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( "MSA entropy: " );
185 if ( Test.testMsaEntropy() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Basic node methods: " );
194 if ( Test.testBasicNodeMethods() ) {
195 System.out.println( "OK." );
199 System.out.println( "failed." );
202 System.out.print( "Protein id: " );
203 if ( !testProteinId() ) {
204 System.out.println( "failed." );
210 System.out.println( "OK." );
211 System.out.print( "Species: " );
212 if ( !testSpecies() ) {
213 System.out.println( "failed." );
219 System.out.println( "OK." );
220 System.out.print( "Basic domain: " );
221 if ( !testBasicDomain() ) {
222 System.out.println( "failed." );
228 System.out.println( "OK." );
229 System.out.print( "Basic protein: " );
230 if ( !testBasicProtein() ) {
231 System.out.println( "failed." );
237 System.out.println( "OK." );
238 System.out.print( "Sequence writer: " );
239 if ( testSequenceWriter() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "Sequence id parsing: " );
248 if ( testSequenceIdParsing() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "UniProtKB id extraction: " );
257 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "Sequence DB tools 1: " );
266 if ( testSequenceDbWsTools1() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "Hmmscan output parser: " );
275 if ( testHmmscanOutputParser() ) {
276 System.out.println( "OK." );
280 System.out.println( "failed." );
283 System.out.print( "Overlap removal: " );
284 if ( !org.forester.test.Test.testOverlapRemoval() ) {
285 System.out.println( "failed." );
291 System.out.println( "OK." );
292 System.out.print( "Engulfing overlap removal: " );
293 if ( !Test.testEngulfingOverlapRemoval() ) {
294 System.out.println( "failed." );
300 System.out.println( "OK." );
301 System.out.print( "Taxonomy data extraction: " );
302 if ( Test.testExtractTaxonomyDataFromNodeName() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "Taxonomy code extraction: " );
311 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "SN extraction: " );
320 if ( Test.testExtractSNFromNodeName() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Taxonomy extraction (general): " );
329 if ( Test.testTaxonomyExtraction() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "Uri for Aptx web sequence accession: " );
338 if ( Test.testCreateUriForSeqWeb() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "Basic node construction and parsing of NHX (node level): " );
347 if ( Test.testNHXNodeParsing() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "NHX parsing iterating: " );
356 if ( Test.testNHParsingIter() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "NH parsing: " );
365 if ( Test.testNHParsing() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "Conversion to NHX (node level): " );
374 if ( Test.testNHXconversion() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "NHX parsing: " );
383 if ( Test.testNHXParsing() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "NHX parsing with quotes: " );
392 if ( Test.testNHXParsingQuotes() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "NHX parsing (MrBayes): " );
401 if ( Test.testNHXParsingMB() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Nexus characters parsing: " );
410 if ( Test.testNexusCharactersParsing() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Nexus tree parsing iterating: " );
419 if ( Test.testNexusTreeParsingIterating() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Nexus tree parsing: " );
428 if ( Test.testNexusTreeParsing() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Nexus tree parsing (translating): " );
437 if ( Test.testNexusTreeParsingTranslating() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Nexus matrix parsing: " );
446 if ( Test.testNexusMatrixParsing() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Basic phyloXML parsing: " );
455 if ( Test.testBasicPhyloXMLparsing() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Basic phyloXML parsing (validating against schema): " );
464 if ( testBasicPhyloXMLparsingValidating() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
473 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "phyloXML Distribution Element: " );
482 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "Tol XML parsing: " );
491 if ( Test.testBasicTolXMLparsing() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Copying of node data: " );
500 if ( Test.testCopyOfNodeData() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "Tree copy: " );
509 if ( Test.testTreeCopy() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "Basic tree methods: " );
518 if ( Test.testBasicTreeMethods() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Tree methods: " );
527 if ( Test.testTreeMethods() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Postorder Iterator: " );
536 if ( Test.testPostOrderIterator() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Preorder Iterator: " );
545 if ( Test.testPreOrderIterator() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Levelorder Iterator: " );
554 if ( Test.testLevelOrderIterator() ) {
555 System.out.println( "OK." );
559 System.out.println( "failed." );
562 System.out.print( "Re-id methods: " );
563 if ( Test.testReIdMethods() ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "Methods on last external nodes: " );
572 if ( Test.testLastExternalNodeMethods() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "Methods on external nodes: " );
581 if ( Test.testExternalNodeRelatedMethods() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Deletion of external nodes: " );
590 if ( Test.testDeletionOfExternalNodes() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Subtree deletion: " );
599 if ( Test.testSubtreeDeletion() ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Phylogeny branch: " );
608 if ( Test.testPhylogenyBranch() ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "Rerooting: " );
617 if ( Test.testRerooting() ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Mipoint rooting: " );
626 if ( Test.testMidpointrooting() ) {
627 System.out.println( "OK." );
631 System.out.println( "failed." );
634 System.out.print( "Node removal: " );
635 if ( Test.testNodeRemoval() ) {
636 System.out.println( "OK." );
640 System.out.println( "failed." );
643 System.out.print( "Support count: " );
644 if ( Test.testSupportCount() ) {
645 System.out.println( "OK." );
649 System.out.println( "failed." );
652 System.out.print( "Support transfer: " );
653 if ( Test.testSupportTransfer() ) {
654 System.out.println( "OK." );
658 System.out.println( "failed." );
661 System.out.print( "Finding of LCA: " );
662 if ( Test.testGetLCA() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Finding of LCA 2: " );
671 if ( Test.testGetLCA2() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 System.out.print( "Calculation of distance between nodes: " );
680 if ( Test.testGetDistance() ) {
681 System.out.println( "OK." );
685 System.out.println( "failed." );
688 System.out.print( "Descriptive statistics: " );
689 if ( Test.testDescriptiveStatistics() ) {
690 System.out.println( "OK." );
694 System.out.println( "failed." );
697 System.out.print( "Data objects and methods: " );
698 if ( Test.testDataObjects() ) {
699 System.out.println( "OK." );
703 System.out.println( "failed." );
706 System.out.print( "Properties map: " );
707 if ( Test.testPropertiesMap() ) {
708 System.out.println( "OK." );
712 System.out.println( "failed." );
715 System.out.print( "SDIse: " );
716 if ( Test.testSDIse() ) {
717 System.out.println( "OK." );
721 System.out.println( "failed." );
724 System.out.print( "SDIunrooted: " );
725 if ( Test.testSDIunrooted() ) {
726 System.out.println( "OK." );
730 System.out.println( "failed." );
733 System.out.print( "GSDI: " );
734 if ( TestGSDI.test() ) {
735 System.out.println( "OK." );
739 System.out.println( "failed." );
742 System.out.print( "RIO: " );
743 if ( TestRIO.test() ) {
744 System.out.println( "OK." );
748 System.out.println( "failed." );
751 System.out.print( "Phylogeny reconstruction:" );
752 System.out.println();
753 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
754 System.out.println( "OK." );
758 System.out.println( "failed." );
761 System.out.print( "Analysis of domain architectures: " );
762 System.out.println();
763 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
764 System.out.println( "OK." );
768 System.out.println( "failed." );
771 System.out.print( "GO: " );
772 System.out.println();
773 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
774 System.out.println( "OK." );
778 System.out.println( "failed." );
781 System.out.print( "Modeling tools: " );
782 if ( TestPccx.test() ) {
783 System.out.println( "OK." );
787 System.out.println( "failed." );
790 System.out.print( "Split Matrix strict: " );
791 if ( Test.testSplitStrict() ) {
792 System.out.println( "OK." );
796 System.out.println( "failed." );
799 System.out.print( "Split Matrix: " );
800 if ( Test.testSplit() ) {
801 System.out.println( "OK." );
805 System.out.println( "failed." );
808 System.out.print( "Confidence Assessor: " );
809 if ( Test.testConfidenceAssessor() ) {
810 System.out.println( "OK." );
814 System.out.println( "failed." );
817 System.out.print( "Basic table: " );
818 if ( Test.testBasicTable() ) {
819 System.out.println( "OK." );
823 System.out.println( "failed." );
826 System.out.print( "General table: " );
827 if ( Test.testGeneralTable() ) {
828 System.out.println( "OK." );
832 System.out.println( "failed." );
835 System.out.print( "Amino acid sequence: " );
836 if ( Test.testAminoAcidSequence() ) {
837 System.out.println( "OK." );
841 System.out.println( "failed." );
844 System.out.print( "General MSA parser: " );
845 if ( Test.testGeneralMsaParser() ) {
846 System.out.println( "OK." );
850 System.out.println( "failed." );
853 System.out.print( "Fasta parser for msa: " );
854 if ( Test.testFastaParser() ) {
855 System.out.println( "OK." );
859 System.out.println( "failed." );
862 System.out.print( "Creation of balanced phylogeny: " );
863 if ( Test.testCreateBalancedPhylogeny() ) {
864 System.out.println( "OK." );
868 System.out.println( "failed." );
871 System.out.print( "Genbank accessor parsing: " );
872 if ( Test.testGenbankAccessorParsing() ) {
873 System.out.println( "OK." );
877 System.out.println( "failed." );
881 final String os = ForesterUtil.OS_NAME.toLowerCase();
882 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
883 path = "/usr/local/bin/mafft";
885 else if ( os.indexOf( "win" ) >= 0 ) {
886 path = "C:\\Program Files\\mafft-win\\mafft.bat";
890 if ( !MsaInferrer.isInstalled( path ) ) {
891 path = "/usr/bin/mafft";
893 if ( !MsaInferrer.isInstalled( path ) ) {
894 path = "/usr/local/bin/mafft";
897 if ( MsaInferrer.isInstalled( path ) ) {
898 System.out.print( "MAFFT (external program): " );
899 if ( Test.testMafft( path ) ) {
900 System.out.println( "OK." );
904 System.out.println( "failed [will not count towards failed tests]" );
907 System.out.print( "Next nodes with collapsed: " );
908 if ( Test.testNextNodeWithCollapsing() ) {
909 System.out.println( "OK." );
913 System.out.println( "failed." );
916 System.out.print( "Simple MSA quality: " );
917 if ( Test.testMsaQualityMethod() ) {
918 System.out.println( "OK." );
922 System.out.println( "failed." );
925 System.out.print( "Deleteable MSA: " );
926 if ( Test.testDeleteableMsa() ) {
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" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1782 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1783 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1786 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1789 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1792 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1795 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1796 .equals( "apoptosis" ) ) {
1799 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1800 .equals( "GO:0006915" ) ) {
1803 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1804 .equals( "UniProtKB" ) ) {
1807 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1808 .equals( "experimental" ) ) {
1811 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1812 .equals( "function" ) ) {
1815 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1816 .getValue() != 1 ) {
1819 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1820 .getType().equals( "ml" ) ) {
1823 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1824 .equals( "apoptosis" ) ) {
1827 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1828 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1831 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1832 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1835 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1836 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1839 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1840 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1843 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1844 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1847 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1848 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1851 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1852 .equals( "GO:0005829" ) ) {
1855 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1856 .equals( "intracellular organelle" ) ) {
1859 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1862 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1863 .equals( "UniProt link" ) ) ) {
1866 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1869 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1870 if ( x.size() != 4 ) {
1874 for( final Accession acc : x ) {
1876 if ( !acc.getSource().equals( "KEGG" ) ) {
1879 if ( !acc.getValue().equals( "hsa:596" ) ) {
1886 catch ( final Exception e ) {
1887 e.printStackTrace( System.out );
1893 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1896 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1897 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1898 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1901 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1903 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1905 if ( xml_parser.getErrorCount() > 0 ) {
1906 System.out.println( xml_parser.getErrorMessages().toString() );
1909 if ( phylogenies_0.length != 4 ) {
1912 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1913 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1914 if ( phylogenies_t1.length != 1 ) {
1917 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1918 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1921 if ( !t1_rt.isRooted() ) {
1924 if ( t1_rt.isRerootable() ) {
1927 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1930 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1931 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1932 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1933 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1936 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1939 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1942 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1945 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1946 .startsWith( "actgtgggggt" ) ) {
1949 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1950 .startsWith( "ctgtgatgcat" ) ) {
1953 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1954 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1955 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1956 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1957 if ( phylogenies_1.length != 1 ) {
1960 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1961 if ( !t3_rt.getName().equals( "t3" ) ) {
1964 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1967 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1970 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1973 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1976 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1977 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1980 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1983 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1986 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1987 .equals( "UniProtKB" ) ) {
1990 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1991 .equals( "apoptosis" ) ) {
1994 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1995 .equals( "GO:0006915" ) ) {
1998 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1999 .equals( "UniProtKB" ) ) {
2002 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
2003 .equals( "experimental" ) ) {
2006 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
2007 .equals( "function" ) ) {
2010 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2011 .getValue() != 1 ) {
2014 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2015 .getType().equals( "ml" ) ) {
2018 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2019 .equals( "apoptosis" ) ) {
2022 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2023 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
2026 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2027 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
2030 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2031 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
2034 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2035 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
2038 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2039 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
2042 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2043 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
2046 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
2047 .equals( "GO:0005829" ) ) {
2050 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
2051 .equals( "intracellular organelle" ) ) {
2054 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
2057 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
2058 .equals( "UniProt link" ) ) ) {
2061 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
2064 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
2067 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
2068 .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." ) ) ) {
2071 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
2074 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
2077 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
2080 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
2083 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
2084 .equals( "ncbi" ) ) {
2087 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
2090 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2091 .getName().equals( "B" ) ) {
2094 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2095 .getFrom() != 21 ) {
2098 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
2101 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2102 .getLength() != 24 ) {
2105 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2106 .getConfidence() != 2144 ) {
2109 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2110 .equals( "pfam" ) ) {
2113 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2116 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2119 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2122 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2125 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2126 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2129 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2132 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2135 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2138 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2141 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2144 if ( taxbb.getSynonyms().size() != 2 ) {
2147 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2150 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2153 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2156 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2159 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2162 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2163 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2166 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2169 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2172 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2175 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2178 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2181 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2184 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2187 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2190 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2191 .equalsIgnoreCase( "435" ) ) {
2194 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2197 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2198 .equalsIgnoreCase( "443.7" ) ) {
2201 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2204 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2207 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2208 .equalsIgnoreCase( "433" ) ) {
2211 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2212 .getCrossReferences();
2213 if ( x.size() != 4 ) {
2217 for( final Accession acc : x ) {
2219 if ( !acc.getSource().equals( "KEGG" ) ) {
2222 if ( !acc.getValue().equals( "hsa:596" ) ) {
2229 catch ( final Exception e ) {
2230 e.printStackTrace( System.out );
2236 private static boolean testBasicPhyloXMLparsingValidating() {
2238 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2239 PhyloXmlParser xml_parser = null;
2241 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2243 catch ( final Exception e ) {
2244 // Do nothing -- means were not running from jar.
2246 if ( xml_parser == null ) {
2247 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2248 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2249 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2252 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2255 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2257 if ( xml_parser.getErrorCount() > 0 ) {
2258 System.out.println( xml_parser.getErrorMessages().toString() );
2261 if ( phylogenies_0.length != 4 ) {
2264 final Phylogeny t1 = phylogenies_0[ 0 ];
2265 final Phylogeny t2 = phylogenies_0[ 1 ];
2266 final Phylogeny t3 = phylogenies_0[ 2 ];
2267 final Phylogeny t4 = phylogenies_0[ 3 ];
2268 if ( !t1.getName().equals( "t1" ) ) {
2271 if ( !t2.getName().equals( "t2" ) ) {
2274 if ( !t3.getName().equals( "t3" ) ) {
2277 if ( !t4.getName().equals( "t4" ) ) {
2280 if ( t1.getNumberOfExternalNodes() != 1 ) {
2283 if ( t2.getNumberOfExternalNodes() != 2 ) {
2286 if ( t3.getNumberOfExternalNodes() != 4 ) {
2289 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2290 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2291 if ( xml_parser.getErrorCount() > 0 ) {
2292 System.out.println( "errors:" );
2293 System.out.println( xml_parser.getErrorMessages().toString() );
2296 if ( phylogenies_1.length != 4 ) {
2299 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2301 if ( xml_parser.getErrorCount() > 0 ) {
2302 System.out.println( "errors:" );
2303 System.out.println( xml_parser.getErrorMessages().toString() );
2306 if ( phylogenies_2.length != 1 ) {
2309 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2312 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2314 if ( xml_parser.getErrorCount() > 0 ) {
2315 System.out.println( xml_parser.getErrorMessages().toString() );
2318 if ( phylogenies_3.length != 2 ) {
2321 final Phylogeny a = phylogenies_3[ 0 ];
2322 if ( !a.getName().equals( "tree 4" ) ) {
2325 if ( a.getNumberOfExternalNodes() != 3 ) {
2328 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2331 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2334 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2336 if ( xml_parser.getErrorCount() > 0 ) {
2337 System.out.println( xml_parser.getErrorMessages().toString() );
2340 if ( phylogenies_4.length != 1 ) {
2343 final Phylogeny s = phylogenies_4[ 0 ];
2344 if ( s.getNumberOfExternalNodes() != 6 ) {
2347 s.getNode( "first" );
2349 s.getNode( "\"<a'b&c'd\">\"" );
2350 s.getNode( "'''\"" );
2351 s.getNode( "\"\"\"" );
2352 s.getNode( "dick & doof" );
2354 catch ( final Exception e ) {
2355 e.printStackTrace( System.out );
2361 private static boolean testBasicProtein() {
2363 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2364 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2365 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2366 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2367 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2368 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2369 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2370 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2371 p0.addProteinDomain( y );
2372 p0.addProteinDomain( e );
2373 p0.addProteinDomain( b );
2374 p0.addProteinDomain( c );
2375 p0.addProteinDomain( d );
2376 p0.addProteinDomain( a );
2377 p0.addProteinDomain( x );
2378 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2381 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2385 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2386 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2387 aa0.addProteinDomain( a1 );
2388 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2391 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2395 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2396 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2397 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2398 aa1.addProteinDomain( a11 );
2399 aa1.addProteinDomain( a12 );
2400 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2403 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2406 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2407 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2410 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2413 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2416 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2417 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2420 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2423 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2426 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2429 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2430 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2433 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2436 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2439 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2442 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2443 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2446 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2449 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2452 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2456 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2457 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2458 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2459 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2460 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2461 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2462 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2463 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2464 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2465 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2466 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2467 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2468 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2469 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2470 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2471 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2472 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2473 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2474 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2475 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2476 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2477 p00.addProteinDomain( y0 );
2478 p00.addProteinDomain( e0 );
2479 p00.addProteinDomain( b0 );
2480 p00.addProteinDomain( c0 );
2481 p00.addProteinDomain( d0 );
2482 p00.addProteinDomain( a0 );
2483 p00.addProteinDomain( x0 );
2484 p00.addProteinDomain( y1 );
2485 p00.addProteinDomain( y2 );
2486 p00.addProteinDomain( y3 );
2487 p00.addProteinDomain( e1 );
2488 p00.addProteinDomain( e2 );
2489 p00.addProteinDomain( e3 );
2490 p00.addProteinDomain( e4 );
2491 p00.addProteinDomain( e5 );
2492 p00.addProteinDomain( z0 );
2493 p00.addProteinDomain( z1 );
2494 p00.addProteinDomain( z2 );
2495 p00.addProteinDomain( zz0 );
2496 p00.addProteinDomain( zz1 );
2497 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2500 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2503 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2506 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2509 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" ) ) {
2512 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2513 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2514 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2515 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2516 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2517 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2518 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2519 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2520 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2521 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2522 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2523 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2524 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2525 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2526 p.addProteinDomain( B15 );
2527 p.addProteinDomain( C50 );
2528 p.addProteinDomain( A60 );
2529 p.addProteinDomain( A30 );
2530 p.addProteinDomain( C70 );
2531 p.addProteinDomain( B35 );
2532 p.addProteinDomain( B40 );
2533 p.addProteinDomain( A0 );
2534 p.addProteinDomain( A10 );
2535 p.addProteinDomain( A20 );
2536 p.addProteinDomain( B25 );
2537 p.addProteinDomain( D80 );
2538 List<String> domains_ids = new ArrayList<String>();
2539 domains_ids.add( "A" );
2540 domains_ids.add( "B" );
2541 domains_ids.add( "C" );
2542 if ( !p.contains( domains_ids, false ) ) {
2545 if ( !p.contains( domains_ids, true ) ) {
2548 domains_ids.add( "X" );
2549 if ( p.contains( domains_ids, false ) ) {
2552 if ( p.contains( domains_ids, true ) ) {
2555 domains_ids = new ArrayList<String>();
2556 domains_ids.add( "A" );
2557 domains_ids.add( "C" );
2558 domains_ids.add( "D" );
2559 if ( !p.contains( domains_ids, false ) ) {
2562 if ( !p.contains( domains_ids, true ) ) {
2565 domains_ids = new ArrayList<String>();
2566 domains_ids.add( "A" );
2567 domains_ids.add( "D" );
2568 domains_ids.add( "C" );
2569 if ( !p.contains( domains_ids, false ) ) {
2572 if ( p.contains( domains_ids, true ) ) {
2575 domains_ids = new ArrayList<String>();
2576 domains_ids.add( "A" );
2577 domains_ids.add( "A" );
2578 domains_ids.add( "B" );
2579 if ( !p.contains( domains_ids, false ) ) {
2582 if ( !p.contains( domains_ids, true ) ) {
2585 domains_ids = new ArrayList<String>();
2586 domains_ids.add( "A" );
2587 domains_ids.add( "A" );
2588 domains_ids.add( "A" );
2589 domains_ids.add( "B" );
2590 domains_ids.add( "B" );
2591 if ( !p.contains( domains_ids, false ) ) {
2594 if ( !p.contains( domains_ids, true ) ) {
2597 domains_ids = new ArrayList<String>();
2598 domains_ids.add( "A" );
2599 domains_ids.add( "A" );
2600 domains_ids.add( "B" );
2601 domains_ids.add( "A" );
2602 domains_ids.add( "B" );
2603 domains_ids.add( "B" );
2604 domains_ids.add( "A" );
2605 domains_ids.add( "B" );
2606 domains_ids.add( "C" );
2607 domains_ids.add( "A" );
2608 domains_ids.add( "C" );
2609 domains_ids.add( "D" );
2610 if ( !p.contains( domains_ids, false ) ) {
2613 if ( p.contains( domains_ids, true ) ) {
2617 catch ( final Exception e ) {
2618 e.printStackTrace( System.out );
2624 private static boolean testBasicTable() {
2626 final BasicTable<String> t0 = new BasicTable<String>();
2627 if ( t0.getNumberOfColumns() != 0 ) {
2630 if ( t0.getNumberOfRows() != 0 ) {
2633 t0.setValue( 3, 2, "23" );
2634 t0.setValue( 10, 1, "error" );
2635 t0.setValue( 10, 1, "110" );
2636 t0.setValue( 9, 1, "19" );
2637 t0.setValue( 1, 10, "101" );
2638 t0.setValue( 10, 10, "1010" );
2639 t0.setValue( 100, 10, "10100" );
2640 t0.setValue( 0, 0, "00" );
2641 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2644 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2647 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2650 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2653 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2656 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2659 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2662 if ( t0.getNumberOfColumns() != 101 ) {
2665 if ( t0.getNumberOfRows() != 11 ) {
2668 if ( t0.getValueAsString( 49, 4 ) != null ) {
2671 final String l = ForesterUtil.getLineSeparator();
2672 final StringBuffer source = new StringBuffer();
2673 source.append( "" + l );
2674 source.append( "# 1 1 1 1 1 1 1 1" + l );
2675 source.append( " 00 01 02 03" + l );
2676 source.append( " 10 11 12 13 " + l );
2677 source.append( "20 21 22 23 " + l );
2678 source.append( " 30 31 32 33" + l );
2679 source.append( "40 41 42 43" + l );
2680 source.append( " # 1 1 1 1 1 " + l );
2681 source.append( "50 51 52 53 54" + l );
2682 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2683 if ( t1.getNumberOfColumns() != 5 ) {
