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();
1225 public static final boolean testNHXparsingFromURL() {
1227 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1228 final URL u = new URL( s );
1229 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1230 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1231 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1234 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1235 System.out.println( phys[ 0 ].toNewHampshire() );
1238 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1239 System.out.println( phys[ 1 ].toNewHampshire() );
1242 final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
1243 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1246 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1247 System.out.println( phys2[ 0 ].toNewHampshire() );
1250 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1251 final NHXParser p = new NHXParser();
1252 final URL u2 = new URL( s );
1254 if ( !p.hasNext() ) {
1257 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1260 if ( !p.hasNext() ) {
1264 if ( !p.hasNext() ) {
1267 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1270 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1274 if ( !p.hasNext() ) {
1277 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1280 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1284 catch ( final Exception e ) {
1285 e.printStackTrace();
1290 public static boolean testOverlapRemoval() {
1292 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1293 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1294 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1295 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1296 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1297 final List<Boolean> covered = new ArrayList<Boolean>();
1298 covered.add( true ); // 0
1299 covered.add( false ); // 1
1300 covered.add( true ); // 2
1301 covered.add( false ); // 3
1302 covered.add( true ); // 4
1303 covered.add( true ); // 5
1304 covered.add( false ); // 6
1305 covered.add( true ); // 7
1306 covered.add( true ); // 8
1307 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1310 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1313 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1316 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1319 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1322 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1323 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1324 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1325 ab.addProteinDomain( a );
1326 ab.addProteinDomain( b );
1327 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1328 if ( ab.getNumberOfProteinDomains() != 2 ) {
1331 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1334 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1337 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1338 if ( ab.getNumberOfProteinDomains() != 2 ) {
1341 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1344 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1345 final Domain d = new BasicDomain( "d",
1352 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1353 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1354 cde.addProteinDomain( c );
1355 cde.addProteinDomain( d );
1356 cde.addProteinDomain( e );
1357 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1358 if ( cde.getNumberOfProteinDomains() != 3 ) {
1361 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1364 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1365 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1366 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1367 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1368 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1369 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1370 fghi.addProteinDomain( f );
1371 fghi.addProteinDomain( g );
1372 fghi.addProteinDomain( h );
1373 fghi.addProteinDomain( i );
1374 fghi.addProteinDomain( i );
1375 fghi.addProteinDomain( i );
1376 fghi.addProteinDomain( i2 );
1377 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1378 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1381 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1384 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1387 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1388 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1391 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1394 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1395 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1396 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1397 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1398 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1399 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1400 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1401 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1402 jklm.addProteinDomain( j );
1403 jklm.addProteinDomain( k );
1404 jklm.addProteinDomain( l );
1405 jklm.addProteinDomain( m );
1406 jklm.addProteinDomain( m0 );
1407 jklm.addProteinDomain( m1 );
1408 jklm.addProteinDomain( m2 );
1409 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1410 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1413 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1416 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1419 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1420 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1423 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1426 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1427 final Protein od = new BasicProtein( "od", "varanus", 0 );
1428 od.addProteinDomain( only );
1429 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1430 if ( od.getNumberOfProteinDomains() != 1 ) {
1433 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1437 catch ( final Exception e ) {
1438 e.printStackTrace( System.out );
1444 public static final boolean testPfamTreeReading() {
1446 final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
1447 final NHXParser parser = new NHXParser();
1448 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1449 parser.setReplaceUnderscores( false );
1450 parser.setGuessRootedness( true );
1451 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1452 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1453 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1456 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1460 catch ( final Exception e ) {
1461 e.printStackTrace();
1466 public static final boolean testPhyloXMLparsingFromURL() {
1468 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1469 final URL u = new URL( s );
1470 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1471 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1472 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1476 catch ( final Exception e ) {
1477 e.printStackTrace();
1482 public static final boolean testToLReading() {
1484 final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
1485 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1486 final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
1487 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1490 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
1493 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
1496 if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
1500 catch ( final Exception e ) {
1501 e.printStackTrace();
1506 public static final boolean testTreeBaseReading() {
1508 final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
1509 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1510 parser.setReplaceUnderscores( true );
1511 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1512 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1513 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1516 final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
1517 final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
1518 parser2.setReplaceUnderscores( true );
1519 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1520 final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
1521 if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
1525 catch ( final Exception e ) {
1526 e.printStackTrace();
1531 public static final boolean testTreeFamReading() {
1533 final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
1534 final NHXParser parser = new NHXParser();
1535 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
1536 parser.setReplaceUnderscores( false );
1537 parser.setGuessRootedness( true );
1538 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1539 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1540 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1543 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1547 catch ( final Exception e ) {
1548 e.printStackTrace();
1553 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1554 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1558 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1559 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1562 private static boolean testAminoAcidSequence() {
1564 final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1565 if ( aa1.getLength() != 13 ) {
1568 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1571 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1574 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1577 final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1578 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
1581 final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1582 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1585 final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1586 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1590 catch ( final Exception e ) {
1591 e.printStackTrace();
1597 private static boolean testBasicDomain() {
1599 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1600 if ( !pd.getDomainId().equals( "id" ) ) {
1603 if ( pd.getNumber() != 1 ) {
1606 if ( pd.getTotalCount() != 4 ) {
1609 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1612 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1613 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1614 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1615 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1616 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1617 if ( !a1.equals( a1 ) ) {
1620 if ( !a1.equals( a1_copy ) ) {
1623 if ( !a1.equals( a1_equal ) ) {
1626 if ( !a1.equals( a2 ) ) {
1629 if ( a1.equals( a3 ) ) {
1632 if ( a1.compareTo( a1 ) != 0 ) {
1635 if ( a1.compareTo( a1_copy ) != 0 ) {
1638 if ( a1.compareTo( a1_equal ) != 0 ) {
1641 if ( a1.compareTo( a2 ) != 0 ) {
1644 if ( a1.compareTo( a3 ) == 0 ) {
1648 catch ( final Exception e ) {
1649 e.printStackTrace( System.out );
1655 private static boolean testBasicNodeMethods() {
1657 if ( PhylogenyNode.getNodeCount() != 0 ) {
1660 final PhylogenyNode n1 = new PhylogenyNode();
1661 final PhylogenyNode n2 = PhylogenyNode
1662 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1663 final PhylogenyNode n3 = PhylogenyNode
1664 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1665 final PhylogenyNode n4 = PhylogenyNode
1666 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1667 if ( n1.isHasAssignedEvent() ) {
1670 if ( PhylogenyNode.getNodeCount() != 4 ) {
1673 if ( n3.getIndicator() != 0 ) {
1676 if ( n3.getNumberOfExternalNodes() != 1 ) {
1679 if ( !n3.isExternal() ) {
1682 if ( !n3.isRoot() ) {
1685 if ( !n4.getName().equals( "n4" ) ) {
1689 catch ( final Exception e ) {
1690 e.printStackTrace( System.out );
1696 private static boolean testBasicPhyloXMLparsing() {
1698 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1699 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1700 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1702 if ( xml_parser.getErrorCount() > 0 ) {
1703 System.out.println( xml_parser.getErrorMessages().toString() );
1706 if ( phylogenies_0.length != 4 ) {
1709 final Phylogeny t1 = phylogenies_0[ 0 ];
1710 final Phylogeny t2 = phylogenies_0[ 1 ];
1711 final Phylogeny t3 = phylogenies_0[ 2 ];
1712 final Phylogeny t4 = phylogenies_0[ 3 ];
1713 if ( t1.getNumberOfExternalNodes() != 1 ) {
1716 if ( !t1.isRooted() ) {
1719 if ( t1.isRerootable() ) {
1722 if ( !t1.getType().equals( "gene_tree" ) ) {
1725 if ( t2.getNumberOfExternalNodes() != 2 ) {
1728 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1731 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1734 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1737 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1740 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1743 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1746 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1747 .startsWith( "actgtgggggt" ) ) {
1750 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1751 .startsWith( "ctgtgatgcat" ) ) {
1754 if ( t3.getNumberOfExternalNodes() != 4 ) {
1757 if ( !t1.getName().equals( "t1" ) ) {
1760 if ( !t2.getName().equals( "t2" ) ) {
1763 if ( !t3.getName().equals( "t3" ) ) {
1766 if ( !t4.getName().equals( "t4" ) ) {
1769 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1772 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1775 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1778 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1779 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1782 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1785 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1788 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1791 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1792 .equals( "apoptosis" ) ) {
1795 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1796 .equals( "GO:0006915" ) ) {
1799 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1800 .equals( "UniProtKB" ) ) {
1803 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1804 .equals( "experimental" ) ) {
1807 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1808 .equals( "function" ) ) {
1811 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1812 .getValue() != 1 ) {
1815 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1816 .getType().equals( "ml" ) ) {
1819 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1820 .equals( "apoptosis" ) ) {
1823 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1824 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1827 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1828 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1831 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1832 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1835 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1836 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1839 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1840 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1843 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1844 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1847 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1848 .equals( "GO:0005829" ) ) {
1851 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1852 .equals( "intracellular organelle" ) ) {
1855 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1858 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1859 .equals( "UniProt link" ) ) ) {
1862 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1865 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1866 if ( x.size() != 4 ) {
1870 for( final Accession acc : x ) {
1872 if ( !acc.getSource().equals( "KEGG" ) ) {
1875 if ( !acc.getValue().equals( "hsa:596" ) ) {
1882 catch ( final Exception e ) {
1883 e.printStackTrace( System.out );
1889 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1891 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1892 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1893 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1894 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1897 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1899 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1901 if ( xml_parser.getErrorCount() > 0 ) {
1902 System.out.println( xml_parser.getErrorMessages().toString() );
1905 if ( phylogenies_0.length != 4 ) {
1908 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1909 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1910 if ( phylogenies_t1.length != 1 ) {
1913 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1914 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1917 if ( !t1_rt.isRooted() ) {
1920 if ( t1_rt.isRerootable() ) {
1923 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1926 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1927 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1928 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1929 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1932 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1935 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1938 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1941 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1942 .startsWith( "actgtgggggt" ) ) {
1945 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1946 .startsWith( "ctgtgatgcat" ) ) {
1949 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1950 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1951 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1952 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1953 if ( phylogenies_1.length != 1 ) {
1956 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1957 if ( !t3_rt.getName().equals( "t3" ) ) {
1960 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1963 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1966 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1969 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1972 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1973 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1976 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1979 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1982 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1983 .equals( "UniProtKB" ) ) {
1986 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1987 .equals( "apoptosis" ) ) {
1990 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1991 .equals( "GO:0006915" ) ) {
1994 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1995 .equals( "UniProtKB" ) ) {
1998 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1999 .equals( "experimental" ) ) {
2002 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
2003 .equals( "function" ) ) {
2006 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2007 .getValue() != 1 ) {
2010 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2011 .getType().equals( "ml" ) ) {
2014 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2015 .equals( "apoptosis" ) ) {
2018 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2019 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
2022 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2023 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
2026 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2027 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
2030 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2031 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
2034 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2035 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
2038 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2039 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
2042 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
2043 .equals( "GO:0005829" ) ) {
2046 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
2047 .equals( "intracellular organelle" ) ) {
2050 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
2053 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
2054 .equals( "UniProt link" ) ) ) {
2057 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
2060 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
2063 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
2064 .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." ) ) ) {
2067 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
2070 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
2073 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
2076 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
2079 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
2080 .equals( "ncbi" ) ) {
2083 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
2086 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2087 .getName().equals( "B" ) ) {
2090 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2091 .getFrom() != 21 ) {
2094 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
2097 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2098 .getLength() != 24 ) {
2101 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2102 .getConfidence() != 2144 ) {
2105 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2106 .equals( "pfam" ) ) {
2109 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2112 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2115 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2118 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2121 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2122 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2125 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2128 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2131 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2134 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2137 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2140 if ( taxbb.getSynonyms().size() != 2 ) {
2143 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2146 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2149 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2152 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2155 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2158 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2159 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2162 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2165 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2168 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2171 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2174 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2177 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2180 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2183 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2186 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2187 .equalsIgnoreCase( "435" ) ) {
2190 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2193 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2194 .equalsIgnoreCase( "443.7" ) ) {
2197 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2200 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2203 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2204 .equalsIgnoreCase( "433" ) ) {
2207 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2208 .getCrossReferences();
2209 if ( x.size() != 4 ) {
2213 for( final Accession acc : x ) {
2215 if ( !acc.getSource().equals( "KEGG" ) ) {
2218 if ( !acc.getValue().equals( "hsa:596" ) ) {
2225 catch ( final Exception e ) {
2226 e.printStackTrace( System.out );
2232 private static boolean testBasicPhyloXMLparsingValidating() {
2234 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2235 PhyloXmlParser xml_parser = null;
2237 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2239 catch ( final Exception e ) {
2240 // Do nothing -- means were not running from jar.
2242 if ( xml_parser == null ) {
2243 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2244 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2245 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2248 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2251 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2253 if ( xml_parser.getErrorCount() > 0 ) {
2254 System.out.println( xml_parser.getErrorMessages().toString() );
2257 if ( phylogenies_0.length != 4 ) {
2260 final Phylogeny t1 = phylogenies_0[ 0 ];
2261 final Phylogeny t2 = phylogenies_0[ 1 ];
2262 final Phylogeny t3 = phylogenies_0[ 2 ];
2263 final Phylogeny t4 = phylogenies_0[ 3 ];
2264 if ( !t1.getName().equals( "t1" ) ) {
2267 if ( !t2.getName().equals( "t2" ) ) {
2270 if ( !t3.getName().equals( "t3" ) ) {
2273 if ( !t4.getName().equals( "t4" ) ) {
2276 if ( t1.getNumberOfExternalNodes() != 1 ) {
2279 if ( t2.getNumberOfExternalNodes() != 2 ) {
2282 if ( t3.getNumberOfExternalNodes() != 4 ) {
2285 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2286 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2287 if ( xml_parser.getErrorCount() > 0 ) {
2288 System.out.println( "errors:" );
2289 System.out.println( xml_parser.getErrorMessages().toString() );
2292 if ( phylogenies_1.length != 4 ) {
2295 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2297 if ( xml_parser.getErrorCount() > 0 ) {
2298 System.out.println( "errors:" );
2299 System.out.println( xml_parser.getErrorMessages().toString() );
2302 if ( phylogenies_2.length != 1 ) {
2305 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2308 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2310 if ( xml_parser.getErrorCount() > 0 ) {
2311 System.out.println( xml_parser.getErrorMessages().toString() );
2314 if ( phylogenies_3.length != 2 ) {
2317 final Phylogeny a = phylogenies_3[ 0 ];
2318 if ( !a.getName().equals( "tree 4" ) ) {
2321 if ( a.getNumberOfExternalNodes() != 3 ) {
2324 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2327 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2330 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2332 if ( xml_parser.getErrorCount() > 0 ) {
2333 System.out.println( xml_parser.getErrorMessages().toString() );
2336 if ( phylogenies_4.length != 1 ) {
2339 final Phylogeny s = phylogenies_4[ 0 ];
2340 if ( s.getNumberOfExternalNodes() != 6 ) {
2343 s.getNode( "first" );
2345 s.getNode( "\"<a'b&c'd\">\"" );
2346 s.getNode( "'''\"" );
2347 s.getNode( "\"\"\"" );
2348 s.getNode( "dick & doof" );
2350 catch ( final Exception e ) {
2351 e.printStackTrace( System.out );
2357 private static boolean testBasicProtein() {
2359 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2360 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2361 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2362 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2363 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2364 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2365 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2366 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2367 p0.addProteinDomain( y );
2368 p0.addProteinDomain( e );
2369 p0.addProteinDomain( b );
2370 p0.addProteinDomain( c );
2371 p0.addProteinDomain( d );
2372 p0.addProteinDomain( a );
2373 p0.addProteinDomain( x );
2374 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2377 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2381 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2382 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2383 aa0.addProteinDomain( a1 );
2384 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2387 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2391 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2392 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2393 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2394 aa1.addProteinDomain( a11 );
2395 aa1.addProteinDomain( a12 );
2396 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2399 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2402 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2403 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2406 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2409 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2412 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2413 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2416 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2419 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2422 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2425 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2426 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2429 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2432 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2435 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2438 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2439 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2442 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2445 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2448 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2452 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2453 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2454 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2455 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2456 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2457 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2458 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2459 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2460 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2461 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2462 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2463 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2464 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2465 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2466 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2467 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2468 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2469 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2470 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2471 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2472 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2473 p00.addProteinDomain( y0 );
2474 p00.addProteinDomain( e0 );
2475 p00.addProteinDomain( b0 );
2476 p00.addProteinDomain( c0 );
2477 p00.addProteinDomain( d0 );
2478 p00.addProteinDomain( a0 );
2479 p00.addProteinDomain( x0 );
2480 p00.addProteinDomain( y1 );
2481 p00.addProteinDomain( y2 );
2482 p00.addProteinDomain( y3 );
2483 p00.addProteinDomain( e1 );
2484 p00.addProteinDomain( e2 );
2485 p00.addProteinDomain( e3 );
2486 p00.addProteinDomain( e4 );
2487 p00.addProteinDomain( e5 );
2488 p00.addProteinDomain( z0 );
2489 p00.addProteinDomain( z1 );
2490 p00.addProteinDomain( z2 );
2491 p00.addProteinDomain( zz0 );
2492 p00.addProteinDomain( zz1 );
2493 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2496 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2499 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2502 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2505 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" ) ) {
2508 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2509 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2510 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2511 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2512 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2513 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2514 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2515 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2516 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2517 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2518 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2519 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2520 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2521 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2522 p.addProteinDomain( B15 );
2523 p.addProteinDomain( C50 );
2524 p.addProteinDomain( A60 );
2525 p.addProteinDomain( A30 );
2526 p.addProteinDomain( C70 );
2527 p.addProteinDomain( B35 );
2528 p.addProteinDomain( B40 );
2529 p.addProteinDomain( A0 );
2530 p.addProteinDomain( A10 );
2531 p.addProteinDomain( A20 );
2532 p.addProteinDomain( B25 );
2533 p.addProteinDomain( D80 );
2534 List<String> domains_ids = new ArrayList<String>();
2535 domains_ids.add( "A" );
2536 domains_ids.add( "B" );
2537 domains_ids.add( "C" );
2538 if ( !p.contains( domains_ids, false ) ) {
2541 if ( !p.contains( domains_ids, true ) ) {
2544 domains_ids.add( "X" );
2545 if ( p.contains( domains_ids, false ) ) {
2548 if ( p.contains( domains_ids, true ) ) {
2551 domains_ids = new ArrayList<String>();
2552 domains_ids.add( "A" );
2553 domains_ids.add( "C" );
2554 domains_ids.add( "D" );
2555 if ( !p.contains( domains_ids, false ) ) {
2558 if ( !p.contains( domains_ids, true ) ) {
2561 domains_ids = new ArrayList<String>();
2562 domains_ids.add( "A" );
2563 domains_ids.add( "D" );
2564 domains_ids.add( "C" );
2565 if ( !p.contains( domains_ids, false ) ) {
2568 if ( p.contains( domains_ids, true ) ) {
2571 domains_ids = new ArrayList<String>();
2572 domains_ids.add( "A" );
2573 domains_ids.add( "A" );
2574 domains_ids.add( "B" );
2575 if ( !p.contains( domains_ids, false ) ) {
2578 if ( !p.contains( domains_ids, true ) ) {
2581 domains_ids = new ArrayList<String>();
2582 domains_ids.add( "A" );
2583 domains_ids.add( "A" );
2584 domains_ids.add( "A" );
2585 domains_ids.add( "B" );
2586 domains_ids.add( "B" );
2587 if ( !p.contains( domains_ids, false ) ) {
2590 if ( !p.contains( domains_ids, true ) ) {
2593 domains_ids = new ArrayList<String>();
2594 domains_ids.add( "A" );
2595 domains_ids.add( "A" );
2596 domains_ids.add( "B" );
