getNode( "B" ) );
10444 t2.reRoot( t2.getNode( "AB" ) );
10445 t2.reRoot( t2.getNode( "C" ) );
10446 t2.reRoot( t2.getNode( "D" ) );
10447 t2.reRoot( t2.getNode( "ABC" ) );
10448 t2.reRoot( t2.getNode( "D" ) );
10449 t2.reRoot( t2.getNode( "A" ) );
10450 t2.reRoot( t2.getNode( "B" ) );
10451 t2.reRoot( t2.getNode( "AB" ) );
10452 t2.reRoot( t2.getNode( "C" ) );
10453 t2.reRoot( t2.getNode( "D" ) );
10454 t2.reRoot( t2.getNode( "ABC" ) );
10455 t2.reRoot( t2.getNode( "D" ) );
10456 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10459 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10462 t2.reRoot( t2.getNode( "ABC" ) );
10463 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10466 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10469 t2.reRoot( t2.getNode( "AB" ) );
10470 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10473 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10476 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10479 t2.reRoot( t2.getNode( "AB" ) );
10480 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10483 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10486 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10489 t2.reRoot( t2.getNode( "D" ) );
10490 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10493 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10496 t2.reRoot( t2.getNode( "ABC" ) );
10497 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10500 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10503 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10504 new NHXParser() )[ 0 ];
10505 t3.reRoot( t3.getNode( "B" ) );
10506 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10509 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10512 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10515 t3.reRoot( t3.getNode( "B" ) );
10516 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10519 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10522 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10525 t3.reRoot( t3.getRoot() );
10526 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10529 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10532 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10536 catch ( final Exception e ) {
10537 e.printStackTrace( System.out );
10543 private static boolean testSDIse() {
10545 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10546 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10547 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10548 gene1.setRooted( true );
10549 species1.setRooted( true );
10550 final SDI sdi = new SDI( gene1, species1 );
10551 if ( !gene1.getRoot().isDuplication() ) {
10554 final Phylogeny species2 = factory
10555 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10556 new NHXParser() )[ 0 ];
10557 final Phylogeny gene2 = factory
10558 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10559 new NHXParser() )[ 0 ];
10560 species2.setRooted( true );
10561 gene2.setRooted( true );
10562 final SDI sdi2 = new SDI( gene2, species2 );
10563 if ( sdi2.getDuplicationsSum() != 0 ) {
10566 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10569 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10572 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10575 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10578 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10581 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10584 final Phylogeny species3 = factory
10585 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10586 new NHXParser() )[ 0 ];
10587 final Phylogeny gene3 = factory
10588 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10589 new NHXParser() )[ 0 ];
10590 species3.setRooted( true );
10591 gene3.setRooted( true );
10592 final SDI sdi3 = new SDI( gene3, species3 );
10593 if ( sdi3.getDuplicationsSum() != 1 ) {
10596 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10599 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10602 final Phylogeny species4 = factory
10603 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10604 new NHXParser() )[ 0 ];
10605 final Phylogeny gene4 = factory
10606 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10607 new NHXParser() )[ 0 ];
10608 species4.setRooted( true );
10609 gene4.setRooted( true );
10610 final SDI sdi4 = new SDI( gene4, species4 );
10611 if ( sdi4.getDuplicationsSum() != 1 ) {
10614 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10617 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10620 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10623 if ( species4.getNumberOfExternalNodes() != 6 ) {
10626 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10629 final Phylogeny species5 = factory
10630 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10631 new NHXParser() )[ 0 ];
10632 final Phylogeny gene5 = factory
10633 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10634 new NHXParser() )[ 0 ];
10635 species5.setRooted( true );
10636 gene5.setRooted( true );
10637 final SDI sdi5 = new SDI( gene5, species5 );
10638 if ( sdi5.getDuplicationsSum() != 2 ) {
10641 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10644 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10647 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10650 if ( species5.getNumberOfExternalNodes() != 6 ) {
10653 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10656 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10657 // Conjecture for Comparing Molecular Phylogenies"
10658 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10659 final Phylogeny species6 = factory
10660 .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,"
10661 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10662 new NHXParser() )[ 0 ];
10663 final Phylogeny gene6 = factory
10664 .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,"
10665 + "((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,"
10666 + "(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;",
10667 new NHXParser() )[ 0 ];
10668 species6.setRooted( true );
10669 gene6.setRooted( true );
10670 final SDI sdi6 = new SDI( gene6, species6 );
10671 if ( sdi6.getDuplicationsSum() != 3 ) {
10674 if ( !gene6.getNode( "r" ).isDuplication() ) {
10677 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10680 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10683 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10686 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10689 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10692 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10695 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10698 sdi6.computeMappingCostL();
10699 if ( sdi6.computeMappingCostL() != 17 ) {
10702 if ( species6.getNumberOfExternalNodes() != 9 ) {
10705 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10708 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10709 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10710 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10711 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10712 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10713 species7.setRooted( true );
10714 final Phylogeny gene7_1 = Test
10715 .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])" );
10716 gene7_1.setRooted( true );
10717 final SDI sdi7 = new SDI( gene7_1, species7 );
10718 if ( sdi7.getDuplicationsSum() != 0 ) {
10721 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10724 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10727 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10730 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10733 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10736 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10739 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10742 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10745 final Phylogeny gene7_2 = Test
10746 .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])" );
10747 gene7_2.setRooted( true );