2686 if ( t1.getNumberOfRows() != 6 ) {
2689 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2692 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2695 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2698 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2701 final StringBuffer source1 = new StringBuffer();
2702 source1.append( "" + l );
2703 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2704 source1.append( " 00; 01 ;02;03" + l );
2705 source1.append( " 10; 11; 12; 13 " + l );
2706 source1.append( "20; 21; 22; 23 " + l );
2707 source1.append( " 30; 31; 32; 33" + l );
2708 source1.append( "40;41;42;43" + l );
2709 source1.append( " # 1 1 1 1 1 " + l );
2710 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2711 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2712 if ( t2.getNumberOfColumns() != 5 ) {
2715 if ( t2.getNumberOfRows() != 6 ) {
2718 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2721 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2724 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2727 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2730 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2733 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2736 final StringBuffer source2 = new StringBuffer();
2737 source2.append( "" + l );
2738 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2739 source2.append( " 00; 01 ;02;03" + l );
2740 source2.append( " 10; 11; 12; 13 " + l );
2741 source2.append( "20; 21; 22; 23 " + l );
2742 source2.append( " " + l );
2743 source2.append( " 30; 31; 32; 33" + l );
2744 source2.append( "40;41;42;43" + l );
2745 source2.append( " comment: 1 1 1 1 1 " + l );
2746 source2.append( ";;;50 ; 52; 53;;54 " + l );
2747 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2753 if ( tl.size() != 2 ) {
2756 final BasicTable<String> t3 = tl.get( 0 );
2757 final BasicTable<String> t4 = tl.get( 1 );
2758 if ( t3.getNumberOfColumns() != 4 ) {
2761 if ( t3.getNumberOfRows() != 3 ) {
2764 if ( t4.getNumberOfColumns() != 4 ) {
2767 if ( t4.getNumberOfRows() != 3 ) {
2770 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2773 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2777 catch ( final Exception e ) {
2778 e.printStackTrace( System.out );
2784 private static boolean testBasicTolXMLparsing() {
2786 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2787 final TolParser parser = new TolParser();
2788 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2789 if ( parser.getErrorCount() > 0 ) {
2790 System.out.println( parser.getErrorMessages().toString() );
2793 if ( phylogenies_0.length != 1 ) {
2796 final Phylogeny t1 = phylogenies_0[ 0 ];
2797 if ( t1.getNumberOfExternalNodes() != 5 ) {
2800 if ( !t1.isRooted() ) {
2803 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2806 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2809 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2812 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2815 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2816 if ( parser.getErrorCount() > 0 ) {
2817 System.out.println( parser.getErrorMessages().toString() );
2820 if ( phylogenies_1.length != 1 ) {
2823 final Phylogeny t2 = phylogenies_1[ 0 ];
2824 if ( t2.getNumberOfExternalNodes() != 664 ) {
2827 if ( !t2.isRooted() ) {
2830 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2833 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2836 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2839 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2842 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2845 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2846 .equals( "Aquifex" ) ) {
2849 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2850 if ( parser.getErrorCount() > 0 ) {
2851 System.out.println( parser.getErrorMessages().toString() );
2854 if ( phylogenies_2.length != 1 ) {
2857 final Phylogeny t3 = phylogenies_2[ 0 ];
2858 if ( t3.getNumberOfExternalNodes() != 184 ) {
2861 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2864 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2867 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2870 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2871 if ( parser.getErrorCount() > 0 ) {
2872 System.out.println( parser.getErrorMessages().toString() );
2875 if ( phylogenies_3.length != 1 ) {
2878 final Phylogeny t4 = phylogenies_3[ 0 ];
2879 if ( t4.getNumberOfExternalNodes() != 1 ) {
2882 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2885 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2888 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2891 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2892 if ( parser.getErrorCount() > 0 ) {
2893 System.out.println( parser.getErrorMessages().toString() );
2896 if ( phylogenies_4.length != 1 ) {
2899 final Phylogeny t5 = phylogenies_4[ 0 ];
2900 if ( t5.getNumberOfExternalNodes() != 13 ) {
2903 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2906 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2909 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2913 catch ( final Exception e ) {
2914 e.printStackTrace( System.out );
2920 private static boolean testBasicTreeMethods() {
2922 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2923 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2924 if ( t2.getNumberOfExternalNodes() != 4 ) {
2927 if ( t2.getHeight() != 8.5 ) {
2930 if ( !t2.isCompletelyBinary() ) {
2933 if ( t2.isEmpty() ) {
2936 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2937 if ( t3.getNumberOfExternalNodes() != 5 ) {
2940 if ( t3.getHeight() != 11 ) {
2943 if ( t3.isCompletelyBinary() ) {
2946 final PhylogenyNode n = t3.getNode( "ABC" );
2947 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 ];
2948 if ( t4.getNumberOfExternalNodes() != 9 ) {
2951 if ( t4.getHeight() != 11 ) {
2954 if ( t4.isCompletelyBinary() ) {
2957 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)" );
2958 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2959 if ( t5.getNumberOfExternalNodes() != 8 ) {
2962 if ( t5.getHeight() != 15 ) {
2965 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)" );
2966 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2967 if ( t6.getHeight() != 15 ) {
2970 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)" );
2971 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2972 if ( t7.getHeight() != 15 ) {
2975 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)" );
2976 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2977 if ( t8.getNumberOfExternalNodes() != 10 ) {
2980 if ( t8.getHeight() != 15 ) {
2983 final char[] a9 = new char[] { 'a' };
2984 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2985 if ( t9.getHeight() != 0 ) {
2988 final char[] a10 = new char[] { 'a', ':', '6' };
2989 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2990 if ( t10.getHeight() != 6 ) {
2994 catch ( final Exception e ) {
2995 e.printStackTrace( System.out );
3001 private static boolean testConfidenceAssessor() {
3003 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3004 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3005 final Phylogeny[] ev0 = factory
3006 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
3008 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
3009 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3012 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3015 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3016 final Phylogeny[] ev1 = factory
3017 .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)));",
3019 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
3020 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
3023 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3026 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3027 final Phylogeny[] ev_b = factory
3028 .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",
3030 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
3031 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
3034 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3038 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3039 final Phylogeny[] ev1x = factory
3040 .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)));",
3042 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
3043 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3046 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3049 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3050 final Phylogeny[] ev_bx = factory
3051 .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",
3053 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
3054 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3057 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3060 final Phylogeny[] t2 = factory
3061 .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);",
3063 final Phylogeny[] ev2 = factory
3064 .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);",
3066 for( final Phylogeny target : t2 ) {
3067 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
3069 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
3070 new NHXParser() )[ 0 ];
3071 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
3072 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
3073 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3076 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
3079 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3083 catch ( final Exception e ) {
3084 e.printStackTrace();
3090 private static boolean testCopyOfNodeData() {
3092 final PhylogenyNode n1 = PhylogenyNode
3093 .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]" );
3094 final PhylogenyNode n2 = n1.copyNodeData();
3095 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
3099 catch ( final Exception e ) {
3100 e.printStackTrace();
3106 private static boolean testCreateBalancedPhylogeny() {
3108 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3109 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3112 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3115 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3116 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3119 if ( p1.getNumberOfExternalNodes() != 100 ) {
3123 catch ( final Exception e ) {
3124 e.printStackTrace();
3130 private static boolean testCreateUriForSeqWeb() {
3132 final PhylogenyNode n = new PhylogenyNode();
3133 n.setName( "tr|B3RJ64" );
3134 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3137 n.setName( "B0LM41_HUMAN" );
3138 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3141 n.setName( "NP_001025424" );
3142 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3145 n.setName( "_NM_001030253-" );
3146 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3149 n.setName( "XM_002122186" );
3150 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3153 n.setName( "dgh_AAA34956_gdg" );
3154 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3157 n.setName( "AAA34956" );
3158 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3161 n.setName( "GI:394892" );
3162 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3163 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3166 n.setName( "gi_394892" );
3167 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3168 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3171 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3172 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3173 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3176 n.setName( "P12345" );
3177 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3178 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3181 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3182 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3183 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3187 catch ( final Exception e ) {
3188 e.printStackTrace( System.out );
3194 private static boolean testDataObjects() {
3196 final Confidence s0 = new Confidence();
3197 final Confidence s1 = new Confidence();
3198 if ( !s0.isEqual( s1 ) ) {
3201 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3202 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3203 if ( s2.isEqual( s1 ) ) {
3206 if ( !s2.isEqual( s3 ) ) {
3209 final Confidence s4 = ( Confidence ) s3.copy();
3210 if ( !s4.isEqual( s3 ) ) {
3217 final Taxonomy t1 = new Taxonomy();
3218 final Taxonomy t2 = new Taxonomy();
3219 final Taxonomy t3 = new Taxonomy();
3220 final Taxonomy t4 = new Taxonomy();
3221 final Taxonomy t5 = new Taxonomy();
3222 t1.setIdentifier( new Identifier( "ecoli" ) );
3223 t1.setTaxonomyCode( "ECOLI" );
3224 t1.setScientificName( "E. coli" );
3225 t1.setCommonName( "coli" );
3226 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3227 if ( !t1.isEqual( t0 ) ) {
3230 t2.setIdentifier( new Identifier( "ecoli" ) );
3231 t2.setTaxonomyCode( "OTHER" );
3232 t2.setScientificName( "what" );
3233 t2.setCommonName( "something" );
3234 if ( !t1.isEqual( t2 ) ) {
3237 t2.setIdentifier( new Identifier( "nemve" ) );
3238 if ( t1.isEqual( t2 ) ) {
3241 t1.setIdentifier( null );
3242 t3.setTaxonomyCode( "ECOLI" );
3243 t3.setScientificName( "what" );
3244 t3.setCommonName( "something" );
3245 if ( !t1.isEqual( t3 ) ) {
3248 t1.setIdentifier( null );
3249 t1.setTaxonomyCode( "" );
3250 t4.setScientificName( "E. ColI" );
3251 t4.setCommonName( "something" );
3252 if ( !t1.isEqual( t4 ) ) {
3255 t4.setScientificName( "B. subtilis" );
3256 t4.setCommonName( "something" );
3257 if ( t1.isEqual( t4 ) ) {
3260 t1.setIdentifier( null );
3261 t1.setTaxonomyCode( "" );
3262 t1.setScientificName( "" );
3263 t5.setCommonName( "COLI" );
3264 if ( !t1.isEqual( t5 ) ) {
3267 t5.setCommonName( "vibrio" );
3268 if ( t1.isEqual( t5 ) ) {
3273 final Identifier id0 = new Identifier( "123", "pfam" );
3274 final Identifier id1 = ( Identifier ) id0.copy();
3275 if ( !id1.isEqual( id1 ) ) {
3278 if ( !id1.isEqual( id0 ) ) {
3281 if ( !id0.isEqual( id1 ) ) {
3288 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3289 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3290 if ( !pd1.isEqual( pd1 ) ) {
3293 if ( !pd1.isEqual( pd0 ) ) {
3298 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3299 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3300 if ( !pd3.isEqual( pd3 ) ) {
3303 if ( !pd2.isEqual( pd3 ) ) {
3306 if ( !pd0.isEqual( pd3 ) ) {
3311 // DomainArchitecture
3312 // ------------------
3313 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3314 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3315 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3316 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3317 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3318 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3323 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3324 if ( ds0.getNumberOfDomains() != 4 ) {
3327 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3328 if ( !ds0.isEqual( ds0 ) ) {
3331 if ( !ds0.isEqual( ds1 ) ) {
3334 if ( ds1.getNumberOfDomains() != 4 ) {
3337 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3342 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3343 if ( ds0.isEqual( ds2 ) ) {
3349 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3350 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3351 System.out.println( ds3.toNHX() );
3354 if ( ds3.getNumberOfDomains() != 3 ) {
3359 final Event e1 = new Event( Event.EventType.fusion );
3360 if ( e1.isDuplication() ) {
3363 if ( !e1.isFusion() ) {
3366 if ( !e1.asText().toString().equals( "fusion" ) ) {
3369 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3372 final Event e11 = new Event( Event.EventType.fusion );
3373 if ( !e11.isEqual( e1 ) ) {
3376 if ( !e11.toNHX().toString().equals( "" ) ) {
3379 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3380 if ( e2.isDuplication() ) {
3383 if ( !e2.isSpeciationOrDuplication() ) {
3386 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3389 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3392 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3395 if ( e11.isEqual( e2 ) ) {
3398 final Event e2c = ( Event ) e2.copy();
3399 if ( !e2c.isEqual( e2 ) ) {
3402 Event e3 = new Event( 1, 2, 3 );
3403 if ( e3.isDuplication() ) {
3406 if ( e3.isSpeciation() ) {
3409 if ( e3.isGeneLoss() ) {
3412 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3415 final Event e3c = ( Event ) e3.copy();
3416 final Event e3cc = ( Event ) e3c.copy();
3417 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3421 if ( !e3c.isEqual( e3cc ) ) {
3424 Event e4 = new Event( 1, 2, 3 );
3425 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3428 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3431 final Event e4c = ( Event ) e4.copy();
3433 final Event e4cc = ( Event ) e4c.copy();
3434 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3437 if ( !e4c.isEqual( e4cc ) ) {
3440 final Event e5 = new Event();
3441 if ( !e5.isUnassigned() ) {
3444 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3447 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3450 final Event e6 = new Event( 1, 0, 0 );
3451 if ( !e6.asText().toString().equals( "duplication" ) ) {
3454 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3457 final Event e7 = new Event( 0, 1, 0 );
3458 if ( !e7.asText().toString().equals( "speciation" ) ) {
3461 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3464 final Event e8 = new Event( 0, 0, 1 );
3465 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3468 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3472 catch ( final Exception e ) {
3473 e.printStackTrace( System.out );
3479 private static boolean testDeletionOfExternalNodes() {
3481 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3482 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3483 final PhylogenyWriter w = new PhylogenyWriter();
3484 if ( t0.isEmpty() ) {
3487 if ( t0.getNumberOfExternalNodes() != 1 ) {
3490 t0.deleteSubtree( t0.getNode( "A" ), false );
3491 if ( t0.getNumberOfExternalNodes() != 0 ) {
3494 if ( !t0.isEmpty() ) {
3497 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3498 if ( t1.getNumberOfExternalNodes() != 2 ) {
3501 t1.deleteSubtree( t1.getNode( "A" ), false );
3502 if ( t1.getNumberOfExternalNodes() != 1 ) {
3505 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3508 t1.deleteSubtree( t1.getNode( "B" ), false );
3509 if ( t1.getNumberOfExternalNodes() != 1 ) {
3512 t1.deleteSubtree( t1.getNode( "r" ), false );
3513 if ( !t1.isEmpty() ) {
3516 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3517 if ( t2.getNumberOfExternalNodes() != 3 ) {
3520 t2.deleteSubtree( t2.getNode( "B" ), false );
3521 if ( t2.getNumberOfExternalNodes() != 2 ) {
3524 t2.toNewHampshireX();
3525 PhylogenyNode n = t2.getNode( "A" );
3526 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3529 t2.deleteSubtree( t2.getNode( "A" ), false );
3530 if ( t2.getNumberOfExternalNodes() != 2 ) {
3533 t2.deleteSubtree( t2.getNode( "C" ), true );
3534 if ( t2.getNumberOfExternalNodes() != 1 ) {
3537 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3538 if ( t3.getNumberOfExternalNodes() != 4 ) {
3541 t3.deleteSubtree( t3.getNode( "B" ), true );
3542 if ( t3.getNumberOfExternalNodes() != 3 ) {
3545 n = t3.getNode( "A" );
3546 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3549 n = n.getNextExternalNode();
3550 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3553 t3.deleteSubtree( t3.getNode( "A" ), true );
3554 if ( t3.getNumberOfExternalNodes() != 2 ) {
3557 n = t3.getNode( "C" );
3558 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3561 t3.deleteSubtree( t3.getNode( "C" ), true );
3562 if ( t3.getNumberOfExternalNodes() != 1 ) {
3565 t3.deleteSubtree( t3.getNode( "D" ), true );
3566 if ( t3.getNumberOfExternalNodes() != 0 ) {
3569 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3570 if ( t4.getNumberOfExternalNodes() != 6 ) {
3573 t4.deleteSubtree( t4.getNode( "B2" ), true );
3574 if ( t4.getNumberOfExternalNodes() != 5 ) {
3577 String s = w.toNewHampshire( t4, true ).toString();
3578 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3581 t4.deleteSubtree( t4.getNode( "B11" ), true );
3582 if ( t4.getNumberOfExternalNodes() != 4 ) {
3585 t4.deleteSubtree( t4.getNode( "C" ), true );
3586 if ( t4.getNumberOfExternalNodes() != 3 ) {
3589 n = t4.getNode( "A" );
3590 n = n.getNextExternalNode();
3591 if ( !n.getName().equals( "B12" ) ) {
3594 n = n.getNextExternalNode();
3595 if ( !n.getName().equals( "D" ) ) {
3598 s = w.toNewHampshire( t4, true ).toString();
3599 if ( !s.equals( "((A,B12),D);" ) ) {
3602 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3603 t5.deleteSubtree( t5.getNode( "A" ), true );
3604 if ( t5.getNumberOfExternalNodes() != 5 ) {
3607 s = w.toNewHampshire( t5, true ).toString();
3608 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3611 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3612 t6.deleteSubtree( t6.getNode( "B11" ), true );
3613 if ( t6.getNumberOfExternalNodes() != 5 ) {
3616 s = w.toNewHampshire( t6, false ).toString();
3617 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3620 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3621 t7.deleteSubtree( t7.getNode( "B12" ), true );
3622 if ( t7.getNumberOfExternalNodes() != 5 ) {
3625 s = w.toNewHampshire( t7, true ).toString();
3626 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3629 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3630 t8.deleteSubtree( t8.getNode( "B2" ), true );
3631 if ( t8.getNumberOfExternalNodes() != 5 ) {
3634 s = w.toNewHampshire( t8, false ).toString();
3635 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3638 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3639 t9.deleteSubtree( t9.getNode( "C" ), true );
3640 if ( t9.getNumberOfExternalNodes() != 5 ) {
3643 s = w.toNewHampshire( t9, true ).toString();
3644 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3647 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3648 t10.deleteSubtree( t10.getNode( "D" ), true );
3649 if ( t10.getNumberOfExternalNodes() != 5 ) {
3652 s = w.toNewHampshire( t10, true ).toString();
3653 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3656 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3657 t11.deleteSubtree( t11.getNode( "A" ), true );
3658 if ( t11.getNumberOfExternalNodes() != 2 ) {
3661 s = w.toNewHampshire( t11, true ).toString();
3662 if ( !s.equals( "(B,C);" ) ) {
3665 t11.deleteSubtree( t11.getNode( "C" ), true );
3666 if ( t11.getNumberOfExternalNodes() != 1 ) {
3669 s = w.toNewHampshire( t11, false ).toString();
3670 if ( !s.equals( "B;" ) ) {
3673 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3674 t12.deleteSubtree( t12.getNode( "B2" ), true );
3675 if ( t12.getNumberOfExternalNodes() != 8 ) {
3678 s = w.toNewHampshire( t12, true ).toString();
3679 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3682 t12.deleteSubtree( t12.getNode( "B3" ), true );
3683 if ( t12.getNumberOfExternalNodes() != 7 ) {
3686 s = w.toNewHampshire( t12, true ).toString();
3687 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3690 t12.deleteSubtree( t12.getNode( "C3" ), true );
3691 if ( t12.getNumberOfExternalNodes() != 6 ) {
3694 s = w.toNewHampshire( t12, true ).toString();
3695 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3698 t12.deleteSubtree( t12.getNode( "A1" ), true );
3699 if ( t12.getNumberOfExternalNodes() != 5 ) {
3702 s = w.toNewHampshire( t12, true ).toString();
3703 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3706 t12.deleteSubtree( t12.getNode( "B1" ), true );
3707 if ( t12.getNumberOfExternalNodes() != 4 ) {
3710 s = w.toNewHampshire( t12, true ).toString();
3711 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3714 t12.deleteSubtree( t12.getNode( "A3" ), true );
3715 if ( t12.getNumberOfExternalNodes() != 3 ) {
3718 s = w.toNewHampshire( t12, true ).toString();
3719 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3722 t12.deleteSubtree( t12.getNode( "A2" ), true );
3723 if ( t12.getNumberOfExternalNodes() != 2 ) {
3726 s = w.toNewHampshire( t12, true ).toString();
3727 if ( !s.equals( "(C1,C2);" ) ) {
3730 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3731 t13.deleteSubtree( t13.getNode( "D" ), true );
3732 if ( t13.getNumberOfExternalNodes() != 4 ) {
3735 s = w.toNewHampshire( t13, true ).toString();
3736 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3739 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3740 t14.deleteSubtree( t14.getNode( "E" ), true );
3741 if ( t14.getNumberOfExternalNodes() != 5 ) {
3744 s = w.toNewHampshire( t14, true ).toString();
3745 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3748 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3749 t15.deleteSubtree( t15.getNode( "B2" ), true );
3750 if ( t15.getNumberOfExternalNodes() != 11 ) {
3753 t15.deleteSubtree( t15.getNode( "B1" ), true );
3754 if ( t15.getNumberOfExternalNodes() != 10 ) {
3757 t15.deleteSubtree( t15.getNode( "B3" ), true );
3758 if ( t15.getNumberOfExternalNodes() != 9 ) {
3761 t15.deleteSubtree( t15.getNode( "B4" ), true );
3762 if ( t15.getNumberOfExternalNodes() != 8 ) {
3765 t15.deleteSubtree( t15.getNode( "A1" ), true );
3766 if ( t15.getNumberOfExternalNodes() != 7 ) {
3769 t15.deleteSubtree( t15.getNode( "C4" ), true );
3770 if ( t15.getNumberOfExternalNodes() != 6 ) {
3774 catch ( final Exception e ) {
3775 e.printStackTrace( System.out );
3781 private static boolean testDescriptiveStatistics() {
3783 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3784 dss1.addValue( 82 );
3785 dss1.addValue( 78 );
3786 dss1.addValue( 70 );
3787 dss1.addValue( 58 );
3788 dss1.addValue( 42 );
3789 if ( dss1.getN() != 5 ) {
3792 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3795 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3798 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3801 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3804 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3807 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3810 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3813 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3816 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3819 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3822 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3825 dss1.addValue( 123 );
3826 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3829 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3832 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3835 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3836 dss2.addValue( -1.85 );
3837 dss2.addValue( 57.5 );
3838 dss2.addValue( 92.78 );
3839 dss2.addValue( 57.78 );
3840 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3843 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3846 final double[] a = dss2.getDataAsDoubleArray();
3847 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3850 dss2.addValue( -100 );
3851 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3854 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3857 final double[] ds = new double[ 14 ];
3872 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3873 if ( bins.length != 4 ) {
3876 if ( bins[ 0 ] != 2 ) {
3879 if ( bins[ 1 ] != 3 ) {
3882 if ( bins[ 2 ] != 4 ) {
3885 if ( bins[ 3 ] != 5 ) {
3888 final double[] ds1 = new double[ 9 ];
3898 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3899 if ( bins1.length != 4 ) {
3902 if ( bins1[ 0 ] != 2 ) {
3905 if ( bins1[ 1 ] != 3 ) {
3908 if ( bins1[ 2 ] != 0 ) {
3911 if ( bins1[ 3 ] != 4 ) {
3914 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3915 if ( bins1_1.length != 3 ) {
3918 if ( bins1_1[ 0 ] != 3 ) {
3921 if ( bins1_1[ 1 ] != 2 ) {
3924 if ( bins1_1[ 2 ] != 4 ) {
3927 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3928 if ( bins1_2.length != 3 ) {
3931 if ( bins1_2[ 0 ] != 2 ) {
3934 if ( bins1_2[ 1 ] != 2 ) {
3937 if ( bins1_2[ 2 ] != 2 ) {
3940 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3954 dss3.addValue( 10 );
3955 dss3.addValue( 10 );
3956 dss3.addValue( 10 );
3957 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3958 histo.toStringBuffer( 10, '=', 40, 5 );
3959 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3961 catch ( final Exception e ) {
3962 e.printStackTrace( System.out );
3968 private static boolean testDir( final String file ) {
3970 final File f = new File( file );
3971 if ( !f.exists() ) {
3974 if ( !f.isDirectory() ) {
3977 if ( !f.canRead() ) {
3981 catch ( final Exception e ) {
3987 private static boolean testEbiEntryRetrieval() {
3989 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3990 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3991 System.out.println( entry.getAccession() );
3994 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
3995 System.out.println( entry.getTaxonomyScientificName() );
3998 if ( !entry.getSequenceName()
3999 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
4000 System.out.println( entry.getSequenceName() );
4003 if ( !entry.getGeneName().equals( "treX-like" ) ) {
4004 System.out.println( entry.getGeneName() );
4007 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
4008 System.out.println( entry.getTaxonomyIdentifier() );
4011 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
4012 System.out.println( entry.getAnnotations().first().getRefValue() );
4015 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
4016 System.out.println( entry.getAnnotations().first().getRefSource() );
4019 if ( entry.getCrossReferences().size() != 5 ) {
4022 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
4023 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
4026 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
4027 System.out.println( entry1.getTaxonomyScientificName() );
4030 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
4031 System.out.println( entry1.getSequenceName() );
4034 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
4035 System.out.println( entry1.getTaxonomyIdentifier() );
4038 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
4039 System.out.println( entry1.getGeneName() );
4042 if ( entry1.getCrossReferences().size() != 6 ) {
4045 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
4046 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
4049 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4050 System.out.println( entry2.getTaxonomyScientificName() );
4053 if ( !entry2.getSequenceName()
4054 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
4055 System.out.println( entry2.getSequenceName() );
4058 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
4059 System.out.println( entry2.getTaxonomyIdentifier() );
4062 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
4063 System.out.println( entry2.getGeneName() );
4066 if ( entry2.getCrossReferences().size() != 3 ) {
4070 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
4071 if ( !entry3.getAccession().equals( "HM043801" ) ) {
4074 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
4075 System.out.println( entry3.getTaxonomyScientificName() );
4078 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
4079 System.out.println( entry3.getSequenceName() );
4082 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
4083 System.out.println( entry3.getTaxonomyIdentifier() );
4086 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
4087 System.out.println( entry3.getSequenceSymbol() );
4090 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
4093 if ( entry3.getCrossReferences().size() < 7 ) {
4096 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
4097 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4100 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4101 System.out.println( entry4.getTaxonomyScientificName() );
4104 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4105 System.out.println( entry4.getSequenceName() );
4108 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4109 System.out.println( entry4.getTaxonomyIdentifier() );
4112 if ( !entry4.getGeneName().equals( "ras" ) ) {
4113 System.out.println( entry4.getGeneName() );
4116 // if ( !entry4.getChromosome().equals( "ras" ) ) {
4117 // System.out.println( entry4.getChromosome() );
4120 // if ( !entry4.getMap().equals( "ras" ) ) {
4121 // System.out.println( entry4.getMap() );
4127 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
4128 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
4131 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4132 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4135 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4136 System.out.println( entry5.getTaxonomyScientificName() );
4139 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4140 System.out.println( entry5.getSequenceName() );
4143 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4144 System.out.println( entry5.getTaxonomyIdentifier() );
4148 catch ( final IOException e ) {
4149 System.out.println();
4150 System.out.println( "the following might be due to absence internet connection:" );
4151 e.printStackTrace( System.out );
4154 catch ( final Exception e ) {
4155 e.printStackTrace();
4161 private static boolean testExternalNodeRelatedMethods() {
4163 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4164 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4165 PhylogenyNode n = t1.getNode( "A" );
4166 n = n.getNextExternalNode();
4167 if ( !n.getName().equals( "B" ) ) {
4170 n = n.getNextExternalNode();
4171 if ( !n.getName().equals( "C" ) ) {
4174 n = n.getNextExternalNode();
4175 if ( !n.getName().equals( "D" ) ) {
4178 n = t1.getNode( "B" );
4179 while ( !n.isLastExternalNode() ) {
4180 n = n.getNextExternalNode();
4182 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4183 n = t2.getNode( "A" );