2597 domains_ids.add( "A" );
2598 domains_ids.add( "B" );
2599 domains_ids.add( "B" );
2600 domains_ids.add( "A" );
2601 domains_ids.add( "B" );
2602 domains_ids.add( "C" );
2603 domains_ids.add( "A" );
2604 domains_ids.add( "C" );
2605 domains_ids.add( "D" );
2606 if ( !p.contains( domains_ids, false ) ) {
2609 if ( p.contains( domains_ids, true ) ) {
2613 catch ( final Exception e ) {
2614 e.printStackTrace( System.out );
2620 private static boolean testBasicTable() {
2622 final BasicTable<String> t0 = new BasicTable<String>();
2623 if ( t0.getNumberOfColumns() != 0 ) {
2626 if ( t0.getNumberOfRows() != 0 ) {
2629 t0.setValue( 3, 2, "23" );
2630 t0.setValue( 10, 1, "error" );
2631 t0.setValue( 10, 1, "110" );
2632 t0.setValue( 9, 1, "19" );
2633 t0.setValue( 1, 10, "101" );
2634 t0.setValue( 10, 10, "1010" );
2635 t0.setValue( 100, 10, "10100" );
2636 t0.setValue( 0, 0, "00" );
2637 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2640 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2643 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2646 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2649 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2652 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2655 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2658 if ( t0.getNumberOfColumns() != 101 ) {
2661 if ( t0.getNumberOfRows() != 11 ) {
2664 if ( t0.getValueAsString( 49, 4 ) != null ) {
2667 final String l = ForesterUtil.getLineSeparator();
2668 final StringBuffer source = new StringBuffer();
2669 source.append( "" + l );
2670 source.append( "# 1 1 1 1 1 1 1 1" + l );
2671 source.append( " 00 01 02 03" + l );
2672 source.append( " 10 11 12 13 " + l );
2673 source.append( "20 21 22 23 " + l );
2674 source.append( " 30 31 32 33" + l );
2675 source.append( "40 41 42 43" + l );
2676 source.append( " # 1 1 1 1 1 " + l );
2677 source.append( "50 51 52 53 54" + l );
2678 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2679 if ( t1.getNumberOfColumns() != 5 ) {
2682 if ( t1.getNumberOfRows() != 6 ) {
2685 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2688 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2691 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2694 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2697 final StringBuffer source1 = new StringBuffer();
2698 source1.append( "" + l );
2699 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2700 source1.append( " 00; 01 ;02;03" + l );
2701 source1.append( " 10; 11; 12; 13 " + l );
2702 source1.append( "20; 21; 22; 23 " + l );
2703 source1.append( " 30; 31; 32; 33" + l );
2704 source1.append( "40;41;42;43" + l );
2705 source1.append( " # 1 1 1 1 1 " + l );
2706 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2707 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2708 if ( t2.getNumberOfColumns() != 5 ) {
2711 if ( t2.getNumberOfRows() != 6 ) {
2714 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2717 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2720 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2723 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2726 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2729 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2732 final StringBuffer source2 = new StringBuffer();
2733 source2.append( "" + l );
2734 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2735 source2.append( " 00; 01 ;02;03" + l );
2736 source2.append( " 10; 11; 12; 13 " + l );
2737 source2.append( "20; 21; 22; 23 " + l );
2738 source2.append( " " + l );
2739 source2.append( " 30; 31; 32; 33" + l );
2740 source2.append( "40;41;42;43" + l );
2741 source2.append( " comment: 1 1 1 1 1 " + l );
2742 source2.append( ";;;50 ; 52; 53;;54 " + l );
2743 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2749 if ( tl.size() != 2 ) {
2752 final BasicTable<String> t3 = tl.get( 0 );
2753 final BasicTable<String> t4 = tl.get( 1 );
2754 if ( t3.getNumberOfColumns() != 4 ) {
2757 if ( t3.getNumberOfRows() != 3 ) {
2760 if ( t4.getNumberOfColumns() != 4 ) {
2763 if ( t4.getNumberOfRows() != 3 ) {
2766 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2769 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2773 catch ( final Exception e ) {
2774 e.printStackTrace( System.out );
2780 private static boolean testBasicTolXMLparsing() {
2782 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2783 final TolParser parser = new TolParser();
2784 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2785 if ( parser.getErrorCount() > 0 ) {
2786 System.out.println( parser.getErrorMessages().toString() );
2789 if ( phylogenies_0.length != 1 ) {
2792 final Phylogeny t1 = phylogenies_0[ 0 ];
2793 if ( t1.getNumberOfExternalNodes() != 5 ) {
2796 if ( !t1.isRooted() ) {
2799 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2802 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2805 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2808 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2811 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2812 if ( parser.getErrorCount() > 0 ) {
2813 System.out.println( parser.getErrorMessages().toString() );
2816 if ( phylogenies_1.length != 1 ) {
2819 final Phylogeny t2 = phylogenies_1[ 0 ];
2820 if ( t2.getNumberOfExternalNodes() != 664 ) {
2823 if ( !t2.isRooted() ) {
2826 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2829 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2832 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2835 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2838 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2841 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2842 .equals( "Aquifex" ) ) {
2845 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2846 if ( parser.getErrorCount() > 0 ) {
2847 System.out.println( parser.getErrorMessages().toString() );
2850 if ( phylogenies_2.length != 1 ) {
2853 final Phylogeny t3 = phylogenies_2[ 0 ];
2854 if ( t3.getNumberOfExternalNodes() != 184 ) {
2857 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2860 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2863 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2866 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2867 if ( parser.getErrorCount() > 0 ) {
2868 System.out.println( parser.getErrorMessages().toString() );
2871 if ( phylogenies_3.length != 1 ) {
2874 final Phylogeny t4 = phylogenies_3[ 0 ];
2875 if ( t4.getNumberOfExternalNodes() != 1 ) {
2878 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2881 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2884 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2887 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2888 if ( parser.getErrorCount() > 0 ) {
2889 System.out.println( parser.getErrorMessages().toString() );
2892 if ( phylogenies_4.length != 1 ) {
2895 final Phylogeny t5 = phylogenies_4[ 0 ];
2896 if ( t5.getNumberOfExternalNodes() != 13 ) {
2899 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2902 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2905 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2909 catch ( final Exception e ) {
2910 e.printStackTrace( System.out );
2916 private static boolean testBasicTreeMethods() {
2918 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2919 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2920 if ( t2.getNumberOfExternalNodes() != 4 ) {
2923 if ( t2.getHeight() != 8.5 ) {
2926 if ( !t2.isCompletelyBinary() ) {
2929 if ( t2.isEmpty() ) {
2932 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2933 if ( t3.getNumberOfExternalNodes() != 5 ) {
2936 if ( t3.getHeight() != 11 ) {
2939 if ( t3.isCompletelyBinary() ) {
2942 final PhylogenyNode n = t3.getNode( "ABC" );
2943 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 ];
2944 if ( t4.getNumberOfExternalNodes() != 9 ) {
2947 if ( t4.getHeight() != 11 ) {
2950 if ( t4.isCompletelyBinary() ) {
2953 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)" );
2954 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2955 if ( t5.getNumberOfExternalNodes() != 8 ) {
2958 if ( t5.getHeight() != 15 ) {
2961 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)" );
2962 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2963 if ( t6.getHeight() != 15 ) {
2966 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)" );
2967 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2968 if ( t7.getHeight() != 15 ) {
2971 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)" );
2972 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2973 if ( t8.getNumberOfExternalNodes() != 10 ) {
2976 if ( t8.getHeight() != 15 ) {
2979 final char[] a9 = new char[] { 'a' };
2980 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2981 if ( t9.getHeight() != 0 ) {
2984 final char[] a10 = new char[] { 'a', ':', '6' };
2985 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2986 if ( t10.getHeight() != 6 ) {
2990 catch ( final Exception e ) {
2991 e.printStackTrace( System.out );
2997 private static boolean testConfidenceAssessor() {
2999 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3000 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3001 final Phylogeny[] ev0 = factory
3002 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
3004 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
3005 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3008 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3011 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3012 final Phylogeny[] ev1 = factory
3013 .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)));",
3015 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
3016 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
3019 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3022 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3023 final Phylogeny[] ev_b = factory
3024 .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",
3026 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
3027 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
3030 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3034 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3035 final Phylogeny[] ev1x = factory
3036 .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)));",
3038 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
3039 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3042 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3045 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3046 final Phylogeny[] ev_bx = factory
3047 .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",
3049 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
3050 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3053 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3056 final Phylogeny[] t2 = factory
3057 .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);",
3059 final Phylogeny[] ev2 = factory
3060 .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);",
3062 for( final Phylogeny target : t2 ) {
3063 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
3065 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
3066 new NHXParser() )[ 0 ];
3067 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
3068 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
3069 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3072 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
3075 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3079 catch ( final Exception e ) {
3080 e.printStackTrace();
3086 private static boolean testCopyOfNodeData() {
3088 final PhylogenyNode n1 = PhylogenyNode
3089 .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]" );
3090 final PhylogenyNode n2 = n1.copyNodeData();
3091 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
3095 catch ( final Exception e ) {
3096 e.printStackTrace();
3102 private static boolean testCreateBalancedPhylogeny() {
3104 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3105 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3108 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3111 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3112 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3115 if ( p1.getNumberOfExternalNodes() != 100 ) {
3119 catch ( final Exception e ) {
3120 e.printStackTrace();
3126 private static boolean testCreateUriForSeqWeb() {
3128 final PhylogenyNode n = new PhylogenyNode();
3129 n.setName( "tr|B3RJ64" );
3130 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3133 n.setName( "B0LM41_HUMAN" );
3134 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3137 n.setName( "NP_001025424" );
3138 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3141 n.setName( "_NM_001030253-" );
3142 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3145 n.setName( "XM_002122186" );
3146 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3149 n.setName( "dgh_AAA34956_gdg" );
3150 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3153 n.setName( "AAA34956" );
3154 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3157 n.setName( "GI:394892" );
3158 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3159 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3162 n.setName( "gi_394892" );
3163 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3164 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3167 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3168 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3169 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3172 n.setName( "P12345" );
3173 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3174 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3177 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3178 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3179 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3183 catch ( final Exception e ) {
3184 e.printStackTrace( System.out );
3190 private static boolean testDataObjects() {
3192 final Confidence s0 = new Confidence();
3193 final Confidence s1 = new Confidence();
3194 if ( !s0.isEqual( s1 ) ) {
3197 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3198 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3199 if ( s2.isEqual( s1 ) ) {
3202 if ( !s2.isEqual( s3 ) ) {
3205 final Confidence s4 = ( Confidence ) s3.copy();
3206 if ( !s4.isEqual( s3 ) ) {
3213 final Taxonomy t1 = new Taxonomy();
3214 final Taxonomy t2 = new Taxonomy();
3215 final Taxonomy t3 = new Taxonomy();
3216 final Taxonomy t4 = new Taxonomy();
3217 final Taxonomy t5 = new Taxonomy();
3218 t1.setIdentifier( new Identifier( "ecoli" ) );
3219 t1.setTaxonomyCode( "ECOLI" );
3220 t1.setScientificName( "E. coli" );
3221 t1.setCommonName( "coli" );
3222 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3223 if ( !t1.isEqual( t0 ) ) {
3226 t2.setIdentifier( new Identifier( "ecoli" ) );
3227 t2.setTaxonomyCode( "OTHER" );
3228 t2.setScientificName( "what" );
3229 t2.setCommonName( "something" );
3230 if ( !t1.isEqual( t2 ) ) {
3233 t2.setIdentifier( new Identifier( "nemve" ) );
3234 if ( t1.isEqual( t2 ) ) {
3237 t1.setIdentifier( null );
3238 t3.setTaxonomyCode( "ECOLI" );
3239 t3.setScientificName( "what" );
3240 t3.setCommonName( "something" );
3241 if ( !t1.isEqual( t3 ) ) {
3244 t1.setIdentifier( null );
3245 t1.setTaxonomyCode( "" );
3246 t4.setScientificName( "E. ColI" );
3247 t4.setCommonName( "something" );
3248 if ( !t1.isEqual( t4 ) ) {
3251 t4.setScientificName( "B. subtilis" );
3252 t4.setCommonName( "something" );
3253 if ( t1.isEqual( t4 ) ) {
3256 t1.setIdentifier( null );
3257 t1.setTaxonomyCode( "" );
3258 t1.setScientificName( "" );
3259 t5.setCommonName( "COLI" );
3260 if ( !t1.isEqual( t5 ) ) {
3263 t5.setCommonName( "vibrio" );
3264 if ( t1.isEqual( t5 ) ) {
3269 final Identifier id0 = new Identifier( "123", "pfam" );
3270 final Identifier id1 = ( Identifier ) id0.copy();
3271 if ( !id1.isEqual( id1 ) ) {
3274 if ( !id1.isEqual( id0 ) ) {
3277 if ( !id0.isEqual( id1 ) ) {
3284 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3285 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3286 if ( !pd1.isEqual( pd1 ) ) {
3289 if ( !pd1.isEqual( pd0 ) ) {
3294 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3295 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3296 if ( !pd3.isEqual( pd3 ) ) {
3299 if ( !pd2.isEqual( pd3 ) ) {
3302 if ( !pd0.isEqual( pd3 ) ) {
3307 // DomainArchitecture
3308 // ------------------
3309 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3310 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3311 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3312 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3313 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3314 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3319 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3320 if ( ds0.getNumberOfDomains() != 4 ) {
3323 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3324 if ( !ds0.isEqual( ds0 ) ) {
3327 if ( !ds0.isEqual( ds1 ) ) {
3330 if ( ds1.getNumberOfDomains() != 4 ) {
3333 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3338 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3339 if ( ds0.isEqual( ds2 ) ) {
3345 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3346 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3347 System.out.println( ds3.toNHX() );
3350 if ( ds3.getNumberOfDomains() != 3 ) {
3355 final Event e1 = new Event( Event.EventType.fusion );
3356 if ( e1.isDuplication() ) {
3359 if ( !e1.isFusion() ) {
3362 if ( !e1.asText().toString().equals( "fusion" ) ) {
3365 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3368 final Event e11 = new Event( Event.EventType.fusion );
3369 if ( !e11.isEqual( e1 ) ) {
3372 if ( !e11.toNHX().toString().equals( "" ) ) {
3375 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3376 if ( e2.isDuplication() ) {
3379 if ( !e2.isSpeciationOrDuplication() ) {
3382 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3385 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3388 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3391 if ( e11.isEqual( e2 ) ) {
3394 final Event e2c = ( Event ) e2.copy();
3395 if ( !e2c.isEqual( e2 ) ) {
3398 Event e3 = new Event( 1, 2, 3 );
3399 if ( e3.isDuplication() ) {
3402 if ( e3.isSpeciation() ) {
3405 if ( e3.isGeneLoss() ) {
3408 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3411 final Event e3c = ( Event ) e3.copy();
3412 final Event e3cc = ( Event ) e3c.copy();
3413 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3417 if ( !e3c.isEqual( e3cc ) ) {
3420 Event e4 = new Event( 1, 2, 3 );
3421 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3424 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3427 final Event e4c = ( Event ) e4.copy();
3429 final Event e4cc = ( Event ) e4c.copy();
3430 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3433 if ( !e4c.isEqual( e4cc ) ) {
3436 final Event e5 = new Event();
3437 if ( !e5.isUnassigned() ) {
3440 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3443 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3446 final Event e6 = new Event( 1, 0, 0 );
3447 if ( !e6.asText().toString().equals( "duplication" ) ) {
3450 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3453 final Event e7 = new Event( 0, 1, 0 );
3454 if ( !e7.asText().toString().equals( "speciation" ) ) {
3457 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3460 final Event e8 = new Event( 0, 0, 1 );
3461 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3464 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3468 catch ( final Exception e ) {
3469 e.printStackTrace( System.out );
3475 private static boolean testDeletionOfExternalNodes() {
3477 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3478 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3479 final PhylogenyWriter w = new PhylogenyWriter();
3480 if ( t0.isEmpty() ) {
3483 if ( t0.getNumberOfExternalNodes() != 1 ) {
3486 t0.deleteSubtree( t0.getNode( "A" ), false );
3487 if ( t0.getNumberOfExternalNodes() != 0 ) {
3490 if ( !t0.isEmpty() ) {
3493 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3494 if ( t1.getNumberOfExternalNodes() != 2 ) {
3497 t1.deleteSubtree( t1.getNode( "A" ), false );
3498 if ( t1.getNumberOfExternalNodes() != 1 ) {
3501 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3504 t1.deleteSubtree( t1.getNode( "B" ), false );
3505 if ( t1.getNumberOfExternalNodes() != 1 ) {
3508 t1.deleteSubtree( t1.getNode( "r" ), false );
3509 if ( !t1.isEmpty() ) {
3512 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3513 if ( t2.getNumberOfExternalNodes() != 3 ) {
3516 t2.deleteSubtree( t2.getNode( "B" ), false );
3517 if ( t2.getNumberOfExternalNodes() != 2 ) {
3520 t2.toNewHampshireX();
3521 PhylogenyNode n = t2.getNode( "A" );
3522 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3525 t2.deleteSubtree( t2.getNode( "A" ), false );
3526 if ( t2.getNumberOfExternalNodes() != 2 ) {
3529 t2.deleteSubtree( t2.getNode( "C" ), true );
3530 if ( t2.getNumberOfExternalNodes() != 1 ) {
3533 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3534 if ( t3.getNumberOfExternalNodes() != 4 ) {
3537 t3.deleteSubtree( t3.getNode( "B" ), true );
3538 if ( t3.getNumberOfExternalNodes() != 3 ) {
3541 n = t3.getNode( "A" );
3542 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3545 n = n.getNextExternalNode();
3546 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3549 t3.deleteSubtree( t3.getNode( "A" ), true );
3550 if ( t3.getNumberOfExternalNodes() != 2 ) {
3553 n = t3.getNode( "C" );
3554 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3557 t3.deleteSubtree( t3.getNode( "C" ), true );
3558 if ( t3.getNumberOfExternalNodes() != 1 ) {
3561 t3.deleteSubtree( t3.getNode( "D" ), true );
3562 if ( t3.getNumberOfExternalNodes() != 0 ) {
3565 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3566 if ( t4.getNumberOfExternalNodes() != 6 ) {
3569 t4.deleteSubtree( t4.getNode( "B2" ), true );
3570 if ( t4.getNumberOfExternalNodes() != 5 ) {
3573 String s = w.toNewHampshire( t4, true ).toString();
3574 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3577 t4.deleteSubtree( t4.getNode( "B11" ), true );
3578 if ( t4.getNumberOfExternalNodes() != 4 ) {
3581 t4.deleteSubtree( t4.getNode( "C" ), true );
3582 if ( t4.getNumberOfExternalNodes() != 3 ) {
3585 n = t4.getNode( "A" );
3586 n = n.getNextExternalNode();
3587 if ( !n.getName().equals( "B12" ) ) {
3590 n = n.getNextExternalNode();
3591 if ( !n.getName().equals( "D" ) ) {
3594 s = w.toNewHampshire( t4, true ).toString();
3595 if ( !s.equals( "((A,B12),D);" ) ) {
3598 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3599 t5.deleteSubtree( t5.getNode( "A" ), true );
3600 if ( t5.getNumberOfExternalNodes() != 5 ) {
3603 s = w.toNewHampshire( t5, true ).toString();
3604 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3607 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3608 t6.deleteSubtree( t6.getNode( "B11" ), true );
3609 if ( t6.getNumberOfExternalNodes() != 5 ) {
3612 s = w.toNewHampshire( t6, false ).toString();
3613 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3616 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3617 t7.deleteSubtree( t7.getNode( "B12" ), true );
3618 if ( t7.getNumberOfExternalNodes() != 5 ) {
3621 s = w.toNewHampshire( t7, true ).toString();
3622 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3625 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3626 t8.deleteSubtree( t8.getNode( "B2" ), true );
3627 if ( t8.getNumberOfExternalNodes() != 5 ) {
3630 s = w.toNewHampshire( t8, false ).toString();
3631 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3634 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3635 t9.deleteSubtree( t9.getNode( "C" ), true );
3636 if ( t9.getNumberOfExternalNodes() != 5 ) {
3639 s = w.toNewHampshire( t9, true ).toString();
3640 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3643 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3644 t10.deleteSubtree( t10.getNode( "D" ), true );
3645 if ( t10.getNumberOfExternalNodes() != 5 ) {
3648 s = w.toNewHampshire( t10, true ).toString();
3649 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3652 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3653 t11.deleteSubtree( t11.getNode( "A" ), true );
3654 if ( t11.getNumberOfExternalNodes() != 2 ) {
3657 s = w.toNewHampshire( t11, true ).toString();
3658 if ( !s.equals( "(B,C);" ) ) {
3661 t11.deleteSubtree( t11.getNode( "C" ), true );
3662 if ( t11.getNumberOfExternalNodes() != 1 ) {
3665 s = w.toNewHampshire( t11, false ).toString();
3666 if ( !s.equals( "B;" ) ) {
3669 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3670 t12.deleteSubtree( t12.getNode( "B2" ), true );
3671 if ( t12.getNumberOfExternalNodes() != 8 ) {
3674 s = w.toNewHampshire( t12, true ).toString();
3675 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3678 t12.deleteSubtree( t12.getNode( "B3" ), true );
3679 if ( t12.getNumberOfExternalNodes() != 7 ) {
3682 s = w.toNewHampshire( t12, true ).toString();
3683 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3686 t12.deleteSubtree( t12.getNode( "C3" ), true );
3687 if ( t12.getNumberOfExternalNodes() != 6 ) {
3690 s = w.toNewHampshire( t12, true ).toString();
3691 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3694 t12.deleteSubtree( t12.getNode( "A1" ), true );
3695 if ( t12.getNumberOfExternalNodes() != 5 ) {
3698 s = w.toNewHampshire( t12, true ).toString();
3699 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3702 t12.deleteSubtree( t12.getNode( "B1" ), true );
3703 if ( t12.getNumberOfExternalNodes() != 4 ) {
3706 s = w.toNewHampshire( t12, true ).toString();
3707 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3710 t12.deleteSubtree( t12.getNode( "A3" ), true );
3711 if ( t12.getNumberOfExternalNodes() != 3 ) {
3714 s = w.toNewHampshire( t12, true ).toString();
3715 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3718 t12.deleteSubtree( t12.getNode( "A2" ), true );
3719 if ( t12.getNumberOfExternalNodes() != 2 ) {
3722 s = w.toNewHampshire( t12, true ).toString();
3723 if ( !s.equals( "(C1,C2);" ) ) {
3726 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3727 t13.deleteSubtree( t13.getNode( "D" ), true );
3728 if ( t13.getNumberOfExternalNodes() != 4 ) {
3731 s = w.toNewHampshire( t13, true ).toString();
3732 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3735 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3736 t14.deleteSubtree( t14.getNode( "E" ), true );
3737 if ( t14.getNumberOfExternalNodes() != 5 ) {
3740 s = w.toNewHampshire( t14, true ).toString();
3741 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3744 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3745 t15.deleteSubtree( t15.getNode( "B2" ), true );
3746 if ( t15.getNumberOfExternalNodes() != 11 ) {
3749 t15.deleteSubtree( t15.getNode( "B1" ), true );
3750 if ( t15.getNumberOfExternalNodes() != 10 ) {
3753 t15.deleteSubtree( t15.getNode( "B3" ), true );
3754 if ( t15.getNumberOfExternalNodes() != 9 ) {
3757 t15.deleteSubtree( t15.getNode( "B4" ), true );
3758 if ( t15.getNumberOfExternalNodes() != 8 ) {
3761 t15.deleteSubtree( t15.getNode( "A1" ), true );
3762 if ( t15.getNumberOfExternalNodes() != 7 ) {
3765 t15.deleteSubtree( t15.getNode( "C4" ), true );
3766 if ( t15.getNumberOfExternalNodes() != 6 ) {
3770 catch ( final Exception e ) {
3771 e.printStackTrace( System.out );
3777 private static boolean testDescriptiveStatistics() {
3779 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3780 dss1.addValue( 82 );
3781 dss1.addValue( 78 );
3782 dss1.addValue( 70 );
3783 dss1.addValue( 58 );
3784 dss1.addValue( 42 );
3785 if ( dss1.getN() != 5 ) {
3788 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3791 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3794 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3797 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3800 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3803 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3806 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3809 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3812 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3815 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3818 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3821 dss1.addValue( 123 );
3822 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3825 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3828 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3831 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3832 dss2.addValue( -1.85 );
3833 dss2.addValue( 57.5 );
3834 dss2.addValue( 92.78 );
3835 dss2.addValue( 57.78 );
3836 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3839 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3842 final double[] a = dss2.getDataAsDoubleArray();
3843 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3846 dss2.addValue( -100 );
3847 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3850 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3853 final double[] ds = new double[ 14 ];
3868 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3869 if ( bins.length != 4 ) {
3872 if ( bins[ 0 ] != 2 ) {
3875 if ( bins[ 1 ] != 3 ) {
3878 if ( bins[ 2 ] != 4 ) {
3881 if ( bins[ 3 ] != 5 ) {
3884 final double[] ds1 = new double[ 9 ];
3894 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3895 if ( bins1.length != 4 ) {
3898 if ( bins1[ 0 ] != 2 ) {
3901 if ( bins1[ 1 ] != 3 ) {
3904 if ( bins1[ 2 ] != 0 ) {
3907 if ( bins1[ 3 ] != 4 ) {
3910 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3911 if ( bins1_1.length != 3 ) {
3914 if ( bins1_1[ 0 ] != 3 ) {
3917 if ( bins1_1[ 1 ] != 2 ) {
3920 if ( bins1_1[ 2 ] != 4 ) {
3923 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3924 if ( bins1_2.length != 3 ) {
3927 if ( bins1_2[ 0 ] != 2 ) {
3930 if ( bins1_2[ 1 ] != 2 ) {
3933 if ( bins1_2[ 2 ] != 2 ) {
3936 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3950 dss3.addValue( 10 );
3951 dss3.addValue( 10 );
3952 dss3.addValue( 10 );
3953 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3954 histo.toStringBuffer( 10, '=', 40, 5 );
3955 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3957 catch ( final Exception e ) {
3958 e.printStackTrace( System.out );
3964 private static boolean testDir( final String file ) {
3966 final File f = new File( file );
3967 if ( !f.exists() ) {
3970 if ( !f.isDirectory() ) {
3973 if ( !f.canRead() ) {
3977 catch ( final Exception e ) {
3983 private static boolean testEbiEntryRetrieval() {
3985 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3986 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3987 System.out.println( entry.getAccession() );
3990 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
3991 System.out.println( entry.getTaxonomyScientificName() );
3994 if ( !entry.getSequenceName()
3995 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
3996 System.out.println( entry.getSequenceName() );
3999 if ( !entry.getGeneName().equals( "treX-like" ) ) {
4000 System.out.println( entry.getGeneName() );
4003 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
4004 System.out.println( entry.getTaxonomyIdentifier() );
4007 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
4008 System.out.println( entry.getAnnotations().first().getRefValue() );
4011 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
4012 System.out.println( entry.getAnnotations().first().getRefSource() );
4015 if ( entry.getCrossReferences().size() != 5 ) {
4018 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
4019 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
4022 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
4023 System.out.println( entry1.getTaxonomyScientificName() );
4026 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
4027 System.out.println( entry1.getSequenceName() );
4030 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
4031 System.out.println( entry1.getTaxonomyIdentifier() );
4034 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
4035 System.out.println( entry1.getGeneName() );
4038 if ( entry1.getCrossReferences().size() != 6 ) {
4041 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
4042 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
4045 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4046 System.out.println( entry2.getTaxonomyScientificName() );
4049 if ( !entry2.getSequenceName()
4050 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
4051 System.out.println( entry2.getSequenceName() );
4054 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
4055 System.out.println( entry2.getTaxonomyIdentifier() );
4058 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
4059 System.out.println( entry2.getGeneName() );
4062 if ( entry2.getCrossReferences().size() != 3 ) {
4066 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
4067 if ( !entry3.getAccession().equals( "HM043801" ) ) {
4070 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
4071 System.out.println( entry3.getTaxonomyScientificName() );
4074 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
4075 System.out.println( entry3.getSequenceName() );
4078 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
4079 System.out.println( entry3.getTaxonomyIdentifier() );
4082 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
4083 System.out.println( entry3.getSequenceSymbol() );
4086 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
4089 if ( entry3.getCrossReferences().size() < 7 ) {
4092 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
4093 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4096 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4097 System.out.println( entry4.getTaxonomyScientificName() );
