2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
6 // Copyright (C) 2014 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.test;
27 import java.io.ByteArrayInputStream;
29 import java.io.FileInputStream;
30 import java.io.IOException;
31 import java.io.StringWriter;
32 import java.io.Writer;
34 import java.util.ArrayList;
35 import java.util.Date;
36 import java.util.HashSet;
37 import java.util.Iterator;
38 import java.util.List;
39 import java.util.Locale;
41 import java.util.SortedSet;
43 import org.forester.application.support_transfer;
44 import org.forester.archaeopteryx.AptxUtil;
45 import org.forester.archaeopteryx.TreePanelUtil;
46 import org.forester.archaeopteryx.webservices.WebserviceUtil;
47 import org.forester.development.DevelopmentTools;
48 import org.forester.evoinference.TestPhylogenyReconstruction;
49 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
50 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
51 import org.forester.go.TestGo;
52 import org.forester.io.parsers.FastaParser;
53 import org.forester.io.parsers.GeneralMsaParser;
54 import org.forester.io.parsers.HmmscanPerDomainTableParser;
55 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
56 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
57 import org.forester.io.parsers.nexus.NexusCharactersParser;
58 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
59 import org.forester.io.parsers.nhx.NHXParser;
60 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
61 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
62 import org.forester.io.parsers.tol.TolParser;
63 import org.forester.io.parsers.util.ParserUtils;
64 import org.forester.io.writers.PhylogenyWriter;
65 import org.forester.io.writers.SequenceWriter;
66 import org.forester.msa.BasicMsa;
67 import org.forester.msa.DeleteableMsa;
68 import org.forester.msa.Mafft;
69 import org.forester.msa.Msa;
70 import org.forester.msa.Msa.MSA_FORMAT;
71 import org.forester.msa.MsaInferrer;
72 import org.forester.msa.MsaMethods;
73 import org.forester.pccx.TestPccx;
74 import org.forester.phylogeny.Phylogeny;
75 import org.forester.phylogeny.PhylogenyBranch;
76 import org.forester.phylogeny.PhylogenyMethods;
77 import org.forester.phylogeny.PhylogenyNode;
78 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
79 import org.forester.phylogeny.data.Accession;
80 import org.forester.phylogeny.data.Accession.Source;
81 import org.forester.phylogeny.data.BinaryCharacters;
82 import org.forester.phylogeny.data.BranchWidth;
83 import org.forester.phylogeny.data.Confidence;
84 import org.forester.phylogeny.data.Distribution;
85 import org.forester.phylogeny.data.DomainArchitecture;
86 import org.forester.phylogeny.data.Event;
87 import org.forester.phylogeny.data.Identifier;
88 import org.forester.phylogeny.data.PhylogenyData;
89 import org.forester.phylogeny.data.PhylogenyDataUtil;
90 import org.forester.phylogeny.data.Polygon;
91 import org.forester.phylogeny.data.PropertiesMap;
92 import org.forester.phylogeny.data.Property;
93 import org.forester.phylogeny.data.Property.AppliesTo;
94 import org.forester.phylogeny.data.ProteinDomain;
95 import org.forester.phylogeny.data.Taxonomy;
96 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
97 import org.forester.phylogeny.factories.PhylogenyFactory;
98 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
99 import org.forester.protein.BasicDomain;
100 import org.forester.protein.BasicProtein;
101 import org.forester.protein.Domain;
102 import org.forester.protein.Protein;
103 import org.forester.protein.ProteinId;
104 import org.forester.rio.TestRIO;
105 import org.forester.sdi.SDI;
106 import org.forester.sdi.SDIR;
107 import org.forester.sdi.TestGSDI;
108 import org.forester.sequence.BasicSequence;
109 import org.forester.sequence.MolecularSequence;
110 import org.forester.species.BasicSpecies;
111 import org.forester.species.Species;
112 import org.forester.surfacing.TestSurfacing;
113 import org.forester.tools.ConfidenceAssessor;
114 import org.forester.tools.SupportCount;
115 import org.forester.tools.TreeSplitMatrix;
116 import org.forester.util.AsciiHistogram;
117 import org.forester.util.BasicDescriptiveStatistics;
118 import org.forester.util.BasicTable;
119 import org.forester.util.BasicTableParser;
120 import org.forester.util.DescriptiveStatistics;
121 import org.forester.util.ForesterConstants;
122 import org.forester.util.ForesterUtil;
123 import org.forester.util.GeneralTable;
124 import org.forester.util.SequenceAccessionTools;
125 import org.forester.ws.seqdb.SequenceDatabaseEntry;
126 import org.forester.ws.seqdb.SequenceDbWsTools;
127 import org.forester.ws.seqdb.UniProtTaxonomy;
128 import org.forester.ws.wabi.TxSearch;
129 import org.forester.ws.wabi.TxSearch.RANKS;
130 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
131 import org.forester.ws.wabi.TxSearch.TAX_RANK;
133 @SuppressWarnings( "unused")
134 public final class Test {
136 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
137 + ForesterUtil.getFileSeparator() + "resources"
138 + ForesterUtil.getFileSeparator();
139 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
140 + ForesterUtil.getFileSeparator() + "test_data"
141 + ForesterUtil.getFileSeparator();
142 private final static boolean PERFORM_DB_TESTS = true;
143 private static final boolean PERFORM_WEB_TREE_ACCESS = true;
144 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
145 + ForesterConstants.PHYLO_XML_VERSION + "/"
146 + ForesterConstants.PHYLO_XML_XSD;
147 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
148 + ForesterConstants.PHYLO_XML_VERSION + "/"
149 + ForesterConstants.PHYLO_XML_XSD;
150 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
151 private final static double ZERO_DIFF = 1.0E-9;
153 public static boolean isEqual( final double a, final double b ) {
154 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
157 public static void main( final String[] args ) {
158 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
159 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
161 Locale.setDefault( Locale.US );
162 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
165 System.out.print( "[Test if directory with files for testing exists/is readable: " );
166 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
171 System.out.println( "Testing aborted." );
174 System.out.print( "[Test if resources directory exists/is readable: " );
175 if ( testDir( PATH_TO_RESOURCES ) ) {
176 System.out.println( "OK.]" );
179 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
180 System.out.println( "Testing aborted." );
183 final long start_time = new Date().getTime();
184 System.out.print( "Basic node methods: " );
185 if ( Test.testBasicNodeMethods() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Protein id: " );
194 if ( !testProteinId() ) {
195 System.out.println( "failed." );
201 System.out.println( "OK." );
202 System.out.print( "Species: " );
203 if ( !testSpecies() ) {
204 System.out.println( "failed." );
210 System.out.println( "OK." );
211 System.out.print( "Basic domain: " );
212 if ( !testBasicDomain() ) {
213 System.out.println( "failed." );
219 System.out.println( "OK." );
220 System.out.print( "Basic protein: " );
221 if ( !testBasicProtein() ) {
222 System.out.println( "failed." );
228 System.out.println( "OK." );
229 System.out.print( "Sequence writer: " );
230 if ( testSequenceWriter() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "Sequence id parsing: " );
239 if ( testSequenceIdParsing() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "UniProtKB id extraction: " );
248 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "Sequence DB tools 1: " );
257 if ( testSequenceDbWsTools1() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "Hmmscan output parser: " );
266 if ( testHmmscanOutputParser() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "Overlap removal: " );
275 if ( !org.forester.test.Test.testOverlapRemoval() ) {
276 System.out.println( "failed." );
282 System.out.println( "OK." );
283 System.out.print( "Engulfing overlap removal: " );
284 if ( !Test.testEngulfingOverlapRemoval() ) {
285 System.out.println( "failed." );
291 System.out.println( "OK." );
292 System.out.print( "Taxonomy data extraction: " );
293 if ( Test.testExtractTaxonomyDataFromNodeName() ) {
294 System.out.println( "OK." );
298 System.out.println( "failed." );
301 System.out.print( "Taxonomy code extraction: " );
302 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "SN extraction: " );
311 if ( Test.testExtractSNFromNodeName() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "Taxonomy extraction (general): " );
320 if ( Test.testTaxonomyExtraction() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Uri for Aptx web sequence accession: " );
329 if ( Test.testCreateUriForSeqWeb() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "Basic node construction and parsing of NHX (node level): " );
338 if ( Test.testNHXNodeParsing() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "NHX parsing iterating: " );
347 if ( Test.testNHParsingIter() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "NH parsing: " );
356 if ( Test.testNHParsing() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "Conversion to NHX (node level): " );
365 if ( Test.testNHXconversion() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "NHX parsing: " );
374 if ( Test.testNHXParsing() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "NHX parsing with quotes: " );
383 if ( Test.testNHXParsingQuotes() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "NHX parsing (MrBayes): " );
392 if ( Test.testNHXParsingMB() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "Nexus characters parsing: " );
401 if ( Test.testNexusCharactersParsing() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Nexus tree parsing iterating: " );
410 if ( Test.testNexusTreeParsingIterating() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Nexus tree parsing: " );
419 if ( Test.testNexusTreeParsing() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Nexus tree parsing (translating): " );
428 if ( Test.testNexusTreeParsingTranslating() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Nexus matrix parsing: " );
437 if ( Test.testNexusMatrixParsing() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Basic phyloXML parsing: " );
446 if ( Test.testBasicPhyloXMLparsing() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Basic phyloXML parsing (validating against schema): " );
455 if ( testBasicPhyloXMLparsingValidating() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
464 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "phyloXML Distribution Element: " );
473 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "Tol XML parsing: " );
482 if ( Test.testBasicTolXMLparsing() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "Copying of node data: " );
491 if ( Test.testCopyOfNodeData() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Tree copy: " );
500 if ( Test.testTreeCopy() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "Basic tree methods: " );
509 if ( Test.testBasicTreeMethods() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "Tree methods: " );
518 if ( Test.testTreeMethods() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Postorder Iterator: " );
527 if ( Test.testPostOrderIterator() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Preorder Iterator: " );
536 if ( Test.testPreOrderIterator() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Levelorder Iterator: " );
545 if ( Test.testLevelOrderIterator() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Re-id methods: " );
554 if ( Test.testReIdMethods() ) {
555 System.out.println( "OK." );
559 System.out.println( "failed." );
562 System.out.print( "Methods on last external nodes: " );
563 if ( Test.testLastExternalNodeMethods() ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "Methods on external nodes: " );
572 if ( Test.testExternalNodeRelatedMethods() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "Deletion of external nodes: " );
581 if ( Test.testDeletionOfExternalNodes() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Subtree deletion: " );