4184 n = n.getNextExternalNode();
4185 if ( !n.getName().equals( "B" ) ) {
4188 n = n.getNextExternalNode();
4189 if ( !n.getName().equals( "C" ) ) {
4192 n = n.getNextExternalNode();
4193 if ( !n.getName().equals( "D" ) ) {
4196 n = t2.getNode( "B" );
4197 while ( !n.isLastExternalNode() ) {
4198 n = n.getNextExternalNode();
4200 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4201 n = t3.getNode( "A" );
4202 n = n.getNextExternalNode();
4203 if ( !n.getName().equals( "B" ) ) {
4206 n = n.getNextExternalNode();
4207 if ( !n.getName().equals( "C" ) ) {
4210 n = n.getNextExternalNode();
4211 if ( !n.getName().equals( "D" ) ) {
4214 n = n.getNextExternalNode();
4215 if ( !n.getName().equals( "E" ) ) {
4218 n = n.getNextExternalNode();
4219 if ( !n.getName().equals( "F" ) ) {
4222 n = n.getNextExternalNode();
4223 if ( !n.getName().equals( "G" ) ) {
4226 n = n.getNextExternalNode();
4227 if ( !n.getName().equals( "H" ) ) {
4230 n = t3.getNode( "B" );
4231 while ( !n.isLastExternalNode() ) {
4232 n = n.getNextExternalNode();
4234 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4235 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4236 final PhylogenyNode node = iter.next();
4238 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4239 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4240 final PhylogenyNode node = iter.next();
4242 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4243 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4244 if ( !iter.next().getName().equals( "A" ) ) {
4247 if ( !iter.next().getName().equals( "B" ) ) {
4250 if ( !iter.next().getName().equals( "C" ) ) {
4253 if ( !iter.next().getName().equals( "D" ) ) {
4256 if ( !iter.next().getName().equals( "E" ) ) {
4259 if ( !iter.next().getName().equals( "F" ) ) {
4262 if ( iter.hasNext() ) {
4266 catch ( final Exception e ) {
4267 e.printStackTrace( System.out );
4273 private static boolean testExtractSNFromNodeName() {
4275 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4278 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4281 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4284 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4285 .equals( "Mus musculus musculus" ) ) {
4288 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4289 .equals( "Mus musculus musculus" ) ) {
4292 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4293 .equals( "Mus musculus musculus" ) ) {
4296 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4297 .equals( "Mus musculus musculus" ) ) {
4300 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4303 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4304 .equals( "Mus musculus musculus" ) ) {
4307 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4308 .equals( "Mus musculus musculus" ) ) {
4311 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4314 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4317 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4320 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4323 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4324 .equals( "Mus musculus musculus" ) ) {
4327 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4330 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4333 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4336 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4339 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4342 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4345 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4348 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4351 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4352 .equals( "Mus musculus" ) ) {
4355 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4356 .equals( "Mus musculus" ) ) {
4359 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4362 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4363 .equals( "Mus musculus musculus" ) ) {
4366 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4367 .equals( "Mus musculus musculus" ) ) {
4370 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4371 .equals( "Mus musculus musculus" ) ) {
4374 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4377 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4378 .equals( "Pilostyles mexicana" ) ) {
4381 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4382 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4385 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4386 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4389 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4390 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4393 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4394 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4397 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4398 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4401 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4402 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4405 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
4406 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4409 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
4410 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4413 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
4414 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4417 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4418 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4421 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4422 .equals( "Escherichia coli (strain K12)" ) ) {
4425 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4426 .equals( "Escherichia coli (strain K12)" ) ) {
4429 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4430 .equals( "Escherichia coli (str. K12)" ) ) {
4433 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4434 .equals( "Escherichia coli (str. K12)" ) ) {
4437 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4438 .equals( "Escherichia coli (str. K12)" ) ) {
4441 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4442 .equals( "Escherichia coli (var. K12)" ) ) {
4445 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4446 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4449 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4450 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4454 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4455 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4458 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4459 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4463 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4464 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4467 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4468 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4471 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4472 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4475 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4478 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4481 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4484 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4485 .equals( "Macrocera sp." ) ) {
4488 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4491 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4492 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4495 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
4496 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4499 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
4500 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4503 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
4504 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4508 catch ( final Exception e ) {
4509 e.printStackTrace( System.out );
4515 private static boolean testExtractTaxonomyDataFromNodeName() {
4517 PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
4518 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4521 n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
4522 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4525 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
4526 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4529 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" );
4530 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4533 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" );
4534 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4537 n = new PhylogenyNode( "HNRPR_HUMAN" );
4538 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4541 n = new PhylogenyNode( "HNRPR_HUMAN_X" );
4542 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4546 catch ( final Exception e ) {
4547 e.printStackTrace( System.out );
4553 private static boolean testExtractTaxonomyCodeFromNodeName() {
4555 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4558 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4559 .equals( "SOYBN" ) ) {
4562 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4563 .equals( "ARATH" ) ) {
4566 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4567 .equals( "ARATH" ) ) {
4570 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4573 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4576 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4579 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4580 .equals( "SOYBN" ) ) {
4583 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4584 .equals( "SOYBN" ) ) {
4587 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4588 .equals( "SOYBN" ) ) {
4591 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4592 .equals( "SOYBN" ) ) {
4595 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4596 .equals( "SOYBN" ) ) {
4599 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4600 .equals( "SOYBN" ) ) {
4603 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4604 .equals( "SOYBN" ) ) {
4607 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4608 .equals( "SOYBN" ) ) {
4611 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4614 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4615 .equals( "SOYBN" ) ) {
4618 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4619 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4622 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4623 .equals( "9YX45" ) ) {
4626 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4627 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4628 .equals( "MOUSE" ) ) {
4631 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4632 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4633 .equals( "MOUSE" ) ) {
4636 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4637 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4638 .equals( "MOUSE" ) ) {
4641 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4642 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4645 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4646 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4649 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4650 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4653 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4654 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4657 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4658 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4661 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4662 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4665 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4666 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4669 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4670 .equals( "RAT" ) ) {
4673 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4674 .equals( "PIG" ) ) {
4678 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4679 .equals( "MOUSE" ) ) {
4682 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4683 .equals( "MOUSE" ) ) {
4686 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4690 catch ( final Exception e ) {
4691 e.printStackTrace( System.out );
4697 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4699 PhylogenyNode n = new PhylogenyNode();
4700 n.setName( "tr|B3RJ64" );
4701 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4704 n.setName( "tr.B3RJ64" );
4705 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4708 n.setName( "tr=B3RJ64" );
4709 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4712 n.setName( "tr-B3RJ64" );
4713 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4716 n.setName( "tr/B3RJ64" );
4717 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4720 n.setName( "tr\\B3RJ64" );
4721 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
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_tr|B3RJ64_sp|123 " );
4745 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4748 n.setName( "B3RJ64" );
4749 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4752 n.setName( "sp|B3RJ64" );
4753 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4756 n.setName( "sp|B3RJ64C" );
4757 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4760 n.setName( "sp B3RJ64" );
4761 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4764 n.setName( "sp|B3RJ6X" );
4765 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4768 n.setName( "sp|B3RJ6" );
4769 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4772 n.setName( "K1PYK7_CRAGI" );
4773 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4776 n.setName( "K1PYK7_PEA" );
4777 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4780 n.setName( "K1PYK7_RAT" );
4781 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4784 n.setName( "K1PYK7_PIG" );
4785 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4788 n.setName( "~K1PYK7_PIG~" );
4789 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4792 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4793 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4796 n.setName( "K1PYKX_CRAGI" );
4797 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4800 n.setName( "XXXXX_CRAGI" );
4801 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4804 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4805 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4808 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4809 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4812 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4813 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4816 n = new PhylogenyNode();
4817 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4818 seq.setSymbol( "K1PYK7_CRAGI" );
4819 n.getNodeData().addSequence( seq );
4820 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4823 seq.setSymbol( "tr|B3RJ64" );
4824 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4827 n = new PhylogenyNode();
4828 seq = new org.forester.phylogeny.data.Sequence();
4829 seq.setName( "K1PYK7_CRAGI" );
4830 n.getNodeData().addSequence( seq );
4831 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4834 seq.setName( "tr|B3RJ64" );
4835 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4838 n = new PhylogenyNode();
4839 seq = new org.forester.phylogeny.data.Sequence();
4840 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4841 n.getNodeData().addSequence( seq );
4842 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4845 n = new PhylogenyNode();
4846 seq = new org.forester.phylogeny.data.Sequence();
4847 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4848 n.getNodeData().addSequence( seq );
4849 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4853 n = new PhylogenyNode();
4854 n.setName( "ACP19736" );
4855 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4858 n = new PhylogenyNode();
4859 n.setName( "|ACP19736|" );
4860 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4864 catch ( final Exception e ) {
4865 e.printStackTrace( System.out );
4871 private static boolean testFastaParser() {
4873 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4876 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4879 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4880 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4883 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4886 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4889 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
4892 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4895 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4899 catch ( final Exception e ) {
4900 e.printStackTrace();
4906 private static boolean testGenbankAccessorParsing() {
4907 //The format for GenBank Accession numbers are:
4908 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4909 //Protein: 3 letters + 5 numerals
4910 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4911 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4914 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4917 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4920 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4923 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4926 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4929 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4932 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4935 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4938 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4941 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4944 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4947 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4950 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4956 private static boolean testGeneralMsaParser() {
4958 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4959 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4960 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4961 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4962 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4963 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4964 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4965 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4966 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4969 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4972 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4975 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4978 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4981 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4984 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4987 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4990 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4993 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4996 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4999 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5002 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
5003 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5006 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5009 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5012 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
5013 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
5016 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
5019 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
5022 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
5023 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5026 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5029 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5033 catch ( final Exception e ) {
5034 e.printStackTrace();
5040 private static boolean testGeneralTable() {
5042 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
5043 t0.setValue( 3, 2, "23" );
5044 t0.setValue( 10, 1, "error" );
5045 t0.setValue( 10, 1, "110" );
5046 t0.setValue( 9, 1, "19" );
5047 t0.setValue( 1, 10, "101" );
5048 t0.setValue( 10, 10, "1010" );
5049 t0.setValue( 100, 10, "10100" );
5050 t0.setValue( 0, 0, "00" );
5051 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
5054 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
5057 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
5060 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
5063 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
5066 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
5069 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
5072 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
5075 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
5078 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
5079 t1.setValue( "3", "2", "23" );
5080 t1.setValue( "10", "1", "error" );
5081 t1.setValue( "10", "1", "110" );
5082 t1.setValue( "9", "1", "19" );
5083 t1.setValue( "1", "10", "101" );
5084 t1.setValue( "10", "10", "1010" );
5085 t1.setValue( "100", "10", "10100" );
5086 t1.setValue( "0", "0", "00" );
5087 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
5088 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
5091 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
5094 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
5097 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
5100 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
5103 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
5106 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
5109 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
5112 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
5115 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
5119 catch ( final Exception e ) {
5120 e.printStackTrace( System.out );
5126 private static boolean testGetDistance() {
5128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5129 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",
5130 new NHXParser() )[ 0 ];
5131 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
5134 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5137 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5140 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5143 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5146 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5149 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5152 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5155 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5158 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5161 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5164 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5167 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5170 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5173 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5176 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5179 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5182 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5185 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5188 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5191 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5194 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5197 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5200 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5203 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5206 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5209 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5212 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5215 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5218 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5221 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5224 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",
5225 new NHXParser() )[ 0 ];
5226 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5229 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5232 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5235 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5238 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5241 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5244 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5247 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5250 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5253 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5256 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5260 catch ( final Exception e ) {
5261 e.printStackTrace( System.out );
5267 private static boolean testGetLCA() {
5269 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5270 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5271 new NHXParser() )[ 0 ];
5272 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5273 if ( !A.getName().equals( "A" ) ) {
5276 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5277 if ( !gh.getName().equals( "gh" ) ) {
5280 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5281 if ( !ab.getName().equals( "ab" ) ) {
5284 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5285 if ( !ab2.getName().equals( "ab" ) ) {
5288 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5289 if ( !gh2.getName().equals( "gh" ) ) {
5292 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5293 if ( !gh3.getName().equals( "gh" ) ) {
5296 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5297 if ( !abc.getName().equals( "abc" ) ) {
5300 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5301 if ( !abc2.getName().equals( "abc" ) ) {
5304 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5305 if ( !abcd.getName().equals( "abcd" ) ) {
5308 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5309 if ( !abcd2.getName().equals( "abcd" ) ) {
5312 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5313 if ( !abcdef.getName().equals( "abcdef" ) ) {
5316 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5317 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5320 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5321 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5324 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5325 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5328 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5329 if ( !abcde.getName().equals( "abcde" ) ) {
5332 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5333 if ( !abcde2.getName().equals( "abcde" ) ) {
5336 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5337 if ( !r.getName().equals( "abcdefgh" ) ) {
5340 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5341 if ( !r2.getName().equals( "abcdefgh" ) ) {
5344 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5345 if ( !r3.getName().equals( "abcdefgh" ) ) {
5348 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5349 if ( !abcde3.getName().equals( "abcde" ) ) {
5352 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5353 if ( !abcde4.getName().equals( "abcde" ) ) {
5356 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5357 if ( !ab3.getName().equals( "ab" ) ) {
5360 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5361 if ( !ab4.getName().equals( "ab" ) ) {
5364 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5365 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5366 if ( !cd.getName().equals( "cd" ) ) {
5369 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5370 if ( !cd2.getName().equals( "cd" ) ) {
5373 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5374 if ( !cde.getName().equals( "cde" ) ) {
5377 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5378 if ( !cde2.getName().equals( "cde" ) ) {
5381 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5382 if ( !cdef.getName().equals( "cdef" ) ) {
5385 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5386 if ( !cdef2.getName().equals( "cdef" ) ) {
5389 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5390 if ( !cdef3.getName().equals( "cdef" ) ) {
5393 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5394 if ( !rt.getName().equals( "r" ) ) {
5397 final Phylogeny p3 = factory
5398 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5399 new NHXParser() )[ 0 ];
5400 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5401 if ( !bc_3.getName().equals( "bc" ) ) {
5404 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5405 if ( !ac_3.getName().equals( "abc" ) ) {
5408 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5409 if ( !ad_3.getName().equals( "abcde" ) ) {
5412 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5413 if ( !af_3.getName().equals( "abcdef" ) ) {
5416 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5417 if ( !ag_3.getName().equals( "" ) ) {
5420 if ( !ag_3.isRoot() ) {
5423 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5424 if ( !al_3.getName().equals( "" ) ) {
5427 if ( !al_3.isRoot() ) {
5430 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5431 if ( !kl_3.getName().equals( "" ) ) {
5434 if ( !kl_3.isRoot() ) {
5437 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5438 if ( !fl_3.getName().equals( "" ) ) {
5441 if ( !fl_3.isRoot() ) {
5444 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5445 if ( !gk_3.getName().equals( "ghijk" ) ) {
5448 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5449 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5450 if ( !r_4.getName().equals( "r" ) ) {
5453 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5454 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5455 if ( !r_5.getName().equals( "root" ) ) {
5458 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5459 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5460 if ( !r_6.getName().equals( "rot" ) ) {
5463 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5464 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5465 if ( !r_7.getName().equals( "rott" ) ) {
5469 catch ( final Exception e ) {
5470 e.printStackTrace( System.out );
5476 private static boolean testGetLCA2() {
5478 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5479 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5480 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5481 PhylogenyMethods.preOrderReId( p_a );
5482 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5483 p_a.getNode( "a" ) );
5484 if ( !p_a_1.getName().equals( "a" ) ) {
5487 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5488 PhylogenyMethods.preOrderReId( p_b );
5489 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5490 p_b.getNode( "a" ) );
5491 if ( !p_b_1.getName().equals( "b" ) ) {
5494 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5495 p_b.getNode( "b" ) );
5496 if ( !p_b_2.getName().equals( "b" ) ) {
5499 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5500 PhylogenyMethods.preOrderReId( p_c );
5501 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5502 p_c.getNode( "a" ) );
5503 if ( !p_c_1.getName().equals( "b" ) ) {
5506 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5507 p_c.getNode( "c" ) );
5508 if ( !p_c_2.getName().equals( "c" ) ) {
5509 System.out.println( p_c_2.getName() );
5513 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5514 p_c.getNode( "b" ) );
5515 if ( !p_c_3.getName().equals( "b" ) ) {
5518 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5519 p_c.getNode( "a" ) );
5520 if ( !p_c_4.getName().equals( "c" ) ) {
5523 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5524 new NHXParser() )[ 0 ];
5525 PhylogenyMethods.preOrderReId( p1 );
5526 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5527 p1.getNode( "A" ) );
5528 if ( !A.getName().equals( "A" ) ) {
5531 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5532 p1.getNode( "gh" ) );
5533 if ( !gh.getName().equals( "gh" ) ) {
5536 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5537 p1.getNode( "B" ) );
5538 if ( !ab.getName().equals( "ab" ) ) {
5541 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5542 p1.getNode( "A" ) );
5543 if ( !ab2.getName().equals( "ab" ) ) {
5546 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5547 p1.getNode( "G" ) );
5548 if ( !gh2.getName().equals( "gh" ) ) {
5551 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5552 p1.getNode( "H" ) );
5553 if ( !gh3.getName().equals( "gh" ) ) {
5556 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5557 p1.getNode( "A" ) );
5558 if ( !abc.getName().equals( "abc" ) ) {
5561 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5562 p1.getNode( "C" ) );
5563 if ( !abc2.getName().equals( "abc" ) ) {
5566 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5567 p1.getNode( "D" ) );
5568 if ( !abcd.getName().equals( "abcd" ) ) {
5571 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5572 p1.getNode( "A" ) );
5573 if ( !abcd2.getName().equals( "abcd" ) ) {
5576 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5577 p1.getNode( "F" ) );
5578 if ( !abcdef.getName().equals( "abcdef" ) ) {
5581 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5582 p1.getNode( "A" ) );
5583 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5586 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5587 p1.getNode( "F" ) );
5588 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5591 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5592 p1.getNode( "ab" ) );
5593 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5596 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5597 p1.getNode( "E" ) );
5598 if ( !abcde.getName().equals( "abcde" ) ) {
5601 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5602 p1.getNode( "A" ) );
5603 if ( !abcde2.getName().equals( "abcde" ) ) {
5606 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5607 p1.getNode( "abcdefgh" ) );
5608 if ( !r.getName().equals( "abcdefgh" ) ) {
5611 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5612 p1.getNode( "H" ) );
5613 if ( !r2.getName().equals( "abcdefgh" ) ) {
5616 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5617 p1.getNode( "A" ) );
5618 if ( !r3.getName().equals( "abcdefgh" ) ) {
5621 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5622 p1.getNode( "abcde" ) );
5623 if ( !abcde3.getName().equals( "abcde" ) ) {