4100 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4101 System.out.println( entry4.getSequenceName() );
4104 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4105 System.out.println( entry4.getTaxonomyIdentifier() );
4108 if ( !entry4.getGeneName().equals( "ras" ) ) {
4109 System.out.println( entry4.getGeneName() );
4112 // if ( !entry4.getChromosome().equals( "ras" ) ) {
4113 // System.out.println( entry4.getChromosome() );
4116 // if ( !entry4.getMap().equals( "ras" ) ) {
4117 // System.out.println( entry4.getMap() );
4123 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
4124 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
4127 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4128 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4131 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4132 System.out.println( entry5.getTaxonomyScientificName() );
4135 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4136 System.out.println( entry5.getSequenceName() );
4139 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4140 System.out.println( entry5.getTaxonomyIdentifier() );
4144 catch ( final IOException e ) {
4145 System.out.println();
4146 System.out.println( "the following might be due to absence internet connection:" );
4147 e.printStackTrace( System.out );
4150 catch ( final Exception e ) {
4151 e.printStackTrace();
4157 private static boolean testExternalNodeRelatedMethods() {
4159 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4160 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4161 PhylogenyNode n = t1.getNode( "A" );
4162 n = n.getNextExternalNode();
4163 if ( !n.getName().equals( "B" ) ) {
4166 n = n.getNextExternalNode();
4167 if ( !n.getName().equals( "C" ) ) {
4170 n = n.getNextExternalNode();
4171 if ( !n.getName().equals( "D" ) ) {
4174 n = t1.getNode( "B" );
4175 while ( !n.isLastExternalNode() ) {
4176 n = n.getNextExternalNode();
4178 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4179 n = t2.getNode( "A" );
4180 n = n.getNextExternalNode();
4181 if ( !n.getName().equals( "B" ) ) {
4184 n = n.getNextExternalNode();
4185 if ( !n.getName().equals( "C" ) ) {
4188 n = n.getNextExternalNode();
4189 if ( !n.getName().equals( "D" ) ) {
4192 n = t2.getNode( "B" );
4193 while ( !n.isLastExternalNode() ) {
4194 n = n.getNextExternalNode();
4196 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4197 n = t3.getNode( "A" );
4198 n = n.getNextExternalNode();
4199 if ( !n.getName().equals( "B" ) ) {
4202 n = n.getNextExternalNode();
4203 if ( !n.getName().equals( "C" ) ) {
4206 n = n.getNextExternalNode();
4207 if ( !n.getName().equals( "D" ) ) {
4210 n = n.getNextExternalNode();
4211 if ( !n.getName().equals( "E" ) ) {
4214 n = n.getNextExternalNode();
4215 if ( !n.getName().equals( "F" ) ) {
4218 n = n.getNextExternalNode();
4219 if ( !n.getName().equals( "G" ) ) {
4222 n = n.getNextExternalNode();
4223 if ( !n.getName().equals( "H" ) ) {
4226 n = t3.getNode( "B" );
4227 while ( !n.isLastExternalNode() ) {
4228 n = n.getNextExternalNode();
4230 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4231 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4232 final PhylogenyNode node = iter.next();
4234 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4235 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4236 final PhylogenyNode node = iter.next();
4238 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4239 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4240 if ( !iter.next().getName().equals( "A" ) ) {
4243 if ( !iter.next().getName().equals( "B" ) ) {
4246 if ( !iter.next().getName().equals( "C" ) ) {
4249 if ( !iter.next().getName().equals( "D" ) ) {
4252 if ( !iter.next().getName().equals( "E" ) ) {
4255 if ( !iter.next().getName().equals( "F" ) ) {
4258 if ( iter.hasNext() ) {
4262 catch ( final Exception e ) {
4263 e.printStackTrace( System.out );
4269 private static boolean testExtractSNFromNodeName() {
4271 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4274 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4277 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4280 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4281 .equals( "Mus musculus musculus" ) ) {
4284 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4285 .equals( "Mus musculus musculus" ) ) {
4288 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4289 .equals( "Mus musculus musculus" ) ) {
4292 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4293 .equals( "Mus musculus musculus" ) ) {
4296 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4299 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4300 .equals( "Mus musculus musculus" ) ) {
4303 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4304 .equals( "Mus musculus musculus" ) ) {
4307 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4310 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4313 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4316 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4319 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4320 .equals( "Mus musculus musculus" ) ) {
4323 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4326 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4329 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4332 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4335 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4338 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4341 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4344 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4347 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4348 .equals( "Mus musculus" ) ) {
4351 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4352 .equals( "Mus musculus" ) ) {
4355 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4358 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4359 .equals( "Mus musculus musculus" ) ) {
4362 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4363 .equals( "Mus musculus musculus" ) ) {
4366 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4367 .equals( "Mus musculus musculus" ) ) {
4370 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4373 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4374 .equals( "Pilostyles mexicana" ) ) {
4377 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4378 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4381 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4382 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4385 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4386 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4389 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4390 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4393 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4394 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4397 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4398 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4401 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
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 subspecies lyrata bcl2" )
4410 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4413 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4414 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4417 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4418 .equals( "Escherichia coli (strain K12)" ) ) {
4421 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4422 .equals( "Escherichia coli (strain K12)" ) ) {
4425 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4426 .equals( "Escherichia coli (str. K12)" ) ) {
4429 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4430 .equals( "Escherichia coli (str. K12)" ) ) {
4433 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4434 .equals( "Escherichia coli (str. K12)" ) ) {
4437 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4438 .equals( "Escherichia coli (var. K12)" ) ) {
4441 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4442 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4445 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4446 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4450 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4451 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4454 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4455 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4459 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4460 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4463 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
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( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4474 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4477 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4480 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4481 .equals( "Macrocera sp." ) ) {
4484 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4487 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4488 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4491 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
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)" ) ) {
4504 catch ( final Exception e ) {
4505 e.printStackTrace( System.out );
4511 private static boolean testExtractTaxonomyDataFromNodeName() {
4513 PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
4514 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4517 n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
4518 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4521 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
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~12" );
4530 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4533 n = new PhylogenyNode( "HNRPR_HUMAN" );
4534 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4537 n = new PhylogenyNode( "HNRPR_HUMAN_X" );
4538 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4542 catch ( final Exception e ) {
4543 e.printStackTrace( System.out );
4549 private static boolean testExtractTaxonomyCodeFromNodeName() {
4551 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4554 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4555 .equals( "SOYBN" ) ) {
4558 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4559 .equals( "ARATH" ) ) {
4562 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4563 .equals( "ARATH" ) ) {
4566 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4569 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4572 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4575 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4576 .equals( "SOYBN" ) ) {
4579 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4580 .equals( "SOYBN" ) ) {
4583 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4584 .equals( "SOYBN" ) ) {
4587 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4588 .equals( "SOYBN" ) ) {
4591 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4592 .equals( "SOYBN" ) ) {
4595 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4596 .equals( "SOYBN" ) ) {
4599 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4600 .equals( "SOYBN" ) ) {
4603 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4604 .equals( "SOYBN" ) ) {
4607 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4610 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4611 .equals( "SOYBN" ) ) {
4614 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4615 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4618 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4619 .equals( "9YX45" ) ) {
4622 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4623 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4624 .equals( "MOUSE" ) ) {
4627 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4628 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4629 .equals( "MOUSE" ) ) {
4632 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4633 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4634 .equals( "MOUSE" ) ) {
4637 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4638 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4641 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4642 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4645 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4646 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
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_RATfunction = 23445",
4658 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4661 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4662 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4665 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4666 .equals( "RAT" ) ) {
4669 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4670 .equals( "PIG" ) ) {
4674 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4675 .equals( "MOUSE" ) ) {
4678 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4679 .equals( "MOUSE" ) ) {
4682 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4686 catch ( final Exception e ) {
4687 e.printStackTrace( System.out );
4693 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4695 PhylogenyNode n = new PhylogenyNode();
4696 n.setName( "tr|B3RJ64" );
4697 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
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_tr|B3RJ64_sp|123 " );
4741 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4744 n.setName( "B3RJ64" );
4745 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4748 n.setName( "sp|B3RJ64" );
4749 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4752 n.setName( "sp|B3RJ64C" );
4753 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4756 n.setName( "sp B3RJ64" );
4757 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4760 n.setName( "sp|B3RJ6X" );
4761 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4764 n.setName( "sp|B3RJ6" );
4765 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4768 n.setName( "K1PYK7_CRAGI" );
4769 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4772 n.setName( "K1PYK7_PEA" );
4773 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4776 n.setName( "K1PYK7_RAT" );
4777 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4780 n.setName( "K1PYK7_PIG" );
4781 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4784 n.setName( "~K1PYK7_PIG~" );
4785 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4788 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4789 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4792 n.setName( "K1PYKX_CRAGI" );
4793 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4796 n.setName( "XXXXX_CRAGI" );
4797 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4800 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4801 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4804 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4805 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4808 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4809 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4812 n = new PhylogenyNode();
4813 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4814 seq.setSymbol( "K1PYK7_CRAGI" );
4815 n.getNodeData().addSequence( seq );
4816 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4819 seq.setSymbol( "tr|B3RJ64" );
4820 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4823 n = new PhylogenyNode();
4824 seq = new org.forester.phylogeny.data.Sequence();
4825 seq.setName( "K1PYK7_CRAGI" );
4826 n.getNodeData().addSequence( seq );
4827 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4830 seq.setName( "tr|B3RJ64" );
4831 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4834 n = new PhylogenyNode();
4835 seq = new org.forester.phylogeny.data.Sequence();
4836 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4837 n.getNodeData().addSequence( seq );
4838 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4841 n = new PhylogenyNode();
4842 seq = new org.forester.phylogeny.data.Sequence();
4843 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4844 n.getNodeData().addSequence( seq );
4845 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4849 n = new PhylogenyNode();
4850 n.setName( "ACP19736" );
4851 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4854 n = new PhylogenyNode();
4855 n.setName( "|ACP19736|" );
4856 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4860 catch ( final Exception e ) {
4861 e.printStackTrace( System.out );
4867 private static boolean testFastaParser() {
4869 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4872 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4875 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4876 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4879 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4882 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4885 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
4888 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4891 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4895 catch ( final Exception e ) {
4896 e.printStackTrace();
4902 private static boolean testGenbankAccessorParsing() {
4903 //The format for GenBank Accession numbers are:
4904 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4905 //Protein: 3 letters + 5 numerals
4906 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4907 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4910 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4913 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4916 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4919 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4922 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4925 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4928 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4931 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4934 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4937 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4940 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4943 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4946 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4952 private static boolean testGeneralMsaParser() {
4954 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4955 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4956 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4957 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4958 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4959 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4960 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4961 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4962 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4965 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4968 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4971 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4974 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4977 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4980 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4983 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4986 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4989 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4992 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4995 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4998 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
4999 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5002 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5005 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5008 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
5009 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
5012 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
5015 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
5018 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
5019 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5022 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5025 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5029 catch ( final Exception e ) {
5030 e.printStackTrace();
5036 private static boolean testGeneralTable() {
5038 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
5039 t0.setValue( 3, 2, "23" );
5040 t0.setValue( 10, 1, "error" );
5041 t0.setValue( 10, 1, "110" );
5042 t0.setValue( 9, 1, "19" );
5043 t0.setValue( 1, 10, "101" );
5044 t0.setValue( 10, 10, "1010" );
5045 t0.setValue( 100, 10, "10100" );
5046 t0.setValue( 0, 0, "00" );
5047 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
5050 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
5053 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
5056 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
5059 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
5062 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
5065 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
5068 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
5071 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
5074 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
5075 t1.setValue( "3", "2", "23" );
5076 t1.setValue( "10", "1", "error" );
5077 t1.setValue( "10", "1", "110" );
5078 t1.setValue( "9", "1", "19" );
5079 t1.setValue( "1", "10", "101" );
5080 t1.setValue( "10", "10", "1010" );
5081 t1.setValue( "100", "10", "10100" );
5082 t1.setValue( "0", "0", "00" );
5083 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
5084 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
5087 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
5090 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
5093 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
5096 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
5099 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
5102 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
5105 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
5108 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
5111 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
5115 catch ( final Exception e ) {
5116 e.printStackTrace( System.out );
5122 private static boolean testGetDistance() {
5124 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5125 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",
5126 new NHXParser() )[ 0 ];
5127 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
5130 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5133 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5136 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5139 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5142 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5145 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5148 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5151 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5154 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5157 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5160 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5163 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5166 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5169 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5172 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5175 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5178 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5181 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5184 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5187 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5190 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5193 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5196 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5199 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5202 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5205 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5208 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5211 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5214 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5217 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5220 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",
5221 new NHXParser() )[ 0 ];
5222 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5225 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5228 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5231 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5234 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5237 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5240 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5243 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5246 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5249 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5252 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5256 catch ( final Exception e ) {
5257 e.printStackTrace( System.out );
5263 private static boolean testGetLCA() {
5265 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5266 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5267 new NHXParser() )[ 0 ];
5268 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5269 if ( !A.getName().equals( "A" ) ) {
5272 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5273 if ( !gh.getName().equals( "gh" ) ) {
5276 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5277 if ( !ab.getName().equals( "ab" ) ) {
5280 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5281 if ( !ab2.getName().equals( "ab" ) ) {
5284 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5285 if ( !gh2.getName().equals( "gh" ) ) {
5288 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5289 if ( !gh3.getName().equals( "gh" ) ) {
5292 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5293 if ( !abc.getName().equals( "abc" ) ) {
5296 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5297 if ( !abc2.getName().equals( "abc" ) ) {
5300 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5301 if ( !abcd.getName().equals( "abcd" ) ) {
5304 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5305 if ( !abcd2.getName().equals( "abcd" ) ) {
5308 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5309 if ( !abcdef.getName().equals( "abcdef" ) ) {
5312 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5313 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5316 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5317 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5320 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5321 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5324 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5325 if ( !abcde.getName().equals( "abcde" ) ) {
5328 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5329 if ( !abcde2.getName().equals( "abcde" ) ) {
5332 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5333 if ( !r.getName().equals( "abcdefgh" ) ) {
5336 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5337 if ( !r2.getName().equals( "abcdefgh" ) ) {
5340 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5341 if ( !r3.getName().equals( "abcdefgh" ) ) {
5344 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5345 if ( !abcde3.getName().equals( "abcde" ) ) {
5348 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5349 if ( !abcde4.getName().equals( "abcde" ) ) {
5352 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5353 if ( !ab3.getName().equals( "ab" ) ) {
5356 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5357 if ( !ab4.getName().equals( "ab" ) ) {
5360 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5361 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5362 if ( !cd.getName().equals( "cd" ) ) {
5365 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5366 if ( !cd2.getName().equals( "cd" ) ) {
5369 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5370 if ( !cde.getName().equals( "cde" ) ) {
5373 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5374 if ( !cde2.getName().equals( "cde" ) ) {
5377 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5378 if ( !cdef.getName().equals( "cdef" ) ) {
5381 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5382 if ( !cdef2.getName().equals( "cdef" ) ) {
5385 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5386 if ( !cdef3.getName().equals( "cdef" ) ) {
5389 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5390 if ( !rt.getName().equals( "r" ) ) {
5393 final Phylogeny p3 = factory
5394 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5395 new NHXParser() )[ 0 ];
5396 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5397 if ( !bc_3.getName().equals( "bc" ) ) {
5400 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5401 if ( !ac_3.getName().equals( "abc" ) ) {
5404 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5405 if ( !ad_3.getName().equals( "abcde" ) ) {
5408 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5409 if ( !af_3.getName().equals( "abcdef" ) ) {
5412 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5413 if ( !ag_3.getName().equals( "" ) ) {
5416 if ( !ag_3.isRoot() ) {
5419 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5420 if ( !al_3.getName().equals( "" ) ) {
5423 if ( !al_3.isRoot() ) {
5426 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5427 if ( !kl_3.getName().equals( "" ) ) {
5430 if ( !kl_3.isRoot() ) {
5433 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5434 if ( !fl_3.getName().equals( "" ) ) {
5437 if ( !fl_3.isRoot() ) {
5440 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5441 if ( !gk_3.getName().equals( "ghijk" ) ) {
5444 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5445 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5446 if ( !r_4.getName().equals( "r" ) ) {
5449 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5450 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5451 if ( !r_5.getName().equals( "root" ) ) {
5454 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5455 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5456 if ( !r_6.getName().equals( "rot" ) ) {
5459 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5460 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5461 if ( !r_7.getName().equals( "rott" ) ) {
5465 catch ( final Exception e ) {
5466 e.printStackTrace( System.out );
5472 private static boolean testGetLCA2() {
5474 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5475 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5476 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5477 PhylogenyMethods.preOrderReId( p_a );
5478 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5479 p_a.getNode( "a" ) );
5480 if ( !p_a_1.getName().equals( "a" ) ) {
5483 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5484 PhylogenyMethods.preOrderReId( p_b );
5485 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5486 p_b.getNode( "a" ) );
5487 if ( !p_b_1.getName().equals( "b" ) ) {
5490 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5491 p_b.getNode( "b" ) );
5492 if ( !p_b_2.getName().equals( "b" ) ) {
5495 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5496 PhylogenyMethods.preOrderReId( p_c );
5497 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5498 p_c.getNode( "a" ) );
5499 if ( !p_c_1.getName().equals( "b" ) ) {
5502 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5503 p_c.getNode( "c" ) );
5504 if ( !p_c_2.getName().equals( "c" ) ) {
5505 System.out.println( p_c_2.getName() );
5509 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5510 p_c.getNode( "b" ) );
5511 if ( !p_c_3.getName().equals( "b" ) ) {
5514 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5515 p_c.getNode( "a" ) );
5516 if ( !p_c_4.getName().equals( "c" ) ) {
5519 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5520 new NHXParser() )[ 0 ];
5521 PhylogenyMethods.preOrderReId( p1 );
5522 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5523 p1.getNode( "A" ) );
5524 if ( !A.getName().equals( "A" ) ) {
5527 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5528 p1.getNode( "gh" ) );
5529 if ( !gh.getName().equals( "gh" ) ) {
5532 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5533 p1.getNode( "B" ) );
5534 if ( !ab.getName().equals( "ab" ) ) {
5537 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5538 p1.getNode( "A" ) );
5539 if ( !ab2.getName().equals( "ab" ) ) {
5542 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5543 p1.getNode( "G" ) );
5544 if ( !gh2.getName().equals( "gh" ) ) {
5547 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5548 p1.getNode( "H" ) );
5549 if ( !gh3.getName().equals( "gh" ) ) {
5552 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5553 p1.getNode( "A" ) );
5554 if ( !abc.getName().equals( "abc" ) ) {
5557 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5558 p1.getNode( "C" ) );
5559 if ( !abc2.getName().equals( "abc" ) ) {
5562 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5563 p1.getNode( "D" ) );
5564 if ( !abcd.getName().equals( "abcd" ) ) {
5567 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5568 p1.getNode( "A" ) );
5569 if ( !abcd2.getName().equals( "abcd" ) ) {
5572 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5573 p1.getNode( "F" ) );
5574 if ( !abcdef.getName().equals( "abcdef" ) ) {
5577 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5578 p1.getNode( "A" ) );
5579 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5582 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5583 p1.getNode( "F" ) );
5584 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5587 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5588 p1.getNode( "ab" ) );
5589 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5592 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5593 p1.getNode( "E" ) );