590 if ( Test.testSubtreeDeletion() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Phylogeny branch: " );
599 if ( Test.testPhylogenyBranch() ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Rerooting: " );
608 if ( Test.testRerooting() ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "Mipoint rooting: " );
617 if ( Test.testMidpointrooting() ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Node removal: " );
626 if ( Test.testNodeRemoval() ) {
627 System.out.println( "OK." );
631 System.out.println( "failed." );
634 System.out.print( "Support count: " );
635 if ( Test.testSupportCount() ) {
636 System.out.println( "OK." );
640 System.out.println( "failed." );
643 System.out.print( "Support transfer: " );
644 if ( Test.testSupportTransfer() ) {
645 System.out.println( "OK." );
649 System.out.println( "failed." );
652 System.out.print( "Finding of LCA: " );
653 if ( Test.testGetLCA() ) {
654 System.out.println( "OK." );
658 System.out.println( "failed." );
661 System.out.print( "Finding of LCA 2: " );
662 if ( Test.testGetLCA2() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Calculation of distance between nodes: " );
671 if ( Test.testGetDistance() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 System.out.print( "Descriptive statistics: " );
680 if ( Test.testDescriptiveStatistics() ) {
681 System.out.println( "OK." );
685 System.out.println( "failed." );
688 System.out.print( "Data objects and methods: " );
689 if ( Test.testDataObjects() ) {
690 System.out.println( "OK." );
694 System.out.println( "failed." );
697 System.out.print( "Properties map: " );
698 if ( Test.testPropertiesMap() ) {
699 System.out.println( "OK." );
703 System.out.println( "failed." );
706 System.out.print( "SDIse: " );
707 if ( Test.testSDIse() ) {
708 System.out.println( "OK." );
712 System.out.println( "failed." );
715 System.out.print( "SDIunrooted: " );
716 if ( Test.testSDIunrooted() ) {
717 System.out.println( "OK." );
721 System.out.println( "failed." );
724 System.out.print( "GSDI: " );
725 if ( TestGSDI.test() ) {
726 System.out.println( "OK." );
730 System.out.println( "failed." );
733 System.out.print( "RIO: " );
734 if ( TestRIO.test() ) {
735 System.out.println( "OK." );
739 System.out.println( "failed." );
742 System.out.print( "Phylogeny reconstruction:" );
743 System.out.println();
744 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
745 System.out.println( "OK." );
749 System.out.println( "failed." );
752 System.out.print( "Analysis of domain architectures: " );
753 System.out.println();
754 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
755 System.out.println( "OK." );
759 System.out.println( "failed." );
762 System.out.print( "GO: " );
763 System.out.println();
764 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
765 System.out.println( "OK." );
769 System.out.println( "failed." );
772 System.out.print( "Modeling tools: " );
773 if ( TestPccx.test() ) {
774 System.out.println( "OK." );
778 System.out.println( "failed." );
781 System.out.print( "Split Matrix strict: " );
782 if ( Test.testSplitStrict() ) {
783 System.out.println( "OK." );
787 System.out.println( "failed." );
790 System.out.print( "Split Matrix: " );
791 if ( Test.testSplit() ) {
792 System.out.println( "OK." );
796 System.out.println( "failed." );
799 System.out.print( "Confidence Assessor: " );
800 if ( Test.testConfidenceAssessor() ) {
801 System.out.println( "OK." );
805 System.out.println( "failed." );
808 System.out.print( "Basic table: " );
809 if ( Test.testBasicTable() ) {
810 System.out.println( "OK." );
814 System.out.println( "failed." );
817 System.out.print( "General table: " );
818 if ( Test.testGeneralTable() ) {
819 System.out.println( "OK." );
823 System.out.println( "failed." );
826 System.out.print( "Amino acid sequence: " );
827 if ( Test.testAminoAcidSequence() ) {
828 System.out.println( "OK." );
832 System.out.println( "failed." );
835 System.out.print( "General MSA parser: " );
836 if ( Test.testGeneralMsaParser() ) {
837 System.out.println( "OK." );
841 System.out.println( "failed." );
844 System.out.print( "Fasta parser for msa: " );
845 if ( Test.testFastaParser() ) {
846 System.out.println( "OK." );
850 System.out.println( "failed." );
853 System.out.print( "Creation of balanced phylogeny: " );
854 if ( Test.testCreateBalancedPhylogeny() ) {
855 System.out.println( "OK." );
859 System.out.println( "failed." );
862 System.out.print( "Genbank accessor parsing: " );
863 if ( Test.testGenbankAccessorParsing() ) {
864 System.out.println( "OK." );
868 System.out.println( "failed." );
872 final String os = ForesterUtil.OS_NAME.toLowerCase();
873 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
874 path = "/usr/local/bin/mafft";
876 else if ( os.indexOf( "win" ) >= 0 ) {
877 path = "C:\\Program Files\\mafft-win\\mafft.bat";
881 if ( !MsaInferrer.isInstalled( path ) ) {
882 path = "/usr/bin/mafft";
884 if ( !MsaInferrer.isInstalled( path ) ) {
885 path = "/usr/local/bin/mafft";
888 if ( MsaInferrer.isInstalled( path ) ) {
889 System.out.print( "MAFFT (external program): " );
890 if ( Test.testMafft( path ) ) {
891 System.out.println( "OK." );
895 System.out.println( "failed [will not count towards failed tests]" );
898 System.out.print( "Next nodes with collapsed: " );
899 if ( Test.testNextNodeWithCollapsing() ) {
900 System.out.println( "OK." );
904 System.out.println( "failed." );
907 System.out.print( "Simple MSA quality: " );
908 if ( Test.testMsaQualityMethod() ) {
909 System.out.println( "OK." );
913 System.out.println( "failed." );
916 System.out.print( "Deleteable MSA: " );
917 if ( Test.testDeleteableMsa() ) {
918 System.out.println( "OK." );
922 System.out.println( "failed." );
925 System.out.print( "MSA entropy: " );
926 if ( Test.testMsaEntropy() ) {
927 System.out.println( "OK." );
931 System.out.println( "failed." );
934 if ( PERFORM_DB_TESTS ) {
935 System.out.print( "Uniprot Entry Retrieval: " );
936 if ( Test.testUniprotEntryRetrieval() ) {
937 System.out.println( "OK." );
941 System.out.println( "failed." );
944 System.out.print( "Ebi Entry Retrieval: " );
945 if ( Test.testEbiEntryRetrieval() ) {
946 System.out.println( "OK." );
950 System.out.println( "failed." );
953 System.out.print( "Sequence DB tools 2: " );
954 if ( testSequenceDbWsTools2() ) {
955 System.out.println( "OK." );
959 System.out.println( "failed." );
963 System.out.print( "Uniprot Taxonomy Search: " );
964 if ( Test.testUniprotTaxonomySearch() ) {
965 System.out.println( "OK." );
969 System.out.println( "failed." );
973 if ( PERFORM_WEB_TREE_ACCESS ) {
974 System.out.print( "NHX parsing from URL: " );
975 if ( Test.testNHXparsingFromURL() ) {
976 System.out.println( "OK." );
980 System.out.println( "failed." );
983 System.out.print( "NHX parsing from URL 2: " );
984 if ( Test.testNHXparsingFromURL2() ) {
985 System.out.println( "OK." );
989 System.out.println( "failed." );
992 System.out.print( "phyloXML parsing from URL: " );
993 if ( Test.testPhyloXMLparsingFromURL() ) {
994 System.out.println( "OK." );
998 System.out.println( "failed." );
1001 System.out.print( "TreeBase acccess: " );
1002 if ( Test.testTreeBaseReading() ) {
1003 System.out.println( "OK." );
1007 System.out.println( "failed." );
1011 System.out.print( "ToL access: " );
1012 if ( Test.testToLReading() ) {
1013 System.out.println( "OK." );
1017 System.out.println( "failed." );
1021 System.out.print( "TreeFam access: " );
1022 if ( Test.testTreeFamReading() ) {
1023 System.out.println( "OK." );
1027 System.out.println( "failed." );
1032 System.out.print( "Pfam tree access: " );
1033 if ( Test.testPfamTreeReading() ) {
1034 System.out.println( "OK." );
1038 System.out.println( "failed." );
1042 System.out.println();
1043 final Runtime rt = java.lang.Runtime.getRuntime();
1044 final long free_memory = rt.freeMemory() / 1000000;
1045 final long total_memory = rt.totalMemory() / 1000000;
1046 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1047 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1048 System.out.println();
1049 System.out.println( "Successful tests: " + succeeded );
1050 System.out.println( "Failed tests: " + failed );
1051 System.out.println();
1053 System.out.println( "OK." );
1056 System.out.println( "Not OK." );
1060 public static boolean testEngulfingOverlapRemoval() {
1062 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1063 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
1064 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
1065 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1066 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1067 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
1068 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1069 final List<Boolean> covered = new ArrayList<Boolean>();
1070 covered.add( true ); // 0
1071 covered.add( false ); // 1
1072 covered.add( true ); // 2
1073 covered.add( false ); // 3
1074 covered.add( true ); // 4
1075 covered.add( true ); // 5
1076 covered.add( false ); // 6
1077 covered.add( true ); // 7
1078 covered.add( true ); // 8
1079 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
1082 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
1085 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
1088 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
1091 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
1094 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
1097 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
1100 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1101 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
1102 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
1103 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
1104 abc.addProteinDomain( a );
1105 abc.addProteinDomain( b );
1106 abc.addProteinDomain( c );
1107 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
1108 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
1109 if ( abc.getNumberOfProteinDomains() != 3 ) {
1112 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
1115 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
1118 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
1121 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
1124 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1125 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
1126 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
1127 final Protein def = new BasicProtein( "def", "nemve", 0 );
1128 def.addProteinDomain( d );
1129 def.addProteinDomain( e );
1130 def.addProteinDomain( f );
1131 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
1132 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
1133 if ( def.getNumberOfProteinDomains() != 3 ) {
1136 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
1139 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
1142 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
1145 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
1148 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
1152 catch ( final Exception e ) {
1153 e.printStackTrace( System.out );
1159 public static final boolean testNHXparsingFromURL2() {
1161 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1162 final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1166 TAXONOMY_EXTRACTION.NO,
1168 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1171 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1172 System.out.println( phys[ 0 ].toNewHampshire() );
1175 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1176 System.out.println( phys[ 1 ].toNewHampshire() );
1179 final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
1183 TAXONOMY_EXTRACTION.NO,
1185 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1188 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1189 System.out.println( phys2[ 0 ].toNewHampshire() );
1192 if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1193 System.out.println( phys2[ 1 ].toNewHampshire() );
1196 final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1197 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1198 if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