5626 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5627 p1.getNode( "E" ) );
5628 if ( !abcde4.getName().equals( "abcde" ) ) {
5631 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5632 p1.getNode( "B" ) );
5633 if ( !ab3.getName().equals( "ab" ) ) {
5636 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5637 p1.getNode( "ab" ) );
5638 if ( !ab4.getName().equals( "ab" ) ) {
5641 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5642 PhylogenyMethods.preOrderReId( p2 );
5643 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5644 p2.getNode( "d" ) );
5645 if ( !cd.getName().equals( "cd" ) ) {
5648 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5649 p2.getNode( "c" ) );
5650 if ( !cd2.getName().equals( "cd" ) ) {
5653 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5654 p2.getNode( "e" ) );
5655 if ( !cde.getName().equals( "cde" ) ) {
5658 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5659 p2.getNode( "c" ) );
5660 if ( !cde2.getName().equals( "cde" ) ) {
5663 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5664 p2.getNode( "f" ) );
5665 if ( !cdef.getName().equals( "cdef" ) ) {
5668 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5669 p2.getNode( "f" ) );
5670 if ( !cdef2.getName().equals( "cdef" ) ) {
5673 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5674 p2.getNode( "d" ) );
5675 if ( !cdef3.getName().equals( "cdef" ) ) {
5678 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5679 p2.getNode( "a" ) );
5680 if ( !rt.getName().equals( "r" ) ) {
5683 final Phylogeny p3 = factory
5684 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5685 new NHXParser() )[ 0 ];
5686 PhylogenyMethods.preOrderReId( p3 );
5687 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5688 p3.getNode( "c" ) );
5689 if ( !bc_3.getName().equals( "bc" ) ) {
5692 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5693 p3.getNode( "c" ) );
5694 if ( !ac_3.getName().equals( "abc" ) ) {
5697 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5698 p3.getNode( "d" ) );
5699 if ( !ad_3.getName().equals( "abcde" ) ) {
5702 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5703 p3.getNode( "f" ) );
5704 if ( !af_3.getName().equals( "abcdef" ) ) {
5707 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5708 p3.getNode( "g" ) );
5709 if ( !ag_3.getName().equals( "" ) ) {
5712 if ( !ag_3.isRoot() ) {
5715 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5716 p3.getNode( "l" ) );
5717 if ( !al_3.getName().equals( "" ) ) {
5720 if ( !al_3.isRoot() ) {
5723 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5724 p3.getNode( "l" ) );
5725 if ( !kl_3.getName().equals( "" ) ) {
5728 if ( !kl_3.isRoot() ) {
5731 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5732 p3.getNode( "l" ) );
5733 if ( !fl_3.getName().equals( "" ) ) {
5736 if ( !fl_3.isRoot() ) {
5739 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5740 p3.getNode( "k" ) );
5741 if ( !gk_3.getName().equals( "ghijk" ) ) {
5744 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5745 PhylogenyMethods.preOrderReId( p4 );
5746 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5747 p4.getNode( "c" ) );
5748 if ( !r_4.getName().equals( "r" ) ) {
5751 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5752 PhylogenyMethods.preOrderReId( p5 );
5753 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5754 p5.getNode( "c" ) );
5755 if ( !r_5.getName().equals( "root" ) ) {
5758 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5759 PhylogenyMethods.preOrderReId( p6 );
5760 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5761 p6.getNode( "a" ) );
5762 if ( !r_6.getName().equals( "rot" ) ) {
5765 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5766 PhylogenyMethods.preOrderReId( p7 );
5767 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5768 p7.getNode( "e" ) );
5769 if ( !r_7.getName().equals( "rott" ) ) {
5772 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5773 p7.getNode( "a" ) );
5774 if ( !r_71.getName().equals( "rott" ) ) {
5777 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5778 p7.getNode( "rott" ) );
5779 if ( !r_72.getName().equals( "rott" ) ) {
5782 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5783 p7.getNode( "a" ) );
5784 if ( !r_73.getName().equals( "rott" ) ) {
5787 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5788 p7.getNode( "rott" ) );
5789 if ( !r_74.getName().equals( "rott" ) ) {
5792 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5793 p7.getNode( "e" ) );
5794 if ( !r_75.getName().equals( "e" ) ) {
5798 catch ( final Exception e ) {
5799 e.printStackTrace( System.out );
5805 private static boolean testHmmscanOutputParser() {
5806 final String test_dir = Test.PATH_TO_TEST_DATA;
5808 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5809 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5811 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5812 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5813 final List<Protein> proteins = parser2.parse();
5814 if ( parser2.getProteinsEncountered() != 4 ) {
5817 if ( proteins.size() != 4 ) {
5820 if ( parser2.getDomainsEncountered() != 69 ) {
5823 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5826 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5829 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5832 final Protein p1 = proteins.get( 0 );
5833 if ( p1.getNumberOfProteinDomains() != 15 ) {
5836 if ( p1.getLength() != 850 ) {
5839 final Protein p2 = proteins.get( 1 );
5840 if ( p2.getNumberOfProteinDomains() != 51 ) {
5843 if ( p2.getLength() != 1291 ) {
5846 final Protein p3 = proteins.get( 2 );
5847 if ( p3.getNumberOfProteinDomains() != 2 ) {
5850 final Protein p4 = proteins.get( 3 );
5851 if ( p4.getNumberOfProteinDomains() != 1 ) {
5854 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5857 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5860 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5863 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5866 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5869 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5872 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5876 catch ( final Exception e ) {
5877 e.printStackTrace( System.out );
5883 private static boolean testLastExternalNodeMethods() {
5885 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5886 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5887 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5888 final PhylogenyNode n1 = t0.getNode( "A" );
5889 if ( n1.isLastExternalNode() ) {
5892 final PhylogenyNode n2 = t0.getNode( "B" );
5893 if ( n2.isLastExternalNode() ) {
5896 final PhylogenyNode n3 = t0.getNode( "C" );
5897 if ( n3.isLastExternalNode() ) {
5900 final PhylogenyNode n4 = t0.getNode( "D" );
5901 if ( !n4.isLastExternalNode() ) {
5905 catch ( final Exception e ) {
5906 e.printStackTrace( System.out );
5912 private static boolean testLevelOrderIterator() {
5914 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5915 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5916 PhylogenyNodeIterator it0;
5917 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5920 for( it0.reset(); it0.hasNext(); ) {
5923 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5924 if ( !it.next().getName().equals( "r" ) ) {
5927 if ( !it.next().getName().equals( "ab" ) ) {
5930 if ( !it.next().getName().equals( "cd" ) ) {
5933 if ( !it.next().getName().equals( "A" ) ) {
5936 if ( !it.next().getName().equals( "B" ) ) {
5939 if ( !it.next().getName().equals( "C" ) ) {
5942 if ( !it.next().getName().equals( "D" ) ) {
5945 if ( it.hasNext() ) {
5948 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",
5949 new NHXParser() )[ 0 ];
5950 PhylogenyNodeIterator it2;
5951 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5954 for( it2.reset(); it2.hasNext(); ) {
5957 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5958 if ( !it3.next().getName().equals( "r" ) ) {
5961 if ( !it3.next().getName().equals( "abc" ) ) {
5964 if ( !it3.next().getName().equals( "defg" ) ) {
5967 if ( !it3.next().getName().equals( "A" ) ) {
5970 if ( !it3.next().getName().equals( "B" ) ) {
5973 if ( !it3.next().getName().equals( "C" ) ) {
5976 if ( !it3.next().getName().equals( "D" ) ) {
5979 if ( !it3.next().getName().equals( "E" ) ) {
5982 if ( !it3.next().getName().equals( "F" ) ) {
5985 if ( !it3.next().getName().equals( "G" ) ) {
5988 if ( !it3.next().getName().equals( "1" ) ) {
5991 if ( !it3.next().getName().equals( "2" ) ) {
5994 if ( !it3.next().getName().equals( "3" ) ) {
5997 if ( !it3.next().getName().equals( "4" ) ) {
6000 if ( !it3.next().getName().equals( "5" ) ) {
6003 if ( !it3.next().getName().equals( "6" ) ) {
6006 if ( !it3.next().getName().equals( "f1" ) ) {
6009 if ( !it3.next().getName().equals( "f2" ) ) {
6012 if ( !it3.next().getName().equals( "f3" ) ) {
6015 if ( !it3.next().getName().equals( "a" ) ) {
6018 if ( !it3.next().getName().equals( "b" ) ) {
6021 if ( !it3.next().getName().equals( "f21" ) ) {
6024 if ( !it3.next().getName().equals( "X" ) ) {
6027 if ( !it3.next().getName().equals( "Y" ) ) {
6030 if ( !it3.next().getName().equals( "Z" ) ) {
6033 if ( it3.hasNext() ) {
6036 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
6037 PhylogenyNodeIterator it4;
6038 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
6041 for( it4.reset(); it4.hasNext(); ) {
6044 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
6045 if ( !it5.next().getName().equals( "r" ) ) {
6048 if ( !it5.next().getName().equals( "A" ) ) {
6051 if ( !it5.next().getName().equals( "B" ) ) {
6054 if ( !it5.next().getName().equals( "C" ) ) {
6057 if ( !it5.next().getName().equals( "D" ) ) {
6060 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
6061 PhylogenyNodeIterator it6;
6062 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
6065 for( it6.reset(); it6.hasNext(); ) {
6068 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
6069 if ( !it7.next().getName().equals( "A" ) ) {
6072 if ( it.hasNext() ) {
6076 catch ( final Exception e ) {
6077 e.printStackTrace( System.out );
6083 private static boolean testMafft( final String path ) {
6085 final List<String> opts = new ArrayList<String>();
6086 opts.add( "--maxiterate" );
6088 opts.add( "--localpair" );
6089 opts.add( "--quiet" );
6091 final MsaInferrer mafft = Mafft.createInstance( path );
6092 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
6093 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
6096 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
6100 catch ( final Exception e ) {
6101 e.printStackTrace( System.out );
6107 private static boolean testMidpointrooting() {
6109 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6110 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
6111 PhylogenyMethods.midpointRoot( t0 );
6112 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
6115 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
6118 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
6122 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",
6123 new NHXParser() )[ 0 ];
6124 if ( !t1.isRooted() ) {
6127 PhylogenyMethods.midpointRoot( t1 );
6128 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6131 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6134 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6137 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6140 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6143 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6146 t1.reRoot( t1.getNode( "A" ) );
6147 PhylogenyMethods.midpointRoot( t1 );
6148 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6151 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6154 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6157 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6160 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6164 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6168 catch ( final Exception e ) {
6169 e.printStackTrace( System.out );
6175 private static boolean testMsaQualityMethod() {
6177 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6178 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6179 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6180 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6181 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6186 final Msa msa = BasicMsa.createInstance( l );
6187 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6190 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6193 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6196 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6199 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6202 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6205 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6209 catch ( final Exception e ) {
6210 e.printStackTrace( System.out );
6216 private static boolean testMsaEntropy() {
6218 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
6219 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
6220 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
6221 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
6222 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6227 final Msa msa = BasicMsa.createInstance( l );
6228 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
6229 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
6230 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
6231 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
6232 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
6233 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
6234 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
6235 System.out.println();
6236 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
6237 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
6238 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
6239 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
6240 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
6241 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
6242 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
6243 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6244 l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
6245 l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
6246 l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
6247 l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
6248 l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
6249 l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
6250 l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
6251 l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
6252 l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
6253 l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
6254 l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
6255 l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
6256 l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
6257 l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
6258 l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
6259 l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
6260 l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
6261 l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
6262 l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
6263 l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
6264 l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
6265 l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
6266 final Msa msa2 = BasicMsa.createInstance( l2 );
6267 System.out.println();
6268 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
6269 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
6270 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
6272 catch ( final Exception e ) {
6273 e.printStackTrace( System.out );
6279 private static boolean testDeleteableMsa() {
6281 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
6282 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
6283 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
6284 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
6285 final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
6286 final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
6287 final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
6294 final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
6295 dmsa0.deleteRow( "b", false );
6296 if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
6299 dmsa0.deleteRow( "e", false );
6300 dmsa0.deleteRow( "a", false );
6301 dmsa0.deleteRow( "f", false );
6302 if ( dmsa0.getLength() != 4 ) {
6305 if ( dmsa0.getNumberOfSequences() != 2 ) {
6308 if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
6311 if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
6314 if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
6317 if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
6320 if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
6323 dmsa0.deleteRow( "c", false );
6324 dmsa0.deleteRow( "d", false );
6325 if ( dmsa0.getNumberOfSequences() != 0 ) {
6329 final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
6330 final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
6331 final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
6332 final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
6333 final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
6334 final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
6335 final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
6342 final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
6343 dmsa1.deleteGapOnlyColumns();
6344 dmsa1.deleteRow( "a", false );
6345 dmsa1.deleteRow( "f", false );
6346 dmsa1.deleteRow( "d", false );
6347 dmsa1.deleteGapOnlyColumns();
6348 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
6351 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
6354 if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
6357 dmsa1.deleteRow( "c", false );
6358 dmsa1.deleteGapOnlyColumns();
6359 final Writer w0 = new StringWriter();
6360 dmsa1.write( w0, MSA_FORMAT.FASTA );
6361 final Writer w1 = new StringWriter();
6362 dmsa1.write( w1, MSA_FORMAT.PHYLIP );
6363 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
6366 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
6369 final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
6370 final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
6371 final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
6372 final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
6373 final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
6374 final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
6375 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6382 final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
6383 dmsa2.deleteGapColumns( 0.5 );
6384 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
6387 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
6390 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
6393 dmsa2.deleteGapColumns( 0.2 );
6394 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
6397 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
6400 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
6403 dmsa2.deleteGapColumns( 0 );
6404 dmsa2.deleteRow( "a", false );
6405 dmsa2.deleteRow( "b", false );
6406 dmsa2.deleteRow( "f", false );
6407 dmsa2.deleteRow( "e", false );
6408 dmsa2.setIdentifier( 0, "new_c" );
6409 dmsa2.setIdentifier( 1, "new_d" );
6410 dmsa2.setResidueAt( 0, 0, 'x' );
6411 final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
6412 if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
6415 final Writer w = new StringWriter();
6416 dmsa2.write( w, MSA_FORMAT.PHYLIP );
6417 final String phylip = w.toString();
6418 if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
6419 System.out.println( phylip );
6422 final Writer w2 = new StringWriter();
6423 dmsa2.write( w2, MSA_FORMAT.FASTA );
6424 final String fasta = w2.toString();
6425 if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
6426 System.out.println( fasta );
6430 catch ( final Exception e ) {
6431 e.printStackTrace( System.out );
6437 private static boolean testNextNodeWithCollapsing() {
6439 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6441 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6442 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6443 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6444 t0.getNode( "cd" ).setCollapse( true );
6445 t0.getNode( "cde" ).setCollapse( true );
6446 n = t0.getFirstExternalNode();
6447 while ( n != null ) {
6449 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6451 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6454 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6457 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6460 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6463 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6466 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6470 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6471 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6472 t1.getNode( "ab" ).setCollapse( true );
6473 t1.getNode( "cd" ).setCollapse( true );
6474 t1.getNode( "cde" ).setCollapse( true );
6475 n = t1.getNode( "ab" );
6476 ext = new ArrayList<PhylogenyNode>();
6477 while ( n != null ) {
6479 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6481 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6484 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6487 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6490 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6493 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6497 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6498 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6499 t2.getNode( "ab" ).setCollapse( true );
6500 t2.getNode( "cd" ).setCollapse( true );
6501 t2.getNode( "cde" ).setCollapse( true );
6502 t2.getNode( "c" ).setCollapse( true );
6503 t2.getNode( "d" ).setCollapse( true );
6504 t2.getNode( "e" ).setCollapse( true );
6505 t2.getNode( "gh" ).setCollapse( true );
6506 n = t2.getNode( "ab" );
6507 ext = new ArrayList<PhylogenyNode>();
6508 while ( n != null ) {
6510 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6512 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6515 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6518 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6521 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6525 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6526 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6527 t3.getNode( "ab" ).setCollapse( true );
6528 t3.getNode( "cd" ).setCollapse( true );
6529 t3.getNode( "cde" ).setCollapse( true );
6530 t3.getNode( "c" ).setCollapse( true );
6531 t3.getNode( "d" ).setCollapse( true );
6532 t3.getNode( "e" ).setCollapse( true );
6533 t3.getNode( "gh" ).setCollapse( true );
6534 t3.getNode( "fgh" ).setCollapse( true );
6535 n = t3.getNode( "ab" );
6536 ext = new ArrayList<PhylogenyNode>();
6537 while ( n != null ) {
6539 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6541 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6544 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6547 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6551 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6552 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6553 t4.getNode( "ab" ).setCollapse( true );
6554 t4.getNode( "cd" ).setCollapse( true );
6555 t4.getNode( "cde" ).setCollapse( true );
6556 t4.getNode( "c" ).setCollapse( true );
6557 t4.getNode( "d" ).setCollapse( true );
6558 t4.getNode( "e" ).setCollapse( true );
6559 t4.getNode( "gh" ).setCollapse( true );
6560 t4.getNode( "fgh" ).setCollapse( true );
6561 t4.getNode( "abcdefgh" ).setCollapse( true );
6562 n = t4.getNode( "abcdefgh" );
6563 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6566 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6567 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6569 n = t5.getFirstExternalNode();
6570 while ( n != null ) {
6572 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6574 if ( ext.size() != 8 ) {
6577 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6580 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6583 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6586 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6589 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6592 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6595 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6598 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6601 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6602 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6604 t6.getNode( "ab" ).setCollapse( true );
6605 n = t6.getNode( "ab" );
6606 while ( n != null ) {
6608 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6610 if ( ext.size() != 7 ) {
6613 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6616 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6619 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6622 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6625 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6628 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6631 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6634 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6635 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6637 t7.getNode( "cd" ).setCollapse( true );
6638 n = t7.getNode( "a" );
6639 while ( n != null ) {
6641 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6643 if ( ext.size() != 7 ) {
6646 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6649 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6652 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6655 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6658 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6661 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6664 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6667 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6668 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6670 t8.getNode( "cd" ).setCollapse( true );
6671 t8.getNode( "c" ).setCollapse( true );
6672 t8.getNode( "d" ).setCollapse( true );
6673 n = t8.getNode( "a" );
6674 while ( n != null ) {
6676 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6678 if ( ext.size() != 7 ) {
6681 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6684 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6687 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6688 System.out.println( "2 fail" );
6691 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6694 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6697 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6700 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6703 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6704 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6706 t9.getNode( "gh" ).setCollapse( true );
6707 n = t9.getNode( "a" );
6708 while ( n != null ) {
6710 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6712 if ( ext.size() != 7 ) {
6715 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6718 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6721 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6724 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6727 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6730 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6733 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6736 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6737 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6739 t10.getNode( "gh" ).setCollapse( true );
6740 t10.getNode( "g" ).setCollapse( true );
6741 t10.getNode( "h" ).setCollapse( true );
6742 n = t10.getNode( "a" );
6743 while ( n != null ) {
6745 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6747 if ( ext.size() != 7 ) {
6750 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6753 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6756 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6759 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6762 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6765 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6768 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6771 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6772 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6774 t11.getNode( "gh" ).setCollapse( true );
6775 t11.getNode( "fgh" ).setCollapse( true );
6776 n = t11.getNode( "a" );
6777 while ( n != null ) {
6779 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6781 if ( ext.size() != 6 ) {
6784 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6787 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6790 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6793 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6796 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6799 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6802 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6803 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6805 t12.getNode( "gh" ).setCollapse( true );
6806 t12.getNode( "fgh" ).setCollapse( true );
6807 t12.getNode( "g" ).setCollapse( true );
6808 t12.getNode( "h" ).setCollapse( true );
6809 t12.getNode( "f" ).setCollapse( true );
6810 n = t12.getNode( "a" );
6811 while ( n != null ) {
6813 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6815 if ( ext.size() != 6 ) {
6818 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6821 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6824 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6827 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6830 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6833 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6836 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6837 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6839 t13.getNode( "ab" ).setCollapse( true );
6840 t13.getNode( "b" ).setCollapse( true );
6841 t13.getNode( "fgh" ).setCollapse( true );
6842 t13.getNode( "gh" ).setCollapse( true );
6843 n = t13.getNode( "ab" );
6844 while ( n != null ) {
6846 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6848 if ( ext.size() != 5 ) {
6851 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6854 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6857 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6860 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6863 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6866 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6867 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6869 t14.getNode( "ab" ).setCollapse( true );
6870 t14.getNode( "a" ).setCollapse( true );
6871 t14.getNode( "fgh" ).setCollapse( true );
6872 t14.getNode( "gh" ).setCollapse( true );
6873 n = t14.getNode( "ab" );
6874 while ( n != null ) {
6876 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6878 if ( ext.size() != 5 ) {
6881 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6884 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6887 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6890 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6893 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6896 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" );
6897 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6899 t15.getNode( "ab" ).setCollapse( true );
6900 t15.getNode( "a" ).setCollapse( true );
6901 t15.getNode( "fgh" ).setCollapse( true );
6902 t15.getNode( "gh" ).setCollapse( true );
6903 n = t15.getNode( "ab" );
6904 while ( n != null ) {
6906 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6908 if ( ext.size() != 6 ) {
6911 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6914 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6917 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6920 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6923 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6926 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6931 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" );
6932 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6934 t16.getNode( "ab" ).setCollapse( true );
6935 t16.getNode( "a" ).setCollapse( true );
6936 t16.getNode( "fgh" ).setCollapse( true );
6937 t16.getNode( "gh" ).setCollapse( true );
6938 t16.getNode( "cd" ).setCollapse( true );
6939 t16.getNode( "cde" ).setCollapse( true );
6940 t16.getNode( "d" ).setCollapse( true );
6941 t16.getNode( "x" ).setCollapse( true );
6942 n = t16.getNode( "ab" );
6943 while ( n != null ) {
6945 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6947 if ( ext.size() != 4 ) {
6950 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6953 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6956 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6959 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6963 catch ( final Exception e ) {
6964 e.printStackTrace( System.out );
6970 private static boolean testNexusCharactersParsing() {
6972 final NexusCharactersParser parser = new NexusCharactersParser();
6973 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6975 String[] labels = parser.getCharStateLabels();
6976 if ( labels.length != 7 ) {
6979 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6982 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6985 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6988 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6991 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6994 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6997 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7000 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7002 labels = parser.getCharStateLabels();