5594 if ( !abcde.getName().equals( "abcde" ) ) {
5597 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5598 p1.getNode( "A" ) );
5599 if ( !abcde2.getName().equals( "abcde" ) ) {
5602 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5603 p1.getNode( "abcdefgh" ) );
5604 if ( !r.getName().equals( "abcdefgh" ) ) {
5607 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5608 p1.getNode( "H" ) );
5609 if ( !r2.getName().equals( "abcdefgh" ) ) {
5612 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5613 p1.getNode( "A" ) );
5614 if ( !r3.getName().equals( "abcdefgh" ) ) {
5617 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5618 p1.getNode( "abcde" ) );
5619 if ( !abcde3.getName().equals( "abcde" ) ) {
5622 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5623 p1.getNode( "E" ) );
5624 if ( !abcde4.getName().equals( "abcde" ) ) {
5627 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5628 p1.getNode( "B" ) );
5629 if ( !ab3.getName().equals( "ab" ) ) {
5632 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5633 p1.getNode( "ab" ) );
5634 if ( !ab4.getName().equals( "ab" ) ) {
5637 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5638 PhylogenyMethods.preOrderReId( p2 );
5639 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5640 p2.getNode( "d" ) );
5641 if ( !cd.getName().equals( "cd" ) ) {
5644 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5645 p2.getNode( "c" ) );
5646 if ( !cd2.getName().equals( "cd" ) ) {
5649 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5650 p2.getNode( "e" ) );
5651 if ( !cde.getName().equals( "cde" ) ) {
5654 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5655 p2.getNode( "c" ) );
5656 if ( !cde2.getName().equals( "cde" ) ) {
5659 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5660 p2.getNode( "f" ) );
5661 if ( !cdef.getName().equals( "cdef" ) ) {
5664 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5665 p2.getNode( "f" ) );
5666 if ( !cdef2.getName().equals( "cdef" ) ) {
5669 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5670 p2.getNode( "d" ) );
5671 if ( !cdef3.getName().equals( "cdef" ) ) {
5674 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5675 p2.getNode( "a" ) );
5676 if ( !rt.getName().equals( "r" ) ) {
5679 final Phylogeny p3 = factory
5680 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5681 new NHXParser() )[ 0 ];
5682 PhylogenyMethods.preOrderReId( p3 );
5683 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5684 p3.getNode( "c" ) );
5685 if ( !bc_3.getName().equals( "bc" ) ) {
5688 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5689 p3.getNode( "c" ) );
5690 if ( !ac_3.getName().equals( "abc" ) ) {
5693 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5694 p3.getNode( "d" ) );
5695 if ( !ad_3.getName().equals( "abcde" ) ) {
5698 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5699 p3.getNode( "f" ) );
5700 if ( !af_3.getName().equals( "abcdef" ) ) {
5703 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5704 p3.getNode( "g" ) );
5705 if ( !ag_3.getName().equals( "" ) ) {
5708 if ( !ag_3.isRoot() ) {
5711 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5712 p3.getNode( "l" ) );
5713 if ( !al_3.getName().equals( "" ) ) {
5716 if ( !al_3.isRoot() ) {
5719 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5720 p3.getNode( "l" ) );
5721 if ( !kl_3.getName().equals( "" ) ) {
5724 if ( !kl_3.isRoot() ) {
5727 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5728 p3.getNode( "l" ) );
5729 if ( !fl_3.getName().equals( "" ) ) {
5732 if ( !fl_3.isRoot() ) {
5735 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5736 p3.getNode( "k" ) );
5737 if ( !gk_3.getName().equals( "ghijk" ) ) {
5740 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5741 PhylogenyMethods.preOrderReId( p4 );
5742 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5743 p4.getNode( "c" ) );
5744 if ( !r_4.getName().equals( "r" ) ) {
5747 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5748 PhylogenyMethods.preOrderReId( p5 );
5749 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5750 p5.getNode( "c" ) );
5751 if ( !r_5.getName().equals( "root" ) ) {
5754 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5755 PhylogenyMethods.preOrderReId( p6 );
5756 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5757 p6.getNode( "a" ) );
5758 if ( !r_6.getName().equals( "rot" ) ) {
5761 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5762 PhylogenyMethods.preOrderReId( p7 );
5763 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5764 p7.getNode( "e" ) );
5765 if ( !r_7.getName().equals( "rott" ) ) {
5768 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5769 p7.getNode( "a" ) );
5770 if ( !r_71.getName().equals( "rott" ) ) {
5773 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5774 p7.getNode( "rott" ) );
5775 if ( !r_72.getName().equals( "rott" ) ) {
5778 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5779 p7.getNode( "a" ) );
5780 if ( !r_73.getName().equals( "rott" ) ) {
5783 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5784 p7.getNode( "rott" ) );
5785 if ( !r_74.getName().equals( "rott" ) ) {
5788 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5789 p7.getNode( "e" ) );
5790 if ( !r_75.getName().equals( "e" ) ) {
5794 catch ( final Exception e ) {
5795 e.printStackTrace( System.out );
5801 private static boolean testHmmscanOutputParser() {
5802 final String test_dir = Test.PATH_TO_TEST_DATA;
5804 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5805 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5807 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5808 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5809 final List<Protein> proteins = parser2.parse();
5810 if ( parser2.getProteinsEncountered() != 4 ) {
5813 if ( proteins.size() != 4 ) {
5816 if ( parser2.getDomainsEncountered() != 69 ) {
5819 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5822 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5825 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5828 final Protein p1 = proteins.get( 0 );
5829 if ( p1.getNumberOfProteinDomains() != 15 ) {
5832 if ( p1.getLength() != 850 ) {
5835 final Protein p2 = proteins.get( 1 );
5836 if ( p2.getNumberOfProteinDomains() != 51 ) {
5839 if ( p2.getLength() != 1291 ) {
5842 final Protein p3 = proteins.get( 2 );
5843 if ( p3.getNumberOfProteinDomains() != 2 ) {
5846 final Protein p4 = proteins.get( 3 );
5847 if ( p4.getNumberOfProteinDomains() != 1 ) {
5850 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5853 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5856 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5859 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5862 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5865 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5868 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5872 catch ( final Exception e ) {
5873 e.printStackTrace( System.out );
5879 private static boolean testLastExternalNodeMethods() {
5881 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5882 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5883 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5884 final PhylogenyNode n1 = t0.getNode( "A" );
5885 if ( n1.isLastExternalNode() ) {
5888 final PhylogenyNode n2 = t0.getNode( "B" );
5889 if ( n2.isLastExternalNode() ) {
5892 final PhylogenyNode n3 = t0.getNode( "C" );
5893 if ( n3.isLastExternalNode() ) {
5896 final PhylogenyNode n4 = t0.getNode( "D" );
5897 if ( !n4.isLastExternalNode() ) {
5901 catch ( final Exception e ) {
5902 e.printStackTrace( System.out );
5908 private static boolean testLevelOrderIterator() {
5910 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5911 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5912 PhylogenyNodeIterator it0;
5913 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5916 for( it0.reset(); it0.hasNext(); ) {
5919 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5920 if ( !it.next().getName().equals( "r" ) ) {
5923 if ( !it.next().getName().equals( "ab" ) ) {
5926 if ( !it.next().getName().equals( "cd" ) ) {
5929 if ( !it.next().getName().equals( "A" ) ) {
5932 if ( !it.next().getName().equals( "B" ) ) {
5935 if ( !it.next().getName().equals( "C" ) ) {
5938 if ( !it.next().getName().equals( "D" ) ) {
5941 if ( it.hasNext() ) {
5944 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",
5945 new NHXParser() )[ 0 ];
5946 PhylogenyNodeIterator it2;
5947 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5950 for( it2.reset(); it2.hasNext(); ) {
5953 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5954 if ( !it3.next().getName().equals( "r" ) ) {
5957 if ( !it3.next().getName().equals( "abc" ) ) {
5960 if ( !it3.next().getName().equals( "defg" ) ) {
5963 if ( !it3.next().getName().equals( "A" ) ) {
5966 if ( !it3.next().getName().equals( "B" ) ) {
5969 if ( !it3.next().getName().equals( "C" ) ) {
5972 if ( !it3.next().getName().equals( "D" ) ) {
5975 if ( !it3.next().getName().equals( "E" ) ) {
5978 if ( !it3.next().getName().equals( "F" ) ) {
5981 if ( !it3.next().getName().equals( "G" ) ) {
5984 if ( !it3.next().getName().equals( "1" ) ) {
5987 if ( !it3.next().getName().equals( "2" ) ) {
5990 if ( !it3.next().getName().equals( "3" ) ) {
5993 if ( !it3.next().getName().equals( "4" ) ) {
5996 if ( !it3.next().getName().equals( "5" ) ) {
5999 if ( !it3.next().getName().equals( "6" ) ) {
6002 if ( !it3.next().getName().equals( "f1" ) ) {
6005 if ( !it3.next().getName().equals( "f2" ) ) {
6008 if ( !it3.next().getName().equals( "f3" ) ) {
6011 if ( !it3.next().getName().equals( "a" ) ) {
6014 if ( !it3.next().getName().equals( "b" ) ) {
6017 if ( !it3.next().getName().equals( "f21" ) ) {
6020 if ( !it3.next().getName().equals( "X" ) ) {
6023 if ( !it3.next().getName().equals( "Y" ) ) {
6026 if ( !it3.next().getName().equals( "Z" ) ) {
6029 if ( it3.hasNext() ) {
6032 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
6033 PhylogenyNodeIterator it4;
6034 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
6037 for( it4.reset(); it4.hasNext(); ) {
6040 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
6041 if ( !it5.next().getName().equals( "r" ) ) {
6044 if ( !it5.next().getName().equals( "A" ) ) {
6047 if ( !it5.next().getName().equals( "B" ) ) {
6050 if ( !it5.next().getName().equals( "C" ) ) {
6053 if ( !it5.next().getName().equals( "D" ) ) {
6056 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
6057 PhylogenyNodeIterator it6;
6058 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
6061 for( it6.reset(); it6.hasNext(); ) {
6064 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
6065 if ( !it7.next().getName().equals( "A" ) ) {
6068 if ( it.hasNext() ) {
6072 catch ( final Exception e ) {
6073 e.printStackTrace( System.out );
6079 private static boolean testMafft( final String path ) {
6081 final List<String> opts = new ArrayList<String>();
6082 opts.add( "--maxiterate" );
6084 opts.add( "--localpair" );
6085 opts.add( "--quiet" );
6087 final MsaInferrer mafft = Mafft.createInstance( path );
6088 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
6089 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
6092 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
6096 catch ( final Exception e ) {
6097 e.printStackTrace( System.out );
6103 private static boolean testMidpointrooting() {
6105 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6106 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
6107 PhylogenyMethods.midpointRoot( t0 );
6108 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
6111 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
6114 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
6118 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",
6119 new NHXParser() )[ 0 ];
6120 if ( !t1.isRooted() ) {
6123 PhylogenyMethods.midpointRoot( t1 );
6124 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6127 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6130 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6133 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6136 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6139 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6142 t1.reRoot( t1.getNode( "A" ) );
6143 PhylogenyMethods.midpointRoot( t1 );
6144 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6147 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6150 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6153 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6156 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6160 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6164 catch ( final Exception e ) {
6165 e.printStackTrace( System.out );
6171 private static boolean testMsaQualityMethod() {
6173 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6174 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6175 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6176 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6177 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6182 final Msa msa = BasicMsa.createInstance( l );
6183 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6186 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6189 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6192 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6195 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6198 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6201 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6205 catch ( final Exception e ) {
6206 e.printStackTrace( System.out );
6212 private static boolean testMsaEntropy() {
6214 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
6215 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
6216 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
6217 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
6218 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6223 final Msa msa = BasicMsa.createInstance( l );
6224 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
6225 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
6226 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
6227 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
6228 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
6229 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
6230 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
6231 System.out.println();
6232 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
6233 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
6234 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
6235 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
6236 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
6237 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
6238 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
6239 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6240 l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
6241 l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
6242 l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
6243 l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
6244 l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
6245 l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
6246 l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
6247 l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
6248 l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
6249 l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
6250 l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
6251 l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
6252 l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
6253 l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
6254 l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
6255 l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
6256 l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
6257 l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
6258 l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
6259 l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
6260 l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
6261 l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
6262 final Msa msa2 = BasicMsa.createInstance( l2 );
6263 System.out.println();
6264 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
6265 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
6266 System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
6268 catch ( final Exception e ) {
6269 e.printStackTrace( System.out );
6275 private static boolean testDeleteableMsa() {
6277 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
6278 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
6279 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
6280 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
6281 final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
6282 final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
6283 final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
6290 final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
6291 dmsa0.deleteRow( "b", false );
6292 if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
6295 dmsa0.deleteRow( "e", false );
6296 dmsa0.deleteRow( "a", false );
6297 dmsa0.deleteRow( "f", false );
6298 if ( dmsa0.getLength() != 4 ) {
6301 if ( dmsa0.getNumberOfSequences() != 2 ) {
6304 if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
6307 if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
6310 if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
6313 if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
6316 if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
6319 dmsa0.deleteRow( "c", false );
6320 dmsa0.deleteRow( "d", false );
6321 if ( dmsa0.getNumberOfSequences() != 0 ) {
6325 final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
6326 final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
6327 final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
6328 final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
6329 final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
6330 final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
6331 final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
6338 final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
6339 dmsa1.deleteGapOnlyColumns();
6340 dmsa1.deleteRow( "a", false );
6341 dmsa1.deleteRow( "f", false );
6342 dmsa1.deleteRow( "d", false );
6343 dmsa1.deleteGapOnlyColumns();
6344 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
6347 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
6350 if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
6353 dmsa1.deleteRow( "c", false );
6354 dmsa1.deleteGapOnlyColumns();
6355 final Writer w0 = new StringWriter();
6356 dmsa1.write( w0, MSA_FORMAT.FASTA );
6357 final Writer w1 = new StringWriter();
6358 dmsa1.write( w1, MSA_FORMAT.PHYLIP );
6359 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
6362 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
6365 final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
6366 final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
6367 final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
6368 final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
6369 final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
6370 final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
6371 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6378 final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
6379 dmsa2.deleteGapColumns( 0.5 );
6380 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
6383 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
6386 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
6389 dmsa2.deleteGapColumns( 0.2 );
6390 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
6393 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
6396 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
6399 dmsa2.deleteGapColumns( 0 );
6400 dmsa2.deleteRow( "a", false );
6401 dmsa2.deleteRow( "b", false );
6402 dmsa2.deleteRow( "f", false );
6403 dmsa2.deleteRow( "e", false );
6404 dmsa2.setIdentifier( 0, "new_c" );
6405 dmsa2.setIdentifier( 1, "new_d" );
6406 dmsa2.setResidueAt( 0, 0, 'x' );
6407 final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
6408 if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
6411 final Writer w = new StringWriter();
6412 dmsa2.write( w, MSA_FORMAT.PHYLIP );
6413 final String phylip = w.toString();
6414 if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
6415 System.out.println( phylip );
6418 final Writer w2 = new StringWriter();
6419 dmsa2.write( w2, MSA_FORMAT.FASTA );
6420 final String fasta = w2.toString();
6421 if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
6422 System.out.println( fasta );
6426 catch ( final Exception e ) {
6427 e.printStackTrace( System.out );
6433 private static boolean testNextNodeWithCollapsing() {
6435 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6437 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6438 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6439 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6440 t0.getNode( "cd" ).setCollapse( true );
6441 t0.getNode( "cde" ).setCollapse( true );
6442 n = t0.getFirstExternalNode();
6443 while ( n != null ) {
6445 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6447 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6450 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6453 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6456 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6459 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6462 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6466 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6467 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6468 t1.getNode( "ab" ).setCollapse( true );
6469 t1.getNode( "cd" ).setCollapse( true );
6470 t1.getNode( "cde" ).setCollapse( true );
6471 n = t1.getNode( "ab" );
6472 ext = new ArrayList<PhylogenyNode>();
6473 while ( n != null ) {
6475 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6477 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6480 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6483 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6486 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6489 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6493 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6494 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6495 t2.getNode( "ab" ).setCollapse( true );
6496 t2.getNode( "cd" ).setCollapse( true );
6497 t2.getNode( "cde" ).setCollapse( true );
6498 t2.getNode( "c" ).setCollapse( true );
6499 t2.getNode( "d" ).setCollapse( true );
6500 t2.getNode( "e" ).setCollapse( true );
6501 t2.getNode( "gh" ).setCollapse( true );
6502 n = t2.getNode( "ab" );
6503 ext = new ArrayList<PhylogenyNode>();
6504 while ( n != null ) {
6506 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6508 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6511 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6514 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6517 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6521 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6522 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6523 t3.getNode( "ab" ).setCollapse( true );
6524 t3.getNode( "cd" ).setCollapse( true );
6525 t3.getNode( "cde" ).setCollapse( true );
6526 t3.getNode( "c" ).setCollapse( true );
6527 t3.getNode( "d" ).setCollapse( true );
6528 t3.getNode( "e" ).setCollapse( true );
6529 t3.getNode( "gh" ).setCollapse( true );
6530 t3.getNode( "fgh" ).setCollapse( true );
6531 n = t3.getNode( "ab" );
6532 ext = new ArrayList<PhylogenyNode>();
6533 while ( n != null ) {
6535 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6537 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6540 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6543 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6547 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6548 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6549 t4.getNode( "ab" ).setCollapse( true );
6550 t4.getNode( "cd" ).setCollapse( true );
6551 t4.getNode( "cde" ).setCollapse( true );
6552 t4.getNode( "c" ).setCollapse( true );
6553 t4.getNode( "d" ).setCollapse( true );
6554 t4.getNode( "e" ).setCollapse( true );
6555 t4.getNode( "gh" ).setCollapse( true );
6556 t4.getNode( "fgh" ).setCollapse( true );
6557 t4.getNode( "abcdefgh" ).setCollapse( true );
6558 n = t4.getNode( "abcdefgh" );
6559 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6562 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6563 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6565 n = t5.getFirstExternalNode();
6566 while ( n != null ) {
6568 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6570 if ( ext.size() != 8 ) {
6573 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6576 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6579 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6582 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6585 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6588 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6591 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6594 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6597 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6598 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6600 t6.getNode( "ab" ).setCollapse( true );
6601 n = t6.getNode( "ab" );
6602 while ( n != null ) {
6604 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6606 if ( ext.size() != 7 ) {
6609 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6612 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6615 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6618 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6621 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6624 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6627 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6630 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6631 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6633 t7.getNode( "cd" ).setCollapse( true );
6634 n = t7.getNode( "a" );
6635 while ( n != null ) {
6637 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6639 if ( ext.size() != 7 ) {
6642 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6645 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6648 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6651 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6654 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6657 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6660 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6663 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6664 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6666 t8.getNode( "cd" ).setCollapse( true );
6667 t8.getNode( "c" ).setCollapse( true );
6668 t8.getNode( "d" ).setCollapse( true );
6669 n = t8.getNode( "a" );
6670 while ( n != null ) {
6672 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6674 if ( ext.size() != 7 ) {
6677 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6680 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6683 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6684 System.out.println( "2 fail" );
6687 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6690 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6693 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6696 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6699 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6700 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6702 t9.getNode( "gh" ).setCollapse( true );
6703 n = t9.getNode( "a" );
6704 while ( n != null ) {
6706 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6708 if ( ext.size() != 7 ) {
6711 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6714 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6717 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6720 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6723 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6726 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6729 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6732 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6733 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6735 t10.getNode( "gh" ).setCollapse( true );
6736 t10.getNode( "g" ).setCollapse( true );
6737 t10.getNode( "h" ).setCollapse( true );
6738 n = t10.getNode( "a" );
6739 while ( n != null ) {
6741 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6743 if ( ext.size() != 7 ) {
6746 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6749 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6752 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6755 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6758 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6761 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6764 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6767 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6768 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6770 t11.getNode( "gh" ).setCollapse( true );
6771 t11.getNode( "fgh" ).setCollapse( true );
6772 n = t11.getNode( "a" );
6773 while ( n != null ) {
6775 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6777 if ( ext.size() != 6 ) {
6780 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6783 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6786 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6789 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6792 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6795 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6798 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6799 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6801 t12.getNode( "gh" ).setCollapse( true );
6802 t12.getNode( "fgh" ).setCollapse( true );
6803 t12.getNode( "g" ).setCollapse( true );
6804 t12.getNode( "h" ).setCollapse( true );
6805 t12.getNode( "f" ).setCollapse( true );
6806 n = t12.getNode( "a" );
6807 while ( n != null ) {
6809 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6811 if ( ext.size() != 6 ) {
6814 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6817 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6820 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6823 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6826 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6829 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6832 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6833 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6835 t13.getNode( "ab" ).setCollapse( true );
6836 t13.getNode( "b" ).setCollapse( true );
6837 t13.getNode( "fgh" ).setCollapse( true );
6838 t13.getNode( "gh" ).setCollapse( true );
6839 n = t13.getNode( "ab" );
6840 while ( n != null ) {
6842 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6844 if ( ext.size() != 5 ) {
6847 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6850 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6853 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6856 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6859 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6862 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6863 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6865 t14.getNode( "ab" ).setCollapse( true );
6866 t14.getNode( "a" ).setCollapse( true );
6867 t14.getNode( "fgh" ).setCollapse( true );
6868 t14.getNode( "gh" ).setCollapse( true );
6869 n = t14.getNode( "ab" );
6870 while ( n != null ) {
6872 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6874 if ( ext.size() != 5 ) {
6877 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6880 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6883 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6886 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6889 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6892 final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6893 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6895 t15.getNode( "ab" ).setCollapse( true );
6896 t15.getNode( "a" ).setCollapse( true );
6897 t15.getNode( "fgh" ).setCollapse( true );
6898 t15.getNode( "gh" ).setCollapse( true );
6899 n = t15.getNode( "ab" );
6900 while ( n != null ) {
6902 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6904 if ( ext.size() != 6 ) {
6907 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6910 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6913 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6916 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6919 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6922 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6927 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" );
6928 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6930 t16.getNode( "ab" ).setCollapse( true );
6931 t16.getNode( "a" ).setCollapse( true );
6932 t16.getNode( "fgh" ).setCollapse( true );
6933 t16.getNode( "gh" ).setCollapse( true );
6934 t16.getNode( "cd" ).setCollapse( true );
6935 t16.getNode( "cde" ).setCollapse( true );
6936 t16.getNode( "d" ).setCollapse( true );
6937 t16.getNode( "x" ).setCollapse( true );
6938 n = t16.getNode( "ab" );
6939 while ( n != null ) {
6941 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6943 if ( ext.size() != 4 ) {
6946 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6949 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6952 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6955 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6959 catch ( final Exception e ) {