10748 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10749 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10752 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10755 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10758 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10761 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10764 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10767 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10770 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10773 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10776 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10780 catch ( final Exception e ) {
10786 private static boolean testSDIunrooted() {
10788 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10789 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10790 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10791 final Iterator<PhylogenyBranch> iter = l.iterator();
10792 PhylogenyBranch br = iter.next();
10793 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10796 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10800 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10803 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10807 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10810 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10814 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10817 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10821 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10824 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10828 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10831 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10835 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10838 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10842 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10845 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10849 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10852 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10856 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10859 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10863 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10866 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10870 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10873 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10877 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10880 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10884 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10887 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10891 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10894 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10897 if ( iter.hasNext() ) {
10900 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10901 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10902 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10904 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10907 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10911 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10914 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10918 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10921 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10924 if ( iter1.hasNext() ) {
10927 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10928 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10929 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10931 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10934 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10938 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10941 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10945 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10948 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10951 if ( iter2.hasNext() ) {
10954 final Phylogeny species0 = factory
10955 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10956 new NHXParser() )[ 0 ];
10957 final Phylogeny gene1 = factory
10958 .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])",
10959 new NHXParser() )[ 0 ];
10960 species0.setRooted( true );
10961 gene1.setRooted( true );
10962 final SDIR sdi_unrooted = new SDIR();
10963 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10964 if ( sdi_unrooted.getCount() != 1 ) {
10967 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10970 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10973 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10976 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10979 final Phylogeny gene2 = factory
10980 .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])",
10981 new NHXParser() )[ 0 ];
10982 gene2.setRooted( true );
10983 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10984 if ( sdi_unrooted.getCount() != 1 ) {
10987 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10990 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10993 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10996 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10999 final Phylogeny species6 = factory
11000 .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,"
11001 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11002 new NHXParser() )[ 0 ];
11003 final Phylogeny gene6 = factory
11004 .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],"
11005 + "(((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],"
11006 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11007 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11008 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11009 new NHXParser() )[ 0 ];
11010 species6.setRooted( true );
11011 gene6.setRooted( true );
11012 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
11013 if ( sdi_unrooted.getCount() != 1 ) {
11016 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11019 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11022 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11025 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11028 if ( !p6[ 0 ].getRoot().isDuplication() ) {
11031 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11034 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11037 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
11040 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11043 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
11046 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
11049 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11053 final Phylogeny species7 = factory
11054 .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,"
11055 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11056 new NHXParser() )[ 0 ];
11057 final Phylogeny gene7 = factory
11058 .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],"
11059 + "(((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],"
11060 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11061 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11062 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11063 new NHXParser() )[ 0 ];
11064 species7.setRooted( true );
11065 gene7.setRooted( true );
11066 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
11067 if ( sdi_unrooted.getCount() != 1 ) {
11070 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11073 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11076 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11079 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
11082 if ( !p7[ 0 ].getRoot().isDuplication() ) {
11085 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11088 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11091 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
11094 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11097 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
11100 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
11103 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11107 final Phylogeny species8 = factory
11108 .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,"
11109 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11110 new NHXParser() )[ 0 ];