7003 if ( labels.length != 7 ) {
7006 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7009 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7012 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7015 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7018 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7021 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7024 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7028 catch ( final Exception e ) {
7029 e.printStackTrace( System.out );
7035 private static boolean testNexusMatrixParsing() {
7037 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
7038 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
7040 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
7041 if ( m.getNumberOfCharacters() != 9 ) {
7044 if ( m.getNumberOfIdentifiers() != 5 ) {
7047 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
7050 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
7053 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
7056 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
7059 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
7062 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
7065 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
7068 // if ( labels.length != 7 ) {
7071 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7074 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7077 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7080 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7083 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7086 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7089 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7092 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7094 // labels = parser.getCharStateLabels();
7095 // if ( labels.length != 7 ) {
7098 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7101 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7104 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7107 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7110 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7113 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7116 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7120 catch ( final Exception e ) {
7121 e.printStackTrace( System.out );
7127 private static boolean testNexusTreeParsing() {
7129 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7130 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7131 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
7132 if ( phylogenies.length != 1 ) {
7135 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
7138 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7142 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
7143 if ( phylogenies.length != 1 ) {
7146 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7149 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
7153 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
7154 if ( phylogenies.length != 1 ) {
7157 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7160 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7163 if ( phylogenies[ 0 ].isRooted() ) {
7167 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
7168 if ( phylogenies.length != 18 ) {
7171 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7174 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
7177 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
7180 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
7183 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7186 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
7189 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
7192 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
7195 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
7198 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
7201 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
7204 if ( phylogenies[ 8 ].isRooted() ) {
7207 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
7210 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
7213 if ( !phylogenies[ 9 ].isRooted() ) {
7216 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
7219 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
7222 if ( !phylogenies[ 10 ].isRooted() ) {
7225 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
7228 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
7231 if ( phylogenies[ 11 ].isRooted() ) {
7234 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
7237 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
7240 if ( !phylogenies[ 12 ].isRooted() ) {
7243 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
7246 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
7249 if ( !phylogenies[ 13 ].isRooted() ) {
7252 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
7255 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
7258 if ( !phylogenies[ 14 ].isRooted() ) {
7261 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
7264 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
7267 if ( phylogenies[ 15 ].isRooted() ) {
7270 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
7273 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
7276 if ( !phylogenies[ 16 ].isRooted() ) {
7279 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
7282 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
7285 if ( phylogenies[ 17 ].isRooted() ) {
7288 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
7291 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7293 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
7294 if ( phylogenies.length != 9 ) {
7297 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
7298 .getDistanceToParent() ) ) {
7301 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
7302 .getDistanceToParent() ) ) {
7305 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
7308 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7311 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7314 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7317 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7321 catch ( final Exception e ) {
7322 e.printStackTrace( System.out );
7328 private static boolean testNexusTreeParsingIterating() {
7330 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7331 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7332 if ( !p.hasNext() ) {
7335 Phylogeny phy = p.next();
7336 if ( phy == null ) {
7339 if ( phy.getNumberOfExternalNodes() != 25 ) {
7342 if ( !phy.getName().equals( "" ) ) {
7345 if ( p.hasNext() ) {
7349 if ( phy != null ) {
7353 if ( !p.hasNext() ) {
7357 if ( phy == null ) {
7360 if ( phy.getNumberOfExternalNodes() != 25 ) {
7363 if ( !phy.getName().equals( "" ) ) {
7366 if ( p.hasNext() ) {
7370 if ( phy != null ) {
7373 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7374 if ( !p.hasNext() ) {
7378 if ( phy == null ) {
7381 if ( phy.getNumberOfExternalNodes() != 10 ) {
7384 if ( !phy.getName().equals( "name" ) ) {
7387 if ( p.hasNext() ) {
7391 if ( phy != null ) {
7395 if ( !p.hasNext() ) {
7399 if ( phy == null ) {
7402 if ( phy.getNumberOfExternalNodes() != 10 ) {
7405 if ( !phy.getName().equals( "name" ) ) {
7408 if ( p.hasNext() ) {
7412 if ( phy != null ) {
7415 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7416 if ( !p.hasNext() ) {
7420 if ( phy == null ) {
7423 if ( phy.getNumberOfExternalNodes() != 3 ) {
7426 if ( !phy.getName().equals( "" ) ) {
7429 if ( phy.isRooted() ) {
7432 if ( p.hasNext() ) {
7436 if ( phy != null ) {
7441 if ( !p.hasNext() ) {
7445 if ( phy == null ) {
7448 if ( phy.getNumberOfExternalNodes() != 3 ) {
7451 if ( !phy.getName().equals( "" ) ) {
7454 if ( p.hasNext() ) {
7458 if ( phy != null ) {
7462 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7463 if ( !p.hasNext() ) {
7468 if ( phy == null ) {
7471 if ( phy.getNumberOfExternalNodes() != 10 ) {
7474 if ( !phy.getName().equals( "tree 0" ) ) {
7478 if ( !p.hasNext() ) {
7482 if ( phy == null ) {
7485 if ( phy.getNumberOfExternalNodes() != 10 ) {
7488 if ( !phy.getName().equals( "tree 1" ) ) {
7492 if ( !p.hasNext() ) {
7496 if ( phy == null ) {
7499 if ( phy.getNumberOfExternalNodes() != 3 ) {
7500 System.out.println( phy.toString() );
7503 if ( !phy.getName().equals( "" ) ) {
7506 if ( phy.isRooted() ) {
7510 if ( !p.hasNext() ) {
7514 if ( phy == null ) {
7517 if ( phy.getNumberOfExternalNodes() != 4 ) {
7520 if ( !phy.getName().equals( "" ) ) {
7523 if ( !phy.isRooted() ) {
7527 if ( !p.hasNext() ) {
7531 if ( phy == null ) {
7534 if ( phy.getNumberOfExternalNodes() != 5 ) {
7535 System.out.println( phy.getNumberOfExternalNodes() );
7538 if ( !phy.getName().equals( "" ) ) {
7541 if ( !phy.isRooted() ) {
7545 if ( !p.hasNext() ) {
7549 if ( phy == null ) {
7552 if ( phy.getNumberOfExternalNodes() != 3 ) {
7555 if ( !phy.getName().equals( "" ) ) {
7558 if ( phy.isRooted() ) {
7562 if ( !p.hasNext() ) {
7566 if ( phy == null ) {
7569 if ( phy.getNumberOfExternalNodes() != 2 ) {
7572 if ( !phy.getName().equals( "" ) ) {
7575 if ( !phy.isRooted() ) {
7579 if ( !p.hasNext() ) {
7583 if ( phy.getNumberOfExternalNodes() != 3 ) {
7586 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7589 if ( !phy.isRooted() ) {
7593 if ( !p.hasNext() ) {
7597 if ( phy.getNumberOfExternalNodes() != 3 ) {
7600 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7603 if ( !phy.getName().equals( "tree 8" ) ) {
7607 if ( !p.hasNext() ) {
7611 if ( phy.getNumberOfExternalNodes() != 3 ) {
7614 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7617 if ( !phy.getName().equals( "tree 9" ) ) {
7621 if ( !p.hasNext() ) {
7625 if ( phy.getNumberOfExternalNodes() != 3 ) {
7628 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7631 if ( !phy.getName().equals( "tree 10" ) ) {
7634 if ( !phy.isRooted() ) {
7638 if ( !p.hasNext() ) {
7642 if ( phy.getNumberOfExternalNodes() != 3 ) {
7645 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7648 if ( !phy.getName().equals( "tree 11" ) ) {
7651 if ( phy.isRooted() ) {
7655 if ( !p.hasNext() ) {
7659 if ( phy.getNumberOfExternalNodes() != 3 ) {
7662 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7665 if ( !phy.getName().equals( "tree 12" ) ) {
7668 if ( !phy.isRooted() ) {
7672 if ( !p.hasNext() ) {
7676 if ( phy.getNumberOfExternalNodes() != 3 ) {
7679 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7682 if ( !phy.getName().equals( "tree 13" ) ) {
7685 if ( !phy.isRooted() ) {
7689 if ( !p.hasNext() ) {
7693 if ( phy.getNumberOfExternalNodes() != 10 ) {
7694 System.out.println( phy.getNumberOfExternalNodes() );
7699 .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;" ) ) {
7700 System.out.println( phy.toNewHampshire() );
7703 if ( !phy.getName().equals( "tree 14" ) ) {
7706 if ( !phy.isRooted() ) {
7710 if ( !p.hasNext() ) {
7714 if ( phy.getNumberOfExternalNodes() != 10 ) {
7715 System.out.println( phy.getNumberOfExternalNodes() );
7720 .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;" ) ) {
7721 System.out.println( phy.toNewHampshire() );
7724 if ( !phy.getName().equals( "tree 15" ) ) {
7727 if ( phy.isRooted() ) {
7731 if ( !p.hasNext() ) {
7735 if ( phy.getNumberOfExternalNodes() != 10 ) {
7736 System.out.println( phy.getNumberOfExternalNodes() );
7741 .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;" ) ) {
7742 System.out.println( phy.toNewHampshire() );
7745 if ( !phy.getName().equals( "tree 16" ) ) {
7748 if ( !phy.isRooted() ) {
7752 if ( !p.hasNext() ) {
7756 if ( phy.getNumberOfExternalNodes() != 10 ) {
7757 System.out.println( phy.getNumberOfExternalNodes() );
7762 .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;" ) ) {
7763 System.out.println( phy.toNewHampshire() );
7766 if ( !phy.getName().equals( "tree 17" ) ) {
7769 if ( phy.isRooted() ) {
7773 if ( p.hasNext() ) {
7777 if ( phy != null ) {
7782 if ( !p.hasNext() ) {
7786 if ( phy == null ) {
7789 if ( phy.getNumberOfExternalNodes() != 10 ) {
7792 if ( !phy.getName().equals( "tree 0" ) ) {
7796 if ( !p.hasNext() ) {
7800 if ( phy == null ) {
7803 if ( phy.getNumberOfExternalNodes() != 10 ) {
7806 if ( !phy.getName().equals( "tree 1" ) ) {
7810 if ( !p.hasNext() ) {
7814 if ( phy == null ) {
7817 if ( phy.getNumberOfExternalNodes() != 3 ) {
7820 if ( !phy.getName().equals( "" ) ) {
7823 if ( phy.isRooted() ) {
7827 if ( !p.hasNext() ) {
7831 if ( phy == null ) {
7834 if ( phy.getNumberOfExternalNodes() != 4 ) {
7837 if ( !phy.getName().equals( "" ) ) {
7840 if ( !phy.isRooted() ) {
7844 if ( !p.hasNext() ) {
7848 if ( phy == null ) {
7851 if ( phy.getNumberOfExternalNodes() != 5 ) {
7852 System.out.println( phy.getNumberOfExternalNodes() );
7855 if ( !phy.getName().equals( "" ) ) {
7858 if ( !phy.isRooted() ) {
7862 if ( !p.hasNext() ) {
7866 if ( phy == null ) {
7869 if ( phy.getNumberOfExternalNodes() != 3 ) {
7872 if ( !phy.getName().equals( "" ) ) {
7875 if ( phy.isRooted() ) {
7879 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7880 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7882 if ( !p2.hasNext() ) {
7886 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7889 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7893 if ( !p2.hasNext() ) {
7898 if ( !p2.hasNext() ) {
7903 if ( !p2.hasNext() ) {
7908 if ( !p2.hasNext() ) {
7913 if ( !p2.hasNext() ) {
7918 if ( !p2.hasNext() ) {
7923 if ( !p2.hasNext() ) {
7928 if ( !p2.hasNext() ) {
7932 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7935 if ( p2.hasNext() ) {
7939 if ( phy != null ) {
7944 if ( !p2.hasNext() ) {
7948 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7951 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7955 catch ( final Exception e ) {
7956 e.printStackTrace( System.out );
7962 private static boolean testNexusTreeParsingTranslating() {
7964 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7965 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7966 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7967 if ( phylogenies.length != 1 ) {
7970 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7973 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7976 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7979 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7982 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7983 .equals( "Aranaeus" ) ) {
7987 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7988 if ( phylogenies.length != 3 ) {
7991 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7994 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7997 if ( phylogenies[ 0 ].isRooted() ) {
8000 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8003 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8006 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8007 .equals( "Aranaeus" ) ) {
8010 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8013 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8016 if ( phylogenies[ 1 ].isRooted() ) {
8019 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8022 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8025 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8026 .equals( "Aranaeus" ) ) {
8029 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8032 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8035 if ( !phylogenies[ 2 ].isRooted() ) {
8038 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8041 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8044 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8045 .equals( "Aranaeus" ) ) {
8049 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
8050 if ( phylogenies.length != 3 ) {
8053 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8056 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8059 if ( phylogenies[ 0 ].isRooted() ) {
8062 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8065 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8068 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8069 .equals( "Aranaeus" ) ) {
8072 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8075 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8078 if ( phylogenies[ 1 ].isRooted() ) {
8081 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8084 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8087 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8088 .equals( "Aranaeus" ) ) {
8091 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8094 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8097 if ( !phylogenies[ 2 ].isRooted() ) {
8100 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8103 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8106 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8107 .equals( "Aranaeus" ) ) {
8110 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
8111 if ( phylogenies.length != 3 ) {
8114 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
8119 catch ( final Exception e ) {
8120 e.printStackTrace( System.out );
8126 private static boolean testNHParsing() {
8128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8129 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
8130 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
8133 final NHXParser nhxp = new NHXParser();
8134 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
8135 nhxp.setReplaceUnderscores( true );
8136 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
8137 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
8140 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
8143 final Phylogeny p1b = factory
8144 .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 ",
8145 new NHXParser() )[ 0 ];
8146 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
8149 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
8152 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
8153 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
8154 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
8155 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
8156 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
8157 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
8158 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
8159 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
8160 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
8161 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
8162 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
8163 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
8164 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
8166 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
8169 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
8172 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
8175 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
8178 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
8179 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
8180 final String p16_S = "((A,B),C)";
8181 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
8182 if ( p16.length != 1 ) {
8185 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
8188 final String p17_S = "(C,(A,B))";
8189 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
8190 if ( p17.length != 1 ) {
8193 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
8196 final String p18_S = "((A,B),(C,D))";
8197 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
8198 if ( p18.length != 1 ) {
8201 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
8204 final String p19_S = "(((A,B),C),D)";
8205 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
8206 if ( p19.length != 1 ) {
8209 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
8212 final String p20_S = "(A,(B,(C,D)))";
8213 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
8214 if ( p20.length != 1 ) {
8217 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
8220 final String p21_S = "(A,(B,(C,(D,E))))";
8221 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
8222 if ( p21.length != 1 ) {
8225 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
8228 final String p22_S = "((((A,B),C),D),E)";
8229 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
8230 if ( p22.length != 1 ) {
8233 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
8236 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8237 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
8238 if ( p23.length != 1 ) {
8239 System.out.println( "xl=" + p23.length );
8243 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
8246 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8247 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
8248 if ( p24.length != 1 ) {
8251 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
8254 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8255 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8256 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
8257 if ( p241.length != 2 ) {
8260 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
8263 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
8266 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
8267 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
8268 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
8269 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
8270 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
8271 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
8272 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
8273 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
8274 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
8275 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
8278 final String p26_S = "(A,B)ab";
8279 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
8280 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
8283 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8284 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
8285 if ( p27s.length != 1 ) {
8286 System.out.println( "xxl=" + p27s.length );
8290 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8291 System.out.println( p27s[ 0 ].toNewHampshireX() );
8295 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
8297 if ( p27.length != 1 ) {
8298 System.out.println( "yl=" + p27.length );
8302 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8303 System.out.println( p27[ 0 ].toNewHampshireX() );
8307 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8308 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8309 final String p28_S3 = "(A,B)ab";
8310 final String p28_S4 = "((((A,B),C),D),;E;)";
8311 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
8313 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
8316 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
8319 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
8322 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
8325 if ( p28.length != 4 ) {
8328 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";
8329 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8330 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8333 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";
8334 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8335 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8338 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8339 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8340 if ( ( p32.length != 0 ) ) {
8343 final String p33_S = "A";
8344 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8345 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8348 final String p34_S = "B;";
8349 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8350 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8353 final String p35_S = "B:0.2";
8354 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8355 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8358 final String p36_S = "(A)";
8359 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8360 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8363 final String p37_S = "((A))";
8364 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8365 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8368 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8369 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8370 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8373 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8374 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8375 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8378 final String p40_S = "(A,B,C)";
8379 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8380 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8383 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8384 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8385 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8388 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8389 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8390 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8393 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)";
8394 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8395 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8398 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)))";
8399 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8400 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8403 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8404 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8405 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8408 final String p46_S = "";
8409 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8410 if ( p46.length != 0 ) {
8413 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8414 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8417 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8418 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8421 final Phylogeny p49 = factory
8422 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8423 new NHXParser() )[ 0 ];
8424 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8427 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8428 if ( p50.getNode( "A" ) == null ) {
8431 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8432 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8435 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8438 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8439 .equals( "((A,B)88:2.0,C);" ) ) {
8442 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8443 if ( p51.getNode( "A(A" ) == null ) {
8446 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8447 if ( p52.getNode( "A(A" ) == null ) {
8450 final Phylogeny p53 = factory
8451 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8452 new NHXParser() )[ 0 ];
8453 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8456 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8457 if ( p54.getNode( "A" ) == null ) {
8460 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8463 final Phylogeny p55 = factory
8464 .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);" ),
8465 new NHXParser() )[ 0 ];
8468 .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);" ) ) {
8469 System.out.println( p55.toNewHampshire() );
8472 final Phylogeny p56 = factory
8473 .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);" ),
8474 new NHXParser() )[ 0 ];
8477 .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);" ) ) {
8478 System.out.println( p56.toNewHampshire() );
8481 final Phylogeny p57 = factory
8482 .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);" ),
8483 new NHXParser() )[ 0 ];
8486 .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);" ) ) {
8487 System.out.println( p56.toNewHampshire() );
8490 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8491 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8492 if ( !p58.toNewHampshire().equals( s58 ) ) {
8493 System.out.println( p58.toNewHampshire() );
8496 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8497 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8498 if ( !p59.toNewHampshire().equals( s59 ) ) {
8499 System.out.println( p59.toNewHampshire() );
8502 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8503 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8504 if ( !p60.toNewHampshire().equals( s60 ) ) {
8505 System.out.println( p60.toNewHampshire() );
8508 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8509 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8510 if ( !p61.toNewHampshire()
8511 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8512 System.out.println( p61.toNewHampshire() );
8516 catch ( final Exception e ) {
8517 e.printStackTrace( System.out );
8523 private static boolean testNHParsingIter() {
8525 final String p0_str = "(A,B);";
8526 final NHXParser p = new NHXParser();
8527 p.setSource( p0_str );
8528 if ( !p.hasNext() ) {
8531 final Phylogeny p0 = p.next();
8532 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8533 System.out.println( p0.toNewHampshire() );
8536 if ( p.hasNext() ) {
8539 if ( p.next() != null ) {
8543 final String p00_str = "(A,B)root;";
8544 p.setSource( p00_str );
8545 final Phylogeny p00 = p.next();
8546 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8547 System.out.println( p00.toNewHampshire() );
8551 final String p000_str = "A;";
8552 p.setSource( p000_str );
8553 final Phylogeny p000 = p.next();
8554 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8555 System.out.println( p000.toNewHampshire() );
8559 final String p0000_str = "A";
8560 p.setSource( p0000_str );
8561 final Phylogeny p0000 = p.next();
8562 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8563 System.out.println( p0000.toNewHampshire() );
8567 p.setSource( "(A)" );
8568 final Phylogeny p00000 = p.next();
8569 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8570 System.out.println( p00000.toNewHampshire() );
8574 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8575 p.setSource( p1_str );
8576 if ( !p.hasNext() ) {
8579 final Phylogeny p1_0 = p.next();
8580 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8581 System.out.println( p1_0.toNewHampshire() );
8584 if ( !p.hasNext() ) {
8587 final Phylogeny p1_1 = p.next();
8588 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8589 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8592 if ( !p.hasNext() ) {
8595 final Phylogeny p1_2 = p.next();
8596 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8597 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8600 if ( !p.hasNext() ) {
8603 final Phylogeny p1_3 = p.next();
8604 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8605 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8608 if ( p.hasNext() ) {
8611 if ( p.next() != null ) {
8615 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8616 p.setSource( p2_str );
8617 if ( !p.hasNext() ) {
8620 Phylogeny p2_0 = p.next();
8621 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8622 System.out.println( p2_0.toNewHampshire() );
8625 if ( !p.hasNext() ) {
8628 Phylogeny p2_1 = p.next();
8629 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8630 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8633 if ( !p.hasNext() ) {
8636 Phylogeny p2_2 = p.next();
8637 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8638 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8641 if ( !p.hasNext() ) {
8644 Phylogeny p2_3 = p.next();
8645 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8646 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8649 if ( !p.hasNext() ) {
8652 Phylogeny p2_4 = p.next();
8653 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8654 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8657 if ( p.hasNext() ) {
8660 if ( p.next() != null ) {
8665 if ( !p.hasNext() ) {
8669 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8670 System.out.println( p2_0.toNewHampshire() );
8673 if ( !p.hasNext() ) {
8677 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8678 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8681 if ( !p.hasNext() ) {
8685 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8686 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8689 if ( !p.hasNext() ) {
8693 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8694 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8697 if ( !p.hasNext() ) {
8701 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8702 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8705 if ( p.hasNext() ) {
8708 if ( p.next() != null ) {
8712 final String p3_str = "((A,B),C)abc";
8713 p.setSource( p3_str );
8714 if ( !p.hasNext() ) {
8717 final Phylogeny p3_0 = p.next();
8718 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8721 if ( p.hasNext() ) {
8724 if ( p.next() != null ) {
8728 final String p4_str = "((A,B)ab,C)abc";
8729 p.setSource( p4_str );
8730 if ( !p.hasNext() ) {
8733 final Phylogeny p4_0 = p.next();
8734 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8737 if ( p.hasNext() ) {
8740 if ( p.next() != null ) {
8744 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8745 p.setSource( p5_str );
8746 if ( !p.hasNext() ) {
8749 final Phylogeny p5_0 = p.next();
8750 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8753 if ( p.hasNext() ) {
8756 if ( p.next() != null ) {
8760 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8761 p.setSource( p6_str );
8762 if ( !p.hasNext() ) {
8765 Phylogeny p6_0 = p.next();
8766 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8769 if ( p.hasNext() ) {
8772 if ( p.next() != null ) {
8776 if ( !p.hasNext() ) {
8780 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8783 if ( p.hasNext() ) {
8786 if ( p.next() != null ) {
8790 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8791 p.setSource( p7_str );
8792 if ( !p.hasNext() ) {
8795 Phylogeny p7_0 = p.next();
8796 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8799 if ( p.hasNext() ) {
8802 if ( p.next() != null ) {
8806 if ( !p.hasNext() ) {