6960 e.printStackTrace( System.out );
6966 private static boolean testNexusCharactersParsing() {
6968 final NexusCharactersParser parser = new NexusCharactersParser();
6969 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6971 String[] labels = parser.getCharStateLabels();
6972 if ( labels.length != 7 ) {
6975 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6978 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6981 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6984 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6987 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6990 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6993 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6996 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6998 labels = parser.getCharStateLabels();
6999 if ( labels.length != 7 ) {
7002 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7005 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7008 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7011 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7014 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7017 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7020 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7024 catch ( final Exception e ) {
7025 e.printStackTrace( System.out );
7031 private static boolean testNexusMatrixParsing() {
7033 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
7034 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
7036 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
7037 if ( m.getNumberOfCharacters() != 9 ) {
7040 if ( m.getNumberOfIdentifiers() != 5 ) {
7043 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
7046 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
7049 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
7052 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
7055 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
7058 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
7061 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
7064 // if ( labels.length != 7 ) {
7067 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7070 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7073 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7076 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7079 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7082 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7085 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7088 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7090 // labels = parser.getCharStateLabels();
7091 // if ( labels.length != 7 ) {
7094 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7097 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7100 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7103 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7106 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7109 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7112 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7116 catch ( final Exception e ) {
7117 e.printStackTrace( System.out );
7123 private static boolean testNexusTreeParsing() {
7125 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7126 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7127 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
7128 if ( phylogenies.length != 1 ) {
7131 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
7134 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7138 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
7139 if ( phylogenies.length != 1 ) {
7142 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7145 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
7149 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
7150 if ( phylogenies.length != 1 ) {
7153 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7156 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7159 if ( phylogenies[ 0 ].isRooted() ) {
7163 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
7164 if ( phylogenies.length != 18 ) {
7167 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7170 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
7173 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
7176 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
7179 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7182 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
7185 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
7188 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
7191 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
7194 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
7197 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
7200 if ( phylogenies[ 8 ].isRooted() ) {
7203 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
7206 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
7209 if ( !phylogenies[ 9 ].isRooted() ) {
7212 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
7215 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
7218 if ( !phylogenies[ 10 ].isRooted() ) {
7221 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
7224 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
7227 if ( phylogenies[ 11 ].isRooted() ) {
7230 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
7233 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
7236 if ( !phylogenies[ 12 ].isRooted() ) {
7239 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
7242 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
7245 if ( !phylogenies[ 13 ].isRooted() ) {
7248 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
7251 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
7254 if ( !phylogenies[ 14 ].isRooted() ) {
7257 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
7260 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
7263 if ( phylogenies[ 15 ].isRooted() ) {
7266 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
7269 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
7272 if ( !phylogenies[ 16 ].isRooted() ) {
7275 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
7278 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
7281 if ( phylogenies[ 17 ].isRooted() ) {
7284 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
7287 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7289 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
7290 if ( phylogenies.length != 9 ) {
7293 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
7294 .getDistanceToParent() ) ) {
7297 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
7298 .getDistanceToParent() ) ) {
7301 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
7304 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7307 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7310 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7313 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7317 catch ( final Exception e ) {
7318 e.printStackTrace( System.out );
7324 private static boolean testNexusTreeParsingIterating() {
7326 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7327 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7328 if ( !p.hasNext() ) {
7331 Phylogeny phy = p.next();
7332 if ( phy == null ) {
7335 if ( phy.getNumberOfExternalNodes() != 25 ) {
7338 if ( !phy.getName().equals( "" ) ) {
7341 if ( p.hasNext() ) {
7345 if ( phy != null ) {
7349 if ( !p.hasNext() ) {
7353 if ( phy == null ) {
7356 if ( phy.getNumberOfExternalNodes() != 25 ) {
7359 if ( !phy.getName().equals( "" ) ) {
7362 if ( p.hasNext() ) {
7366 if ( phy != null ) {
7369 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7370 if ( !p.hasNext() ) {
7374 if ( phy == null ) {
7377 if ( phy.getNumberOfExternalNodes() != 10 ) {
7380 if ( !phy.getName().equals( "name" ) ) {
7383 if ( p.hasNext() ) {
7387 if ( phy != null ) {
7391 if ( !p.hasNext() ) {
7395 if ( phy == null ) {
7398 if ( phy.getNumberOfExternalNodes() != 10 ) {
7401 if ( !phy.getName().equals( "name" ) ) {
7404 if ( p.hasNext() ) {
7408 if ( phy != null ) {
7411 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7412 if ( !p.hasNext() ) {
7416 if ( phy == null ) {
7419 if ( phy.getNumberOfExternalNodes() != 3 ) {
7422 if ( !phy.getName().equals( "" ) ) {
7425 if ( phy.isRooted() ) {
7428 if ( p.hasNext() ) {
7432 if ( phy != null ) {
7437 if ( !p.hasNext() ) {
7441 if ( phy == null ) {
7444 if ( phy.getNumberOfExternalNodes() != 3 ) {
7447 if ( !phy.getName().equals( "" ) ) {
7450 if ( p.hasNext() ) {
7454 if ( phy != null ) {
7458 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7459 if ( !p.hasNext() ) {
7464 if ( phy == null ) {
7467 if ( phy.getNumberOfExternalNodes() != 10 ) {
7470 if ( !phy.getName().equals( "tree 0" ) ) {
7474 if ( !p.hasNext() ) {
7478 if ( phy == null ) {
7481 if ( phy.getNumberOfExternalNodes() != 10 ) {
7484 if ( !phy.getName().equals( "tree 1" ) ) {
7488 if ( !p.hasNext() ) {
7492 if ( phy == null ) {
7495 if ( phy.getNumberOfExternalNodes() != 3 ) {
7496 System.out.println( phy.toString() );
7499 if ( !phy.getName().equals( "" ) ) {
7502 if ( phy.isRooted() ) {
7506 if ( !p.hasNext() ) {
7510 if ( phy == null ) {
7513 if ( phy.getNumberOfExternalNodes() != 4 ) {
7516 if ( !phy.getName().equals( "" ) ) {
7519 if ( !phy.isRooted() ) {
7523 if ( !p.hasNext() ) {
7527 if ( phy == null ) {
7530 if ( phy.getNumberOfExternalNodes() != 5 ) {
7531 System.out.println( phy.getNumberOfExternalNodes() );
7534 if ( !phy.getName().equals( "" ) ) {
7537 if ( !phy.isRooted() ) {
7541 if ( !p.hasNext() ) {
7545 if ( phy == null ) {
7548 if ( phy.getNumberOfExternalNodes() != 3 ) {
7551 if ( !phy.getName().equals( "" ) ) {
7554 if ( phy.isRooted() ) {
7558 if ( !p.hasNext() ) {
7562 if ( phy == null ) {
7565 if ( phy.getNumberOfExternalNodes() != 2 ) {
7568 if ( !phy.getName().equals( "" ) ) {
7571 if ( !phy.isRooted() ) {
7575 if ( !p.hasNext() ) {
7579 if ( phy.getNumberOfExternalNodes() != 3 ) {
7582 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7585 if ( !phy.isRooted() ) {
7589 if ( !p.hasNext() ) {
7593 if ( phy.getNumberOfExternalNodes() != 3 ) {
7596 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7599 if ( !phy.getName().equals( "tree 8" ) ) {
7603 if ( !p.hasNext() ) {
7607 if ( phy.getNumberOfExternalNodes() != 3 ) {
7610 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7613 if ( !phy.getName().equals( "tree 9" ) ) {
7617 if ( !p.hasNext() ) {
7621 if ( phy.getNumberOfExternalNodes() != 3 ) {
7624 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7627 if ( !phy.getName().equals( "tree 10" ) ) {
7630 if ( !phy.isRooted() ) {
7634 if ( !p.hasNext() ) {
7638 if ( phy.getNumberOfExternalNodes() != 3 ) {
7641 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7644 if ( !phy.getName().equals( "tree 11" ) ) {
7647 if ( phy.isRooted() ) {
7651 if ( !p.hasNext() ) {
7655 if ( phy.getNumberOfExternalNodes() != 3 ) {
7658 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7661 if ( !phy.getName().equals( "tree 12" ) ) {
7664 if ( !phy.isRooted() ) {
7668 if ( !p.hasNext() ) {
7672 if ( phy.getNumberOfExternalNodes() != 3 ) {
7675 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7678 if ( !phy.getName().equals( "tree 13" ) ) {
7681 if ( !phy.isRooted() ) {
7685 if ( !p.hasNext() ) {
7689 if ( phy.getNumberOfExternalNodes() != 10 ) {
7690 System.out.println( phy.getNumberOfExternalNodes() );
7695 .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;" ) ) {
7696 System.out.println( phy.toNewHampshire() );
7699 if ( !phy.getName().equals( "tree 14" ) ) {
7702 if ( !phy.isRooted() ) {
7706 if ( !p.hasNext() ) {
7710 if ( phy.getNumberOfExternalNodes() != 10 ) {
7711 System.out.println( phy.getNumberOfExternalNodes() );
7716 .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;" ) ) {
7717 System.out.println( phy.toNewHampshire() );
7720 if ( !phy.getName().equals( "tree 15" ) ) {
7723 if ( phy.isRooted() ) {
7727 if ( !p.hasNext() ) {
7731 if ( phy.getNumberOfExternalNodes() != 10 ) {
7732 System.out.println( phy.getNumberOfExternalNodes() );
7737 .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;" ) ) {
7738 System.out.println( phy.toNewHampshire() );
7741 if ( !phy.getName().equals( "tree 16" ) ) {
7744 if ( !phy.isRooted() ) {
7748 if ( !p.hasNext() ) {
7752 if ( phy.getNumberOfExternalNodes() != 10 ) {
7753 System.out.println( phy.getNumberOfExternalNodes() );
7758 .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;" ) ) {
7759 System.out.println( phy.toNewHampshire() );
7762 if ( !phy.getName().equals( "tree 17" ) ) {
7765 if ( phy.isRooted() ) {
7769 if ( p.hasNext() ) {
7773 if ( phy != null ) {
7778 if ( !p.hasNext() ) {
7782 if ( phy == null ) {
7785 if ( phy.getNumberOfExternalNodes() != 10 ) {
7788 if ( !phy.getName().equals( "tree 0" ) ) {
7792 if ( !p.hasNext() ) {
7796 if ( phy == null ) {
7799 if ( phy.getNumberOfExternalNodes() != 10 ) {
7802 if ( !phy.getName().equals( "tree 1" ) ) {
7806 if ( !p.hasNext() ) {
7810 if ( phy == null ) {
7813 if ( phy.getNumberOfExternalNodes() != 3 ) {
7816 if ( !phy.getName().equals( "" ) ) {
7819 if ( phy.isRooted() ) {
7823 if ( !p.hasNext() ) {
7827 if ( phy == null ) {
7830 if ( phy.getNumberOfExternalNodes() != 4 ) {
7833 if ( !phy.getName().equals( "" ) ) {
7836 if ( !phy.isRooted() ) {
7840 if ( !p.hasNext() ) {
7844 if ( phy == null ) {
7847 if ( phy.getNumberOfExternalNodes() != 5 ) {
7848 System.out.println( phy.getNumberOfExternalNodes() );
7851 if ( !phy.getName().equals( "" ) ) {
7854 if ( !phy.isRooted() ) {
7858 if ( !p.hasNext() ) {
7862 if ( phy == null ) {
7865 if ( phy.getNumberOfExternalNodes() != 3 ) {
7868 if ( !phy.getName().equals( "" ) ) {
7871 if ( phy.isRooted() ) {
7875 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7876 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7878 if ( !p2.hasNext() ) {
7882 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7885 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7889 if ( !p2.hasNext() ) {
7894 if ( !p2.hasNext() ) {
7899 if ( !p2.hasNext() ) {
7904 if ( !p2.hasNext() ) {
7909 if ( !p2.hasNext() ) {
7914 if ( !p2.hasNext() ) {
7919 if ( !p2.hasNext() ) {
7924 if ( !p2.hasNext() ) {
7928 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7931 if ( p2.hasNext() ) {
7935 if ( phy != null ) {
7940 if ( !p2.hasNext() ) {
7944 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7947 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7951 catch ( final Exception e ) {
7952 e.printStackTrace( System.out );
7958 private static boolean testNexusTreeParsingTranslating() {
7960 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7961 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7962 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7963 if ( phylogenies.length != 1 ) {
7966 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7969 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7972 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7975 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7978 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7979 .equals( "Aranaeus" ) ) {
7983 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7984 if ( phylogenies.length != 3 ) {
7987 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7990 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7993 if ( phylogenies[ 0 ].isRooted() ) {
7996 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7999 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8002 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8003 .equals( "Aranaeus" ) ) {
8006 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8009 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8012 if ( phylogenies[ 1 ].isRooted() ) {
8015 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8018 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8021 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8022 .equals( "Aranaeus" ) ) {
8025 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8028 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8031 if ( !phylogenies[ 2 ].isRooted() ) {
8034 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8037 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8040 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8041 .equals( "Aranaeus" ) ) {
8045 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
8046 if ( phylogenies.length != 3 ) {
8049 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8052 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8055 if ( phylogenies[ 0 ].isRooted() ) {
8058 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8061 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8064 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8065 .equals( "Aranaeus" ) ) {
8068 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8071 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8074 if ( phylogenies[ 1 ].isRooted() ) {
8077 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8080 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8083 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8084 .equals( "Aranaeus" ) ) {
8087 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8090 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8093 if ( !phylogenies[ 2 ].isRooted() ) {
8096 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8099 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8102 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8103 .equals( "Aranaeus" ) ) {
8106 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
8107 if ( phylogenies.length != 3 ) {
8110 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
8115 catch ( final Exception e ) {
8116 e.printStackTrace( System.out );
8122 private static boolean testNHParsing() {
8124 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8125 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
8126 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
8129 final NHXParser nhxp = new NHXParser();
8130 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
8131 nhxp.setReplaceUnderscores( true );
8132 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
8133 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
8136 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
8139 final Phylogeny p1b = factory
8140 .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 ",
8141 new NHXParser() )[ 0 ];
8142 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
8145 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
8148 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
8149 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
8150 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
8151 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
8152 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
8153 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
8154 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
8155 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
8156 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
8157 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
8158 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
8159 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
8160 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
8162 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
8165 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
8168 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
8171 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
8174 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
8175 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
8176 final String p16_S = "((A,B),C)";
8177 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
8178 if ( p16.length != 1 ) {
8181 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
8184 final String p17_S = "(C,(A,B))";
8185 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
8186 if ( p17.length != 1 ) {
8189 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
8192 final String p18_S = "((A,B),(C,D))";
8193 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
8194 if ( p18.length != 1 ) {
8197 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
8200 final String p19_S = "(((A,B),C),D)";
8201 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
8202 if ( p19.length != 1 ) {
8205 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
8208 final String p20_S = "(A,(B,(C,D)))";
8209 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
8210 if ( p20.length != 1 ) {
8213 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
8216 final String p21_S = "(A,(B,(C,(D,E))))";
8217 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
8218 if ( p21.length != 1 ) {
8221 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
8224 final String p22_S = "((((A,B),C),D),E)";
8225 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
8226 if ( p22.length != 1 ) {
8229 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
8232 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8233 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
8234 if ( p23.length != 1 ) {
8235 System.out.println( "xl=" + p23.length );
8239 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
8242 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8243 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
8244 if ( p24.length != 1 ) {
8247 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
8250 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8251 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8252 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
8253 if ( p241.length != 2 ) {
8256 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
8259 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
8262 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
8263 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
8264 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
8265 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
8266 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
8267 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
8268 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
8269 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
8270 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
8271 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
8274 final String p26_S = "(A,B)ab";
8275 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
8276 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
8279 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8280 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
8281 if ( p27s.length != 1 ) {
8282 System.out.println( "xxl=" + p27s.length );
8286 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8287 System.out.println( p27s[ 0 ].toNewHampshireX() );
8291 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
8293 if ( p27.length != 1 ) {
8294 System.out.println( "yl=" + p27.length );
8298 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8299 System.out.println( p27[ 0 ].toNewHampshireX() );
8303 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8304 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8305 final String p28_S3 = "(A,B)ab";
8306 final String p28_S4 = "((((A,B),C),D),;E;)";
8307 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
8309 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
8312 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
8315 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
8318 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
8321 if ( p28.length != 4 ) {
8324 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";
8325 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8326 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8329 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";
8330 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8331 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8334 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8335 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8336 if ( ( p32.length != 0 ) ) {
8339 final String p33_S = "A";
8340 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8341 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8344 final String p34_S = "B;";
8345 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8346 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8349 final String p35_S = "B:0.2";
8350 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8351 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8354 final String p36_S = "(A)";
8355 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8356 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8359 final String p37_S = "((A))";
8360 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8361 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8364 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8365 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8366 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8369 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8370 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8371 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8374 final String p40_S = "(A,B,C)";
8375 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8376 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8379 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8380 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8381 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8384 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8385 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8386 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8389 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)";
8390 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8391 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8394 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)))";
8395 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8396 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8399 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8400 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8401 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8404 final String p46_S = "";
8405 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8406 if ( p46.length != 0 ) {
8409 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8410 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8413 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8414 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8417 final Phylogeny p49 = factory
8418 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8419 new NHXParser() )[ 0 ];
8420 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8423 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8424 if ( p50.getNode( "A" ) == null ) {
8427 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8428 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8431 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8434 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8435 .equals( "((A,B)88:2.0,C);" ) ) {
8438 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8439 if ( p51.getNode( "A(A" ) == null ) {
8442 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8443 if ( p52.getNode( "A(A" ) == null ) {
8446 final Phylogeny p53 = factory
8447 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8448 new NHXParser() )[ 0 ];
8449 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8452 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8453 if ( p54.getNode( "A" ) == null ) {
8456 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8459 final Phylogeny p55 = factory
8460 .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);" ),
8461 new NHXParser() )[ 0 ];
8464 .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);" ) ) {
8465 System.out.println( p55.toNewHampshire() );
8468 final Phylogeny p56 = factory
8469 .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);" ),
8470 new NHXParser() )[ 0 ];
8473 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8474 System.out.println( p56.toNewHampshire() );
8477 final Phylogeny p57 = factory
8478 .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
8479 new NHXParser() )[ 0 ];
8482 .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
8483 System.out.println( p56.toNewHampshire() );
8486 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8487 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8488 if ( !p58.toNewHampshire().equals( s58 ) ) {
8489 System.out.println( p58.toNewHampshire() );
8492 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8493 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8494 if ( !p59.toNewHampshire().equals( s59 ) ) {
8495 System.out.println( p59.toNewHampshire() );
8498 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8499 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8500 if ( !p60.toNewHampshire().equals( s60 ) ) {
8501 System.out.println( p60.toNewHampshire() );
8504 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8505 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8506 if ( !p61.toNewHampshire()
8507 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8508 System.out.println( p61.toNewHampshire() );
8512 catch ( final Exception e ) {
8513 e.printStackTrace( System.out );
8519 private static boolean testNHParsingIter() {
8521 final String p0_str = "(A,B);";
8522 final NHXParser p = new NHXParser();
8523 p.setSource( p0_str );
8524 if ( !p.hasNext() ) {
8527 final Phylogeny p0 = p.next();
8528 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8529 System.out.println( p0.toNewHampshire() );
8532 if ( p.hasNext() ) {
8535 if ( p.next() != null ) {
8539 final String p00_str = "(A,B)root;";
8540 p.setSource( p00_str );
8541 final Phylogeny p00 = p.next();
8542 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8543 System.out.println( p00.toNewHampshire() );
8547 final String p000_str = "A;";
8548 p.setSource( p000_str );
8549 final Phylogeny p000 = p.next();
8550 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8551 System.out.println( p000.toNewHampshire() );
8555 final String p0000_str = "A";
8556 p.setSource( p0000_str );
8557 final Phylogeny p0000 = p.next();
8558 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8559 System.out.println( p0000.toNewHampshire() );
8563 p.setSource( "(A)" );
8564 final Phylogeny p00000 = p.next();
8565 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8566 System.out.println( p00000.toNewHampshire() );
8570 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8571 p.setSource( p1_str );
8572 if ( !p.hasNext() ) {
8575 final Phylogeny p1_0 = p.next();
8576 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8577 System.out.println( p1_0.toNewHampshire() );
8580 if ( !p.hasNext() ) {
8583 final Phylogeny p1_1 = p.next();
8584 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8585 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8588 if ( !p.hasNext() ) {
8591 final Phylogeny p1_2 = p.next();
8592 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8593 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8596 if ( !p.hasNext() ) {
8599 final Phylogeny p1_3 = p.next();
8600 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8601 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8604 if ( p.hasNext() ) {
8607 if ( p.next() != null ) {
8611 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8612 p.setSource( p2_str );
8613 if ( !p.hasNext() ) {
8616 Phylogeny p2_0 = p.next();
8617 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8618 System.out.println( p2_0.toNewHampshire() );
8621 if ( !p.hasNext() ) {
8624 Phylogeny p2_1 = p.next();
8625 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8626 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8629 if ( !p.hasNext() ) {
8632 Phylogeny p2_2 = p.next();
8633 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8634 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8637 if ( !p.hasNext() ) {
8640 Phylogeny p2_3 = p.next();
8641 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8642 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8645 if ( !p.hasNext() ) {
8648 Phylogeny p2_4 = p.next();
8649 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8650 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8653 if ( p.hasNext() ) {
8656 if ( p.next() != null ) {
8661 if ( !p.hasNext() ) {
8665 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8666 System.out.println( p2_0.toNewHampshire() );
8669 if ( !p.hasNext() ) {
8673 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8674 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8677 if ( !p.hasNext() ) {
8681 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8682 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8685 if ( !p.hasNext() ) {
8689 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8690 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8693 if ( !p.hasNext() ) {
8697 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8698 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8701 if ( p.hasNext() ) {
8704 if ( p.next() != null ) {
8708 final String p3_str = "((A,B),C)abc";
8709 p.setSource( p3_str );
8710 if ( !p.hasNext() ) {
8713 final Phylogeny p3_0 = p.next();
8714 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8717 if ( p.hasNext() ) {
8720 if ( p.next() != null ) {
8724 final String p4_str = "((A,B)ab,C)abc";
8725 p.setSource( p4_str );
8726 if ( !p.hasNext() ) {
8729 final Phylogeny p4_0 = p.next();
8730 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8733 if ( p.hasNext() ) {
8736 if ( p.next() != null ) {
8740 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8741 p.setSource( p5_str );
8742 if ( !p.hasNext() ) {