11111 final Phylogeny gene8 = factory
11112 .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],"
11113 + "(((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],"
11114 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11115 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11116 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11117 new NHXParser() )[ 0 ];
11118 species8.setRooted( true );
11119 gene8.setRooted( true );
11120 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
11121 if ( sdi_unrooted.getCount() != 1 ) {
11124 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11127 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11130 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11133 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11136 if ( !p8[ 0 ].getRoot().isDuplication() ) {
11139 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11142 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11145 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
11148 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11151 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
11154 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
11157 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11162 catch ( final Exception e ) {
11163 e.printStackTrace( System.out );
11169 private static boolean testSequenceDbWsTools1() {
11171 final PhylogenyNode n = new PhylogenyNode();
11172 n.setName( "NP_001025424" );
11173 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11174 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11175 || !acc.getValue().equals( "NP_001025424" ) ) {
11178 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11179 acc = SequenceDbWsTools.obtainSeqAccession( n );
11180 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11181 || !acc.getValue().equals( "NP_001025424" ) ) {
11184 n.setName( "NP_001025424.1" );
11185 acc = SequenceDbWsTools.obtainSeqAccession( n );
11186 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11187 || !acc.getValue().equals( "NP_001025424" ) ) {
11190 n.setName( "NM_001030253" );
11191 acc = SequenceDbWsTools.obtainSeqAccession( n );
11192 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11193 || !acc.getValue().equals( "NM_001030253" ) ) {
11196 n.setName( "BCL2_HUMAN" );
11197 acc = SequenceDbWsTools.obtainSeqAccession( n );
11198 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11199 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11200 System.out.println( acc.toString() );
11203 n.setName( "P10415" );
11204 acc = SequenceDbWsTools.obtainSeqAccession( n );
11205 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11206 || !acc.getValue().equals( "P10415" ) ) {
11207 System.out.println( acc.toString() );
11210 n.setName( " P10415 " );
11211 acc = SequenceDbWsTools.obtainSeqAccession( n );
11212 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11213 || !acc.getValue().equals( "P10415" ) ) {
11214 System.out.println( acc.toString() );
11217 n.setName( "_P10415|" );
11218 acc = SequenceDbWsTools.obtainSeqAccession( n );
11219 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11220 || !acc.getValue().equals( "P10415" ) ) {
11221 System.out.println( acc.toString() );
11224 n.setName( "AY695820" );
11225 acc = SequenceDbWsTools.obtainSeqAccession( n );
11226 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11227 || !acc.getValue().equals( "AY695820" ) ) {
11228 System.out.println( acc.toString() );
11231 n.setName( "_AY695820_" );
11232 acc = SequenceDbWsTools.obtainSeqAccession( n );
11233 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11234 || !acc.getValue().equals( "AY695820" ) ) {
11235 System.out.println( acc.toString() );
11238 n.setName( "AAA59452" );
11239 acc = SequenceDbWsTools.obtainSeqAccession( n );
11240 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11241 || !acc.getValue().equals( "AAA59452" ) ) {
11242 System.out.println( acc.toString() );
11245 n.setName( "_AAA59452_" );
11246 acc = SequenceDbWsTools.obtainSeqAccession( n );
11247 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11248 || !acc.getValue().equals( "AAA59452" ) ) {
11249 System.out.println( acc.toString() );
11252 n.setName( "AAA59452.1" );
11253 acc = SequenceDbWsTools.obtainSeqAccession( n );
11254 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11255 || !acc.getValue().equals( "AAA59452.1" ) ) {
11256 System.out.println( acc.toString() );
11259 n.setName( "_AAA59452.1_" );
11260 acc = SequenceDbWsTools.obtainSeqAccession( n );
11261 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11262 || !acc.getValue().equals( "AAA59452.1" ) ) {
11263 System.out.println( acc.toString() );
11266 n.setName( "GI:94894583" );
11267 acc = SequenceDbWsTools.obtainSeqAccession( n );
11268 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11269 || !acc.getValue().equals( "94894583" ) ) {
11270 System.out.println( acc.toString() );
11273 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11274 acc = SequenceDbWsTools.obtainSeqAccession( n );
11275 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11276 || !acc.getValue().equals( "71845847" ) ) {
11277 System.out.println( acc.toString() );
11280 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11281 acc = SequenceDbWsTools.obtainSeqAccession( n );
11282 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11283 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11284 System.out.println( acc.toString() );
11288 catch ( final Exception e ) {
11294 private static boolean testSequenceDbWsTools2() {
11296 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11297 SequenceDbWsTools.obtainSeqInformation( n1 );
11298 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11301 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11304 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11307 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11310 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11311 SequenceDbWsTools.obtainSeqInformation( n2 );
11312 if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
11315 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11318 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11321 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11324 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11325 SequenceDbWsTools.obtainSeqInformation( n3 );
11326 if ( !n3.getNodeData().getSequence().getName()
11327 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11330 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11333 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11336 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11340 catch ( final IOException e ) {
11341 System.out.println();
11342 System.out.println( "the following might be due to absence internet connection:" );
11343 e.printStackTrace( System.out );
11346 catch ( final Exception e ) {
11347 e.printStackTrace();
11353 private static boolean testSequenceIdParsing() {
11355 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11356 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11357 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11358 if ( id != null ) {
11359 System.out.println( "value =" + id.getValue() );
11360 System.out.println( "provider=" + id.getSource() );
11364 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11365 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11366 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11367 if ( id != null ) {
11368 System.out.println( "value =" + id.getValue() );
11369 System.out.println( "provider=" + id.getSource() );
11373 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11374 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11375 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11376 if ( id != null ) {
11377 System.out.println( "value =" + id.getValue() );
11378 System.out.println( "provider=" + id.getSource() );
11382 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11383 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11384 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11385 if ( id != null ) {