8810 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8813 if ( p.hasNext() ) {
8816 if ( p.next() != null ) {
8820 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8821 p.setSource( p8_str );
8822 if ( !p.hasNext() ) {
8825 Phylogeny p8_0 = p.next();
8826 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8829 if ( !p.hasNext() ) {
8832 if ( !p.hasNext() ) {
8835 Phylogeny p8_1 = p.next();
8836 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8839 if ( p.hasNext() ) {
8842 if ( p.next() != null ) {
8846 if ( !p.hasNext() ) {
8850 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8853 if ( !p.hasNext() ) {
8857 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8860 if ( p.hasNext() ) {
8863 if ( p.next() != null ) {
8869 if ( p.hasNext() ) {
8873 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8874 if ( !p.hasNext() ) {
8877 Phylogeny p_27 = p.next();
8878 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8879 System.out.println( p_27.toNewHampshireX() );
8883 if ( p.hasNext() ) {
8886 if ( p.next() != null ) {
8890 if ( !p.hasNext() ) {
8894 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8895 System.out.println( p_27.toNewHampshireX() );
8899 if ( p.hasNext() ) {
8902 if ( p.next() != null ) {
8906 final String p30_str = "(A,B);(C,D)";
8907 final NHXParser p30 = new NHXParser();
8908 p30.setSource( p30_str );
8909 if ( !p30.hasNext() ) {
8912 Phylogeny phy30 = p30.next();
8913 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8914 System.out.println( phy30.toNewHampshire() );
8917 if ( !p30.hasNext() ) {
8920 Phylogeny phy301 = p30.next();
8921 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8922 System.out.println( phy301.toNewHampshire() );
8925 if ( p30.hasNext() ) {
8928 if ( p30.hasNext() ) {
8931 if ( p30.next() != null ) {
8934 if ( p30.next() != null ) {
8938 if ( !p30.hasNext() ) {
8942 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8943 System.out.println( phy30.toNewHampshire() );
8946 if ( !p30.hasNext() ) {
8949 phy301 = p30.next();
8950 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8951 System.out.println( phy301.toNewHampshire() );
8954 if ( p30.hasNext() ) {
8957 if ( p30.hasNext() ) {
8960 if ( p30.next() != null ) {
8963 if ( p30.next() != null ) {
8967 catch ( final Exception e ) {
8968 e.printStackTrace( System.out );
8974 private static boolean testNHXconversion() {
8976 final PhylogenyNode n1 = new PhylogenyNode();
8977 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8978 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8979 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8980 final PhylogenyNode n5 = PhylogenyNode
8981 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8982 final PhylogenyNode n6 = PhylogenyNode
8983 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8984 if ( !n1.toNewHampshireX().equals( "" ) ) {
8987 if ( !n2.toNewHampshireX().equals( "" ) ) {
8990 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8993 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
8996 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
8999 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
9000 System.out.println( n6.toNewHampshireX() );
9003 final PhylogenyNode n7 = new PhylogenyNode();
9004 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
9005 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
9006 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
9007 System.out.println( n7
9008 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
9012 catch ( final Exception e ) {
9013 e.printStackTrace( System.out );
9019 private static boolean testNHXNodeParsing() {
9021 final PhylogenyNode n1 = new PhylogenyNode();
9022 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9023 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9024 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9025 final PhylogenyNode n5 = PhylogenyNode
9026 .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]" );
9027 if ( !n3.getName().equals( "n3" ) ) {
9030 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9033 if ( n3.isDuplication() ) {
9036 if ( n3.isHasAssignedEvent() ) {
9039 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
9042 if ( !n4.getName().equals( "n4" ) ) {
9045 if ( n4.getDistanceToParent() != 0.01 ) {
9048 if ( !n5.getName().equals( "n5" ) ) {
9051 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
9054 if ( n5.getDistanceToParent() != 0.1 ) {
9057 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
9060 if ( !n5.isDuplication() ) {
9063 if ( !n5.isHasAssignedEvent() ) {
9066 final PhylogenyNode n8 = PhylogenyNode
9067 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
9068 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9069 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9072 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
9075 final PhylogenyNode n9 = PhylogenyNode
9076 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
9077 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9078 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
9081 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
9084 final PhylogenyNode n10 = PhylogenyNode
9085 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9086 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
9089 final PhylogenyNode n20 = PhylogenyNode
9090 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9091 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9094 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
9097 final PhylogenyNode n20x = PhylogenyNode
9098 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9099 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
9102 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
9105 final PhylogenyNode n20xx = PhylogenyNode
9106 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9107 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
9110 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
9113 final PhylogenyNode n20xxx = PhylogenyNode
9114 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9115 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
9118 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
9121 final PhylogenyNode n20xxxx = PhylogenyNode
9122 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9123 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
9126 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
9129 final PhylogenyNode n21 = PhylogenyNode
9130 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9131 if ( !n21.getName().equals( "N21_PIG" ) ) {
9134 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
9137 final PhylogenyNode n21x = PhylogenyNode
9138 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9139 if ( !n21x.getName().equals( "n21_PIG" ) ) {
9142 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
9145 final PhylogenyNode n22 = PhylogenyNode
9146 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9147 if ( !n22.getName().equals( "n22/PIG" ) ) {
9150 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
9153 final PhylogenyNode n23 = PhylogenyNode
9154 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9155 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
9158 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
9161 final PhylogenyNode a = PhylogenyNode
9162 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9163 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9166 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
9169 final PhylogenyNode c1 = PhylogenyNode
9170 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
9171 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9172 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
9175 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
9178 final PhylogenyNode c2 = PhylogenyNode
9179 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
9180 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9181 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
9184 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
9187 final PhylogenyNode e3 = PhylogenyNode
9188 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9189 if ( !e3.getName().equals( "n10_RAT~" ) ) {
9192 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
9195 final PhylogenyNode n11 = PhylogenyNode
9196 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
9197 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9198 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
9201 if ( n11.getDistanceToParent() != 0.4 ) {
9204 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
9207 final PhylogenyNode n12 = PhylogenyNode
9208 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
9209 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9210 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
9213 if ( n12.getDistanceToParent() != 0.4 ) {
9216 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
9219 final PhylogenyNode o = PhylogenyNode
9220 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9221 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
9224 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
9227 if ( n1.getName().compareTo( "" ) != 0 ) {
9230 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9233 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9236 if ( n2.getName().compareTo( "" ) != 0 ) {
9239 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9242 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9245 final PhylogenyNode n00 = PhylogenyNode
9246 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
9247 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
9250 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
9253 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
9254 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
9257 final PhylogenyNode n13 = PhylogenyNode
9258 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9259 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
9262 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
9265 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9268 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9271 final PhylogenyNode n14 = PhylogenyNode
9272 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9273 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
9276 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
9279 final PhylogenyNode n15 = PhylogenyNode
9280 .createInstanceFromNhxString( "something_wicked[123]",
9281 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9282 if ( !n15.getName().equals( "something_wicked" ) ) {
9285 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
9288 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
9291 final PhylogenyNode n16 = PhylogenyNode
9292 .createInstanceFromNhxString( "something_wicked2[9]",
9293 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9294 if ( !n16.getName().equals( "something_wicked2" ) ) {
9297 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
9300 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
9303 final PhylogenyNode n17 = PhylogenyNode
9304 .createInstanceFromNhxString( "something_wicked3[a]",
9305 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9306 if ( !n17.getName().equals( "something_wicked3" ) ) {
9309 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
9312 final PhylogenyNode n18 = PhylogenyNode
9313 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9314 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
9317 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
9320 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
9323 final PhylogenyNode n19 = PhylogenyNode
9324 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9325 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9328 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9331 final PhylogenyNode n30 = PhylogenyNode
9332 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9333 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9334 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9337 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9340 final PhylogenyNode n31 = PhylogenyNode
9341 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9342 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9343 if ( n31.getNodeData().isHasTaxonomy() ) {
9346 final PhylogenyNode n32 = PhylogenyNode
9347 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9348 if ( n32.getNodeData().isHasTaxonomy() ) {
9351 final PhylogenyNode n40 = PhylogenyNode
9352 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9353 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9356 final PhylogenyNode n41 = PhylogenyNode
9357 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9358 if ( n41.getNodeData().isHasTaxonomy() ) {
9361 final PhylogenyNode n42 = PhylogenyNode
9362 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9363 if ( n42.getNodeData().isHasTaxonomy() ) {
9366 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9367 NHXParser.TAXONOMY_EXTRACTION.NO );
9368 if ( n43.getNodeData().isHasTaxonomy() ) {
9371 final PhylogenyNode n44 = PhylogenyNode
9372 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9373 if ( n44.getNodeData().isHasTaxonomy() ) {
9377 catch ( final Exception e ) {
9378 e.printStackTrace( System.out );
9384 private static boolean testNHXParsing() {
9386 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9387 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9388 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9391 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]";
9392 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9393 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9396 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]";
9397 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9398 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9401 final Phylogeny[] p3 = factory
9402 .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]",
9404 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9407 final Phylogeny[] p4 = factory
9408 .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(]",
9410 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9413 final Phylogeny[] p5 = factory
9414 .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(((]",
9416 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9419 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)";
9420 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)";
9421 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9422 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9425 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)))";
9426 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)))";
9427 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9428 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9431 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]) ))[,,, ])))))))";
9432 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9433 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9434 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9437 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9438 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9441 final Phylogeny p10 = factory
9442 .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]",
9443 new NHXParser() )[ 0 ];
9444 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9447 final Phylogeny p11 = factory
9448 .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]",
9449 new NHXParser() )[ 0 ];
9450 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9453 final Phylogeny p12 = factory
9454 .create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
9455 new NHXParser() )[ 0 ];
9456 if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9462 catch ( final Exception e ) {
9463 e.printStackTrace( System.out );
9469 private static boolean testNHXParsingMB() {
9471 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9472 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9473 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9474 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9475 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9476 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9477 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9478 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9479 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9480 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9481 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9484 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9487 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9488 0.1100000000000000e+00 ) ) {
9491 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9494 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9497 final Phylogeny p2 = factory
9498 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9499 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9500 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9501 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9502 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9503 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9504 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9505 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9506 + "7.369400000000000e-02}])",
9507 new NHXParser() )[ 0 ];
9508 if ( p2.getNode( "1" ) == null ) {
9511 if ( p2.getNode( "2" ) == null ) {
9515 catch ( final Exception e ) {
9516 e.printStackTrace( System.out );
9523 private static boolean testNHXParsingQuotes() {
9525 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9526 final NHXParser p = new NHXParser();
9527 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9528 if ( phylogenies_0.length != 5 ) {
9531 final Phylogeny phy = phylogenies_0[ 4 ];
9532 if ( phy.getNumberOfExternalNodes() != 7 ) {
9535 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9538 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9541 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9542 .getScientificName().equals( "hsapiens" ) ) {
9545 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9548 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9551 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9554 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9557 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9560 final NHXParser p1p = new NHXParser();
9561 p1p.setIgnoreQuotes( true );
9562 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9563 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9566 final NHXParser p2p = new NHXParser();
9567 p1p.setIgnoreQuotes( false );
9568 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9569 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9572 final NHXParser p3p = new NHXParser();
9573 p3p.setIgnoreQuotes( false );
9574 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9575 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9578 final NHXParser p4p = new NHXParser();
9579 p4p.setIgnoreQuotes( false );
9580 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9581 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9584 final Phylogeny p10 = factory
9585 .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]",
9586 new NHXParser() )[ 0 ];
9587 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]";
9588 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9591 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9592 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9595 final Phylogeny p12 = factory
9596 .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]",
9597 new NHXParser() )[ 0 ];
9598 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]";
9599 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9602 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9603 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9606 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;";
9607 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9610 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9611 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9615 catch ( final Exception e ) {
9616 e.printStackTrace( System.out );
9622 private static boolean testNodeRemoval() {
9624 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9625 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9626 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9627 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9630 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9631 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9632 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9635 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9636 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9637 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9641 catch ( final Exception e ) {
9642 e.printStackTrace( System.out );
9648 private static boolean testPhylogenyBranch() {
9650 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9651 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9652 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9653 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9654 if ( !a1b1.equals( a1b1 ) ) {
9657 if ( !a1b1.equals( b1a1 ) ) {
9660 if ( !b1a1.equals( a1b1 ) ) {
9663 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9664 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9665 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9666 if ( a1_b1.equals( b1_a1 ) ) {
9669 if ( a1_b1.equals( a1_b1_ ) ) {
9672 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9673 if ( !a1_b1.equals( b1_a1_ ) ) {
9676 if ( a1_b1_.equals( b1_a1_ ) ) {
9679 if ( !a1_b1_.equals( b1_a1 ) ) {
9683 catch ( final Exception e ) {
9684 e.printStackTrace( System.out );
9690 private static boolean testPhyloXMLparsingOfDistributionElement() {
9692 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9693 PhyloXmlParser xml_parser = null;
9695 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9697 catch ( final Exception e ) {
9698 // Do nothing -- means were not running from jar.
9700 if ( xml_parser == null ) {
9701 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9702 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9703 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9706 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9709 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9711 if ( xml_parser.getErrorCount() > 0 ) {
9712 System.out.println( xml_parser.getErrorMessages().toString() );
9715 if ( phylogenies_0.length != 1 ) {
9718 final Phylogeny t1 = phylogenies_0[ 0 ];
9719 PhylogenyNode n = null;
9720 Distribution d = null;
9721 n = t1.getNode( "root node" );
9722 if ( !n.getNodeData().isHasDistribution() ) {
9725 if ( n.getNodeData().getDistributions().size() != 1 ) {
9728 d = n.getNodeData().getDistribution();
9729 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9732 if ( d.getPoints().size() != 1 ) {
9735 if ( d.getPolygons() != null ) {
9738 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9741 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9744 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9747 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9750 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9753 n = t1.getNode( "node a" );
9754 if ( !n.getNodeData().isHasDistribution() ) {
9757 if ( n.getNodeData().getDistributions().size() != 2 ) {
9760 d = n.getNodeData().getDistribution( 1 );
9761 if ( !d.getDesc().equals( "San Diego" ) ) {
9764 if ( d.getPoints().size() != 1 ) {
9767 if ( d.getPolygons() != null ) {
9770 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9773 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9776 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9779 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9782 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9785 n = t1.getNode( "node bb" );
9786 if ( !n.getNodeData().isHasDistribution() ) {
9789 if ( n.getNodeData().getDistributions().size() != 1 ) {
9792 d = n.getNodeData().getDistribution( 0 );
9793 if ( d.getPoints().size() != 3 ) {
9796 if ( d.getPolygons().size() != 2 ) {
9799 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9802 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9805 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9808 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9811 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9814 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9817 Polygon p = d.getPolygons().get( 0 );
9818 if ( p.getPoints().size() != 3 ) {
9821 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9824 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9827 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9830 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9833 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9836 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9839 p = d.getPolygons().get( 1 );
9840 if ( p.getPoints().size() != 3 ) {
9843 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9846 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9849 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9853 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9854 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9855 if ( rt.length != 1 ) {
9858 final Phylogeny t1_rt = rt[ 0 ];
9859 n = t1_rt.getNode( "root node" );
9860 if ( !n.getNodeData().isHasDistribution() ) {
9863 if ( n.getNodeData().getDistributions().size() != 1 ) {
9866 d = n.getNodeData().getDistribution();
9867 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9870 if ( d.getPoints().size() != 1 ) {
9873 if ( d.getPolygons() != null ) {
9876 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9879 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9882 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9885 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9888 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9891 n = t1_rt.getNode( "node a" );
9892 if ( !n.getNodeData().isHasDistribution() ) {
9895 if ( n.getNodeData().getDistributions().size() != 2 ) {
9898 d = n.getNodeData().getDistribution( 1 );
9899 if ( !d.getDesc().equals( "San Diego" ) ) {
9902 if ( d.getPoints().size() != 1 ) {
9905 if ( d.getPolygons() != null ) {
9908 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9911 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9914 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9917 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9920 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9923 n = t1_rt.getNode( "node bb" );
9924 if ( !n.getNodeData().isHasDistribution() ) {
9927 if ( n.getNodeData().getDistributions().size() != 1 ) {
9930 d = n.getNodeData().getDistribution( 0 );
9931 if ( d.getPoints().size() != 3 ) {
9934 if ( d.getPolygons().size() != 2 ) {
9937 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9940 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9943 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9946 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9949 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9952 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9955 p = d.getPolygons().get( 0 );
9956 if ( p.getPoints().size() != 3 ) {
9959 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9962 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9965 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9968 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9971 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9974 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9977 p = d.getPolygons().get( 1 );
9978 if ( p.getPoints().size() != 3 ) {
9981 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9984 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9987 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9991 catch ( final Exception e ) {
9992 e.printStackTrace( System.out );
9998 private static boolean testPostOrderIterator() {
10000 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10001 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10002 PhylogenyNodeIterator it0;
10003 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
10006 for( it0.reset(); it0.hasNext(); ) {
10009 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10010 final PhylogenyNodeIterator it = t1.iteratorPostorder();
10011 if ( !it.next().getName().equals( "A" ) ) {
10014 if ( !it.next().getName().equals( "B" ) ) {
10017 if ( !it.next().getName().equals( "ab" ) ) {
10020 if ( !it.next().getName().equals( "C" ) ) {
10023 if ( !it.next().getName().equals( "D" ) ) {
10026 if ( !it.next().getName().equals( "cd" ) ) {
10029 if ( !it.next().getName().equals( "abcd" ) ) {
10032 if ( !it.next().getName().equals( "E" ) ) {
10035 if ( !it.next().getName().equals( "F" ) ) {
10038 if ( !it.next().getName().equals( "ef" ) ) {
10041 if ( !it.next().getName().equals( "G" ) ) {
10044 if ( !it.next().getName().equals( "H" ) ) {
10047 if ( !it.next().getName().equals( "gh" ) ) {
10050 if ( !it.next().getName().equals( "efgh" ) ) {
10053 if ( !it.next().getName().equals( "r" ) ) {
10056 if ( it.hasNext() ) {
10060 catch ( final Exception e ) {
10061 e.printStackTrace( System.out );
10067 private static boolean testPreOrderIterator() {
10069 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10070 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10071 PhylogenyNodeIterator it0;
10072 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
10075 for( it0.reset(); it0.hasNext(); ) {
10078 PhylogenyNodeIterator it = t0.iteratorPreorder();
10079 if ( !it.next().getName().equals( "r" ) ) {
10082 if ( !it.next().getName().equals( "ab" ) ) {
10085 if ( !it.next().getName().equals( "A" ) ) {
10088 if ( !it.next().getName().equals( "B" ) ) {
10091 if ( !it.next().getName().equals( "cd" ) ) {
10094 if ( !it.next().getName().equals( "C" ) ) {
10097 if ( !it.next().getName().equals( "D" ) ) {
10100 if ( it.hasNext() ) {
10103 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10104 it = t1.iteratorPreorder();
10105 if ( !it.next().getName().equals( "r" ) ) {
10108 if ( !it.next().getName().equals( "abcd" ) ) {
10111 if ( !it.next().getName().equals( "ab" ) ) {
10114 if ( !it.next().getName().equals( "A" ) ) {
10117 if ( !it.next().getName().equals( "B" ) ) {
10120 if ( !it.next().getName().equals( "cd" ) ) {
10123 if ( !it.next().getName().equals( "C" ) ) {
10126 if ( !it.next().getName().equals( "D" ) ) {
10129 if ( !it.next().getName().equals( "efgh" ) ) {
10132 if ( !it.next().getName().equals( "ef" ) ) {
10135 if ( !it.next().getName().equals( "E" ) ) {
10138 if ( !it.next().getName().equals( "F" ) ) {
10141 if ( !it.next().getName().equals( "gh" ) ) {
10144 if ( !it.next().getName().equals( "G" ) ) {
10147 if ( !it.next().getName().equals( "H" ) ) {
10150 if ( it.hasNext() ) {
10154 catch ( final Exception e ) {
10155 e.printStackTrace( System.out );
10161 private static boolean testPropertiesMap() {
10163 final PropertiesMap pm = new PropertiesMap();
10164 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10165 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10166 final Property p2 = new Property( "something:else",
10168 "improbable:research",
10171 pm.addProperty( p0 );
10172 pm.addProperty( p1 );
10173 pm.addProperty( p2 );
10174 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
10177 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
10180 if ( pm.getProperties().size() != 3 ) {
10183 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
10186 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10189 if ( pm.getProperties().size() != 3 ) {
10192 pm.removeProperty( "dimensions:diameter" );
10193 if ( pm.getProperties().size() != 2 ) {
10196 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
10199 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10203 catch ( final Exception e ) {
10204 e.printStackTrace( System.out );
10210 private static boolean testProteinId() {
10212 final ProteinId id1 = new ProteinId( "a" );
10213 final ProteinId id2 = new ProteinId( "a" );
10214 final ProteinId id3 = new ProteinId( "A" );
10215 final ProteinId id4 = new ProteinId( "b" );
10216 if ( !id1.equals( id1 ) ) {
10219 if ( id1.getId().equals( "x" ) ) {
10222 if ( id1.getId().equals( null ) ) {
10225 if ( !id1.equals( id2 ) ) {
10228 if ( id1.equals( id3 ) ) {
10231 if ( id1.hashCode() != id1.hashCode() ) {
10234 if ( id1.hashCode() != id2.hashCode() ) {
10237 if ( id1.hashCode() == id3.hashCode() ) {
10240 if ( id1.compareTo( id1 ) != 0 ) {
10243 if ( id1.compareTo( id2 ) != 0 ) {
10246 if ( id1.compareTo( id3 ) != 0 ) {
10249 if ( id1.compareTo( id4 ) >= 0 ) {
10252 if ( id4.compareTo( id1 ) <= 0 ) {
10255 if ( !id4.getId().equals( "b" ) ) {
10258 final ProteinId id5 = new ProteinId( " C " );
10259 if ( !id5.getId().equals( "C" ) ) {
10262 if ( id5.equals( id1 ) ) {
10266 catch ( final Exception e ) {
10267 e.printStackTrace( System.out );
10273 private static boolean testReIdMethods() {
10275 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10276 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
10277 final long count = PhylogenyNode.getNodeCount();
10278 p.levelOrderReID();
10279 if ( p.getNode( "r" ).getId() != count ) {
10282 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
10285 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
10288 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
10291 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
10294 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
10297 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
10300 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
10303 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
10306 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
10309 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
10312 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