8745 final Phylogeny p5_0 = p.next();
8746 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8749 if ( p.hasNext() ) {
8752 if ( p.next() != null ) {
8756 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8757 p.setSource( p6_str );
8758 if ( !p.hasNext() ) {
8761 Phylogeny p6_0 = p.next();
8762 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8765 if ( p.hasNext() ) {
8768 if ( p.next() != null ) {
8772 if ( !p.hasNext() ) {
8776 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8779 if ( p.hasNext() ) {
8782 if ( p.next() != null ) {
8786 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8787 p.setSource( p7_str );
8788 if ( !p.hasNext() ) {
8791 Phylogeny p7_0 = p.next();
8792 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8795 if ( p.hasNext() ) {
8798 if ( p.next() != null ) {
8802 if ( !p.hasNext() ) {
8806 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8809 if ( p.hasNext() ) {
8812 if ( p.next() != null ) {
8816 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8817 p.setSource( p8_str );
8818 if ( !p.hasNext() ) {
8821 Phylogeny p8_0 = p.next();
8822 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8825 if ( !p.hasNext() ) {
8828 if ( !p.hasNext() ) {
8831 Phylogeny p8_1 = p.next();
8832 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8835 if ( p.hasNext() ) {
8838 if ( p.next() != null ) {
8842 if ( !p.hasNext() ) {
8846 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8849 if ( !p.hasNext() ) {
8853 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8856 if ( p.hasNext() ) {
8859 if ( p.next() != null ) {
8865 if ( p.hasNext() ) {
8869 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8870 if ( !p.hasNext() ) {
8873 Phylogeny p_27 = p.next();
8874 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8875 System.out.println( p_27.toNewHampshireX() );
8879 if ( p.hasNext() ) {
8882 if ( p.next() != null ) {
8886 if ( !p.hasNext() ) {
8890 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8891 System.out.println( p_27.toNewHampshireX() );
8895 if ( p.hasNext() ) {
8898 if ( p.next() != null ) {
8902 final String p30_str = "(A,B);(C,D)";
8903 final NHXParser p30 = new NHXParser();
8904 p30.setSource( p30_str );
8905 if ( !p30.hasNext() ) {
8908 Phylogeny phy30 = p30.next();
8909 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8910 System.out.println( phy30.toNewHampshire() );
8913 if ( !p30.hasNext() ) {
8916 Phylogeny phy301 = p30.next();
8917 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8918 System.out.println( phy301.toNewHampshire() );
8921 if ( p30.hasNext() ) {
8924 if ( p30.hasNext() ) {
8927 if ( p30.next() != null ) {
8930 if ( p30.next() != null ) {
8934 if ( !p30.hasNext() ) {
8938 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8939 System.out.println( phy30.toNewHampshire() );
8942 if ( !p30.hasNext() ) {
8945 phy301 = p30.next();
8946 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8947 System.out.println( phy301.toNewHampshire() );
8950 if ( p30.hasNext() ) {
8953 if ( p30.hasNext() ) {
8956 if ( p30.next() != null ) {
8959 if ( p30.next() != null ) {
8963 catch ( final Exception e ) {
8964 e.printStackTrace( System.out );
8970 private static boolean testNHXconversion() {
8972 final PhylogenyNode n1 = new PhylogenyNode();
8973 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8974 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8975 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8976 final PhylogenyNode n5 = PhylogenyNode
8977 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8978 final PhylogenyNode n6 = PhylogenyNode
8979 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8980 if ( !n1.toNewHampshireX().equals( "" ) ) {
8983 if ( !n2.toNewHampshireX().equals( "" ) ) {
8986 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8989 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
8992 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
8995 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
8996 System.out.println( n6.toNewHampshireX() );
8999 final PhylogenyNode n7 = new PhylogenyNode();
9000 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
9001 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
9002 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
9003 System.out.println( n7
9004 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
9008 catch ( final Exception e ) {
9009 e.printStackTrace( System.out );
9015 private static boolean testNHXNodeParsing() {
9017 final PhylogenyNode n1 = new PhylogenyNode();
9018 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9019 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9020 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9021 final PhylogenyNode n5 = PhylogenyNode
9022 .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]" );
9023 if ( !n3.getName().equals( "n3" ) ) {
9026 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9029 if ( n3.isDuplication() ) {
9032 if ( n3.isHasAssignedEvent() ) {
9035 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
9038 if ( !n4.getName().equals( "n4" ) ) {
9041 if ( n4.getDistanceToParent() != 0.01 ) {
9044 if ( !n5.getName().equals( "n5" ) ) {
9047 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
9050 if ( n5.getDistanceToParent() != 0.1 ) {
9053 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
9056 if ( !n5.isDuplication() ) {
9059 if ( !n5.isHasAssignedEvent() ) {
9062 final PhylogenyNode n8 = PhylogenyNode
9063 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
9064 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9065 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9068 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
9071 final PhylogenyNode n9 = PhylogenyNode
9072 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
9073 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9074 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
9077 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
9080 final PhylogenyNode n10 = PhylogenyNode
9081 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9082 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
9085 final PhylogenyNode n20 = PhylogenyNode
9086 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9087 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9090 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
9093 final PhylogenyNode n20x = PhylogenyNode
9094 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9095 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
9098 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
9101 final PhylogenyNode n20xx = PhylogenyNode
9102 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9103 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
9106 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
9109 final PhylogenyNode n20xxx = PhylogenyNode
9110 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9111 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
9114 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
9117 final PhylogenyNode n20xxxx = PhylogenyNode
9118 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9119 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
9122 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
9125 final PhylogenyNode n21 = PhylogenyNode
9126 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9127 if ( !n21.getName().equals( "N21_PIG" ) ) {
9130 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
9133 final PhylogenyNode n21x = PhylogenyNode
9134 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9135 if ( !n21x.getName().equals( "n21_PIG" ) ) {
9138 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
9141 final PhylogenyNode n22 = PhylogenyNode
9142 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9143 if ( !n22.getName().equals( "n22/PIG" ) ) {
9146 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
9149 final PhylogenyNode n23 = PhylogenyNode
9150 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9151 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
9154 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
9157 final PhylogenyNode a = PhylogenyNode
9158 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9159 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9162 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
9165 final PhylogenyNode c1 = PhylogenyNode
9166 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
9167 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9168 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
9171 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
9174 final PhylogenyNode c2 = PhylogenyNode
9175 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
9176 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9177 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
9180 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
9183 final PhylogenyNode e3 = PhylogenyNode
9184 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9185 if ( !e3.getName().equals( "n10_RAT~" ) ) {
9188 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
9191 final PhylogenyNode n11 = PhylogenyNode
9192 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
9193 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9194 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
9197 if ( n11.getDistanceToParent() != 0.4 ) {
9200 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
9203 final PhylogenyNode n12 = PhylogenyNode
9204 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
9205 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9206 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
9209 if ( n12.getDistanceToParent() != 0.4 ) {
9212 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
9215 final PhylogenyNode o = PhylogenyNode
9216 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9217 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
9220 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
9223 if ( n1.getName().compareTo( "" ) != 0 ) {
9226 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9229 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9232 if ( n2.getName().compareTo( "" ) != 0 ) {
9235 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9238 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9241 final PhylogenyNode n00 = PhylogenyNode
9242 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
9243 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
9246 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
9249 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
9250 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
9253 final PhylogenyNode n13 = PhylogenyNode
9254 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9255 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
9258 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
9261 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9264 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9267 final PhylogenyNode n14 = PhylogenyNode
9268 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9269 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
9272 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
9275 final PhylogenyNode n15 = PhylogenyNode
9276 .createInstanceFromNhxString( "something_wicked[123]",
9277 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9278 if ( !n15.getName().equals( "something_wicked" ) ) {
9281 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
9284 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
9287 final PhylogenyNode n16 = PhylogenyNode
9288 .createInstanceFromNhxString( "something_wicked2[9]",
9289 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9290 if ( !n16.getName().equals( "something_wicked2" ) ) {
9293 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
9296 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
9299 final PhylogenyNode n17 = PhylogenyNode
9300 .createInstanceFromNhxString( "something_wicked3[a]",
9301 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9302 if ( !n17.getName().equals( "something_wicked3" ) ) {
9305 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
9308 final PhylogenyNode n18 = PhylogenyNode
9309 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9310 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
9313 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
9316 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
9319 final PhylogenyNode n19 = PhylogenyNode
9320 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9321 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9324 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9327 final PhylogenyNode n30 = PhylogenyNode
9328 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9329 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9330 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9333 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9336 final PhylogenyNode n31 = PhylogenyNode
9337 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9338 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9339 if ( n31.getNodeData().isHasTaxonomy() ) {
9342 final PhylogenyNode n32 = PhylogenyNode
9343 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9344 if ( n32.getNodeData().isHasTaxonomy() ) {
9347 final PhylogenyNode n40 = PhylogenyNode
9348 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9349 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9352 final PhylogenyNode n41 = PhylogenyNode
9353 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9354 if ( n41.getNodeData().isHasTaxonomy() ) {
9357 final PhylogenyNode n42 = PhylogenyNode
9358 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9359 if ( n42.getNodeData().isHasTaxonomy() ) {
9362 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9363 NHXParser.TAXONOMY_EXTRACTION.NO );
9364 if ( n43.getNodeData().isHasTaxonomy() ) {
9367 final PhylogenyNode n44 = PhylogenyNode
9368 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9369 if ( n44.getNodeData().isHasTaxonomy() ) {
9373 catch ( final Exception e ) {
9374 e.printStackTrace( System.out );
9380 private static boolean testNHXParsing() {
9382 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9383 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9384 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9387 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]";
9388 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9389 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9392 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]";
9393 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9394 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9397 final Phylogeny[] p3 = factory
9398 .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]",
9400 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9403 final Phylogeny[] p4 = factory
9404 .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(]",
9406 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9409 final Phylogeny[] p5 = factory
9410 .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(((]",
9412 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9415 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)";
9416 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)";
9417 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9418 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9421 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)))";
9422 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)))";
9423 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9424 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9427 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]) ))[,,, ])))))))";
9428 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9429 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9430 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9433 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9434 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9437 final Phylogeny p10 = factory
9438 .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]",
9439 new NHXParser() )[ 0 ];
9440 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9443 final Phylogeny p11 = factory
9444 .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]",
9445 new NHXParser() )[ 0 ];
9446 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9450 catch ( final Exception e ) {
9451 e.printStackTrace( System.out );
9457 private static boolean testNHXParsingMB() {
9459 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9460 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9461 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9462 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9463 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9464 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9465 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9466 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9467 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9468 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9469 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9472 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9475 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9476 0.1100000000000000e+00 ) ) {
9479 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9482 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9485 final Phylogeny p2 = factory
9486 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9487 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9488 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9489 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9490 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9491 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9492 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9493 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9494 + "7.369400000000000e-02}])",
9495 new NHXParser() )[ 0 ];
9496 if ( p2.getNode( "1" ) == null ) {
9499 if ( p2.getNode( "2" ) == null ) {
9503 catch ( final Exception e ) {
9504 e.printStackTrace( System.out );
9511 private static boolean testNHXParsingQuotes() {
9513 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9514 final NHXParser p = new NHXParser();
9515 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9516 if ( phylogenies_0.length != 5 ) {
9519 final Phylogeny phy = phylogenies_0[ 4 ];
9520 if ( phy.getNumberOfExternalNodes() != 7 ) {
9523 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9526 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9529 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9530 .getScientificName().equals( "hsapiens" ) ) {
9533 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9536 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9539 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9542 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9545 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9548 final NHXParser p1p = new NHXParser();
9549 p1p.setIgnoreQuotes( true );
9550 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9551 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9554 final NHXParser p2p = new NHXParser();
9555 p1p.setIgnoreQuotes( false );
9556 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9557 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9560 final NHXParser p3p = new NHXParser();
9561 p3p.setIgnoreQuotes( false );
9562 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9563 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9566 final NHXParser p4p = new NHXParser();
9567 p4p.setIgnoreQuotes( false );
9568 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9569 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9572 final Phylogeny p10 = factory
9573 .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]",
9574 new NHXParser() )[ 0 ];
9575 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]";
9576 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9579 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9580 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9583 final Phylogeny p12 = factory
9584 .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]",
9585 new NHXParser() )[ 0 ];
9586 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]";
9587 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9590 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9591 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9594 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;";
9595 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9598 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9599 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9603 catch ( final Exception e ) {
9604 e.printStackTrace( System.out );
9610 private static boolean testNodeRemoval() {
9612 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9613 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9614 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9615 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9618 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9619 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9620 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9623 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9624 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9625 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9629 catch ( final Exception e ) {
9630 e.printStackTrace( System.out );
9636 private static boolean testPhylogenyBranch() {
9638 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9639 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9640 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9641 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9642 if ( !a1b1.equals( a1b1 ) ) {
9645 if ( !a1b1.equals( b1a1 ) ) {
9648 if ( !b1a1.equals( a1b1 ) ) {
9651 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9652 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9653 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9654 if ( a1_b1.equals( b1_a1 ) ) {
9657 if ( a1_b1.equals( a1_b1_ ) ) {
9660 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9661 if ( !a1_b1.equals( b1_a1_ ) ) {
9664 if ( a1_b1_.equals( b1_a1_ ) ) {
9667 if ( !a1_b1_.equals( b1_a1 ) ) {
9671 catch ( final Exception e ) {
9672 e.printStackTrace( System.out );
9678 private static boolean testPhyloXMLparsingOfDistributionElement() {
9680 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9681 PhyloXmlParser xml_parser = null;
9683 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9685 catch ( final Exception e ) {
9686 // Do nothing -- means were not running from jar.
9688 if ( xml_parser == null ) {
9689 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9690 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9691 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9694 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9697 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9699 if ( xml_parser.getErrorCount() > 0 ) {
9700 System.out.println( xml_parser.getErrorMessages().toString() );
9703 if ( phylogenies_0.length != 1 ) {
9706 final Phylogeny t1 = phylogenies_0[ 0 ];
9707 PhylogenyNode n = null;
9708 Distribution d = null;
9709 n = t1.getNode( "root node" );
9710 if ( !n.getNodeData().isHasDistribution() ) {
9713 if ( n.getNodeData().getDistributions().size() != 1 ) {
9716 d = n.getNodeData().getDistribution();
9717 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9720 if ( d.getPoints().size() != 1 ) {
9723 if ( d.getPolygons() != null ) {
9726 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9729 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9732 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9735 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9738 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9741 n = t1.getNode( "node a" );
9742 if ( !n.getNodeData().isHasDistribution() ) {
9745 if ( n.getNodeData().getDistributions().size() != 2 ) {
9748 d = n.getNodeData().getDistribution( 1 );
9749 if ( !d.getDesc().equals( "San Diego" ) ) {
9752 if ( d.getPoints().size() != 1 ) {
9755 if ( d.getPolygons() != null ) {
9758 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9761 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9764 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9767 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9770 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9773 n = t1.getNode( "node bb" );
9774 if ( !n.getNodeData().isHasDistribution() ) {
9777 if ( n.getNodeData().getDistributions().size() != 1 ) {
9780 d = n.getNodeData().getDistribution( 0 );
9781 if ( d.getPoints().size() != 3 ) {
9784 if ( d.getPolygons().size() != 2 ) {
9787 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9790 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9793 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9796 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9799 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9802 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9805 Polygon p = d.getPolygons().get( 0 );
9806 if ( p.getPoints().size() != 3 ) {
9809 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9812 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9815 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9818 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9821 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9824 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9827 p = d.getPolygons().get( 1 );
9828 if ( p.getPoints().size() != 3 ) {
9831 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9834 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9837 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9841 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9842 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9843 if ( rt.length != 1 ) {
9846 final Phylogeny t1_rt = rt[ 0 ];
9847 n = t1_rt.getNode( "root node" );
9848 if ( !n.getNodeData().isHasDistribution() ) {
9851 if ( n.getNodeData().getDistributions().size() != 1 ) {
9854 d = n.getNodeData().getDistribution();
9855 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9858 if ( d.getPoints().size() != 1 ) {
9861 if ( d.getPolygons() != null ) {
9864 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9867 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9870 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9873 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9876 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9879 n = t1_rt.getNode( "node a" );
9880 if ( !n.getNodeData().isHasDistribution() ) {
9883 if ( n.getNodeData().getDistributions().size() != 2 ) {
9886 d = n.getNodeData().getDistribution( 1 );
9887 if ( !d.getDesc().equals( "San Diego" ) ) {
9890 if ( d.getPoints().size() != 1 ) {
9893 if ( d.getPolygons() != null ) {
9896 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9899 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9902 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9905 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9908 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9911 n = t1_rt.getNode( "node bb" );
9912 if ( !n.getNodeData().isHasDistribution() ) {
9915 if ( n.getNodeData().getDistributions().size() != 1 ) {
9918 d = n.getNodeData().getDistribution( 0 );
9919 if ( d.getPoints().size() != 3 ) {
9922 if ( d.getPolygons().size() != 2 ) {
9925 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9928 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9931 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9934 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9937 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9940 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9943 p = d.getPolygons().get( 0 );
9944 if ( p.getPoints().size() != 3 ) {
9947 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9950 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9953 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9956 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9959 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9962 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9965 p = d.getPolygons().get( 1 );
9966 if ( p.getPoints().size() != 3 ) {
9969 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9972 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9975 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9979 catch ( final Exception e ) {
9980 e.printStackTrace( System.out );
9986 private static boolean testPostOrderIterator() {
9988 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9989 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
9990 PhylogenyNodeIterator it0;
9991 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
9994 for( it0.reset(); it0.hasNext(); ) {
9997 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
9998 final PhylogenyNodeIterator it = t1.iteratorPostorder();
9999 if ( !it.next().getName().equals( "A" ) ) {
10002 if ( !it.next().getName().equals( "B" ) ) {
10005 if ( !it.next().getName().equals( "ab" ) ) {
10008 if ( !it.next().getName().equals( "C" ) ) {
10011 if ( !it.next().getName().equals( "D" ) ) {
10014 if ( !it.next().getName().equals( "cd" ) ) {
10017 if ( !it.next().getName().equals( "abcd" ) ) {
10020 if ( !it.next().getName().equals( "E" ) ) {
10023 if ( !it.next().getName().equals( "F" ) ) {
10026 if ( !it.next().getName().equals( "ef" ) ) {
10029 if ( !it.next().getName().equals( "G" ) ) {
10032 if ( !it.next().getName().equals( "H" ) ) {
10035 if ( !it.next().getName().equals( "gh" ) ) {
10038 if ( !it.next().getName().equals( "efgh" ) ) {
10041 if ( !it.next().getName().equals( "r" ) ) {
10044 if ( it.hasNext() ) {
10048 catch ( final Exception e ) {
10049 e.printStackTrace( System.out );
10055 private static boolean testPreOrderIterator() {
10057 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10058 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10059 PhylogenyNodeIterator it0;
10060 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
10063 for( it0.reset(); it0.hasNext(); ) {
10066 PhylogenyNodeIterator it = t0.iteratorPreorder();
10067 if ( !it.next().getName().equals( "r" ) ) {
10070 if ( !it.next().getName().equals( "ab" ) ) {
10073 if ( !it.next().getName().equals( "A" ) ) {
10076 if ( !it.next().getName().equals( "B" ) ) {
10079 if ( !it.next().getName().equals( "cd" ) ) {
10082 if ( !it.next().getName().equals( "C" ) ) {
10085 if ( !it.next().getName().equals( "D" ) ) {
10088 if ( it.hasNext() ) {
10091 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10092 it = t1.iteratorPreorder();
10093 if ( !it.next().getName().equals( "r" ) ) {
10096 if ( !it.next().getName().equals( "abcd" ) ) {
10099 if ( !it.next().getName().equals( "ab" ) ) {
10102 if ( !it.next().getName().equals( "A" ) ) {
10105 if ( !it.next().getName().equals( "B" ) ) {
10108 if ( !it.next().getName().equals( "cd" ) ) {
10111 if ( !it.next().getName().equals( "C" ) ) {
10114 if ( !it.next().getName().equals( "D" ) ) {
10117 if ( !it.next().getName().equals( "efgh" ) ) {
10120 if ( !it.next().getName().equals( "ef" ) ) {
10123 if ( !it.next().getName().equals( "E" ) ) {
10126 if ( !it.next().getName().equals( "F" ) ) {
10129 if ( !it.next().getName().equals( "gh" ) ) {
10132 if ( !it.next().getName().equals( "G" ) ) {
10135 if ( !it.next().getName().equals( "H" ) ) {
10138 if ( it.hasNext() ) {
10142 catch ( final Exception e ) {
10143 e.printStackTrace( System.out );
10149 private static boolean testPropertiesMap() {
10151 final PropertiesMap pm = new PropertiesMap();
10152 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10153 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10154 final Property p2 = new Property( "something:else",
10156 "improbable:research",
10159 pm.addProperty( p0 );
10160 pm.addProperty( p1 );
10161 pm.addProperty( p2 );
10162 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
10165 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
10168 if ( pm.getProperties().size() != 3 ) {
10171 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
10174 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10177 if ( pm.getProperties().size() != 3 ) {
10180 pm.removeProperty( "dimensions:diameter" );
10181 if ( pm.getProperties().size() != 2 ) {
10184 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
10187 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10191 catch ( final Exception e ) {
10192 e.printStackTrace( System.out );
10198 private static boolean testProteinId() {
10200 final ProteinId id1 = new ProteinId( "a" );
10201 final ProteinId id2 = new ProteinId( "a" );
10202 final ProteinId id3 = new ProteinId( "A" );
10203 final ProteinId id4 = new ProteinId( "b" );
10204 if ( !id1.equals( id1 ) ) {
10207 if ( id1.getId().equals( "x" ) ) {
10210 if ( id1.getId().equals( null ) ) {
10213 if ( !id1.equals( id2 ) ) {
10216 if ( id1.equals( id3 ) ) {
10219 if ( id1.hashCode() != id1.hashCode() ) {
10222 if ( id1.hashCode() != id2.hashCode() ) {
10225 if ( id1.hashCode() == id3.hashCode() ) {
10228 if ( id1.compareTo( id1 ) != 0 ) {
10231 if ( id1.compareTo( id2 ) != 0 ) {
10234 if ( id1.compareTo( id3 ) != 0 ) {
10237 if ( id1.compareTo( id4 ) >= 0 ) {
10240 if ( id4.compareTo( id1 ) <= 0 ) {
10243 if ( !id4.getId().equals( "b" ) ) {
10246 final ProteinId id5 = new ProteinId( " C " );
10247 if ( !id5.getId().equals( "C" ) ) {
10250 if ( id5.equals( id1 ) ) {
10254 catch ( final Exception e ) {
10255 e.printStackTrace( System.out );
10261 private static boolean testReIdMethods() {
10263 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10264 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
10265 final long count = PhylogenyNode.getNodeCount();
10266 p.levelOrderReID();