1203 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1204 System.out.println( phys3[ 0 ].toNewHampshire() );
1207 final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
1208 + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
1209 if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
1214 .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
1215 System.out.println( phys4[ 0 ].toNewHampshire() );
1219 catch ( final Exception e ) {
1220 e.printStackTrace();
1226 public static final boolean testNHXparsingFromURL() {
1228 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
1229 final URL u = new URL( s );
1230 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1231 final Phylogeny[] phys = factory.create( u, new NHXParser() );
1232 if ( ( phys == null ) || ( phys.length != 5 ) ) {
1235 if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1236 System.out.println( phys[ 0 ].toNewHampshire() );
1239 if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1240 System.out.println( phys[ 1 ].toNewHampshire() );
1243 final URL u2 = new URL( s );
1244 final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
1245 if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
1248 if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1249 System.out.println( phys2[ 0 ].toNewHampshire() );
1252 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1253 final NHXParser p = new NHXParser();
1254 final URL u3 = new URL( s );
1256 if ( !p.hasNext() ) {
1259 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1262 if ( !p.hasNext() ) {
1266 if ( !p.hasNext() ) {
1269 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1272 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1276 if ( !p.hasNext() ) {
1279 if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
1282 if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
1286 catch ( final Exception e ) {
1287 System.out.println( e.toString() );
1288 e.printStackTrace();
1294 public static boolean testOverlapRemoval() {
1296 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
1297 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1298 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
1299 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
1300 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
1301 final List<Boolean> covered = new ArrayList<Boolean>();
1302 covered.add( true ); // 0
1303 covered.add( false ); // 1
1304 covered.add( true ); // 2
1305 covered.add( false ); // 3
1306 covered.add( true ); // 4
1307 covered.add( true ); // 5
1308 covered.add( false ); // 6
1309 covered.add( true ); // 7
1310 covered.add( true ); // 8
1311 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
1314 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
1317 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
1320 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
1323 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
1326 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
1327 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
1328 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
1329 ab.addProteinDomain( a );
1330 ab.addProteinDomain( b );
1331 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
1332 if ( ab.getNumberOfProteinDomains() != 2 ) {
1335 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
1338 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
1341 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
1342 if ( ab.getNumberOfProteinDomains() != 2 ) {
1345 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
1348 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
1349 final Domain d = new BasicDomain( "d",
1356 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
1357 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
1358 cde.addProteinDomain( c );
1359 cde.addProteinDomain( d );
1360 cde.addProteinDomain( e );
1361 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
1362 if ( cde.getNumberOfProteinDomains() != 3 ) {
1365 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
1368 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1369 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1370 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1371 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
1372 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
1373 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
1374 fghi.addProteinDomain( f );
1375 fghi.addProteinDomain( g );
1376 fghi.addProteinDomain( h );
1377 fghi.addProteinDomain( i );
1378 fghi.addProteinDomain( i );
1379 fghi.addProteinDomain( i );
1380 fghi.addProteinDomain( i2 );
1381 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
1382 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1385 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
1388 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
1391 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
1392 if ( fghi.getNumberOfProteinDomains() != 7 ) {
1395 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
1398 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
1399 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
1400 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
1401 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
1402 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
1403 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
1404 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1405 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
1406 jklm.addProteinDomain( j );
1407 jklm.addProteinDomain( k );
1408 jklm.addProteinDomain( l );
1409 jklm.addProteinDomain( m );
1410 jklm.addProteinDomain( m0 );
1411 jklm.addProteinDomain( m1 );
1412 jklm.addProteinDomain( m2 );
1413 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
1414 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1417 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
1420 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
1423 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
1424 if ( jklm.getNumberOfProteinDomains() != 7 ) {
1427 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
1430 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
1431 final Protein od = new BasicProtein( "od", "varanus", 0 );
1432 od.addProteinDomain( only );
1433 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
1434 if ( od.getNumberOfProteinDomains() != 1 ) {
1437 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
1441 catch ( final Exception e ) {
1442 e.printStackTrace( System.out );
1448 public static final boolean testPfamTreeReading() {
1450 final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
1451 final NHXParser parser = new NHXParser();
1452 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1453 parser.setReplaceUnderscores( false );
1454 parser.setGuessRootedness( true );
1455 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1456 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1457 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1460 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1464 catch ( final Exception e ) {
1465 e.printStackTrace();
1470 public static final boolean testPhyloXMLparsingFromURL() {
1472 final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
1473 final URL u = new URL( s );
1474 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1475 final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
1476 if ( ( phys == null ) || ( phys.length != 2 ) ) {
1480 catch ( final Exception e ) {
1481 e.printStackTrace();
1486 public static final boolean testToLReading() {
1488 final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
1489 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1490 final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
1491 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1494 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
1497 if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
1500 if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
1504 catch ( final Exception e ) {
1505 e.printStackTrace();
1510 public static final boolean testTreeBaseReading() {
1512 final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
1513 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
1514 parser.setReplaceUnderscores( true );
1515 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1516 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1517 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1520 final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
1521 final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
1522 parser2.setReplaceUnderscores( true );
1523 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1524 final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
1525 if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
1529 catch ( final Exception e ) {
1530 e.printStackTrace();
1535 public static final boolean testTreeFamReading() {
1537 final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
1538 final NHXParser parser = new NHXParser();
1539 parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
1540 parser.setReplaceUnderscores( false );
1541 parser.setGuessRootedness( true );
1542 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1543 final Phylogeny[] phys = factory.create( u.openStream(), parser );
1544 if ( ( phys == null ) || ( phys.length != 1 ) ) {
1547 if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
1551 catch ( final Exception e ) {
1552 e.printStackTrace();
1557 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1558 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1562 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1563 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1566 private static boolean testAminoAcidSequence() {
1568 final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1569 if ( aa1.getLength() != 13 ) {
1572 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1575 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1578 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1581 final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1582 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
1585 final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1586 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1589 final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1590 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1594 catch ( final Exception e ) {
1595 e.printStackTrace();
1601 private static boolean testBasicDomain() {
1603 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1604 if ( !pd.getDomainId().equals( "id" ) ) {
1607 if ( pd.getNumber() != 1 ) {
1610 if ( pd.getTotalCount() != 4 ) {
1613 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1616 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1617 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1618 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1619 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1620 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1621 if ( !a1.equals( a1 ) ) {
1624 if ( !a1.equals( a1_copy ) ) {
1627 if ( !a1.equals( a1_equal ) ) {
1630 if ( !a1.equals( a2 ) ) {
1633 if ( a1.equals( a3 ) ) {
1636 if ( a1.compareTo( a1 ) != 0 ) {
1639 if ( a1.compareTo( a1_copy ) != 0 ) {
1642 if ( a1.compareTo( a1_equal ) != 0 ) {
1645 if ( a1.compareTo( a2 ) != 0 ) {
1648 if ( a1.compareTo( a3 ) == 0 ) {
1652 catch ( final Exception e ) {
1653 e.printStackTrace( System.out );
1659 private static boolean testBasicNodeMethods() {
1661 if ( PhylogenyNode.getNodeCount() != 0 ) {
1664 final PhylogenyNode n1 = new PhylogenyNode();
1665 final PhylogenyNode n2 = PhylogenyNode
1666 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1667 final PhylogenyNode n3 = PhylogenyNode
1668 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1669 final PhylogenyNode n4 = PhylogenyNode
1670 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1671 if ( n1.isHasAssignedEvent() ) {
1674 if ( PhylogenyNode.getNodeCount() != 4 ) {
1677 if ( n3.getIndicator() != 0 ) {
1680 if ( n3.getNumberOfExternalNodes() != 1 ) {
1683 if ( !n3.isExternal() ) {
1686 if ( !n3.isRoot() ) {
1689 if ( !n4.getName().equals( "n4" ) ) {