11386 System.out.println( "value =" + id.getValue() );
11387 System.out.println( "provider=" + id.getSource() );
11391 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11392 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11393 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11394 if ( id != null ) {
11395 System.out.println( "value =" + id.getValue() );
11396 System.out.println( "provider=" + id.getSource() );
11400 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11401 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11402 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11403 if ( id != null ) {
11404 System.out.println( "value =" + id.getValue() );
11405 System.out.println( "provider=" + id.getSource() );
11409 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11410 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11411 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11412 if ( id != null ) {
11413 System.out.println( "value =" + id.getValue() );
11414 System.out.println( "provider=" + id.getSource() );
11418 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11419 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11420 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11421 if ( id != null ) {
11422 System.out.println( "value =" + id.getValue() );
11423 System.out.println( "provider=" + id.getSource() );
11427 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11428 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11429 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11430 if ( id != null ) {
11431 System.out.println( "value =" + id.getValue() );
11432 System.out.println( "provider=" + id.getSource() );
11436 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11437 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11438 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11439 if ( id != null ) {
11440 System.out.println( "value =" + id.getValue() );
11441 System.out.println( "provider=" + id.getSource() );
11445 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11446 if ( id != null ) {
11447 System.out.println( "value =" + id.getValue() );
11448 System.out.println( "provider=" + id.getSource() );
11451 id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
11452 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11453 || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
11454 if ( id != null ) {
11455 System.out.println( "value =" + id.getValue() );
11456 System.out.println( "provider=" + id.getSource() );
11460 id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
11461 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11462 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11463 if ( id != null ) {
11464 System.out.println( "value =" + id.getValue() );
11465 System.out.println( "provider=" + id.getSource() );
11469 id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
11470 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11471 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11472 if ( id != null ) {
11473 System.out.println( "value =" + id.getValue() );
11474 System.out.println( "provider=" + id.getSource() );
11478 id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
11479 if ( id != null ) {
11480 System.out.println( "value =" + id.getValue() );
11481 System.out.println( "provider=" + id.getSource() );
11485 catch ( final Exception e ) {
11486 e.printStackTrace( System.out );
11492 private static boolean testSequenceWriter() {
11494 final String n = ForesterUtil.LINE_SEPARATOR;
11495 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11498 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11501 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11504 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11507 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11508 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11511 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11512 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11516 catch ( final Exception e ) {
11517 e.printStackTrace();
11523 private static boolean testSpecies() {
11525 final Species s1 = new BasicSpecies( "a" );
11526 final Species s2 = new BasicSpecies( "a" );
11527 final Species s3 = new BasicSpecies( "A" );
11528 final Species s4 = new BasicSpecies( "b" );
11529 if ( !s1.equals( s1 ) ) {
11532 if ( s1.getSpeciesId().equals( "x" ) ) {
11535 if ( s1.getSpeciesId().equals( null ) ) {
11538 if ( !s1.equals( s2 ) ) {
11541 if ( s1.equals( s3 ) ) {
11544 if ( s1.hashCode() != s1.hashCode() ) {
11547 if ( s1.hashCode() != s2.hashCode() ) {
11550 if ( s1.hashCode() == s3.hashCode() ) {
11553 if ( s1.compareTo( s1 ) != 0 ) {
11556 if ( s1.compareTo( s2 ) != 0 ) {
11559 if ( s1.compareTo( s3 ) != 0 ) {
11562 if ( s1.compareTo( s4 ) >= 0 ) {
11565 if ( s4.compareTo( s1 ) <= 0 ) {
11568 if ( !s4.getSpeciesId().equals( "b" ) ) {
11571 final Species s5 = new BasicSpecies( " C " );
11572 if ( !s5.getSpeciesId().equals( "C" ) ) {
11575 if ( s5.equals( s1 ) ) {
11579 catch ( final Exception e ) {
11580 e.printStackTrace( System.out );
11586 private static boolean testSplit() {
11588 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11589 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11590 //Archaeopteryx.createApplication( p0 );
11591 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11592 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11593 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11594 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11595 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11596 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11597 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11598 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11599 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11600 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11601 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11602 // System.out.println( s0.toString() );
11604 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11607 if ( s0.match( query_nodes ) ) {
11610 query_nodes = new HashSet<PhylogenyNode>();
11611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11618 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 if ( !s0.match( query_nodes ) ) {
11630 query_nodes = new HashSet<PhylogenyNode>();
11631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11635 if ( !s0.match( query_nodes ) ) {
11639 query_nodes = new HashSet<PhylogenyNode>();
11640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11644 if ( !s0.match( query_nodes ) ) {
11648 query_nodes = new HashSet<PhylogenyNode>();
11649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11652 if ( !s0.match( query_nodes ) ) {
11655 query_nodes = new HashSet<PhylogenyNode>();
11656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11658 if ( !s0.match( query_nodes ) ) {
11661 query_nodes = new HashSet<PhylogenyNode>();
11662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11667 if ( !s0.match( query_nodes ) ) {
11670 query_nodes = new HashSet<PhylogenyNode>();
11671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11674 if ( !s0.match( query_nodes ) ) {
11677 query_nodes = new HashSet<PhylogenyNode>();
11678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11682 if ( !s0.match( query_nodes ) ) {
11685 query_nodes = new HashSet<PhylogenyNode>();
11686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11688 if ( s0.match( query_nodes ) ) {
11691 query_nodes = new HashSet<PhylogenyNode>();
11692 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11696 if ( s0.match( query_nodes ) ) {
11699 query_nodes = new HashSet<PhylogenyNode>();
11700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11705 if ( s0.match( query_nodes ) ) {
11708 query_nodes = new HashSet<PhylogenyNode>();
11709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11712 if ( s0.match( query_nodes ) ) {
11715 query_nodes = new HashSet<PhylogenyNode>();
11716 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11718 if ( s0.match( query_nodes ) ) {
11721 query_nodes = new HashSet<PhylogenyNode>();