10267 if ( p.getNode( "r" ).getId() != count ) {
10270 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
10273 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
10276 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
10279 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
10282 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
10285 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
10288 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
10291 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
10294 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
10297 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
10300 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
10303 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
10306 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
10309 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
10313 catch ( final Exception e ) {
10314 e.printStackTrace( System.out );
10320 private static boolean testRerooting() {
10322 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10323 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",
10324 new NHXParser() )[ 0 ];
10325 if ( !t1.isRooted() ) {
10328 t1.reRoot( t1.getNode( "D" ) );
10329 t1.reRoot( t1.getNode( "CD" ) );
10330 t1.reRoot( t1.getNode( "A" ) );
10331 t1.reRoot( t1.getNode( "B" ) );
10332 t1.reRoot( t1.getNode( "AB" ) );
10333 t1.reRoot( t1.getNode( "D" ) );
10334 t1.reRoot( t1.getNode( "C" ) );
10335 t1.reRoot( t1.getNode( "CD" ) );
10336 t1.reRoot( t1.getNode( "A" ) );
10337 t1.reRoot( t1.getNode( "B" ) );
10338 t1.reRoot( t1.getNode( "AB" ) );
10339 t1.reRoot( t1.getNode( "D" ) );
10340 t1.reRoot( t1.getNode( "D" ) );
10341 t1.reRoot( t1.getNode( "C" ) );
10342 t1.reRoot( t1.getNode( "A" ) );
10343 t1.reRoot( t1.getNode( "B" ) );
10344 t1.reRoot( t1.getNode( "AB" ) );
10345 t1.reRoot( t1.getNode( "C" ) );
10346 t1.reRoot( t1.getNode( "D" ) );
10347 t1.reRoot( t1.getNode( "CD" ) );
10348 t1.reRoot( t1.getNode( "D" ) );
10349 t1.reRoot( t1.getNode( "A" ) );
10350 t1.reRoot( t1.getNode( "B" ) );
10351 t1.reRoot( t1.getNode( "AB" ) );
10352 t1.reRoot( t1.getNode( "C" ) );
10353 t1.reRoot( t1.getNode( "D" ) );
10354 t1.reRoot( t1.getNode( "CD" ) );
10355 t1.reRoot( t1.getNode( "D" ) );
10356 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10359 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10362 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10365 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10368 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10371 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10374 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",
10375 new NHXParser() )[ 0 ];
10376 t2.reRoot( t2.getNode( "A" ) );
10377 t2.reRoot( t2.getNode( "D" ) );
10378 t2.reRoot( t2.getNode( "ABC" ) );
10379 t2.reRoot( t2.getNode( "A" ) );
10380 t2.reRoot( t2.getNode( "B" ) );
10381 t2.reRoot( t2.getNode( "D" ) );
10382 t2.reRoot( t2.getNode( "C" ) );
10383 t2.reRoot( t2.getNode( "ABC" ) );
10384 t2.reRoot( t2.getNode( "A" ) );
10385 t2.reRoot( t2.getNode( "B" ) );
10386 t2.reRoot( t2.getNode( "AB" ) );
10387 t2.reRoot( t2.getNode( "AB" ) );
10388 t2.reRoot( t2.getNode( "D" ) );
10389 t2.reRoot( t2.getNode( "C" ) );
10390 t2.reRoot( t2.getNode( "B" ) );
10391 t2.reRoot( t2.getNode( "AB" ) );
10392 t2.reRoot( t2.getNode( "D" ) );
10393 t2.reRoot( t2.getNode( "D" ) );
10394 t2.reRoot( t2.getNode( "ABC" ) );
10395 t2.reRoot( t2.getNode( "A" ) );
10396 t2.reRoot( t2.getNode( "B" ) );
10397 t2.reRoot( t2.getNode( "AB" ) );
10398 t2.reRoot( t2.getNode( "D" ) );
10399 t2.reRoot( t2.getNode( "C" ) );
10400 t2.reRoot( t2.getNode( "ABC" ) );
10401 t2.reRoot( t2.getNode( "A" ) );
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( "C" ) );
10407 t2.reRoot( t2.getNode( "A" ) );
10408 t2.reRoot( t2.getNode( "B" ) );
10409 t2.reRoot( t2.getNode( "AB" ) );
10410 t2.reRoot( t2.getNode( "C" ) );
10411 t2.reRoot( t2.getNode( "D" ) );
10412 t2.reRoot( t2.getNode( "ABC" ) );
10413 t2.reRoot( t2.getNode( "D" ) );
10414 t2.reRoot( t2.getNode( "A" ) );
10415 t2.reRoot( t2.getNode( "B" ) );
10416 t2.reRoot( t2.getNode( "AB" ) );
10417 t2.reRoot( t2.getNode( "C" ) );
10418 t2.reRoot( t2.getNode( "D" ) );
10419 t2.reRoot( t2.getNode( "ABC" ) );
10420 t2.reRoot( t2.getNode( "D" ) );
10421 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10424 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10427 t2.reRoot( t2.getNode( "ABC" ) );
10428 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10431 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10434 t2.reRoot( t2.getNode( "AB" ) );
10435 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10438 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10441 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10444 t2.reRoot( t2.getNode( "AB" ) );
10445 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10448 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10451 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10454 t2.reRoot( t2.getNode( "D" ) );
10455 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10458 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10461 t2.reRoot( t2.getNode( "ABC" ) );
10462 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10465 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10468 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10469 new NHXParser() )[ 0 ];
10470 t3.reRoot( t3.getNode( "B" ) );
10471 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10474 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10477 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10480 t3.reRoot( t3.getNode( "B" ) );
10481 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10484 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10487 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10490 t3.reRoot( t3.getRoot() );
10491 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10494 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10497 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10501 catch ( final Exception e ) {
10502 e.printStackTrace( System.out );
10508 private static boolean testSDIse() {
10510 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10511 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10512 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10513 gene1.setRooted( true );
10514 species1.setRooted( true );
10515 final SDI sdi = new SDI( gene1, species1 );
10516 if ( !gene1.getRoot().isDuplication() ) {
10519 final Phylogeny species2 = factory
10520 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10521 new NHXParser() )[ 0 ];
10522 final Phylogeny gene2 = factory
10523 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10524 new NHXParser() )[ 0 ];
10525 species2.setRooted( true );
10526 gene2.setRooted( true );
10527 final SDI sdi2 = new SDI( gene2, species2 );
10528 if ( sdi2.getDuplicationsSum() != 0 ) {
10531 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10534 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10537 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10540 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10543 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10546 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10549 final Phylogeny species3 = factory
10550 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10551 new NHXParser() )[ 0 ];
10552 final Phylogeny gene3 = factory
10553 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10554 new NHXParser() )[ 0 ];
10555 species3.setRooted( true );
10556 gene3.setRooted( true );
10557 final SDI sdi3 = new SDI( gene3, species3 );
10558 if ( sdi3.getDuplicationsSum() != 1 ) {
10561 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10564 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10567 final Phylogeny species4 = factory
10568 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10569 new NHXParser() )[ 0 ];
10570 final Phylogeny gene4 = factory
10571 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10572 new NHXParser() )[ 0 ];
10573 species4.setRooted( true );
10574 gene4.setRooted( true );
10575 final SDI sdi4 = new SDI( gene4, species4 );
10576 if ( sdi4.getDuplicationsSum() != 1 ) {
10579 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10582 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10585 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10588 if ( species4.getNumberOfExternalNodes() != 6 ) {
10591 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10594 final Phylogeny species5 = factory
10595 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10596 new NHXParser() )[ 0 ];
10597 final Phylogeny gene5 = factory
10598 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10599 new NHXParser() )[ 0 ];
10600 species5.setRooted( true );
10601 gene5.setRooted( true );
10602 final SDI sdi5 = new SDI( gene5, species5 );
10603 if ( sdi5.getDuplicationsSum() != 2 ) {
10606 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10609 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10612 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10615 if ( species5.getNumberOfExternalNodes() != 6 ) {
10618 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10621 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10622 // Conjecture for Comparing Molecular Phylogenies"
10623 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10624 final Phylogeny species6 = factory
10625 .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,"
10626 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10627 new NHXParser() )[ 0 ];
10628 final Phylogeny gene6 = factory
10629 .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,"
10630 + "((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,"
10631 + "(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;",
10632 new NHXParser() )[ 0 ];
10633 species6.setRooted( true );
10634 gene6.setRooted( true );
10635 final SDI sdi6 = new SDI( gene6, species6 );
10636 if ( sdi6.getDuplicationsSum() != 3 ) {
10639 if ( !gene6.getNode( "r" ).isDuplication() ) {
10642 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10645 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10648 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10651 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10654 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10657 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10660 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10663 sdi6.computeMappingCostL();
10664 if ( sdi6.computeMappingCostL() != 17 ) {
10667 if ( species6.getNumberOfExternalNodes() != 9 ) {
10670 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10673 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10674 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10675 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10676 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10677 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10678 species7.setRooted( true );
10679 final Phylogeny gene7_1 = Test
10680 .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])" );
10681 gene7_1.setRooted( true );
10682 final SDI sdi7 = new SDI( gene7_1, species7 );
10683 if ( sdi7.getDuplicationsSum() != 0 ) {
10686 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10689 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10692 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10695 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10698 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10701 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10704 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10707 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10710 final Phylogeny gene7_2 = Test
10711 .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])" );
10712 gene7_2.setRooted( true );
10713 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10714 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10717 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10720 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10723 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10726 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10729 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10732 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10735 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10738 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10741 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10745 catch ( final Exception e ) {
10751 private static boolean testSDIunrooted() {
10753 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10754 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10755 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10756 final Iterator<PhylogenyBranch> iter = l.iterator();
10757 PhylogenyBranch br = iter.next();
10758 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10761 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10765 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10768 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10772 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10775 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10779 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10782 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10786 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10789 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10793 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10796 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10800 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10803 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10807 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10810 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10814 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10817 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10821 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10824 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10828 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10831 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10835 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10838 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10842 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10845 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10849 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10852 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10856 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10859 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10862 if ( iter.hasNext() ) {
10865 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10866 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10867 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10869 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10872 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10876 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10879 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10883 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10886 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10889 if ( iter1.hasNext() ) {
10892 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10893 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10894 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10896 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10899 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10903 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10906 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10910 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10913 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10916 if ( iter2.hasNext() ) {
10919 final Phylogeny species0 = factory
10920 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10921 new NHXParser() )[ 0 ];
10922 final Phylogeny gene1 = factory
10923 .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])",
10924 new NHXParser() )[ 0 ];
10925 species0.setRooted( true );
10926 gene1.setRooted( true );
10927 final SDIR sdi_unrooted = new SDIR();
10928 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10929 if ( sdi_unrooted.getCount() != 1 ) {
10932 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10935 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10938 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10941 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10944 final Phylogeny gene2 = factory
10945 .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])",
10946 new NHXParser() )[ 0 ];
10947 gene2.setRooted( true );
10948 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10949 if ( sdi_unrooted.getCount() != 1 ) {
10952 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10955 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10958 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10961 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10964 final Phylogeny species6 = factory
10965 .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,"
10966 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10967 new NHXParser() )[ 0 ];
10968 final Phylogeny gene6 = factory
10969 .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],"
10970 + "(((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],"
10971 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10972 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10973 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10974 new NHXParser() )[ 0 ];
10975 species6.setRooted( true );
10976 gene6.setRooted( true );
10977 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10978 if ( sdi_unrooted.getCount() != 1 ) {
10981 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10984 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10987 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10990 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10993 if ( !p6[ 0 ].getRoot().isDuplication() ) {
10996 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10999 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11002 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
11005 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11008 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
11011 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
11014 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11018 final Phylogeny species7 = factory
11019 .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,"
11020 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11021 new NHXParser() )[ 0 ];
11022 final Phylogeny gene7 = factory
11023 .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],"
11024 + "(((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],"
11025 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11026 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11027 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11028 new NHXParser() )[ 0 ];
11029 species7.setRooted( true );
11030 gene7.setRooted( true );
11031 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
11032 if ( sdi_unrooted.getCount() != 1 ) {
11035 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11038 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11041 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11044 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
11047 if ( !p7[ 0 ].getRoot().isDuplication() ) {
11050 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11053 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11056 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
11059 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11062 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
11065 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
11068 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11072 final Phylogeny species8 = factory
11073 .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,"
11074 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11075 new NHXParser() )[ 0 ];
11076 final Phylogeny gene8 = factory
11077 .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],"
11078 + "(((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],"
11079 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11080 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11081 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11082 new NHXParser() )[ 0 ];
11083 species8.setRooted( true );
11084 gene8.setRooted( true );
11085 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
11086 if ( sdi_unrooted.getCount() != 1 ) {
11089 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11092 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11095 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11098 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11101 if ( !p8[ 0 ].getRoot().isDuplication() ) {
11104 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11107 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11110 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
11113 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11116 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
11119 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
11122 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11127 catch ( final Exception e ) {
11128 e.printStackTrace( System.out );
11134 private static boolean testSequenceDbWsTools1() {
11136 final PhylogenyNode n = new PhylogenyNode();
11137 n.setName( "NP_001025424" );
11138 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11139 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11140 || !acc.getValue().equals( "NP_001025424" ) ) {
11143 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11144 acc = SequenceDbWsTools.obtainSeqAccession( n );
11145 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11146 || !acc.getValue().equals( "NP_001025424" ) ) {
11149 n.setName( "NP_001025424.1" );
11150 acc = SequenceDbWsTools.obtainSeqAccession( n );
11151 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11152 || !acc.getValue().equals( "NP_001025424" ) ) {
11155 n.setName( "NM_001030253" );
11156 acc = SequenceDbWsTools.obtainSeqAccession( n );
11157 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11158 || !acc.getValue().equals( "NM_001030253" ) ) {
11161 n.setName( "BCL2_HUMAN" );
11162 acc = SequenceDbWsTools.obtainSeqAccession( n );
11163 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11164 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11165 System.out.println( acc.toString() );
11168 n.setName( "P10415" );
11169 acc = SequenceDbWsTools.obtainSeqAccession( n );
11170 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11171 || !acc.getValue().equals( "P10415" ) ) {
11172 System.out.println( acc.toString() );
11175 n.setName( " P10415 " );
11176 acc = SequenceDbWsTools.obtainSeqAccession( n );
11177 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11178 || !acc.getValue().equals( "P10415" ) ) {
11179 System.out.println( acc.toString() );
11182 n.setName( "_P10415|" );
11183 acc = SequenceDbWsTools.obtainSeqAccession( n );
11184 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11185 || !acc.getValue().equals( "P10415" ) ) {
11186 System.out.println( acc.toString() );
11189 n.setName( "AY695820" );
11190 acc = SequenceDbWsTools.obtainSeqAccession( n );
11191 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11192 || !acc.getValue().equals( "AY695820" ) ) {
11193 System.out.println( acc.toString() );
11196 n.setName( "_AY695820_" );
11197 acc = SequenceDbWsTools.obtainSeqAccession( n );
11198 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11199 || !acc.getValue().equals( "AY695820" ) ) {
11200 System.out.println( acc.toString() );
11203 n.setName( "AAA59452" );
11204 acc = SequenceDbWsTools.obtainSeqAccession( n );
11205 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11206 || !acc.getValue().equals( "AAA59452" ) ) {
11207 System.out.println( acc.toString() );
11210 n.setName( "_AAA59452_" );
11211 acc = SequenceDbWsTools.obtainSeqAccession( n );
11212 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11213 || !acc.getValue().equals( "AAA59452" ) ) {
11214 System.out.println( acc.toString() );
11217 n.setName( "AAA59452.1" );
11218 acc = SequenceDbWsTools.obtainSeqAccession( n );
11219 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11220 || !acc.getValue().equals( "AAA59452.1" ) ) {
11221 System.out.println( acc.toString() );
11224 n.setName( "_AAA59452.1_" );
11225 acc = SequenceDbWsTools.obtainSeqAccession( n );
11226 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11227 || !acc.getValue().equals( "AAA59452.1" ) ) {
11228 System.out.println( acc.toString() );
11231 n.setName( "GI:94894583" );
11232 acc = SequenceDbWsTools.obtainSeqAccession( n );
11233 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11234 || !acc.getValue().equals( "94894583" ) ) {
11235 System.out.println( acc.toString() );
11238 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11239 acc = SequenceDbWsTools.obtainSeqAccession( n );
11240 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11241 || !acc.getValue().equals( "71845847" ) ) {
11242 System.out.println( acc.toString() );
11245 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11246 acc = SequenceDbWsTools.obtainSeqAccession( n );
11247 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11248 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11249 System.out.println( acc.toString() );
11253 catch ( final Exception e ) {
11259 private static boolean testSequenceDbWsTools2() {
11261 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11262 SequenceDbWsTools.obtainSeqInformation( n1 );
11263 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11266 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11269 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11272 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11275 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11276 SequenceDbWsTools.obtainSeqInformation( n2 );
11277 if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
11280 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11283 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11286 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11289 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11290 SequenceDbWsTools.obtainSeqInformation( n3 );
11291 if ( !n3.getNodeData().getSequence().getName()
11292 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11295 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11298 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11301 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11305 catch ( final IOException e ) {
11306 System.out.println();
11307 System.out.println( "the following might be due to absence internet connection:" );
11308 e.printStackTrace( System.out );
11311 catch ( final Exception e ) {
11312 e.printStackTrace();
11318 private static boolean testSequenceIdParsing() {
11320 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11321 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11322 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11323 if ( id != null ) {
11324 System.out.println( "value =" + id.getValue() );
11325 System.out.println( "provider=" + id.getSource() );
11329 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11330 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11331 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11332 if ( id != null ) {
11333 System.out.println( "value =" + id.getValue() );
11334 System.out.println( "provider=" + id.getSource() );
11338 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11339 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11340 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11341 if ( id != null ) {
11342 System.out.println( "value =" + id.getValue() );
11343 System.out.println( "provider=" + id.getSource() );
11347 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11348 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11349 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11350 if ( id != null ) {
11351 System.out.println( "value =" + id.getValue() );
11352 System.out.println( "provider=" + id.getSource() );
11356 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11357 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11358 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11359 if ( id != null ) {
11360 System.out.println( "value =" + id.getValue() );
11361 System.out.println( "provider=" + id.getSource() );
11365 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11366 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11367 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11368 if ( id != null ) {
11369 System.out.println( "value =" + id.getValue() );
11370 System.out.println( "provider=" + id.getSource() );
11374 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11375 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11376 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11377 if ( id != null ) {
11378 System.out.println( "value =" + id.getValue() );
11379 System.out.println( "provider=" + id.getSource() );
11383 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11384 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11385 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11386 if ( id != null ) {
11387 System.out.println( "value =" + id.getValue() );
11388 System.out.println( "provider=" + id.getSource() );
11392 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11393 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11394 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11395 if ( id != null ) {
11396 System.out.println( "value =" + id.getValue() );
11397 System.out.println( "provider=" + id.getSource() );
11401 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11402 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11403 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11404 if ( id != null ) {
11405 System.out.println( "value =" + id.getValue() );
11406 System.out.println( "provider=" + id.getSource() );
11410 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11411 if ( id != null ) {
11412 System.out.println( "value =" + id.getValue() );
11413 System.out.println( "provider=" + id.getSource() );
11416 id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
11417 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11418 || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
11419 if ( id != null ) {
11420 System.out.println( "value =" + id.getValue() );
11421 System.out.println( "provider=" + id.getSource() );
11425 id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
11426 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11427 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11428 if ( id != null ) {
11429 System.out.println( "value =" + id.getValue() );
11430 System.out.println( "provider=" + id.getSource() );
11434 id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
11435 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11436 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11437 if ( id != null ) {
11438 System.out.println( "value =" + id.getValue() );
11439 System.out.println( "provider=" + id.getSource() );
11443 id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
11444 if ( id != null ) {
11445 System.out.println( "value =" + id.getValue() );
11446 System.out.println( "provider=" + id.getSource() );
11450 catch ( final Exception e ) {
11451 e.printStackTrace( System.out );
11457 private static boolean testSequenceWriter() {
11459 final String n = ForesterUtil.LINE_SEPARATOR;
11460 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11463 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11466 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11469 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11472 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11473 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11476 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11477 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11481 catch ( final Exception e ) {
11482 e.printStackTrace();
11488 private static boolean testSpecies() {
11490 final Species s1 = new BasicSpecies( "a" );
11491 final Species s2 = new BasicSpecies( "a" );
11492 final Species s3 = new BasicSpecies( "A" );
11493 final Species s4 = new BasicSpecies( "b" );
11494 if ( !s1.equals( s1 ) ) {
11497 if ( s1.getSpeciesId().equals( "x" ) ) {
11500 if ( s1.getSpeciesId().equals( null ) ) {
11503 if ( !s1.equals( s2 ) ) {
11506 if ( s1.equals( s3 ) ) {
11509 if ( s1.hashCode() != s1.hashCode() ) {
11512 if ( s1.hashCode() != s2.hashCode() ) {
11515 if ( s1.hashCode() == s3.hashCode() ) {
11518 if ( s1.compareTo( s1 ) != 0 ) {
11521 if ( s1.compareTo( s2 ) != 0 ) {
11524 if ( s1.compareTo( s3 ) != 0 ) {
11527 if ( s1.compareTo( s4 ) >= 0 ) {
11530 if ( s4.compareTo( s1 ) <= 0 ) {
11533 if ( !s4.getSpeciesId().equals( "b" ) ) {
11536 final Species s5 = new BasicSpecies( " C " );
11537 if ( !s5.getSpeciesId().equals( "C" ) ) {
11540 if ( s5.equals( s1 ) ) {
11544 catch ( final Exception e ) {
11545 e.printStackTrace( System.out );
11551 private static boolean testSplit() {
11553 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11554 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11555 //Archaeopteryx.createApplication( p0 );