1693 catch ( final Exception e ) {
1694 e.printStackTrace( System.out );
1700 private static boolean testBasicPhyloXMLparsing() {
1702 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1703 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1704 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1706 if ( xml_parser.getErrorCount() > 0 ) {
1707 System.out.println( xml_parser.getErrorMessages().toString() );
1710 if ( phylogenies_0.length != 4 ) {
1713 final Phylogeny t1 = phylogenies_0[ 0 ];
1714 final Phylogeny t2 = phylogenies_0[ 1 ];
1715 final Phylogeny t3 = phylogenies_0[ 2 ];
1716 final Phylogeny t4 = phylogenies_0[ 3 ];
1717 if ( t1.getNumberOfExternalNodes() != 1 ) {
1720 if ( !t1.isRooted() ) {
1723 if ( t1.isRerootable() ) {
1726 if ( !t1.getType().equals( "gene_tree" ) ) {
1729 if ( t2.getNumberOfExternalNodes() != 2 ) {
1732 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1735 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1738 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1741 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1744 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1747 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1750 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1751 .startsWith( "actgtgggggt" ) ) {
1754 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1755 .startsWith( "ctgtgatgcat" ) ) {
1758 if ( t3.getNumberOfExternalNodes() != 4 ) {
1761 if ( !t1.getName().equals( "t1" ) ) {
1764 if ( !t2.getName().equals( "t2" ) ) {
1767 if ( !t3.getName().equals( "t3" ) ) {
1770 if ( !t4.getName().equals( "t4" ) ) {
1773 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1776 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1779 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1782 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1783 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1786 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1789 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1792 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1795 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1796 .equals( "apoptosis" ) ) {
1799 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1800 .equals( "GO:0006915" ) ) {
1803 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1804 .equals( "UniProtKB" ) ) {
1807 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1808 .equals( "experimental" ) ) {
1811 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1812 .equals( "function" ) ) {
1815 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1816 .getValue() != 1 ) {
1819 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1820 .getType().equals( "ml" ) ) {
1823 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1824 .equals( "apoptosis" ) ) {
1827 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1828 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1831 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1832 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1835 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1836 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1839 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1840 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1843 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1844 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1847 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1848 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1851 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1852 .equals( "GO:0005829" ) ) {
1855 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1856 .equals( "intracellular organelle" ) ) {
1859 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1862 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1863 .equals( "UniProt link" ) ) ) {
1866 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1869 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1870 if ( x.size() != 4 ) {
1874 for( final Accession acc : x ) {
1876 if ( !acc.getSource().equals( "KEGG" ) ) {
1879 if ( !acc.getValue().equals( "hsa:596" ) ) {
1886 catch ( final Exception e ) {
1887 e.printStackTrace( System.out );
1893 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1896 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1897 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1898 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1901 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1903 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1905 if ( xml_parser.getErrorCount() > 0 ) {
1906 System.out.println( xml_parser.getErrorMessages().toString() );
1909 if ( phylogenies_0.length != 4 ) {
1912 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1913 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1914 if ( phylogenies_t1.length != 1 ) {
1917 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1918 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1921 if ( !t1_rt.isRooted() ) {
1924 if ( t1_rt.isRerootable() ) {
1927 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1930 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1931 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1932 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1933 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1936 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1939 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1942 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1945 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1946 .startsWith( "actgtgggggt" ) ) {
1949 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1950 .startsWith( "ctgtgatgcat" ) ) {
1953 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1954 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1955 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1956 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1957 if ( phylogenies_1.length != 1 ) {
1960 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1961 if ( !t3_rt.getName().equals( "t3" ) ) {
1964 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1967 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1970 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1973 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1976 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1977 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1980 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1983 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1986 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1987 .equals( "UniProtKB" ) ) {
1990 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1991 .equals( "apoptosis" ) ) {
1994 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1995 .equals( "GO:0006915" ) ) {
1998 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1999 .equals( "UniProtKB" ) ) {
2002 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
2003 .equals( "experimental" ) ) {
2006 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
2007 .equals( "function" ) ) {
2010 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2011 .getValue() != 1 ) {
2014 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
2015 .getType().equals( "ml" ) ) {
2018 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
2019 .equals( "apoptosis" ) ) {
2022 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2023 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
2026 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2027 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
2030 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2031 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
2034 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2035 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
2038 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2039 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
2042 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
2043 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
2046 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
2047 .equals( "GO:0005829" ) ) {
2050 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
2051 .equals( "intracellular organelle" ) ) {
2054 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
2057 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
2058 .equals( "UniProt link" ) ) ) {
2061 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
2064 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
2067 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
2068 .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
2071 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
2074 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
2077 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
2080 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
2083 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
2084 .equals( "ncbi" ) ) {
2087 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
2090 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2091 .getName().equals( "B" ) ) {
2094 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2095 .getFrom() != 21 ) {
2098 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
2101 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2102 .getLength() != 24 ) {
2105 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
2106 .getConfidence() != 0 ) {
2109 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
2110 .equals( "pfam" ) ) {
2113 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
2116 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2119 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
2122 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
2125 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
2126 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
2129 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
2132 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
2135 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
2138 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
2141 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
2144 if ( taxbb.getSynonyms().size() != 2 ) {
2147 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
2150 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
2153 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
2156 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
2159 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
2162 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
2163 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
2166 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
2169 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
2172 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
2175 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
2178 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
2181 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
2184 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
2187 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
2190 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
2191 .equalsIgnoreCase( "435" ) ) {
2194 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
2197 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
2198 .equalsIgnoreCase( "443.7" ) ) {
2201 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
2204 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
2207 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
2208 .equalsIgnoreCase( "433" ) ) {
2211 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
2212 .getCrossReferences();
2213 if ( x.size() != 4 ) {
2217 for( final Accession acc : x ) {
2219 if ( !acc.getSource().equals( "KEGG" ) ) {
2222 if ( !acc.getValue().equals( "hsa:596" ) ) {
2229 catch ( final Exception e ) {
2230 e.printStackTrace( System.out );
2236 private static boolean testBasicPhyloXMLparsingValidating() {
2238 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2239 PhyloXmlParser xml_parser = null;
2241 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
2243 catch ( final Exception e ) {
2244 // Do nothing -- means were not running from jar.