11722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11724 if ( s0.match( query_nodes ) ) {
11727 query_nodes = new HashSet<PhylogenyNode>();
11728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11730 if ( s0.match( query_nodes ) ) {
11733 query_nodes = new HashSet<PhylogenyNode>();
11734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11736 if ( s0.match( query_nodes ) ) {
11739 query_nodes = new HashSet<PhylogenyNode>();
11740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11742 if ( s0.match( query_nodes ) ) {
11745 query_nodes = new HashSet<PhylogenyNode>();
11746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11748 if ( s0.match( query_nodes ) ) {
11751 query_nodes = new HashSet<PhylogenyNode>();
11752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11755 if ( s0.match( query_nodes ) ) {
11758 query_nodes = new HashSet<PhylogenyNode>();
11759 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11760 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11761 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11762 if ( s0.match( query_nodes ) ) {
11765 query_nodes = new HashSet<PhylogenyNode>();
11766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11767 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11768 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11769 if ( s0.match( query_nodes ) ) {
11772 query_nodes = new HashSet<PhylogenyNode>();
11773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11774 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11777 if ( s0.match( query_nodes ) ) {
11781 // query_nodes = new HashSet<PhylogenyNode>();
11782 // query_nodes.add( new PhylogenyNode( "X" ) );
11783 // query_nodes.add( new PhylogenyNode( "Y" ) );
11784 // query_nodes.add( new PhylogenyNode( "A" ) );
11785 // query_nodes.add( new PhylogenyNode( "B" ) );
11786 // query_nodes.add( new PhylogenyNode( "C" ) );
11787 // query_nodes.add( new PhylogenyNode( "D" ) );
11788 // query_nodes.add( new PhylogenyNode( "E" ) );
11789 // query_nodes.add( new PhylogenyNode( "F" ) );
11790 // query_nodes.add( new PhylogenyNode( "G" ) );
11791 // if ( !s0.match( query_nodes ) ) {
11794 // query_nodes = new HashSet<PhylogenyNode>();
11795 // query_nodes.add( new PhylogenyNode( "X" ) );
11796 // query_nodes.add( new PhylogenyNode( "Y" ) );
11797 // query_nodes.add( new PhylogenyNode( "A" ) );
11798 // query_nodes.add( new PhylogenyNode( "B" ) );
11799 // query_nodes.add( new PhylogenyNode( "C" ) );
11800 // if ( !s0.match( query_nodes ) ) {
11804 // query_nodes = new HashSet<PhylogenyNode>();
11805 // query_nodes.add( new PhylogenyNode( "X" ) );
11806 // query_nodes.add( new PhylogenyNode( "Y" ) );
11807 // query_nodes.add( new PhylogenyNode( "D" ) );
11808 // query_nodes.add( new PhylogenyNode( "E" ) );
11809 // query_nodes.add( new PhylogenyNode( "F" ) );
11810 // query_nodes.add( new PhylogenyNode( "G" ) );
11811 // if ( !s0.match( query_nodes ) ) {
11815 // query_nodes = new HashSet<PhylogenyNode>();
11816 // query_nodes.add( new PhylogenyNode( "X" ) );
11817 // query_nodes.add( new PhylogenyNode( "Y" ) );
11818 // query_nodes.add( new PhylogenyNode( "A" ) );
11819 // query_nodes.add( new PhylogenyNode( "B" ) );
11820 // query_nodes.add( new PhylogenyNode( "C" ) );
11821 // query_nodes.add( new PhylogenyNode( "D" ) );
11822 // if ( !s0.match( query_nodes ) ) {
11826 // query_nodes = new HashSet<PhylogenyNode>();
11827 // query_nodes.add( new PhylogenyNode( "X" ) );
11828 // query_nodes.add( new PhylogenyNode( "Y" ) );
11829 // query_nodes.add( new PhylogenyNode( "E" ) );
11830 // query_nodes.add( new PhylogenyNode( "F" ) );
11831 // query_nodes.add( new PhylogenyNode( "G" ) );
11832 // if ( !s0.match( query_nodes ) ) {
11836 // query_nodes = new HashSet<PhylogenyNode>();
11837 // query_nodes.add( new PhylogenyNode( "X" ) );
11838 // query_nodes.add( new PhylogenyNode( "Y" ) );
11839 // query_nodes.add( new PhylogenyNode( "F" ) );
11840 // query_nodes.add( new PhylogenyNode( "G" ) );
11841 // if ( !s0.match( query_nodes ) ) {
11845 query_nodes = new HashSet<PhylogenyNode>();
11846 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11847 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11850 if ( s0.match( query_nodes ) ) {
11854 query_nodes = new HashSet<PhylogenyNode>();
11855 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11856 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11857 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11859 if ( s0.match( query_nodes ) ) {
11862 ///////////////////////////
11864 query_nodes = new HashSet<PhylogenyNode>();
11865 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11866 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11867 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11868 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11869 if ( s0.match( query_nodes ) ) {
11873 query_nodes = new HashSet<PhylogenyNode>();
11874 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11875 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11876 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11878 if ( s0.match( query_nodes ) ) {
11882 query_nodes = new HashSet<PhylogenyNode>();
11883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11887 if ( s0.match( query_nodes ) ) {
11891 query_nodes = new HashSet<PhylogenyNode>();
11892 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11893 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11896 if ( s0.match( query_nodes ) ) {
11900 query_nodes = new HashSet<PhylogenyNode>();
11901 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11905 if ( s0.match( query_nodes ) ) {
11909 query_nodes = new HashSet<PhylogenyNode>();
11910 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11913 if ( s0.match( query_nodes ) ) {
11917 query_nodes = new HashSet<PhylogenyNode>();
11918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11923 if ( s0.match( query_nodes ) ) {
11927 query_nodes = new HashSet<PhylogenyNode>();
11928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11933 if ( s0.match( query_nodes ) ) {
11937 query_nodes = new HashSet<PhylogenyNode>();
11938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11943 if ( s0.match( query_nodes ) ) {
11947 query_nodes = new HashSet<PhylogenyNode>();
11948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11952 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11954 if ( s0.match( query_nodes ) ) {
11958 catch ( final Exception e ) {
11959 e.printStackTrace();
11965 private static boolean testSplitStrict() {
11967 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11968 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11969 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11970 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11971 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11972 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11973 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11974 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11975 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11976 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11977 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11978 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11981 if ( s0.match( query_nodes ) ) {
11984 query_nodes = new HashSet<PhylogenyNode>();
11985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11992 if ( !s0.match( query_nodes ) ) {
11996 query_nodes = new HashSet<PhylogenyNode>();
11997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12000 if ( !s0.match( query_nodes ) ) {
12004 query_nodes = new HashSet<PhylogenyNode>();
12005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12009 if ( !s0.match( query_nodes ) ) {
12013 query_nodes = new HashSet<PhylogenyNode>();
12014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12018 if ( !s0.match( query_nodes ) ) {
12022 query_nodes = new HashSet<PhylogenyNode>();
12023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12026 if ( !s0.match( query_nodes ) ) {
12030 query_nodes = new HashSet<PhylogenyNode>();
12031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12033 if ( !s0.match( query_nodes ) ) {