11556 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11557 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11558 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11559 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11560 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11561 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11562 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11563 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11564 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11565 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11566 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11567 // System.out.println( s0.toString() );
11569 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11571 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11572 if ( s0.match( query_nodes ) ) {
11575 query_nodes = new HashSet<PhylogenyNode>();
11576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11583 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 if ( !s0.match( query_nodes ) ) {
11595 query_nodes = new HashSet<PhylogenyNode>();
11596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11600 if ( !s0.match( query_nodes ) ) {
11604 query_nodes = new HashSet<PhylogenyNode>();
11605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11609 if ( !s0.match( query_nodes ) ) {
11613 query_nodes = new HashSet<PhylogenyNode>();
11614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11617 if ( !s0.match( query_nodes ) ) {
11620 query_nodes = new HashSet<PhylogenyNode>();
11621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11623 if ( !s0.match( query_nodes ) ) {
11626 query_nodes = new HashSet<PhylogenyNode>();
11627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11632 if ( !s0.match( query_nodes ) ) {
11635 query_nodes = new HashSet<PhylogenyNode>();
11636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11639 if ( !s0.match( query_nodes ) ) {
11642 query_nodes = new HashSet<PhylogenyNode>();
11643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11647 if ( !s0.match( query_nodes ) ) {
11650 query_nodes = new HashSet<PhylogenyNode>();
11651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11653 if ( s0.match( query_nodes ) ) {
11656 query_nodes = new HashSet<PhylogenyNode>();
11657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11661 if ( s0.match( query_nodes ) ) {
11664 query_nodes = new HashSet<PhylogenyNode>();
11665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11670 if ( s0.match( query_nodes ) ) {
11673 query_nodes = new HashSet<PhylogenyNode>();
11674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11677 if ( s0.match( query_nodes ) ) {
11680 query_nodes = new HashSet<PhylogenyNode>();
11681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11683 if ( s0.match( query_nodes ) ) {
11686 query_nodes = new HashSet<PhylogenyNode>();
11687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
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( "C" ) );
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( "E" ) );
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( "F" ) );
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( "G" ) );
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 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11720 if ( s0.match( query_nodes ) ) {
11723 query_nodes = new HashSet<PhylogenyNode>();
11724 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11727 if ( s0.match( query_nodes ) ) {
11730 query_nodes = new HashSet<PhylogenyNode>();
11731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11734 if ( s0.match( query_nodes ) ) {
11737 query_nodes = new HashSet<PhylogenyNode>();
11738 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11742 if ( s0.match( query_nodes ) ) {
11746 // query_nodes = new HashSet<PhylogenyNode>();
11747 // query_nodes.add( new PhylogenyNode( "X" ) );
11748 // query_nodes.add( new PhylogenyNode( "Y" ) );
11749 // query_nodes.add( new PhylogenyNode( "A" ) );
11750 // query_nodes.add( new PhylogenyNode( "B" ) );
11751 // query_nodes.add( new PhylogenyNode( "C" ) );
11752 // query_nodes.add( new PhylogenyNode( "D" ) );
11753 // query_nodes.add( new PhylogenyNode( "E" ) );
11754 // query_nodes.add( new PhylogenyNode( "F" ) );
11755 // query_nodes.add( new PhylogenyNode( "G" ) );
11756 // if ( !s0.match( query_nodes ) ) {
11759 // query_nodes = new HashSet<PhylogenyNode>();
11760 // query_nodes.add( new PhylogenyNode( "X" ) );
11761 // query_nodes.add( new PhylogenyNode( "Y" ) );
11762 // query_nodes.add( new PhylogenyNode( "A" ) );
11763 // query_nodes.add( new PhylogenyNode( "B" ) );
11764 // query_nodes.add( new PhylogenyNode( "C" ) );
11765 // if ( !s0.match( query_nodes ) ) {
11769 // query_nodes = new HashSet<PhylogenyNode>();
11770 // query_nodes.add( new PhylogenyNode( "X" ) );
11771 // query_nodes.add( new PhylogenyNode( "Y" ) );
11772 // query_nodes.add( new PhylogenyNode( "D" ) );
11773 // query_nodes.add( new PhylogenyNode( "E" ) );
11774 // query_nodes.add( new PhylogenyNode( "F" ) );
11775 // query_nodes.add( new PhylogenyNode( "G" ) );
11776 // if ( !s0.match( query_nodes ) ) {
11780 // query_nodes = new HashSet<PhylogenyNode>();
11781 // query_nodes.add( new PhylogenyNode( "X" ) );
11782 // query_nodes.add( new PhylogenyNode( "Y" ) );
11783 // query_nodes.add( new PhylogenyNode( "A" ) );
11784 // query_nodes.add( new PhylogenyNode( "B" ) );
11785 // query_nodes.add( new PhylogenyNode( "C" ) );
11786 // query_nodes.add( new PhylogenyNode( "D" ) );
11787 // if ( !s0.match( query_nodes ) ) {
11791 // query_nodes = new HashSet<PhylogenyNode>();
11792 // query_nodes.add( new PhylogenyNode( "X" ) );
11793 // query_nodes.add( new PhylogenyNode( "Y" ) );
11794 // query_nodes.add( new PhylogenyNode( "E" ) );
11795 // query_nodes.add( new PhylogenyNode( "F" ) );
11796 // query_nodes.add( new PhylogenyNode( "G" ) );
11797 // if ( !s0.match( query_nodes ) ) {
11801 // query_nodes = new HashSet<PhylogenyNode>();
11802 // query_nodes.add( new PhylogenyNode( "X" ) );
11803 // query_nodes.add( new PhylogenyNode( "Y" ) );
11804 // query_nodes.add( new PhylogenyNode( "F" ) );
11805 // query_nodes.add( new PhylogenyNode( "G" ) );
11806 // if ( !s0.match( query_nodes ) ) {
11810 query_nodes = new HashSet<PhylogenyNode>();
11811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11815 if ( s0.match( query_nodes ) ) {
11819 query_nodes = new HashSet<PhylogenyNode>();
11820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11821 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11824 if ( s0.match( query_nodes ) ) {
11827 ///////////////////////////
11829 query_nodes = new HashSet<PhylogenyNode>();
11830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11834 if ( s0.match( query_nodes ) ) {
11838 query_nodes = new HashSet<PhylogenyNode>();
11839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11843 if ( s0.match( query_nodes ) ) {
11847 query_nodes = new HashSet<PhylogenyNode>();
11848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11852 if ( s0.match( query_nodes ) ) {
11856 query_nodes = new HashSet<PhylogenyNode>();
11857 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11861 if ( s0.match( query_nodes ) ) {
11865 query_nodes = new HashSet<PhylogenyNode>();
11866 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11867 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11868 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11870 if ( s0.match( query_nodes ) ) {
11874 query_nodes = new HashSet<PhylogenyNode>();
11875 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11876 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11878 if ( s0.match( query_nodes ) ) {
11882 query_nodes = new HashSet<PhylogenyNode>();
11883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11888 if ( s0.match( query_nodes ) ) {
11892 query_nodes = new HashSet<PhylogenyNode>();
11893 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11898 if ( s0.match( query_nodes ) ) {
11902 query_nodes = new HashSet<PhylogenyNode>();
11903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11908 if ( s0.match( query_nodes ) ) {
11912 query_nodes = new HashSet<PhylogenyNode>();
11913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11919 if ( s0.match( query_nodes ) ) {
11923 catch ( final Exception e ) {
11924 e.printStackTrace();
11930 private static boolean testSplitStrict() {
11932 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11933 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11934 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11935 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11936 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11937 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11938 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11939 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11940 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11941 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11942 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11943 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11944 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11946 if ( s0.match( query_nodes ) ) {
11949 query_nodes = new HashSet<PhylogenyNode>();
11950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11952 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11957 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 if ( !s0.match( query_nodes ) ) {
11969 query_nodes = new HashSet<PhylogenyNode>();
11970 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11971 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11974 if ( !s0.match( query_nodes ) ) {
11978 query_nodes = new HashSet<PhylogenyNode>();
11979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11983 if ( !s0.match( query_nodes ) ) {
11987 query_nodes = new HashSet<PhylogenyNode>();
11988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11991 if ( !s0.match( query_nodes ) ) {
11995 query_nodes = new HashSet<PhylogenyNode>();
11996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11998 if ( !s0.match( query_nodes ) ) {
12002 query_nodes = new HashSet<PhylogenyNode>();
12003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12008 if ( !s0.match( query_nodes ) ) {
12012 query_nodes = new HashSet<PhylogenyNode>();
12013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12016 if ( !s0.match( query_nodes ) ) {
12020 query_nodes = new HashSet<PhylogenyNode>();
12021 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12025 if ( !s0.match( query_nodes ) ) {
12029 query_nodes = new HashSet<PhylogenyNode>();
12030 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12032 if ( s0.match( query_nodes ) ) {
12036 query_nodes = new HashSet<PhylogenyNode>();
12037 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12041 if ( s0.match( query_nodes ) ) {
12045 query_nodes = new HashSet<PhylogenyNode>();
12046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12051 if ( s0.match( query_nodes ) ) {
12055 query_nodes = new HashSet<PhylogenyNode>();
12056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12059 if ( s0.match( query_nodes ) ) {
12063 query_nodes = new HashSet<PhylogenyNode>();
12064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12066 if ( s0.match( query_nodes ) ) {
12070 query_nodes = new HashSet<PhylogenyNode>();
12071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12073 if ( s0.match( query_nodes ) ) {
12077 query_nodes = new HashSet<PhylogenyNode>();
12078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12080 if ( s0.match( query_nodes ) ) {
12084 query_nodes = new HashSet<PhylogenyNode>();
12085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12087 if ( s0.match( query_nodes ) ) {
12091 query_nodes = new HashSet<PhylogenyNode>();
12092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12094 if ( s0.match( query_nodes ) ) {
12098 query_nodes = new HashSet<PhylogenyNode>();
12099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12101 if ( s0.match( query_nodes ) ) {
12105 query_nodes = new HashSet<PhylogenyNode>();
12106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12109 if ( s0.match( query_nodes ) ) {
12113 query_nodes = new HashSet<PhylogenyNode>();
12114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12117 if ( s0.match( query_nodes ) ) {
12121 query_nodes = new HashSet<PhylogenyNode>();
12122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12124 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12125 if ( s0.match( query_nodes ) ) {
12129 query_nodes = new HashSet<PhylogenyNode>();
12130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12134 if ( s0.match( query_nodes ) ) {
12138 catch ( final Exception e ) {
12139 e.printStackTrace();
12145 private static boolean testSubtreeDeletion() {
12147 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12148 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12149 t1.deleteSubtree( t1.getNode( "A" ), false );
12150 if ( t1.getNumberOfExternalNodes() != 5 ) {
12153 t1.toNewHampshireX();
12154 t1.deleteSubtree( t1.getNode( "E" ), false );
12155 if ( t1.getNumberOfExternalNodes() != 4 ) {
12158 t1.toNewHampshireX();
12159 t1.deleteSubtree( t1.getNode( "F" ), false );
12160 if ( t1.getNumberOfExternalNodes() != 3 ) {
12163 t1.toNewHampshireX();
12164 t1.deleteSubtree( t1.getNode( "D" ), false );
12165 t1.toNewHampshireX();
12166 if ( t1.getNumberOfExternalNodes() != 3 ) {
12169 t1.deleteSubtree( t1.getNode( "def" ), false );
12170 t1.toNewHampshireX();
12171 if ( t1.getNumberOfExternalNodes() != 2 ) {
12174 t1.deleteSubtree( t1.getNode( "B" ), false );
12175 t1.toNewHampshireX();
12176 if ( t1.getNumberOfExternalNodes() != 1 ) {
12179 t1.deleteSubtree( t1.getNode( "C" ), false );
12180 t1.toNewHampshireX();
12181 if ( t1.getNumberOfExternalNodes() != 1 ) {
12184 t1.deleteSubtree( t1.getNode( "abc" ), false );
12185 t1.toNewHampshireX();
12186 if ( t1.getNumberOfExternalNodes() != 1 ) {
12189 t1.deleteSubtree( t1.getNode( "r" ), false );
12190 if ( t1.getNumberOfExternalNodes() != 0 ) {
12193 if ( !t1.isEmpty() ) {
12196 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12197 t2.deleteSubtree( t2.getNode( "A" ), false );
12198 t2.toNewHampshireX();
12199 if ( t2.getNumberOfExternalNodes() != 5 ) {
12202 t2.deleteSubtree( t2.getNode( "abc" ), false );
12203 t2.toNewHampshireX();
12204 if ( t2.getNumberOfExternalNodes() != 3 ) {
12207 t2.deleteSubtree( t2.getNode( "def" ), false );
12208 t2.toNewHampshireX();
12209 if ( t2.getNumberOfExternalNodes() != 1 ) {
12213 catch ( final Exception e ) {
12214 e.printStackTrace( System.out );
12220 private static boolean testSupportCount() {
12222 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12223 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
12224 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
12225 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
12226 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
12227 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
12228 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
12230 SupportCount.count( t0_1, phylogenies_1, true, false );
12231 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
12232 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
12233 + "(((((A,B),C),D),E),((F,G),X))"
12234 + "(((((A,Y),B),C),D),((F,G),E))"
12235 + "(((((A,B),C),D),E),(F,G))"
12236 + "(((((A,B),C),D),E),(F,G))"
12237 + "(((((A,B),C),D),E),(F,G))"
12238 + "(((((A,B),C),D),E),(F,G),Z)"
12239 + "(((((A,B),C),D),E),(F,G))"
12240 + "((((((A,B),C),D),E),F),G)"
12241 + "(((((X,Y),F,G),E),((A,B),C)),D)",
12243 SupportCount.count( t0_2, phylogenies_2, true, false );
12244 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
12245 while ( it.hasNext() ) {
12246 final PhylogenyNode n = it.next();
12247 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
12251 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
12252 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
12253 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
12254 SupportCount.count( t0_3, phylogenies_3, true, false );
12255 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
12256 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
12259 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
12262 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
12265 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
12268 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
12271 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
12274 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
12277 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
12280 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
12283 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
12286 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12287 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
12288 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
12289 SupportCount.count( t0_4, phylogenies_4, true, false );
12290 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
12291 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
12294 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
12297 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
12300 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
12303 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
12306 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
12309 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
12312 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
12315 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
12318 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
12321 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12322 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12323 double d = SupportCount.compare( b1, a, true, true, true );
12324 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12327 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12328 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12329 d = SupportCount.compare( b2, a, true, true, true );
12330 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12333 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12334 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12335 d = SupportCount.compare( b3, a, true, true, true );
12336 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12339 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12340 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12341 d = SupportCount.compare( b4, a, true, true, false );
12342 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12346 catch ( final Exception e ) {
12347 e.printStackTrace( System.out );
12353 private static boolean testSupportTransfer() {
12355 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12356 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)",
12357 new NHXParser() )[ 0 ];
12358 final Phylogeny p2 = factory
12359 .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 ];
12360 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12363 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12366 support_transfer.moveBranchLengthsToBootstrap( p1 );
12367 support_transfer.transferSupportValues( p1, p2 );
12368 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12371 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12374 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12377 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12380 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12383 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12386 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12389 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12393 catch ( final Exception e ) {
12394 e.printStackTrace( System.out );
12400 private static boolean testTaxonomyExtraction() {
12402 final PhylogenyNode n0 = PhylogenyNode
12403 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12404 if ( n0.getNodeData().isHasTaxonomy() ) {
12407 final PhylogenyNode n1 = PhylogenyNode
12408 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12409 if ( n1.getNodeData().isHasTaxonomy() ) {
12410 System.out.println( n1.toString() );
12413 final PhylogenyNode n2x = PhylogenyNode
12414 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12415 if ( n2x.getNodeData().isHasTaxonomy() ) {
12418 final PhylogenyNode n3 = PhylogenyNode
12419 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12420 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12421 System.out.println( n3.toString() );
12424 final PhylogenyNode n4 = PhylogenyNode
12425 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12426 if ( n4.getNodeData().isHasTaxonomy() ) {
12427 System.out.println( n4.toString() );
12430 final PhylogenyNode n5 = PhylogenyNode
12431 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12432 if ( n5.getNodeData().isHasTaxonomy() ) {
12433 System.out.println( n5.toString() );
12436 final PhylogenyNode n6 = PhylogenyNode
12437 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12438 if ( n6.getNodeData().isHasTaxonomy() ) {
12439 System.out.println( n6.toString() );
12442 final PhylogenyNode n7 = PhylogenyNode
12443 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12444 if ( n7.getNodeData().isHasTaxonomy() ) {
12445 System.out.println( n7.toString() );
12448 final PhylogenyNode n8 = PhylogenyNode
12449 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12450 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12451 System.out.println( n8.toString() );
12454 final PhylogenyNode n9 = PhylogenyNode
12455 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12456 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12457 System.out.println( n9.toString() );
12460 final PhylogenyNode n10x = PhylogenyNode
12461 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12462 if ( n10x.getNodeData().isHasTaxonomy() ) {
12463 System.out.println( n10x.toString() );
12466 final PhylogenyNode n10xx = PhylogenyNode
12467 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12468 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12469 System.out.println( n10xx.toString() );
12472 final PhylogenyNode n10 = PhylogenyNode
12473 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12474 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12475 System.out.println( n10.toString() );
12478 final PhylogenyNode n11 = PhylogenyNode
12479 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12480 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12481 System.out.println( n11.toString() );
12484 final PhylogenyNode n12 = PhylogenyNode
12485 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12486 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12487 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12488 System.out.println( n12.toString() );
12491 final PhylogenyNode n13 = PhylogenyNode
12492 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12493 if ( n13.getNodeData().isHasTaxonomy() ) {
12494 System.out.println( n13.toString() );
12497 final PhylogenyNode n14 = PhylogenyNode
12498 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12499 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12500 System.out.println( n14.toString() );
12503 final PhylogenyNode n15 = PhylogenyNode
12504 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12505 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12506 System.out.println( n15.toString() );
12509 final PhylogenyNode n16 = PhylogenyNode
12510 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12511 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12512 System.out.println( n16.toString() );
12515 final PhylogenyNode n17 = PhylogenyNode
12516 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12517 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12518 System.out.println( n17.toString() );
12521 final PhylogenyNode n18 = PhylogenyNode
12522 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12523 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12524 System.out.println( n18.toString() );
12527 final PhylogenyNode n19 = PhylogenyNode
12528 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12529 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12530 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12531 System.out.println( n19.toString() );
12534 final PhylogenyNode n20 = PhylogenyNode
12535 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12536 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12537 System.out.println( n20.toString() );
12540 final PhylogenyNode n21 = PhylogenyNode
12541 .createInstanceFromNhxString( "Mus musculus musculus K392",
12542 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12543 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12544 System.out.println( n21.toString() );
12547 final PhylogenyNode n23 = PhylogenyNode
12548 .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
12549 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12550 if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12551 System.out.println( n23.toString() );
12554 final PhylogenyNode n24 = PhylogenyNode
12555 .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12556 if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12557 System.out.println( n24.toString() );
12561 final PhylogenyNode n25 = PhylogenyNode
12562 .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
12563 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12564 if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
12565 System.out.println( n25.toString() );
12568 final PhylogenyNode n26 = PhylogenyNode
12569 .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
12570 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12571 if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12572 System.out.println( n26.toString() );
12575 final PhylogenyNode n27 = PhylogenyNode
12576 .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12577 if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12578 System.out.println( n27.toString() );
12582 catch ( final Exception e ) {
12583 e.printStackTrace( System.out );
12589 private static boolean testTreeCopy() {
12591 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12592 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12593 final Phylogeny t1 = t0.copy();
12594 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12597 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12600 t0.deleteSubtree( t0.getNode( "c" ), true );
12601 t0.deleteSubtree( t0.getNode( "a" ), true );
12602 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12603 t0.getNode( "b" ).setName( "Bee" );
12604 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12607 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12610 t0.deleteSubtree( t0.getNode( "e" ), true );
12611 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12612 t0.deleteSubtree( t0.getNode( "d" ), true );
12613 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12617 catch ( final Exception e ) {
12618 e.printStackTrace();
12624 private static boolean testTreeMethods() {
12626 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12627 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12628 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12629 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12630 System.out.println( t0.toNewHampshireX() );
12633 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12634 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12635 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12638 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12641 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12645 catch ( final Exception e ) {
12646 e.printStackTrace( System.out );
12652 private static boolean testUniprotEntryRetrieval() {
12654 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
12655 if ( !entry.getAccession().equals( "P12345" ) ) {
12658 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12661 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12664 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12667 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12670 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12674 .getMolecularSequence()
12675 .getMolecularSequenceAsString()
12676 .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
12677 || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
12678 System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
12682 catch ( final IOException e ) {
12683 System.out.println();
12684 System.out.println( "the following might be due to absence internet connection:" );
12685 e.printStackTrace( System.out );
12688 catch ( final Exception e ) {
12694 private static boolean testUniprotTaxonomySearch() {
12696 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12698 if ( results.size() != 1 ) {
12701 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12704 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12707 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12710 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12713 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12717 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12718 if ( results.size() != 1 ) {
12721 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12724 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12727 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12730 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12733 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12737 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12738 if ( results.size() != 1 ) {
12741 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12744 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12747 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12750 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12753 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12757 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12758 if ( results.size() != 1 ) {
12761 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12764 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12767 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12770 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12773 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12776 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12779 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12782 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12783 .equals( "Nematostella vectensis" ) ) {
12784 System.out.println( results.get( 0 ).getLineage() );
12789 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12790 if ( results.size() != 1 ) {
12793 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12796 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12799 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12802 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12805 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12808 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12809 .equals( "Xenopus tropicalis" ) ) {
12810 System.out.println( results.get( 0 ).getLineage() );
12815 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12816 if ( results.size() != 1 ) {
12819 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12822 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12825 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12828 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12831 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12834 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12835 .equals( "Xenopus tropicalis" ) ) {
12836 System.out.println( results.get( 0 ).getLineage() );
12841 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12842 if ( results.size() != 1 ) {
12845 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12848 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12851 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12854 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12857 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12860 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12861 .equals( "Xenopus tropicalis" ) ) {
12862 System.out.println( results.get( 0 ).getLineage() );
12866 catch ( final IOException e ) {
12867 System.out.println();
12868 System.out.println( "the following might be due to absence internet connection:" );
12869 e.printStackTrace( System.out );
12872 catch ( final Exception e ) {
12878 private static boolean testWabiTxSearch() {
12880 String result = "";
12881 result = TxSearch.searchSimple( "nematostella" );
12882 result = TxSearch.getTxId( "nematostella" );
12883 if ( !result.equals( "45350" ) ) {
12886 result = TxSearch.getTxName( "45350" );
12887 if ( !result.equals( "Nematostella" ) ) {
12890 result = TxSearch.getTxId( "nematostella vectensis" );
12891 if ( !result.equals( "45351" ) ) {
12894 result = TxSearch.getTxName( "45351" );
12895 if ( !result.equals( "Nematostella vectensis" ) ) {
12898 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12899 if ( !result.equals( "536089" ) ) {
12902 result = TxSearch.getTxName( "536089" );
12903 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12906 final List<String> queries = new ArrayList<String>();
12907 queries.add( "Campylobacter coli" );
12908 queries.add( "Escherichia coli" );
12909 queries.add( "Arabidopsis" );
12910 queries.add( "Trichoplax" );
12911 queries.add( "Samanea saman" );
12912 queries.add( "Kluyveromyces marxianus" );
12913 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12914 queries.add( "Bornavirus parrot/PDD/2008" );
12915 final List<RANKS> ranks = new ArrayList<RANKS>();
12916 ranks.add( RANKS.SUPERKINGDOM );
12917 ranks.add( RANKS.KINGDOM );
12918 ranks.add( RANKS.FAMILY );
12919 ranks.add( RANKS.GENUS );
12920 ranks.add( RANKS.TRIBE );
12921 result = TxSearch.searchLineage( queries, ranks );
12922 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12923 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12925 catch ( final Exception e ) {
12926 System.out.println();
12927 System.out.println( "the following might be due to absence internet connection:" );
12928 e.printStackTrace( System.out );