2246 if ( xml_parser == null ) {
2247 xml_parser = PhyloXmlParser.createPhyloXmlParser();
2248 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
2249 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
2252 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
2255 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
2257 if ( xml_parser.getErrorCount() > 0 ) {
2258 System.out.println( xml_parser.getErrorMessages().toString() );
2261 if ( phylogenies_0.length != 4 ) {
2264 final Phylogeny t1 = phylogenies_0[ 0 ];
2265 final Phylogeny t2 = phylogenies_0[ 1 ];
2266 final Phylogeny t3 = phylogenies_0[ 2 ];
2267 final Phylogeny t4 = phylogenies_0[ 3 ];
2268 if ( !t1.getName().equals( "t1" ) ) {
2271 if ( !t2.getName().equals( "t2" ) ) {
2274 if ( !t3.getName().equals( "t3" ) ) {
2277 if ( !t4.getName().equals( "t4" ) ) {
2280 if ( t1.getNumberOfExternalNodes() != 1 ) {
2283 if ( t2.getNumberOfExternalNodes() != 2 ) {
2286 if ( t3.getNumberOfExternalNodes() != 4 ) {
2289 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2290 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2291 if ( xml_parser.getErrorCount() > 0 ) {
2292 System.out.println( "errors:" );
2293 System.out.println( xml_parser.getErrorMessages().toString() );
2296 if ( phylogenies_1.length != 4 ) {
2299 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2301 if ( xml_parser.getErrorCount() > 0 ) {
2302 System.out.println( "errors:" );
2303 System.out.println( xml_parser.getErrorMessages().toString() );
2306 if ( phylogenies_2.length != 1 ) {
2309 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2312 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2314 if ( xml_parser.getErrorCount() > 0 ) {
2315 System.out.println( xml_parser.getErrorMessages().toString() );
2318 if ( phylogenies_3.length != 2 ) {
2321 final Phylogeny a = phylogenies_3[ 0 ];
2322 if ( !a.getName().equals( "tree 4" ) ) {
2325 if ( a.getNumberOfExternalNodes() != 3 ) {
2328 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2331 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2334 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2336 if ( xml_parser.getErrorCount() > 0 ) {
2337 System.out.println( xml_parser.getErrorMessages().toString() );
2340 if ( phylogenies_4.length != 1 ) {
2343 final Phylogeny s = phylogenies_4[ 0 ];
2344 if ( s.getNumberOfExternalNodes() != 6 ) {
2347 s.getNode( "first" );
2349 s.getNode( "\"<a'b&c'd\">\"" );
2350 s.getNode( "'''\"" );
2351 s.getNode( "\"\"\"" );
2352 s.getNode( "dick & doof" );
2354 catch ( final Exception e ) {
2355 e.printStackTrace( System.out );
2361 private static boolean testBasicProtein() {
2363 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2364 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2365 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2366 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2367 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2368 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2369 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2370 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2371 p0.addProteinDomain( y );
2372 p0.addProteinDomain( e );
2373 p0.addProteinDomain( b );
2374 p0.addProteinDomain( c );
2375 p0.addProteinDomain( d );
2376 p0.addProteinDomain( a );
2377 p0.addProteinDomain( x );
2378 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2381 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2385 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2386 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2387 aa0.addProteinDomain( a1 );
2388 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2391 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2395 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2396 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2397 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2398 aa1.addProteinDomain( a11 );
2399 aa1.addProteinDomain( a12 );
2400 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2403 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2406 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2407 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2410 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2413 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2416 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2417 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2420 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2423 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2426 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2429 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2430 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2433 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2436 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2439 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2442 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2443 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2446 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2449 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2452 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2456 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2457 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2458 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2459 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2460 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2461 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2462 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2463 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2464 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2465 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2466 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2467 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2468 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2469 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2470 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2471 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2472 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2473 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2474 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2475 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2476 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2477 p00.addProteinDomain( y0 );
2478 p00.addProteinDomain( e0 );
2479 p00.addProteinDomain( b0 );
2480 p00.addProteinDomain( c0 );
2481 p00.addProteinDomain( d0 );
2482 p00.addProteinDomain( a0 );
2483 p00.addProteinDomain( x0 );
2484 p00.addProteinDomain( y1 );
2485 p00.addProteinDomain( y2 );
2486 p00.addProteinDomain( y3 );
2487 p00.addProteinDomain( e1 );
2488 p00.addProteinDomain( e2 );
2489 p00.addProteinDomain( e3 );
2490 p00.addProteinDomain( e4 );
2491 p00.addProteinDomain( e5 );
2492 p00.addProteinDomain( z0 );
2493 p00.addProteinDomain( z1 );
2494 p00.addProteinDomain( z2 );
2495 p00.addProteinDomain( zz0 );
2496 p00.addProteinDomain( zz1 );
2497 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2500 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2503 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2506 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2509 if ( !p00.toDomainArchitectureString( "~", 7, "" ).equals( "a~b~c~d~e~e~e~e~e~e~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2512 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2513 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2514 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2515 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2516 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2517 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2518 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2519 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2520 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2521 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2522 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2523 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2524 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2525 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2526 p.addProteinDomain( B15 );
2527 p.addProteinDomain( C50 );
2528 p.addProteinDomain( A60 );
2529 p.addProteinDomain( A30 );
2530 p.addProteinDomain( C70 );
2531 p.addProteinDomain( B35 );
2532 p.addProteinDomain( B40 );
2533 p.addProteinDomain( A0 );
2534 p.addProteinDomain( A10 );
2535 p.addProteinDomain( A20 );
2536 p.addProteinDomain( B25 );
2537 p.addProteinDomain( D80 );
2538 List<String> domains_ids = new ArrayList<String>();
2539 domains_ids.add( "A" );
2540 domains_ids.add( "B" );
2541 domains_ids.add( "C" );
2542 if ( !p.contains( domains_ids, false ) ) {
2545 if ( !p.contains( domains_ids, true ) ) {
2548 domains_ids.add( "X" );
2549 if ( p.contains( domains_ids, false ) ) {
2552 if ( p.contains( domains_ids, true ) ) {
2555 domains_ids = new ArrayList<String>();
2556 domains_ids.add( "A" );
2557 domains_ids.add( "C" );
2558 domains_ids.add( "D" );
2559 if ( !p.contains( domains_ids, false ) ) {
2562 if ( !p.contains( domains_ids, true ) ) {
2565 domains_ids = new ArrayList<String>();
2566 domains_ids.add( "A" );
2567 domains_ids.add( "D" );
2568 domains_ids.add( "C" );
2569 if ( !p.contains( domains_ids, false ) ) {
2572 if ( p.contains( domains_ids, true ) ) {
2575 domains_ids = new ArrayList<String>();
2576 domains_ids.add( "A" );
2577 domains_ids.add( "A" );
2578 domains_ids.add( "B" );
2579 if ( !p.contains( domains_ids, false ) ) {
2582 if ( !p.contains( domains_ids, true ) ) {
2585 domains_ids = new ArrayList<String>();
2586 domains_ids.add( "A" );
2587 domains_ids.add( "A" );
2588 domains_ids.add( "A" );
2589 domains_ids.add( "B" );
2590 domains_ids.add( "B" );
2591 if ( !p.contains( domains_ids, false ) ) {
2594 if ( !p.contains( domains_ids, true ) ) {
2597 domains_ids = new ArrayList<String>();
2598 domains_ids.add( "A" );
2599 domains_ids.add( "A" );
2600 domains_ids.add( "B" );
2601 domains_ids.add( "A" );
2602 domains_ids.add( "B" );
2603 domains_ids.add( "B" );
2604 domains_ids.add( "A" );
2605 domains_ids.add( "B" );
2606 domains_ids.add( "C" );
2607 domains_ids.add( "A" );
2608 domains_ids.add( "C" );