10315 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
10318 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
10321 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
10325 catch ( final Exception e ) {
10326 e.printStackTrace( System.out );
10332 private static boolean testRerooting() {
10334 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10335 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",
10336 new NHXParser() )[ 0 ];
10337 if ( !t1.isRooted() ) {
10340 t1.reRoot( t1.getNode( "D" ) );
10341 t1.reRoot( t1.getNode( "CD" ) );
10342 t1.reRoot( t1.getNode( "A" ) );
10343 t1.reRoot( t1.getNode( "B" ) );
10344 t1.reRoot( t1.getNode( "AB" ) );
10345 t1.reRoot( t1.getNode( "D" ) );
10346 t1.reRoot( t1.getNode( "C" ) );
10347 t1.reRoot( t1.getNode( "CD" ) );
10348 t1.reRoot( t1.getNode( "A" ) );
10349 t1.reRoot( t1.getNode( "B" ) );
10350 t1.reRoot( t1.getNode( "AB" ) );
10351 t1.reRoot( t1.getNode( "D" ) );
10352 t1.reRoot( t1.getNode( "D" ) );
10353 t1.reRoot( t1.getNode( "C" ) );
10354 t1.reRoot( t1.getNode( "A" ) );
10355 t1.reRoot( t1.getNode( "B" ) );
10356 t1.reRoot( t1.getNode( "AB" ) );
10357 t1.reRoot( t1.getNode( "C" ) );
10358 t1.reRoot( t1.getNode( "D" ) );
10359 t1.reRoot( t1.getNode( "CD" ) );
10360 t1.reRoot( t1.getNode( "D" ) );
10361 t1.reRoot( t1.getNode( "A" ) );
10362 t1.reRoot( t1.getNode( "B" ) );
10363 t1.reRoot( t1.getNode( "AB" ) );
10364 t1.reRoot( t1.getNode( "C" ) );
10365 t1.reRoot( t1.getNode( "D" ) );
10366 t1.reRoot( t1.getNode( "CD" ) );
10367 t1.reRoot( t1.getNode( "D" ) );
10368 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10371 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10374 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10377 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10380 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10383 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10386 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",
10387 new NHXParser() )[ 0 ];
10388 t2.reRoot( t2.getNode( "A" ) );
10389 t2.reRoot( t2.getNode( "D" ) );
10390 t2.reRoot( t2.getNode( "ABC" ) );
10391 t2.reRoot( t2.getNode( "A" ) );
10392 t2.reRoot( t2.getNode( "B" ) );
10393 t2.reRoot( t2.getNode( "D" ) );
10394 t2.reRoot( t2.getNode( "C" ) );
10395 t2.reRoot( t2.getNode( "ABC" ) );
10396 t2.reRoot( t2.getNode( "A" ) );
10397 t2.reRoot( t2.getNode( "B" ) );
10398 t2.reRoot( t2.getNode( "AB" ) );
10399 t2.reRoot( t2.getNode( "AB" ) );
10400 t2.reRoot( t2.getNode( "D" ) );
10401 t2.reRoot( t2.getNode( "C" ) );
10402 t2.reRoot( t2.getNode( "B" ) );
10403 t2.reRoot( t2.getNode( "AB" ) );
10404 t2.reRoot( t2.getNode( "D" ) );
10405 t2.reRoot( t2.getNode( "D" ) );
10406 t2.reRoot( t2.getNode( "ABC" ) );
10407 t2.reRoot( t2.getNode( "A" ) );
10408 t2.reRoot( t2.getNode( "B" ) );
10409 t2.reRoot( t2.getNode( "AB" ) );
10410 t2.reRoot( t2.getNode( "D" ) );
10411 t2.reRoot( t2.getNode( "C" ) );
10412 t2.reRoot( t2.getNode( "ABC" ) );
10413 t2.reRoot( t2.getNode( "A" ) );
10414 t2.reRoot( t2.getNode( "B" ) );
10415 t2.reRoot( t2.getNode( "AB" ) );
10416 t2.reRoot( t2.getNode( "D" ) );
10417 t2.reRoot( t2.getNode( "D" ) );
10418 t2.reRoot( t2.getNode( "C" ) );
10419 t2.reRoot( t2.getNode( "A" ) );
10420 t2.reRoot( t2.getNode( "B" ) );
10421 t2.reRoot( t2.getNode( "AB" ) );
10422 t2.reRoot( t2.getNode( "C" ) );
10423 t2.reRoot( t2.getNode( "D" ) );
10424 t2.reRoot( t2.getNode( "ABC" ) );
10425 t2.reRoot( t2.getNode( "D" ) );
10426 t2.reRoot( t2.getNode( "A" ) );
10427 t2.reRoot( t2.getNode( "B" ) );
10428 t2.reRoot( t2.getNode( "AB" ) );
10429 t2.reRoot( t2.getNode( "C" ) );
10430 t2.reRoot( t2.getNode( "D" ) );
10431 t2.reRoot( t2.getNode( "ABC" ) );
10432 t2.reRoot( t2.getNode( "D" ) );
10433 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10436 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10439 t2.reRoot( t2.getNode( "ABC" ) );
10440 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10443 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10446 t2.reRoot( t2.getNode( "AB" ) );
10447 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10450 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10453 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10456 t2.reRoot( t2.getNode( "AB" ) );
10457 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10460 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10463 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10466 t2.reRoot( t2.getNode( "D" ) );
10467 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10470 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10473 t2.reRoot( t2.getNode( "ABC" ) );
10474 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10477 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10480 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10481 new NHXParser() )[ 0 ];
10482 t3.reRoot( t3.getNode( "B" ) );
10483 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10486 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10489 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10492 t3.reRoot( t3.getNode( "B" ) );
10493 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10496 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10499 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10502 t3.reRoot( t3.getRoot() );
10503 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10506 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10509 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10513 catch ( final Exception e ) {
10514 e.printStackTrace( System.out );
10520 private static boolean testSDIse() {
10522 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10523 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10524 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10525 gene1.setRooted( true );
10526 species1.setRooted( true );
10527 final SDI sdi = new SDI( gene1, species1 );
10528 if ( !gene1.getRoot().isDuplication() ) {
10531 final Phylogeny species2 = factory
10532 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10533 new NHXParser() )[ 0 ];
10534 final Phylogeny gene2 = factory
10535 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10536 new NHXParser() )[ 0 ];
10537 species2.setRooted( true );
10538 gene2.setRooted( true );
10539 final SDI sdi2 = new SDI( gene2, species2 );
10540 if ( sdi2.getDuplicationsSum() != 0 ) {
10543 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10546 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10549 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10552 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10555 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10558 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10561 final Phylogeny species3 = factory
10562 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10563 new NHXParser() )[ 0 ];
10564 final Phylogeny gene3 = factory
10565 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10566 new NHXParser() )[ 0 ];
10567 species3.setRooted( true );
10568 gene3.setRooted( true );
10569 final SDI sdi3 = new SDI( gene3, species3 );
10570 if ( sdi3.getDuplicationsSum() != 1 ) {
10573 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10576 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10579 final Phylogeny species4 = factory
10580 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10581 new NHXParser() )[ 0 ];
10582 final Phylogeny gene4 = factory
10583 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10584 new NHXParser() )[ 0 ];
10585 species4.setRooted( true );
10586 gene4.setRooted( true );
10587 final SDI sdi4 = new SDI( gene4, species4 );
10588 if ( sdi4.getDuplicationsSum() != 1 ) {
10591 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10594 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10597 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10600 if ( species4.getNumberOfExternalNodes() != 6 ) {
10603 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10606 final Phylogeny species5 = factory
10607 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10608 new NHXParser() )[ 0 ];
10609 final Phylogeny gene5 = factory
10610 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10611 new NHXParser() )[ 0 ];
10612 species5.setRooted( true );
10613 gene5.setRooted( true );
10614 final SDI sdi5 = new SDI( gene5, species5 );
10615 if ( sdi5.getDuplicationsSum() != 2 ) {
10618 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10621 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10624 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10627 if ( species5.getNumberOfExternalNodes() != 6 ) {
10630 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10633 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10634 // Conjecture for Comparing Molecular Phylogenies"
10635 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10636 final Phylogeny species6 = factory
10637 .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,"
10638 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10639 new NHXParser() )[ 0 ];
10640 final Phylogeny gene6 = factory
10641 .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,"
10642 + "((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,"
10643 + "(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;",
10644 new NHXParser() )[ 0 ];
10645 species6.setRooted( true );
10646 gene6.setRooted( true );
10647 final SDI sdi6 = new SDI( gene6, species6 );
10648 if ( sdi6.getDuplicationsSum() != 3 ) {
10651 if ( !gene6.getNode( "r" ).isDuplication() ) {
10654 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10657 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10660 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10663 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10666 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10669 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10672 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10675 sdi6.computeMappingCostL();
10676 if ( sdi6.computeMappingCostL() != 17 ) {
10679 if ( species6.getNumberOfExternalNodes() != 9 ) {
10682 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10685 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10686 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10687 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10688 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10689 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10690 species7.setRooted( true );
10691 final Phylogeny gene7_1 = Test
10692 .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])" );
10693 gene7_1.setRooted( true );
10694 final SDI sdi7 = new SDI( gene7_1, species7 );
10695 if ( sdi7.getDuplicationsSum() != 0 ) {
10698 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10701 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10704 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10707 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10710 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10713 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10716 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10719 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10722 final Phylogeny gene7_2 = Test
10723 .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])" );
10724 gene7_2.setRooted( true );
10725 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10726 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10729 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10732 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10735 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10738 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10741 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10744 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10747 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10750 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10753 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10757 catch ( final Exception e ) {
10763 private static boolean testSDIunrooted() {
10765 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10766 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10767 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10768 final Iterator<PhylogenyBranch> iter = l.iterator();
10769 PhylogenyBranch br = iter.next();
10770 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10773 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10777 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10780 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10784 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10787 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10791 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10794 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10798 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10801 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10805 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10808 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10812 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10815 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10819 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10822 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10826 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10829 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10833 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10836 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10840 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10843 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10847 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10850 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10854 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10857 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10861 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10864 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10868 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10871 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10874 if ( iter.hasNext() ) {
10877 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10878 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10879 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10881 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10884 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10888 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10891 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10895 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10898 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10901 if ( iter1.hasNext() ) {
10904 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10905 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10906 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10908 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10911 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10915 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10918 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10922 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10925 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10928 if ( iter2.hasNext() ) {
10931 final Phylogeny species0 = factory
10932 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10933 new NHXParser() )[ 0 ];
10934 final Phylogeny gene1 = factory
10935 .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])",
10936 new NHXParser() )[ 0 ];
10937 species0.setRooted( true );
10938 gene1.setRooted( true );
10939 final SDIR sdi_unrooted = new SDIR();
10940 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10941 if ( sdi_unrooted.getCount() != 1 ) {
10944 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10947 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10950 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10953 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10956 final Phylogeny gene2 = factory
10957 .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])",
10958 new NHXParser() )[ 0 ];
10959 gene2.setRooted( true );
10960 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10961 if ( sdi_unrooted.getCount() != 1 ) {
10964 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10967 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10970 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10973 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10976 final Phylogeny species6 = factory
10977 .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,"
10978 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10979 new NHXParser() )[ 0 ];
10980 final Phylogeny gene6 = factory
10981 .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],"
10982 + "(((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],"
10983 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10984 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10985 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10986 new NHXParser() )[ 0 ];
10987 species6.setRooted( true );
10988 gene6.setRooted( true );
10989 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10990 if ( sdi_unrooted.getCount() != 1 ) {
10993 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10996 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10999 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11002 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11005 if ( !p6[ 0 ].getRoot().isDuplication() ) {
11008 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11011 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11014 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
11017 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11020 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
11023 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
11026 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11030 final Phylogeny species7 = factory
11031 .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,"
11032 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11033 new NHXParser() )[ 0 ];
11034 final Phylogeny gene7 = factory
11035 .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],"
11036 + "(((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],"
11037 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11038 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11039 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11040 new NHXParser() )[ 0 ];
11041 species7.setRooted( true );
11042 gene7.setRooted( true );
11043 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
11044 if ( sdi_unrooted.getCount() != 1 ) {
11047 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11050 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11053 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11056 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
11059 if ( !p7[ 0 ].getRoot().isDuplication() ) {
11062 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11065 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11068 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
11071 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11074 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
11077 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
11080 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11084 final Phylogeny species8 = factory
11085 .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,"
11086 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11087 new NHXParser() )[ 0 ];
11088 final Phylogeny gene8 = factory
11089 .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],"
11090 + "(((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],"
11091 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11092 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11093 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11094 new NHXParser() )[ 0 ];
11095 species8.setRooted( true );
11096 gene8.setRooted( true );
11097 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
11098 if ( sdi_unrooted.getCount() != 1 ) {
11101 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11104 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11107 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11110 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11113 if ( !p8[ 0 ].getRoot().isDuplication() ) {
11116 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11119 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11122 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
11125 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11128 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
11131 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
11134 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11139 catch ( final Exception e ) {
11140 e.printStackTrace( System.out );
11146 private static boolean testSequenceDbWsTools1() {
11148 final PhylogenyNode n = new PhylogenyNode();
11149 n.setName( "NP_001025424" );
11150 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11151 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11152 || !acc.getValue().equals( "NP_001025424" ) ) {
11155 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11156 acc = SequenceDbWsTools.obtainSeqAccession( n );
11157 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11158 || !acc.getValue().equals( "NP_001025424" ) ) {
11161 n.setName( "NP_001025424.1" );
11162 acc = SequenceDbWsTools.obtainSeqAccession( n );
11163 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11164 || !acc.getValue().equals( "NP_001025424" ) ) {
11167 n.setName( "NM_001030253" );
11168 acc = SequenceDbWsTools.obtainSeqAccession( n );
11169 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11170 || !acc.getValue().equals( "NM_001030253" ) ) {
11173 n.setName( "BCL2_HUMAN" );
11174 acc = SequenceDbWsTools.obtainSeqAccession( n );
11175 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11176 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11177 System.out.println( acc.toString() );
11180 n.setName( "P10415" );
11181 acc = SequenceDbWsTools.obtainSeqAccession( n );
11182 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11183 || !acc.getValue().equals( "P10415" ) ) {
11184 System.out.println( acc.toString() );
11187 n.setName( " P10415 " );
11188 acc = SequenceDbWsTools.obtainSeqAccession( n );
11189 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11190 || !acc.getValue().equals( "P10415" ) ) {
11191 System.out.println( acc.toString() );
11194 n.setName( "_P10415|" );
11195 acc = SequenceDbWsTools.obtainSeqAccession( n );
11196 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11197 || !acc.getValue().equals( "P10415" ) ) {
11198 System.out.println( acc.toString() );
11201 n.setName( "AY695820" );
11202 acc = SequenceDbWsTools.obtainSeqAccession( n );
11203 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11204 || !acc.getValue().equals( "AY695820" ) ) {
11205 System.out.println( acc.toString() );
11208 n.setName( "_AY695820_" );
11209 acc = SequenceDbWsTools.obtainSeqAccession( n );
11210 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11211 || !acc.getValue().equals( "AY695820" ) ) {
11212 System.out.println( acc.toString() );
11215 n.setName( "AAA59452" );
11216 acc = SequenceDbWsTools.obtainSeqAccession( n );
11217 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11218 || !acc.getValue().equals( "AAA59452" ) ) {
11219 System.out.println( acc.toString() );
11222 n.setName( "_AAA59452_" );
11223 acc = SequenceDbWsTools.obtainSeqAccession( n );
11224 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11225 || !acc.getValue().equals( "AAA59452" ) ) {
11226 System.out.println( acc.toString() );
11229 n.setName( "AAA59452.1" );
11230 acc = SequenceDbWsTools.obtainSeqAccession( n );
11231 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11232 || !acc.getValue().equals( "AAA59452.1" ) ) {
11233 System.out.println( acc.toString() );
11236 n.setName( "_AAA59452.1_" );
11237 acc = SequenceDbWsTools.obtainSeqAccession( n );
11238 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11239 || !acc.getValue().equals( "AAA59452.1" ) ) {
11240 System.out.println( acc.toString() );
11243 n.setName( "GI:94894583" );
11244 acc = SequenceDbWsTools.obtainSeqAccession( n );
11245 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11246 || !acc.getValue().equals( "94894583" ) ) {
11247 System.out.println( acc.toString() );
11250 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11251 acc = SequenceDbWsTools.obtainSeqAccession( n );
11252 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11253 || !acc.getValue().equals( "71845847" ) ) {
11254 System.out.println( acc.toString() );
11257 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11258 acc = SequenceDbWsTools.obtainSeqAccession( n );
11259 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11260 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11261 System.out.println( acc.toString() );
11265 catch ( final Exception e ) {
11271 private static boolean testSequenceDbWsTools2() {
11273 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11274 SequenceDbWsTools.obtainSeqInformation( n1 );
11275 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11278 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11281 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11284 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11287 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11288 SequenceDbWsTools.obtainSeqInformation( n2 );
11289 if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
11292 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11295 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11298 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11301 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11302 SequenceDbWsTools.obtainSeqInformation( n3 );
11303 if ( !n3.getNodeData().getSequence().getName()
11304 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11307 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11310 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11313 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11317 catch ( final IOException e ) {
11318 System.out.println();
11319 System.out.println( "the following might be due to absence internet connection:" );
11320 e.printStackTrace( System.out );
11323 catch ( final Exception e ) {
11324 e.printStackTrace();
11330 private static boolean testSequenceIdParsing() {
11332 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11333 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11334 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11335 if ( id != null ) {
11336 System.out.println( "value =" + id.getValue() );
11337 System.out.println( "provider=" + id.getSource() );
11341 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11342 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11343 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11344 if ( id != null ) {
11345 System.out.println( "value =" + id.getValue() );
11346 System.out.println( "provider=" + id.getSource() );
11350 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11351 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11352 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11353 if ( id != null ) {
11354 System.out.println( "value =" + id.getValue() );
11355 System.out.println( "provider=" + id.getSource() );
11359 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11360 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11361 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11362 if ( id != null ) {
11363 System.out.println( "value =" + id.getValue() );
11364 System.out.println( "provider=" + id.getSource() );
11368 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11369 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11370 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11371 if ( id != null ) {
11372 System.out.println( "value =" + id.getValue() );
11373 System.out.println( "provider=" + id.getSource() );
11377 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11378 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11379 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11380 if ( id != null ) {
11381 System.out.println( "value =" + id.getValue() );
11382 System.out.println( "provider=" + id.getSource() );
11386 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11387 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11388 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11389 if ( id != null ) {
11390 System.out.println( "value =" + id.getValue() );
11391 System.out.println( "provider=" + id.getSource() );
11395 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11396 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11397 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11398 if ( id != null ) {
11399 System.out.println( "value =" + id.getValue() );
11400 System.out.println( "provider=" + id.getSource() );
11404 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11405 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11406 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11407 if ( id != null ) {
11408 System.out.println( "value =" + id.getValue() );
11409 System.out.println( "provider=" + id.getSource() );
11413 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11414 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11415 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11416 if ( id != null ) {
11417 System.out.println( "value =" + id.getValue() );
11418 System.out.println( "provider=" + id.getSource() );
11422 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11423 if ( id != null ) {
11424 System.out.println( "value =" + id.getValue() );
11425 System.out.println( "provider=" + id.getSource() );
11428 id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
11429 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11430 || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
11431 if ( id != null ) {
11432 System.out.println( "value =" + id.getValue() );
11433 System.out.println( "provider=" + id.getSource() );
11437 id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
11438 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11439 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11440 if ( id != null ) {
11441 System.out.println( "value =" + id.getValue() );
11442 System.out.println( "provider=" + id.getSource() );
11446 id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
11447 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11448 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11449 if ( id != null ) {
11450 System.out.println( "value =" + id.getValue() );
11451 System.out.println( "provider=" + id.getSource() );
11455 id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
11456 if ( id != null ) {
11457 System.out.println( "value =" + id.getValue() );
11458 System.out.println( "provider=" + id.getSource() );
11462 catch ( final Exception e ) {
11463 e.printStackTrace( System.out );
11469 private static boolean testSequenceWriter() {
11471 final String n = ForesterUtil.LINE_SEPARATOR;
11472 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11475 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11478 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11481 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11484 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11485 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11488 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11489 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11493 catch ( final Exception e ) {
11494 e.printStackTrace();
11500 private static boolean testSpecies() {
11502 final Species s1 = new BasicSpecies( "a" );
11503 final Species s2 = new BasicSpecies( "a" );
11504 final Species s3 = new BasicSpecies( "A" );
11505 final Species s4 = new BasicSpecies( "b" );
11506 if ( !s1.equals( s1 ) ) {
11509 if ( s1.getSpeciesId().equals( "x" ) ) {
11512 if ( s1.getSpeciesId().equals( null ) ) {
11515 if ( !s1.equals( s2 ) ) {
11518 if ( s1.equals( s3 ) ) {
11521 if ( s1.hashCode() != s1.hashCode() ) {
11524 if ( s1.hashCode() != s2.hashCode() ) {
11527 if ( s1.hashCode() == s3.hashCode() ) {
11530 if ( s1.compareTo( s1 ) != 0 ) {
11533 if ( s1.compareTo( s2 ) != 0 ) {
11536 if ( s1.compareTo( s3 ) != 0 ) {
11539 if ( s1.compareTo( s4 ) >= 0 ) {
11542 if ( s4.compareTo( s1 ) <= 0 ) {
11545 if ( !s4.getSpeciesId().equals( "b" ) ) {
11548 final Species s5 = new BasicSpecies( " C " );
11549 if ( !s5.getSpeciesId().equals( "C" ) ) {
11552 if ( s5.equals( s1 ) ) {
11556 catch ( final Exception e ) {
11557 e.printStackTrace( System.out );
11563 private static boolean testSplit() {
11565 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11566 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11567 //Archaeopteryx.createApplication( p0 );
11568 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11569 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11570 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11571 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11572 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11573 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11574 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11575 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11576 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11577 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11578 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11579 // System.out.println( s0.toString() );
11581 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11584 if ( s0.match( query_nodes ) ) {
11587 query_nodes = new HashSet<PhylogenyNode>();
11588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11594 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11595 if ( !s0.match( query_nodes ) ) {