12037 query_nodes = new HashSet<PhylogenyNode>();
12038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12043 if ( !s0.match( query_nodes ) ) {
12047 query_nodes = new HashSet<PhylogenyNode>();
12048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12051 if ( !s0.match( query_nodes ) ) {
12055 query_nodes = new HashSet<PhylogenyNode>();
12056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12060 if ( !s0.match( query_nodes ) ) {
12064 query_nodes = new HashSet<PhylogenyNode>();
12065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12067 if ( s0.match( query_nodes ) ) {
12071 query_nodes = new HashSet<PhylogenyNode>();
12072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12076 if ( s0.match( query_nodes ) ) {
12080 query_nodes = new HashSet<PhylogenyNode>();
12081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12086 if ( s0.match( query_nodes ) ) {
12090 query_nodes = new HashSet<PhylogenyNode>();
12091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12094 if ( s0.match( query_nodes ) ) {
12098 query_nodes = new HashSet<PhylogenyNode>();
12099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12101 if ( s0.match( query_nodes ) ) {
12105 query_nodes = new HashSet<PhylogenyNode>();
12106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12108 if ( s0.match( query_nodes ) ) {
12112 query_nodes = new HashSet<PhylogenyNode>();
12113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12115 if ( s0.match( query_nodes ) ) {
12119 query_nodes = new HashSet<PhylogenyNode>();
12120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12122 if ( s0.match( query_nodes ) ) {
12126 query_nodes = new HashSet<PhylogenyNode>();
12127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12129 if ( s0.match( query_nodes ) ) {
12133 query_nodes = new HashSet<PhylogenyNode>();
12134 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12135 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12136 if ( s0.match( query_nodes ) ) {
12140 query_nodes = new HashSet<PhylogenyNode>();
12141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12144 if ( s0.match( query_nodes ) ) {
12148 query_nodes = new HashSet<PhylogenyNode>();
12149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12151 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12152 if ( s0.match( query_nodes ) ) {
12156 query_nodes = new HashSet<PhylogenyNode>();
12157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12159 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12160 if ( s0.match( query_nodes ) ) {
12164 query_nodes = new HashSet<PhylogenyNode>();
12165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12169 if ( s0.match( query_nodes ) ) {
12173 catch ( final Exception e ) {
12174 e.printStackTrace();
12180 private static boolean testSubtreeDeletion() {
12182 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12183 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12184 t1.deleteSubtree( t1.getNode( "A" ), false );
12185 if ( t1.getNumberOfExternalNodes() != 5 ) {
12188 t1.toNewHampshireX();
12189 t1.deleteSubtree( t1.getNode( "E" ), false );
12190 if ( t1.getNumberOfExternalNodes() != 4 ) {
12193 t1.toNewHampshireX();
12194 t1.deleteSubtree( t1.getNode( "F" ), false );
12195 if ( t1.getNumberOfExternalNodes() != 3 ) {
12198 t1.toNewHampshireX();
12199 t1.deleteSubtree( t1.getNode( "D" ), false );
12200 t1.toNewHampshireX();
12201 if ( t1.getNumberOfExternalNodes() != 3 ) {
12204 t1.deleteSubtree( t1.getNode( "def" ), false );
12205 t1.toNewHampshireX();
12206 if ( t1.getNumberOfExternalNodes() != 2 ) {
12209 t1.deleteSubtree( t1.getNode( "B" ), false );
12210 t1.toNewHampshireX();
12211 if ( t1.getNumberOfExternalNodes() != 1 ) {
12214 t1.deleteSubtree( t1.getNode( "C" ), false );
12215 t1.toNewHampshireX();
12216 if ( t1.getNumberOfExternalNodes() != 1 ) {
12219 t1.deleteSubtree( t1.getNode( "abc" ), false );
12220 t1.toNewHampshireX();
12221 if ( t1.getNumberOfExternalNodes() != 1 ) {
12224 t1.deleteSubtree( t1.getNode( "r" ), false );
12225 if ( t1.getNumberOfExternalNodes() != 0 ) {
12228 if ( !t1.isEmpty() ) {
12231 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12232 t2.deleteSubtree( t2.getNode( "A" ), false );
12233 t2.toNewHampshireX();
12234 if ( t2.getNumberOfExternalNodes() != 5 ) {
12237 t2.deleteSubtree( t2.getNode( "abc" ), false );
12238 t2.toNewHampshireX();
12239 if ( t2.getNumberOfExternalNodes() != 3 ) {
12242 t2.deleteSubtree( t2.getNode( "def" ), false );
12243 t2.toNewHampshireX();
12244 if ( t2.getNumberOfExternalNodes() != 1 ) {
12248 catch ( final Exception e ) {
12249 e.printStackTrace( System.out );
12255 private static boolean testSupportCount() {
12257 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12258 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
12259 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
12260 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
12261 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
12262 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
12263 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
12265 SupportCount.count( t0_1, phylogenies_1, true, false );
12266 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
12267 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
12268 + "(((((A,B),C),D),E),((F,G),X))"
12269 + "(((((A,Y),B),C),D),((F,G),E))"
12270 + "(((((A,B),C),D),E),(F,G))"
12271 + "(((((A,B),C),D),E),(F,G))"
12272 + "(((((A,B),C),D),E),(F,G))"
12273 + "(((((A,B),C),D),E),(F,G),Z)"
12274 + "(((((A,B),C),D),E),(F,G))"
12275 + "((((((A,B),C),D),E),F),G)"
12276 + "(((((X,Y),F,G),E),((A,B),C)),D)",
12278 SupportCount.count( t0_2, phylogenies_2, true, false );
12279 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
12280 while ( it.hasNext() ) {
12281 final PhylogenyNode n = it.next();
12282 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
12286 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
12287 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
12288 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
12289 SupportCount.count( t0_3, phylogenies_3, true, false );
12290 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
12291 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
12294 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
12297 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
12300 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
12303 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
12306 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
12309 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
12312 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
12315 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
12318 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
12321 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12322 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
12323 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
12324 SupportCount.count( t0_4, phylogenies_4, true, false );
12325 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
12326 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
12329 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
12332 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
12335 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
12338 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
12341 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
12344 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
12347 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
12350 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
12353 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
12356 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12357 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12358 double d = SupportCount.compare( b1, a, true, true, true );
12359 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12362 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12363 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12364 d = SupportCount.compare( b2, a, true, true, true );