2609 domains_ids.add( "D" );
2610 if ( !p.contains( domains_ids, false ) ) {
2613 if ( p.contains( domains_ids, true ) ) {
2617 catch ( final Exception e ) {
2618 e.printStackTrace( System.out );
2624 private static boolean testBasicTable() {
2626 final BasicTable<String> t0 = new BasicTable<String>();
2627 if ( t0.getNumberOfColumns() != 0 ) {
2630 if ( t0.getNumberOfRows() != 0 ) {
2633 t0.setValue( 3, 2, "23" );
2634 t0.setValue( 10, 1, "error" );
2635 t0.setValue( 10, 1, "110" );
2636 t0.setValue( 9, 1, "19" );
2637 t0.setValue( 1, 10, "101" );
2638 t0.setValue( 10, 10, "1010" );
2639 t0.setValue( 100, 10, "10100" );
2640 t0.setValue( 0, 0, "00" );
2641 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2644 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2647 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2650 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2653 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2656 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2659 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2662 if ( t0.getNumberOfColumns() != 101 ) {
2665 if ( t0.getNumberOfRows() != 11 ) {
2668 if ( t0.getValueAsString( 49, 4 ) != null ) {
2671 final String l = ForesterUtil.getLineSeparator();
2672 final StringBuffer source = new StringBuffer();
2673 source.append( "" + l );
2674 source.append( "# 1 1 1 1 1 1 1 1" + l );
2675 source.append( " 00 01 02 03" + l );
2676 source.append( " 10 11 12 13 " + l );
2677 source.append( "20 21 22 23 " + l );
2678 source.append( " 30 31 32 33" + l );
2679 source.append( "40 41 42 43" + l );
2680 source.append( " # 1 1 1 1 1 " + l );
2681 source.append( "50 51 52 53 54" + l );
2682 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2683 if ( t1.getNumberOfColumns() != 5 ) {
2686 if ( t1.getNumberOfRows() != 6 ) {
2689 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2692 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2695 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2698 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2701 final StringBuffer source1 = new StringBuffer();
2702 source1.append( "" + l );
2703 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2704 source1.append( " 00; 01 ;02;03" + l );
2705 source1.append( " 10; 11; 12; 13 " + l );
2706 source1.append( "20; 21; 22; 23 " + l );
2707 source1.append( " 30; 31; 32; 33" + l );
2708 source1.append( "40;41;42;43" + l );
2709 source1.append( " # 1 1 1 1 1 " + l );
2710 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2711 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2712 if ( t2.getNumberOfColumns() != 5 ) {
2715 if ( t2.getNumberOfRows() != 6 ) {
2718 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2721 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2724 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2727 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2730 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2733 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2736 final StringBuffer source2 = new StringBuffer();
2737 source2.append( "" + l );
2738 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2739 source2.append( " 00; 01 ;02;03" + l );
2740 source2.append( " 10; 11; 12; 13 " + l );
2741 source2.append( "20; 21; 22; 23 " + l );
2742 source2.append( " " + l );
2743 source2.append( " 30; 31; 32; 33" + l );
2744 source2.append( "40;41;42;43" + l );
2745 source2.append( " comment: 1 1 1 1 1 " + l );
2746 source2.append( ";;;50 ; 52; 53;;54 " + l );
2747 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2753 if ( tl.size() != 2 ) {
2756 final BasicTable<String> t3 = tl.get( 0 );
2757 final BasicTable<String> t4 = tl.get( 1 );
2758 if ( t3.getNumberOfColumns() != 4 ) {
2761 if ( t3.getNumberOfRows() != 3 ) {
2764 if ( t4.getNumberOfColumns() != 4 ) {
2767 if ( t4.getNumberOfRows() != 3 ) {
2770 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2773 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2777 catch ( final Exception e ) {
2778 e.printStackTrace( System.out );
2784 private static boolean testBasicTolXMLparsing() {
2786 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2787 final TolParser parser = new TolParser();
2788 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2789 if ( parser.getErrorCount() > 0 ) {
2790 System.out.println( parser.getErrorMessages().toString() );
2793 if ( phylogenies_0.length != 1 ) {
2796 final Phylogeny t1 = phylogenies_0[ 0 ];
2797 if ( t1.getNumberOfExternalNodes() != 5 ) {
2800 if ( !t1.isRooted() ) {
2803 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2806 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2809 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2812 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2815 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2816 if ( parser.getErrorCount() > 0 ) {
2817 System.out.println( parser.getErrorMessages().toString() );
2820 if ( phylogenies_1.length != 1 ) {
2823 final Phylogeny t2 = phylogenies_1[ 0 ];
2824 if ( t2.getNumberOfExternalNodes() != 664 ) {
2827 if ( !t2.isRooted() ) {
2830 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2833 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2836 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2839 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2842 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2845 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2846 .equals( "Aquifex" ) ) {
2849 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2850 if ( parser.getErrorCount() > 0 ) {
2851 System.out.println( parser.getErrorMessages().toString() );
2854 if ( phylogenies_2.length != 1 ) {
2857 final Phylogeny t3 = phylogenies_2[ 0 ];
2858 if ( t3.getNumberOfExternalNodes() != 184 ) {
2861 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2864 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2867 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2870 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2871 if ( parser.getErrorCount() > 0 ) {
2872 System.out.println( parser.getErrorMessages().toString() );
2875 if ( phylogenies_3.length != 1 ) {
2878 final Phylogeny t4 = phylogenies_3[ 0 ];
2879 if ( t4.getNumberOfExternalNodes() != 1 ) {
2882 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2885 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2888 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2891 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2892 if ( parser.getErrorCount() > 0 ) {
2893 System.out.println( parser.getErrorMessages().toString() );
2896 if ( phylogenies_4.length != 1 ) {
2899 final Phylogeny t5 = phylogenies_4[ 0 ];
2900 if ( t5.getNumberOfExternalNodes() != 13 ) {
2903 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2906 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2909 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2913 catch ( final Exception e ) {
2914 e.printStackTrace( System.out );
2920 private static boolean testBasicTreeMethods() {
2922 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2923 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2924 if ( t2.getNumberOfExternalNodes() != 4 ) {
2927 if ( t2.getHeight() != 8.5 ) {
2930 if ( !t2.isCompletelyBinary() ) {
2933 if ( t2.isEmpty() ) {
2936 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2937 if ( t3.getNumberOfExternalNodes() != 5 ) {
2940 if ( t3.getHeight() != 11 ) {
2943 if ( t3.isCompletelyBinary() ) {
2946 final PhylogenyNode n = t3.getNode( "ABC" );
2947 final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
2948 if ( t4.getNumberOfExternalNodes() != 9 ) {
2951 if ( t4.getHeight() != 11 ) {
2954 if ( t4.isCompletelyBinary() ) {
2957 final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
2958 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2959 if ( t5.getNumberOfExternalNodes() != 8 ) {
2962 if ( t5.getHeight() != 15 ) {
2965 final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
2966 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2967 if ( t6.getHeight() != 15 ) {
2970 final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
2971 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2972 if ( t7.getHeight() != 15 ) {
2975 final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
2976 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2977 if ( t8.getNumberOfExternalNodes() != 10 ) {
2980 if ( t8.getHeight() != 15 ) {
2983 final char[] a9 = new char[] { 'a' };
2984 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2985 if ( t9.getHeight() != 0 ) {
2988 final char[] a10 = new char[] { 'a', ':', '6' };
2989 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2990 if ( t10.getHeight() != 6 ) {
2994 catch ( final Exception e ) {
2995 e.printStackTrace( System.out );
3001 private static boolean testConfidenceAssessor() {
3003 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3004 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3005 final Phylogeny[] ev0 = factory
3006 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
3008 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
3009 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3012 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
3015 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3016 final Phylogeny[] ev1 = factory
3017 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
3019 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
3020 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
3023 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3026 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3027 final Phylogeny[] ev_b = factory
3028 .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
3030 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
3031 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
3034 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3038 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
3039 final Phylogeny[] ev1x = factory
3040 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
3042 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
3043 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3046 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
3049 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