11599 query_nodes = new HashSet<PhylogenyNode>();
11600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11603 if ( !s0.match( query_nodes ) ) {
11607 query_nodes = new HashSet<PhylogenyNode>();
11608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11612 if ( !s0.match( query_nodes ) ) {
11616 query_nodes = new HashSet<PhylogenyNode>();
11617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11621 if ( !s0.match( query_nodes ) ) {
11625 query_nodes = new HashSet<PhylogenyNode>();
11626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11629 if ( !s0.match( query_nodes ) ) {
11632 query_nodes = new HashSet<PhylogenyNode>();
11633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11635 if ( !s0.match( query_nodes ) ) {
11638 query_nodes = new HashSet<PhylogenyNode>();
11639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11644 if ( !s0.match( query_nodes ) ) {
11647 query_nodes = new HashSet<PhylogenyNode>();
11648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11651 if ( !s0.match( query_nodes ) ) {
11654 query_nodes = new HashSet<PhylogenyNode>();
11655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11659 if ( !s0.match( query_nodes ) ) {
11662 query_nodes = new HashSet<PhylogenyNode>();
11663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11665 if ( s0.match( query_nodes ) ) {
11668 query_nodes = new HashSet<PhylogenyNode>();
11669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11673 if ( s0.match( query_nodes ) ) {
11676 query_nodes = new HashSet<PhylogenyNode>();
11677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11682 if ( s0.match( query_nodes ) ) {
11685 query_nodes = new HashSet<PhylogenyNode>();
11686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11689 if ( s0.match( query_nodes ) ) {
11692 query_nodes = new HashSet<PhylogenyNode>();
11693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11695 if ( s0.match( query_nodes ) ) {
11698 query_nodes = new HashSet<PhylogenyNode>();
11699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11701 if ( s0.match( query_nodes ) ) {
11704 query_nodes = new HashSet<PhylogenyNode>();
11705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11707 if ( s0.match( query_nodes ) ) {
11710 query_nodes = new HashSet<PhylogenyNode>();
11711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11713 if ( s0.match( query_nodes ) ) {
11716 query_nodes = new HashSet<PhylogenyNode>();
11717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11718 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11719 if ( s0.match( query_nodes ) ) {
11722 query_nodes = new HashSet<PhylogenyNode>();
11723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11724 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11725 if ( s0.match( query_nodes ) ) {
11728 query_nodes = new HashSet<PhylogenyNode>();
11729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11732 if ( s0.match( query_nodes ) ) {
11735 query_nodes = new HashSet<PhylogenyNode>();
11736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11739 if ( s0.match( query_nodes ) ) {
11742 query_nodes = new HashSet<PhylogenyNode>();
11743 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11745 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11746 if ( s0.match( query_nodes ) ) {
11749 query_nodes = new HashSet<PhylogenyNode>();
11750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11754 if ( s0.match( query_nodes ) ) {
11758 // query_nodes = new HashSet<PhylogenyNode>();
11759 // query_nodes.add( new PhylogenyNode( "X" ) );
11760 // query_nodes.add( new PhylogenyNode( "Y" ) );
11761 // query_nodes.add( new PhylogenyNode( "A" ) );
11762 // query_nodes.add( new PhylogenyNode( "B" ) );
11763 // query_nodes.add( new PhylogenyNode( "C" ) );
11764 // query_nodes.add( new PhylogenyNode( "D" ) );
11765 // query_nodes.add( new PhylogenyNode( "E" ) );
11766 // query_nodes.add( new PhylogenyNode( "F" ) );
11767 // query_nodes.add( new PhylogenyNode( "G" ) );
11768 // if ( !s0.match( query_nodes ) ) {
11771 // query_nodes = new HashSet<PhylogenyNode>();
11772 // query_nodes.add( new PhylogenyNode( "X" ) );
11773 // query_nodes.add( new PhylogenyNode( "Y" ) );
11774 // query_nodes.add( new PhylogenyNode( "A" ) );
11775 // query_nodes.add( new PhylogenyNode( "B" ) );
11776 // query_nodes.add( new PhylogenyNode( "C" ) );
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( "D" ) );
11785 // query_nodes.add( new PhylogenyNode( "E" ) );
11786 // query_nodes.add( new PhylogenyNode( "F" ) );
11787 // query_nodes.add( new PhylogenyNode( "G" ) );
11788 // if ( !s0.match( query_nodes ) ) {
11792 // query_nodes = new HashSet<PhylogenyNode>();
11793 // query_nodes.add( new PhylogenyNode( "X" ) );
11794 // query_nodes.add( new PhylogenyNode( "Y" ) );
11795 // query_nodes.add( new PhylogenyNode( "A" ) );
11796 // query_nodes.add( new PhylogenyNode( "B" ) );
11797 // query_nodes.add( new PhylogenyNode( "C" ) );
11798 // query_nodes.add( new PhylogenyNode( "D" ) );
11799 // if ( !s0.match( query_nodes ) ) {
11803 // query_nodes = new HashSet<PhylogenyNode>();
11804 // query_nodes.add( new PhylogenyNode( "X" ) );
11805 // query_nodes.add( new PhylogenyNode( "Y" ) );
11806 // query_nodes.add( new PhylogenyNode( "E" ) );
11807 // query_nodes.add( new PhylogenyNode( "F" ) );
11808 // query_nodes.add( new PhylogenyNode( "G" ) );
11809 // if ( !s0.match( query_nodes ) ) {
11813 // query_nodes = new HashSet<PhylogenyNode>();
11814 // query_nodes.add( new PhylogenyNode( "X" ) );
11815 // query_nodes.add( new PhylogenyNode( "Y" ) );
11816 // query_nodes.add( new PhylogenyNode( "F" ) );
11817 // query_nodes.add( new PhylogenyNode( "G" ) );
11818 // if ( !s0.match( query_nodes ) ) {
11822 query_nodes = new HashSet<PhylogenyNode>();
11823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11827 if ( s0.match( query_nodes ) ) {
11831 query_nodes = new HashSet<PhylogenyNode>();
11832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11835 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11836 if ( s0.match( query_nodes ) ) {
11839 ///////////////////////////
11841 query_nodes = new HashSet<PhylogenyNode>();
11842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11843 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11844 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11845 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11846 if ( s0.match( query_nodes ) ) {
11850 query_nodes = new HashSet<PhylogenyNode>();
11851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11854 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11855 if ( s0.match( query_nodes ) ) {
11859 query_nodes = new HashSet<PhylogenyNode>();
11860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11864 if ( s0.match( query_nodes ) ) {
11868 query_nodes = new HashSet<PhylogenyNode>();
11869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11873 if ( s0.match( query_nodes ) ) {
11877 query_nodes = new HashSet<PhylogenyNode>();
11878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11882 if ( s0.match( query_nodes ) ) {
11886 query_nodes = new HashSet<PhylogenyNode>();
11887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11890 if ( s0.match( query_nodes ) ) {
11894 query_nodes = new HashSet<PhylogenyNode>();
11895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11899 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11900 if ( s0.match( query_nodes ) ) {
11904 query_nodes = new HashSet<PhylogenyNode>();
11905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11909 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11910 if ( s0.match( query_nodes ) ) {
11914 query_nodes = new HashSet<PhylogenyNode>();
11915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11920 if ( s0.match( query_nodes ) ) {
11924 query_nodes = new HashSet<PhylogenyNode>();
11925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11931 if ( s0.match( query_nodes ) ) {
11935 catch ( final Exception e ) {
11936 e.printStackTrace();
11942 private static boolean testSplitStrict() {
11944 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11945 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11946 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11947 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11948 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11949 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11950 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11951 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11952 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11953 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11954 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11955 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11958 if ( s0.match( query_nodes ) ) {
11961 query_nodes = new HashSet<PhylogenyNode>();
11962 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11969 if ( !s0.match( query_nodes ) ) {
11973 query_nodes = new HashSet<PhylogenyNode>();
11974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11977 if ( !s0.match( query_nodes ) ) {
11981 query_nodes = new HashSet<PhylogenyNode>();
11982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11986 if ( !s0.match( query_nodes ) ) {
11990 query_nodes = new HashSet<PhylogenyNode>();
11991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11995 if ( !s0.match( query_nodes ) ) {
11999 query_nodes = new HashSet<PhylogenyNode>();
12000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12003 if ( !s0.match( query_nodes ) ) {
12007 query_nodes = new HashSet<PhylogenyNode>();
12008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12010 if ( !s0.match( query_nodes ) ) {
12014 query_nodes = new HashSet<PhylogenyNode>();
12015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12020 if ( !s0.match( query_nodes ) ) {
12024 query_nodes = new HashSet<PhylogenyNode>();
12025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12028 if ( !s0.match( query_nodes ) ) {
12032 query_nodes = new HashSet<PhylogenyNode>();
12033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12036 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12037 if ( !s0.match( query_nodes ) ) {
12041 query_nodes = new HashSet<PhylogenyNode>();
12042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12044 if ( s0.match( query_nodes ) ) {
12048 query_nodes = new HashSet<PhylogenyNode>();
12049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12053 if ( s0.match( query_nodes ) ) {
12057 query_nodes = new HashSet<PhylogenyNode>();
12058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12063 if ( s0.match( query_nodes ) ) {
12067 query_nodes = new HashSet<PhylogenyNode>();
12068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12071 if ( s0.match( query_nodes ) ) {
12075 query_nodes = new HashSet<PhylogenyNode>();
12076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12078 if ( s0.match( query_nodes ) ) {
12082 query_nodes = new HashSet<PhylogenyNode>();
12083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12085 if ( s0.match( query_nodes ) ) {
12089 query_nodes = new HashSet<PhylogenyNode>();
12090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12092 if ( s0.match( query_nodes ) ) {
12096 query_nodes = new HashSet<PhylogenyNode>();
12097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12099 if ( s0.match( query_nodes ) ) {
12103 query_nodes = new HashSet<PhylogenyNode>();
12104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12106 if ( s0.match( query_nodes ) ) {
12110 query_nodes = new HashSet<PhylogenyNode>();
12111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12113 if ( s0.match( query_nodes ) ) {
12117 query_nodes = new HashSet<PhylogenyNode>();
12118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12121 if ( s0.match( query_nodes ) ) {
12125 query_nodes = new HashSet<PhylogenyNode>();
12126 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12129 if ( s0.match( query_nodes ) ) {
12133 query_nodes = new HashSet<PhylogenyNode>();
12134 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12135 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12137 if ( s0.match( query_nodes ) ) {
12141 query_nodes = new HashSet<PhylogenyNode>();
12142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12144 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12146 if ( s0.match( query_nodes ) ) {
12150 catch ( final Exception e ) {
12151 e.printStackTrace();
12157 private static boolean testSubtreeDeletion() {
12159 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12160 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12161 t1.deleteSubtree( t1.getNode( "A" ), false );
12162 if ( t1.getNumberOfExternalNodes() != 5 ) {
12165 t1.toNewHampshireX();
12166 t1.deleteSubtree( t1.getNode( "E" ), false );
12167 if ( t1.getNumberOfExternalNodes() != 4 ) {
12170 t1.toNewHampshireX();
12171 t1.deleteSubtree( t1.getNode( "F" ), false );
12172 if ( t1.getNumberOfExternalNodes() != 3 ) {
12175 t1.toNewHampshireX();
12176 t1.deleteSubtree( t1.getNode( "D" ), false );
12177 t1.toNewHampshireX();
12178 if ( t1.getNumberOfExternalNodes() != 3 ) {
12181 t1.deleteSubtree( t1.getNode( "def" ), false );
12182 t1.toNewHampshireX();
12183 if ( t1.getNumberOfExternalNodes() != 2 ) {
12186 t1.deleteSubtree( t1.getNode( "B" ), false );
12187 t1.toNewHampshireX();
12188 if ( t1.getNumberOfExternalNodes() != 1 ) {
12191 t1.deleteSubtree( t1.getNode( "C" ), false );
12192 t1.toNewHampshireX();
12193 if ( t1.getNumberOfExternalNodes() != 1 ) {
12196 t1.deleteSubtree( t1.getNode( "abc" ), false );
12197 t1.toNewHampshireX();
12198 if ( t1.getNumberOfExternalNodes() != 1 ) {
12201 t1.deleteSubtree( t1.getNode( "r" ), false );
12202 if ( t1.getNumberOfExternalNodes() != 0 ) {
12205 if ( !t1.isEmpty() ) {
12208 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12209 t2.deleteSubtree( t2.getNode( "A" ), false );
12210 t2.toNewHampshireX();
12211 if ( t2.getNumberOfExternalNodes() != 5 ) {
12214 t2.deleteSubtree( t2.getNode( "abc" ), false );
12215 t2.toNewHampshireX();
12216 if ( t2.getNumberOfExternalNodes() != 3 ) {
12219 t2.deleteSubtree( t2.getNode( "def" ), false );
12220 t2.toNewHampshireX();
12221 if ( t2.getNumberOfExternalNodes() != 1 ) {
12225 catch ( final Exception e ) {
12226 e.printStackTrace( System.out );
12232 private static boolean testSupportCount() {
12234 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12235 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
12236 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
12237 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
12238 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
12239 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
12240 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
12242 SupportCount.count( t0_1, phylogenies_1, true, false );
12243 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
12244 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
12245 + "(((((A,B),C),D),E),((F,G),X))"
12246 + "(((((A,Y),B),C),D),((F,G),E))"
12247 + "(((((A,B),C),D),E),(F,G))"
12248 + "(((((A,B),C),D),E),(F,G))"
12249 + "(((((A,B),C),D),E),(F,G))"
12250 + "(((((A,B),C),D),E),(F,G),Z)"
12251 + "(((((A,B),C),D),E),(F,G))"
12252 + "((((((A,B),C),D),E),F),G)"
12253 + "(((((X,Y),F,G),E),((A,B),C)),D)",
12255 SupportCount.count( t0_2, phylogenies_2, true, false );
12256 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
12257 while ( it.hasNext() ) {
12258 final PhylogenyNode n = it.next();
12259 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
12263 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
12264 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
12265 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
12266 SupportCount.count( t0_3, phylogenies_3, true, false );
12267 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
12268 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
12271 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
12274 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
12277 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
12280 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
12283 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
12286 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
12289 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
12292 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
12295 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
12298 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12299 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
12300 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
12301 SupportCount.count( t0_4, phylogenies_4, true, false );
12302 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
12303 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
12306 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
12309 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
12312 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
12315 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
12318 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
12321 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
12324 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
12327 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
12330 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
12333 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12334 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12335 double d = SupportCount.compare( b1, a, true, true, true );
12336 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12339 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12340 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12341 d = SupportCount.compare( b2, a, true, true, true );
12342 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12345 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12346 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12347 d = SupportCount.compare( b3, a, true, true, true );
12348 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12351 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12352 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12353 d = SupportCount.compare( b4, a, true, true, false );
12354 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12358 catch ( final Exception e ) {
12359 e.printStackTrace( System.out );
12365 private static boolean testSupportTransfer() {
12367 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12368 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)",
12369 new NHXParser() )[ 0 ];
12370 final Phylogeny p2 = factory
12371 .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 ];
12372 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12375 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12378 support_transfer.moveBranchLengthsToBootstrap( p1 );
12379 support_transfer.transferSupportValues( p1, p2 );
12380 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12383 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12386 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12389 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12392 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12395 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12398 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12401 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12405 catch ( final Exception e ) {
12406 e.printStackTrace( System.out );
12412 private static boolean testTaxonomyExtraction() {
12414 final PhylogenyNode n0 = PhylogenyNode
12415 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12416 if ( n0.getNodeData().isHasTaxonomy() ) {
12419 final PhylogenyNode n1 = PhylogenyNode
12420 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12421 if ( n1.getNodeData().isHasTaxonomy() ) {
12422 System.out.println( n1.toString() );
12425 final PhylogenyNode n2x = PhylogenyNode
12426 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12427 if ( n2x.getNodeData().isHasTaxonomy() ) {
12430 final PhylogenyNode n3 = PhylogenyNode
12431 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12432 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12433 System.out.println( n3.toString() );
12436 final PhylogenyNode n4 = PhylogenyNode
12437 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12438 if ( n4.getNodeData().isHasTaxonomy() ) {
12439 System.out.println( n4.toString() );
12442 final PhylogenyNode n5 = PhylogenyNode
12443 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12444 if ( n5.getNodeData().isHasTaxonomy() ) {
12445 System.out.println( n5.toString() );
12448 final PhylogenyNode n6 = PhylogenyNode
12449 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12450 if ( n6.getNodeData().isHasTaxonomy() ) {
12451 System.out.println( n6.toString() );
12454 final PhylogenyNode n7 = PhylogenyNode
12455 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12456 if ( n7.getNodeData().isHasTaxonomy() ) {
12457 System.out.println( n7.toString() );
12460 final PhylogenyNode n8 = PhylogenyNode
12461 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12462 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12463 System.out.println( n8.toString() );
12466 final PhylogenyNode n9 = PhylogenyNode
12467 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12468 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12469 System.out.println( n9.toString() );
12472 final PhylogenyNode n10x = PhylogenyNode
12473 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12474 if ( n10x.getNodeData().isHasTaxonomy() ) {
12475 System.out.println( n10x.toString() );
12478 final PhylogenyNode n10xx = PhylogenyNode
12479 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12480 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12481 System.out.println( n10xx.toString() );
12484 final PhylogenyNode n10 = PhylogenyNode
12485 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12486 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12487 System.out.println( n10.toString() );
12490 final PhylogenyNode n11 = PhylogenyNode
12491 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12492 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12493 System.out.println( n11.toString() );
12496 final PhylogenyNode n12 = PhylogenyNode
12497 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12498 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12499 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12500 System.out.println( n12.toString() );
12503 final PhylogenyNode n13 = PhylogenyNode
12504 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12505 if ( n13.getNodeData().isHasTaxonomy() ) {
12506 System.out.println( n13.toString() );
12509 final PhylogenyNode n14 = PhylogenyNode
12510 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12511 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12512 System.out.println( n14.toString() );
12515 final PhylogenyNode n15 = PhylogenyNode
12516 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12517 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12518 System.out.println( n15.toString() );
12521 final PhylogenyNode n16 = PhylogenyNode
12522 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12523 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12524 System.out.println( n16.toString() );
12527 final PhylogenyNode n17 = PhylogenyNode
12528 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12529 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12530 System.out.println( n17.toString() );
12533 final PhylogenyNode n18 = PhylogenyNode
12534 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12535 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12536 System.out.println( n18.toString() );
12539 final PhylogenyNode n19 = PhylogenyNode
12540 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12541 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12542 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12543 System.out.println( n19.toString() );
12546 final PhylogenyNode n20 = PhylogenyNode
12547 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12548 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12549 System.out.println( n20.toString() );
12552 final PhylogenyNode n21 = PhylogenyNode
12553 .createInstanceFromNhxString( "Mus musculus musculus K392",
12554 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12555 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12556 System.out.println( n21.toString() );
12559 final PhylogenyNode n23 = PhylogenyNode
12560 .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
12561 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12562 if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12563 System.out.println( n23.toString() );
12566 final PhylogenyNode n24 = PhylogenyNode
12567 .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12568 if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12569 System.out.println( n24.toString() );
12573 final PhylogenyNode n25 = PhylogenyNode
12574 .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
12575 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12576 if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
12577 System.out.println( n25.toString() );
12580 final PhylogenyNode n26 = PhylogenyNode
12581 .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
12582 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12583 if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12584 System.out.println( n26.toString() );
12587 final PhylogenyNode n27 = PhylogenyNode
12588 .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12589 if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12590 System.out.println( n27.toString() );
12594 catch ( final Exception e ) {
12595 e.printStackTrace( System.out );
12601 private static boolean testTreeCopy() {
12603 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12604 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12605 final Phylogeny t1 = t0.copy();
12606 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12609 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12612 t0.deleteSubtree( t0.getNode( "c" ), true );
12613 t0.deleteSubtree( t0.getNode( "a" ), true );
12614 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12615 t0.getNode( "b" ).setName( "Bee" );
12616 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12619 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12622 t0.deleteSubtree( t0.getNode( "e" ), true );
12623 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12624 t0.deleteSubtree( t0.getNode( "d" ), true );
12625 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12629 catch ( final Exception e ) {
12630 e.printStackTrace();
12636 private static boolean testTreeMethods() {
12638 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12639 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12640 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12641 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12642 System.out.println( t0.toNewHampshireX() );
12645 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12646 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12647 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12650 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12653 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12657 catch ( final Exception e ) {
12658 e.printStackTrace( System.out );
12664 private static boolean testUniprotEntryRetrieval() {
12666 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
12667 if ( !entry.getAccession().equals( "P12345" ) ) {
12670 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12673 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12676 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12679 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12682 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12686 .getMolecularSequence()
12687 .getMolecularSequenceAsString()
12688 .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
12689 || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
12690 System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
12694 catch ( final IOException e ) {
12695 System.out.println();
12696 System.out.println( "the following might be due to absence internet connection:" );
12697 e.printStackTrace( System.out );
12700 catch ( final Exception e ) {
12706 private static boolean testUniprotTaxonomySearch() {
12708 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12710 if ( results.size() != 1 ) {
12713 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12716 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12719 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12722 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12725 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12729 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12730 if ( results.size() != 1 ) {
12733 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12736 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12739 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12742 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12745 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12749 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12750 if ( results.size() != 1 ) {
12753 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12756 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12759 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12762 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12765 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12769 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12770 if ( results.size() != 1 ) {
12773 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12776 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12779 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12782 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12785 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12788 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12791 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12794 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12795 .equals( "Nematostella vectensis" ) ) {
12796 System.out.println( results.get( 0 ).getLineage() );
12801 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12802 if ( results.size() != 1 ) {
12805 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12808 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12811 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12814 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12817 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12820 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12821 .equals( "Xenopus tropicalis" ) ) {
12822 System.out.println( results.get( 0 ).getLineage() );
12827 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12828 if ( results.size() != 1 ) {
12831 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12834 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12837 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12840 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12843 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12846 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12847 .equals( "Xenopus tropicalis" ) ) {
12848 System.out.println( results.get( 0 ).getLineage() );
12853 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12854 if ( results.size() != 1 ) {
12857 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12860 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12863 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12866 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12869 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12872 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12873 .equals( "Xenopus tropicalis" ) ) {
12874 System.out.println( results.get( 0 ).getLineage() );
12878 catch ( final IOException e ) {
12879 System.out.println();
12880 System.out.println( "the following might be due to absence internet connection:" );
12881 e.printStackTrace( System.out );
12884 catch ( final Exception e ) {
12890 private static boolean testWabiTxSearch() {
12892 String result = "";
12893 result = TxSearch.searchSimple( "nematostella" );
12894 result = TxSearch.getTxId( "nematostella" );
12895 if ( !result.equals( "45350" ) ) {
12898 result = TxSearch.getTxName( "45350" );
12899 if ( !result.equals( "Nematostella" ) ) {
12902 result = TxSearch.getTxId( "nematostella vectensis" );
12903 if ( !result.equals( "45351" ) ) {
12906 result = TxSearch.getTxName( "45351" );
12907 if ( !result.equals( "Nematostella vectensis" ) ) {
12910 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12911 if ( !result.equals( "536089" ) ) {
12914 result = TxSearch.getTxName( "536089" );
12915 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12918 final List<String> queries = new ArrayList<String>();
12919 queries.add( "Campylobacter coli" );
12920 queries.add( "Escherichia coli" );
12921 queries.add( "Arabidopsis" );
12922 queries.add( "Trichoplax" );
12923 queries.add( "Samanea saman" );
12924 queries.add( "Kluyveromyces marxianus" );
12925 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12926 queries.add( "Bornavirus parrot/PDD/2008" );
12927 final List<RANKS> ranks = new ArrayList<RANKS>();
12928 ranks.add( RANKS.SUPERKINGDOM );
12929 ranks.add( RANKS.KINGDOM );
12930 ranks.add( RANKS.FAMILY );
12931 ranks.add( RANKS.GENUS );
12932 ranks.add( RANKS.TRIBE );
12933 result = TxSearch.searchLineage( queries, ranks );
12934 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12935 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12937 catch ( final Exception e ) {
12938 System.out.println();
12939 System.out.println( "the following might be due to absence internet connection:" );
12940 e.printStackTrace( System.out );