12365 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12368 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12369 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12370 d = SupportCount.compare( b3, a, true, true, true );
12371 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12374 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12375 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12376 d = SupportCount.compare( b4, a, true, true, false );
12377 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12381 catch ( final Exception e ) {
12382 e.printStackTrace( System.out );
12388 private static boolean testSupportTransfer() {
12390 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12391 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)",
12392 new NHXParser() )[ 0 ];
12393 final Phylogeny p2 = factory
12394 .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 ];
12395 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12398 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12401 support_transfer.moveBranchLengthsToBootstrap( p1 );
12402 support_transfer.transferSupportValues( p1, p2 );
12403 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12406 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12409 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12412 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12415 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12418 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12421 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12424 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12428 catch ( final Exception e ) {
12429 e.printStackTrace( System.out );
12435 private static boolean testTaxonomyExtraction() {
12437 final PhylogenyNode n0 = PhylogenyNode
12438 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12439 if ( n0.getNodeData().isHasTaxonomy() ) {
12442 final PhylogenyNode n1 = PhylogenyNode
12443 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12444 if ( n1.getNodeData().isHasTaxonomy() ) {
12445 System.out.println( n1.toString() );
12448 final PhylogenyNode n2x = PhylogenyNode
12449 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12450 if ( n2x.getNodeData().isHasTaxonomy() ) {
12453 final PhylogenyNode n3 = PhylogenyNode
12454 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12455 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12456 System.out.println( n3.toString() );
12459 final PhylogenyNode n4 = PhylogenyNode
12460 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12461 if ( n4.getNodeData().isHasTaxonomy() ) {
12462 System.out.println( n4.toString() );
12465 final PhylogenyNode n5 = PhylogenyNode
12466 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12467 if ( n5.getNodeData().isHasTaxonomy() ) {
12468 System.out.println( n5.toString() );
12471 final PhylogenyNode n6 = PhylogenyNode
12472 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12473 if ( n6.getNodeData().isHasTaxonomy() ) {
12474 System.out.println( n6.toString() );
12477 final PhylogenyNode n7 = PhylogenyNode
12478 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12479 if ( n7.getNodeData().isHasTaxonomy() ) {
12480 System.out.println( n7.toString() );
12483 final PhylogenyNode n8 = PhylogenyNode
12484 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12485 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12486 System.out.println( n8.toString() );
12489 final PhylogenyNode n9 = PhylogenyNode
12490 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12491 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12492 System.out.println( n9.toString() );
12495 final PhylogenyNode n10x = PhylogenyNode
12496 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12497 if ( n10x.getNodeData().isHasTaxonomy() ) {
12498 System.out.println( n10x.toString() );
12501 final PhylogenyNode n10xx = PhylogenyNode
12502 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12503 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12504 System.out.println( n10xx.toString() );
12507 final PhylogenyNode n10 = PhylogenyNode
12508 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12509 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12510 System.out.println( n10.toString() );
12513 final PhylogenyNode n11 = PhylogenyNode
12514 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12515 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12516 System.out.println( n11.toString() );
12519 final PhylogenyNode n12 = PhylogenyNode
12520 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12521 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12522 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12523 System.out.println( n12.toString() );
12526 final PhylogenyNode n13 = PhylogenyNode
12527 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12528 if ( n13.getNodeData().isHasTaxonomy() ) {
12529 System.out.println( n13.toString() );
12532 final PhylogenyNode n14 = PhylogenyNode
12533 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12534 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12535 System.out.println( n14.toString() );
12538 final PhylogenyNode n15 = PhylogenyNode
12539 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12540 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12541 System.out.println( n15.toString() );
12544 final PhylogenyNode n16 = PhylogenyNode
12545 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12546 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12547 System.out.println( n16.toString() );
12550 final PhylogenyNode n17 = PhylogenyNode
12551 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12552 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12553 System.out.println( n17.toString() );
12556 final PhylogenyNode n18 = PhylogenyNode
12557 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12558 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12559 System.out.println( n18.toString() );
12562 final PhylogenyNode n19 = PhylogenyNode
12563 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12564 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12565 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12566 System.out.println( n19.toString() );
12569 final PhylogenyNode n20 = PhylogenyNode
12570 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12571 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12572 System.out.println( n20.toString() );
12575 final PhylogenyNode n21 = PhylogenyNode
12576 .createInstanceFromNhxString( "Mus musculus musculus K392",
12577 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12578 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12579 System.out.println( n21.toString() );
12582 final PhylogenyNode n23 = PhylogenyNode
12583 .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
12584 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12585 if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12586 System.out.println( n23.toString() );
12589 final PhylogenyNode n24 = PhylogenyNode
12590 .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12591 if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12592 System.out.println( n24.toString() );
12596 final PhylogenyNode n25 = PhylogenyNode
12597 .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
12598 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12599 if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
12600 System.out.println( n25.toString() );
12603 final PhylogenyNode n26 = PhylogenyNode
12604 .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
12605 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12606 if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12607 System.out.println( n26.toString() );
12610 final PhylogenyNode n27 = PhylogenyNode
12611 .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12612 if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12613 System.out.println( n27.toString() );
12617 catch ( final Exception e ) {
12618 e.printStackTrace( System.out );
12624 private static boolean testTreeCopy() {
12626 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12627 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12628 final Phylogeny t1 = t0.copy();