3050 final Phylogeny[] ev_bx = factory
3051 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
3053 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
3054 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3057 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3060 final Phylogeny[] t2 = factory
3061 .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
3063 final Phylogeny[] ev2 = factory
3064 .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
3066 for( final Phylogeny target : t2 ) {
3067 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
3069 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
3070 new NHXParser() )[ 0 ];
3071 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
3072 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
3073 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3076 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
3079 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
3083 catch ( final Exception e ) {
3084 e.printStackTrace();
3090 private static boolean testCopyOfNodeData() {
3092 final PhylogenyNode n1 = PhylogenyNode
3093 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
3094 final PhylogenyNode n2 = n1.copyNodeData();
3095 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
3099 catch ( final Exception e ) {
3100 e.printStackTrace();
3106 private static boolean testCreateBalancedPhylogeny() {
3108 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
3109 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
3112 if ( p0.getNumberOfExternalNodes() != 15625 ) {
3115 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
3116 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
3119 if ( p1.getNumberOfExternalNodes() != 100 ) {
3123 catch ( final Exception e ) {
3124 e.printStackTrace();
3130 private static boolean testCreateUriForSeqWeb() {
3132 final PhylogenyNode n = new PhylogenyNode();
3133 n.setName( "tr|B3RJ64" );
3134 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
3137 n.setName( "B0LM41_HUMAN" );
3138 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
3141 n.setName( "NP_001025424" );
3142 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
3145 n.setName( "_NM_001030253-" );
3146 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
3149 n.setName( "XM_002122186" );
3150 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
3153 n.setName( "dgh_AAA34956_gdg" );
3154 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3157 n.setName( "AAA34956" );
3158 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
3161 n.setName( "GI:394892" );
3162 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3163 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3166 n.setName( "gi_394892" );
3167 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3168 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3171 n.setName( "gi6335_gi_394892_56635_Gi_43" );
3172 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
3173 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3176 n.setName( "P12345" );
3177 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3178 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3181 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
3182 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
3183 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
3187 catch ( final Exception e ) {
3188 e.printStackTrace( System.out );
3194 private static boolean testDataObjects() {
3196 final Confidence s0 = new Confidence();
3197 final Confidence s1 = new Confidence();
3198 if ( !s0.isEqual( s1 ) ) {
3201 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
3202 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
3203 if ( s2.isEqual( s1 ) ) {
3206 if ( !s2.isEqual( s3 ) ) {
3209 final Confidence s4 = ( Confidence ) s3.copy();
3210 if ( !s4.isEqual( s3 ) ) {
3217 final Taxonomy t1 = new Taxonomy();
3218 final Taxonomy t2 = new Taxonomy();
3219 final Taxonomy t3 = new Taxonomy();
3220 final Taxonomy t4 = new Taxonomy();
3221 final Taxonomy t5 = new Taxonomy();
3222 t1.setIdentifier( new Identifier( "ecoli" ) );
3223 t1.setTaxonomyCode( "ECOLI" );
3224 t1.setScientificName( "E. coli" );
3225 t1.setCommonName( "coli" );
3226 final Taxonomy t0 = ( Taxonomy ) t1.copy();
3227 if ( !t1.isEqual( t0 ) ) {
3230 t2.setIdentifier( new Identifier( "ecoli" ) );
3231 t2.setTaxonomyCode( "OTHER" );
3232 t2.setScientificName( "what" );
3233 t2.setCommonName( "something" );
3234 if ( !t1.isEqual( t2 ) ) {
3237 t2.setIdentifier( new Identifier( "nemve" ) );
3238 if ( t1.isEqual( t2 ) ) {
3241 t1.setIdentifier( null );
3242 t3.setTaxonomyCode( "ECOLI" );
3243 t3.setScientificName( "what" );
3244 t3.setCommonName( "something" );
3245 if ( !t1.isEqual( t3 ) ) {
3248 t1.setIdentifier( null );
3249 t1.setTaxonomyCode( "" );
3250 t4.setScientificName( "E. ColI" );
3251 t4.setCommonName( "something" );
3252 if ( !t1.isEqual( t4 ) ) {
3255 t4.setScientificName( "B. subtilis" );
3256 t4.setCommonName( "something" );
3257 if ( t1.isEqual( t4 ) ) {
3260 t1.setIdentifier( null );
3261 t1.setTaxonomyCode( "" );
3262 t1.setScientificName( "" );
3263 t5.setCommonName( "COLI" );
3264 if ( !t1.isEqual( t5 ) ) {
3267 t5.setCommonName( "vibrio" );
3268 if ( t1.isEqual( t5 ) ) {
3273 final Identifier id0 = new Identifier( "123", "pfam" );
3274 final Identifier id1 = ( Identifier ) id0.copy();
3275 if ( !id1.isEqual( id1 ) ) {
3278 if ( !id1.isEqual( id0 ) ) {
3281 if ( !id0.isEqual( id1 ) ) {
3288 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3289 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3290 if ( !pd1.isEqual( pd1 ) ) {
3293 if ( !pd1.isEqual( pd0 ) ) {
3298 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3299 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3300 if ( !pd3.isEqual( pd3 ) ) {
3303 if ( !pd2.isEqual( pd3 ) ) {
3306 if ( !pd0.isEqual( pd3 ) ) {
3311 // DomainArchitecture
3312 // ------------------
3313 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3314 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3315 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3316 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3317 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3318 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3323 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3324 if ( ds0.getNumberOfDomains() != 4 ) {
3327 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3328 if ( !ds0.isEqual( ds0 ) ) {
3331 if ( !ds0.isEqual( ds1 ) ) {
3334 if ( ds1.getNumberOfDomains() != 4 ) {
3337 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3342 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3343 if ( ds0.isEqual( ds2 ) ) {
3349 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3350 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3351 System.out.println( ds3.toNHX() );
3354 if ( ds3.getNumberOfDomains() != 3 ) {
3359 final Event e1 = new Event( Event.EventType.fusion );
3360 if ( e1.isDuplication() ) {
3363 if ( !e1.isFusion() ) {
3366 if ( !e1.asText().toString().equals( "fusion" ) ) {
3369 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3372 final Event e11 = new Event( Event.EventType.fusion );
3373 if ( !e11.isEqual( e1 ) ) {
3376 if ( !e11.toNHX().toString().equals( "" ) ) {
3379 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3380 if ( e2.isDuplication() ) {
3383 if ( !e2.isSpeciationOrDuplication() ) {
3386 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3389 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3392 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3395 if ( e11.isEqual( e2 ) ) {
3398 final Event e2c = ( Event ) e2.copy();
3399 if ( !e2c.isEqual( e2 ) ) {
3402 Event e3 = new Event( 1, 2, 3 );
3403 if ( e3.isDuplication() ) {
3406 if ( e3.isSpeciation() ) {
3409 if ( e3.isGeneLoss() ) {
3412 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3415 final Event e3c = ( Event ) e3.copy();
3416 final Event e3cc = ( Event ) e3c.copy();
3417 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3421 if ( !e3c.isEqual( e3cc ) ) {
3424 Event e4 = new Event( 1, 2, 3 );
3425 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3428 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3431 final Event e4c = ( Event ) e4.copy();
3433 final Event e4cc = ( Event ) e4c.copy();
3434 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3437 if ( !e4c.isEqual( e4cc ) ) {
3440 final Event e5 = new Event();
3441 if ( !e5.isUnassigned() ) {
3444 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3447 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3450 final Event e6 = new Event( 1, 0, 0 );
3451 if ( !e6.asText().toString().equals( "duplication" ) ) {
3454 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3457 final Event e7 = new Event( 0, 1, 0 );
3458 if ( !e7.asText().toString().equals( "speciation" ) ) {
3461 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3464 final Event e8 = new Event( 0, 0, 1 );
3465 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3468 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3472 catch ( final Exception e ) {
3473 e.printStackTrace( System.out );
3479 private static boolean testDeletionOfExternalNodes() {
3481 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3482 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3483 final PhylogenyWriter w = new PhylogenyWriter();
3484 if ( t0.isEmpty() ) {
3487 if ( t0.getNumberOfExternalNodes() != 1 ) {
3490 t0.deleteSubtree( t0.getNode( "A" ), false );
3491 if ( t0.getNumberOfExternalNodes() != 0 ) {
3494 if ( !t0.isEmpty() ) {
3497 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3498 if ( t1.getNumberOfExternalNodes() != 2 ) {
3501 t1.deleteSubtree( t1.getNode( "A" ), false );
3502 if ( t1.getNumberOfExternalNodes() != 1 ) {
3505 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3508 t1.deleteSubtree( t1.getNode( "B" ), false );
3509 if ( t1.getNumberOfExternalNodes() != 1 ) {
3512 t1.deleteSubtree( t1.getNode( "r" ), false );
3513 if ( !t1.isEmpty() ) {
3516 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3517 if ( t2.getNumberOfExternalNodes() != 3 ) {
3520 t2.deleteSubtree( t2.getNode( "B" ), false );
3521 if ( t2.getNumberOfExternalNodes() != 2 ) {
3524 t2.toNewHampshireX();
3525 PhylogenyNode n = t2.getNode( "A" );