12629 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12632 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12635 t0.deleteSubtree( t0.getNode( "c" ), true );
12636 t0.deleteSubtree( t0.getNode( "a" ), true );
12637 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12638 t0.getNode( "b" ).setName( "Bee" );
12639 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12642 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12645 t0.deleteSubtree( t0.getNode( "e" ), true );
12646 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12647 t0.deleteSubtree( t0.getNode( "d" ), true );
12648 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12652 catch ( final Exception e ) {
12653 e.printStackTrace();
12659 private static boolean testTreeMethods() {
12661 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12662 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12663 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12664 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12665 System.out.println( t0.toNewHampshireX() );
12668 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12669 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12670 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12673 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12676 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12680 catch ( final Exception e ) {
12681 e.printStackTrace( System.out );
12687 private static boolean testUniprotEntryRetrieval() {
12689 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
12690 if ( !entry.getAccession().equals( "P12345" ) ) {
12693 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12696 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12699 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12702 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12705 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12708 if ( entry.getMolecularSequence() == null ) {
12712 .getMolecularSequence()
12713 .getMolecularSequenceAsString()
12714 .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
12715 || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
12716 System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() );
12717 System.out.println( "expected something else." );
12721 catch ( final IOException e ) {
12722 System.out.println();
12723 System.out.println( "the following might be due to absence internet connection:" );
12724 e.printStackTrace( System.out );
12727 catch ( final NullPointerException f ) {
12728 f.printStackTrace( System.out );
12731 catch ( final Exception e ) {
12737 private static boolean testUniprotTaxonomySearch() {
12739 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12741 if ( results.size() != 1 ) {
12744 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12747 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12750 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12753 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12756 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12760 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12761 if ( results.size() != 1 ) {
12764 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12767 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12770 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12773 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12776 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12780 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12781 if ( results.size() != 1 ) {
12784 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12787 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12790 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12793 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12796 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12800 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12801 if ( results.size() != 1 ) {
12804 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12807 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12810 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12813 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12816 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12819 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12822 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12825 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12826 .equals( "Nematostella vectensis" ) ) {
12827 System.out.println( results.get( 0 ).getLineage() );
12832 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12833 if ( results.size() != 1 ) {
12836 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12839 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12842 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12845 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12848 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12851 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12852 .equals( "Xenopus tropicalis" ) ) {
12853 System.out.println( results.get( 0 ).getLineage() );
12858 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12859 if ( results.size() != 1 ) {
12862 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12865 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12868 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12871 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12874 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12877 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12878 .equals( "Xenopus tropicalis" ) ) {
12879 System.out.println( results.get( 0 ).getLineage() );
12884 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12885 if ( results.size() != 1 ) {
12888 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12891 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12894 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12897 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12900 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12903 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12904 .equals( "Xenopus tropicalis" ) ) {
12905 System.out.println( results.get( 0 ).getLineage() );
12909 catch ( final IOException e ) {
12910 System.out.println();
12911 System.out.println( "the following might be due to absence internet connection:" );
12912 e.printStackTrace( System.out );
12915 catch ( final Exception e ) {
12921 private static boolean testWabiTxSearch() {
12923 String result = "";
12924 result = TxSearch.searchSimple( "nematostella" );
12925 result = TxSearch.getTxId( "nematostella" );
12926 if ( !result.equals( "45350" ) ) {
12929 result = TxSearch.getTxName( "45350" );
12930 if ( !result.equals( "Nematostella" ) ) {
12933 result = TxSearch.getTxId( "nematostella vectensis" );
12934 if ( !result.equals( "45351" ) ) {
12937 result = TxSearch.getTxName( "45351" );
12938 if ( !result.equals( "Nematostella vectensis" ) ) {
12941 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12942 if ( !result.equals( "536089" ) ) {
12945 result = TxSearch.getTxName( "536089" );
12946 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12949 final List<String> queries = new ArrayList<String>();
12950 queries.add( "Campylobacter coli" );
12951 queries.add( "Escherichia coli" );
12952 queries.add( "Arabidopsis" );
12953 queries.add( "Trichoplax" );
12954 queries.add( "Samanea saman" );
12955 queries.add( "Kluyveromyces marxianus" );
12956 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12957 queries.add( "Bornavirus parrot/PDD/2008" );
12958 final List<RANKS> ranks = new ArrayList<RANKS>();
12959 ranks.add( RANKS.SUPERKINGDOM );
12960 ranks.add( RANKS.KINGDOM );
12961 ranks.add( RANKS.FAMILY );
12962 ranks.add( RANKS.GENUS );
12963 ranks.add( RANKS.TRIBE );
12964 result = TxSearch.searchLineage( queries, ranks );
12965 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12966 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12968 catch ( final Exception e ) {
12969 System.out.println();
12970 System.out.println( "the following might be due to absence internet connection:" );
12971 e.printStackTrace( System.out );