3526 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3529 t2.deleteSubtree( t2.getNode( "A" ), false );
3530 if ( t2.getNumberOfExternalNodes() != 2 ) {
3533 t2.deleteSubtree( t2.getNode( "C" ), true );
3534 if ( t2.getNumberOfExternalNodes() != 1 ) {
3537 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3538 if ( t3.getNumberOfExternalNodes() != 4 ) {
3541 t3.deleteSubtree( t3.getNode( "B" ), true );
3542 if ( t3.getNumberOfExternalNodes() != 3 ) {
3545 n = t3.getNode( "A" );
3546 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3549 n = n.getNextExternalNode();
3550 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3553 t3.deleteSubtree( t3.getNode( "A" ), true );
3554 if ( t3.getNumberOfExternalNodes() != 2 ) {
3557 n = t3.getNode( "C" );
3558 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3561 t3.deleteSubtree( t3.getNode( "C" ), true );
3562 if ( t3.getNumberOfExternalNodes() != 1 ) {
3565 t3.deleteSubtree( t3.getNode( "D" ), true );
3566 if ( t3.getNumberOfExternalNodes() != 0 ) {
3569 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3570 if ( t4.getNumberOfExternalNodes() != 6 ) {
3573 t4.deleteSubtree( t4.getNode( "B2" ), true );
3574 if ( t4.getNumberOfExternalNodes() != 5 ) {
3577 String s = w.toNewHampshire( t4, true ).toString();
3578 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3581 t4.deleteSubtree( t4.getNode( "B11" ), true );
3582 if ( t4.getNumberOfExternalNodes() != 4 ) {
3585 t4.deleteSubtree( t4.getNode( "C" ), true );
3586 if ( t4.getNumberOfExternalNodes() != 3 ) {
3589 n = t4.getNode( "A" );
3590 n = n.getNextExternalNode();
3591 if ( !n.getName().equals( "B12" ) ) {
3594 n = n.getNextExternalNode();
3595 if ( !n.getName().equals( "D" ) ) {
3598 s = w.toNewHampshire( t4, true ).toString();
3599 if ( !s.equals( "((A,B12),D);" ) ) {
3602 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3603 t5.deleteSubtree( t5.getNode( "A" ), true );
3604 if ( t5.getNumberOfExternalNodes() != 5 ) {
3607 s = w.toNewHampshire( t5, true ).toString();
3608 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3611 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3612 t6.deleteSubtree( t6.getNode( "B11" ), true );
3613 if ( t6.getNumberOfExternalNodes() != 5 ) {
3616 s = w.toNewHampshire( t6, false ).toString();
3617 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3620 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3621 t7.deleteSubtree( t7.getNode( "B12" ), true );
3622 if ( t7.getNumberOfExternalNodes() != 5 ) {
3625 s = w.toNewHampshire( t7, true ).toString();
3626 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3629 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3630 t8.deleteSubtree( t8.getNode( "B2" ), true );
3631 if ( t8.getNumberOfExternalNodes() != 5 ) {
3634 s = w.toNewHampshire( t8, false ).toString();
3635 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3638 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3639 t9.deleteSubtree( t9.getNode( "C" ), true );
3640 if ( t9.getNumberOfExternalNodes() != 5 ) {
3643 s = w.toNewHampshire( t9, true ).toString();
3644 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3647 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3648 t10.deleteSubtree( t10.getNode( "D" ), true );
3649 if ( t10.getNumberOfExternalNodes() != 5 ) {
3652 s = w.toNewHampshire( t10, true ).toString();
3653 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3656 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3657 t11.deleteSubtree( t11.getNode( "A" ), true );
3658 if ( t11.getNumberOfExternalNodes() != 2 ) {
3661 s = w.toNewHampshire( t11, true ).toString();
3662 if ( !s.equals( "(B,C);" ) ) {
3665 t11.deleteSubtree( t11.getNode( "C" ), true );
3666 if ( t11.getNumberOfExternalNodes() != 1 ) {
3669 s = w.toNewHampshire( t11, false ).toString();
3670 if ( !s.equals( "B;" ) ) {
3673 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3674 t12.deleteSubtree( t12.getNode( "B2" ), true );
3675 if ( t12.getNumberOfExternalNodes() != 8 ) {
3678 s = w.toNewHampshire( t12, true ).toString();
3679 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3682 t12.deleteSubtree( t12.getNode( "B3" ), true );
3683 if ( t12.getNumberOfExternalNodes() != 7 ) {
3686 s = w.toNewHampshire( t12, true ).toString();
3687 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3690 t12.deleteSubtree( t12.getNode( "C3" ), true );
3691 if ( t12.getNumberOfExternalNodes() != 6 ) {
3694 s = w.toNewHampshire( t12, true ).toString();
3695 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3698 t12.deleteSubtree( t12.getNode( "A1" ), true );
3699 if ( t12.getNumberOfExternalNodes() != 5 ) {
3702 s = w.toNewHampshire( t12, true ).toString();
3703 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3706 t12.deleteSubtree( t12.getNode( "B1" ), true );
3707 if ( t12.getNumberOfExternalNodes() != 4 ) {
3710 s = w.toNewHampshire( t12, true ).toString();
3711 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3714 t12.deleteSubtree( t12.getNode( "A3" ), true );
3715 if ( t12.getNumberOfExternalNodes() != 3 ) {
3718 s = w.toNewHampshire( t12, true ).toString();
3719 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3722 t12.deleteSubtree( t12.getNode( "A2" ), true );
3723 if ( t12.getNumberOfExternalNodes() != 2 ) {
3726 s = w.toNewHampshire( t12, true ).toString();
3727 if ( !s.equals( "(C1,C2);" ) ) {
3730 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3731 t13.deleteSubtree( t13.getNode( "D" ), true );
3732 if ( t13.getNumberOfExternalNodes() != 4 ) {
3735 s = w.toNewHampshire( t13, true ).toString();
3736 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3739 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3740 t14.deleteSubtree( t14.getNode( "E" ), true );
3741 if ( t14.getNumberOfExternalNodes() != 5 ) {
3744 s = w.toNewHampshire( t14, true ).toString();
3745 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3748 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3749 t15.deleteSubtree( t15.getNode( "B2" ), true );
3750 if ( t15.getNumberOfExternalNodes() != 11 ) {
3753 t15.deleteSubtree( t15.getNode( "B1" ), true );
3754 if ( t15.getNumberOfExternalNodes() != 10 ) {
3757 t15.deleteSubtree( t15.getNode( "B3" ), true );
3758 if ( t15.getNumberOfExternalNodes() != 9 ) {
3761 t15.deleteSubtree( t15.getNode( "B4" ), true );
3762 if ( t15.getNumberOfExternalNodes() != 8 ) {
3765 t15.deleteSubtree( t15.getNode( "A1" ), true );
3766 if ( t15.getNumberOfExternalNodes() != 7 ) {
3769 t15.deleteSubtree( t15.getNode( "C4" ), true );
3770 if ( t15.getNumberOfExternalNodes() != 6 ) {
3774 catch ( final Exception e ) {
3775 e.printStackTrace( System.out );
3781 private static boolean testDescriptiveStatistics() {
3783 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3784 dss1.addValue( 82 );
3785 dss1.addValue( 78 );
3786 dss1.addValue( 70 );
3787 dss1.addValue( 58 );
3788 dss1.addValue( 42 );
3789 if ( dss1.getN() != 5 ) {
3792 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3795 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3798 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3801 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3804 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3807 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3810 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3813 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3816 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3819 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3822 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3825 dss1.addValue( 123 );
3826 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3829 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3832 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3835 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3836 dss2.addValue( -1.85 );
3837 dss2.addValue( 57.5 );
3838 dss2.addValue( 92.78 );
3839 dss2.addValue( 57.78 );
3840 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3843 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3846 final double[] a = dss2.getDataAsDoubleArray();
3847 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3850 dss2.addValue( -100 );
3851 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3854 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3857 final double[] ds = new double[ 14 ];
3872 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3873 if ( bins.length != 4 ) {
3876 if ( bins[ 0 ] != 2 ) {
3879 if ( bins[ 1 ] != 3 ) {
3882 if ( bins[ 2 ] != 4 ) {
3885 if ( bins[ 3 ] != 5 ) {
3888 final double[] ds1 = new double[ 9 ];
3898 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3899 if ( bins1.length != 4 ) {
3902 if ( bins1[ 0 ] != 2 ) {
3905 if ( bins1[ 1 ] != 3 ) {
3908 if ( bins1[ 2 ] != 0 ) {
3911 if ( bins1[ 3 ] != 4 ) {
3914 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3915 if ( bins1_1.length != 3 ) {
3918 if ( bins1_1[ 0 ] != 3 ) {
3921 if ( bins1_1[ 1 ] != 2 ) {
3924 if ( bins1_1[ 2 ] != 4 ) {
3927 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3928 if ( bins1_2.length != 3 ) {
3931 if ( bins1_2[ 0 ] != 2 ) {
3934 if ( bins1_2[ 1 ] != 2 ) {
3937 if ( bins1_2[ 2 ] != 2 ) {
3940 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3954 dss3.addValue( 10 );
3955 dss3.addValue( 10 );
3956 dss3.addValue( 10 );
3957 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3958 histo.toStringBuffer( 10, '=', 40, 5 );
3959 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3961 catch ( final Exception e ) {
3962 e.printStackTrace( System.out );
3968 private static boolean testDir( final String file ) {
3970 final File f = new File( file );
3971 if ( !f.exists() ) {
3974 if ( !f.isDirectory() ) {
3977 if ( !f.canRead() ) {
3981 catch ( final Exception e ) {
3987 private static boolean testEbiEntryRetrieval() {
3989 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
3990 if ( !entry.getAccession().equals( "AAK41263" ) ) {
3991 System.out.println( entry.getAccession() );
3994 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
3995 System.out.println( entry.getTaxonomyScientificName() );
3998 if ( !entry.getSequenceName()
3999 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
4000 System.out.println( entry.getSequenceName() );
4003 if ( !entry.getGeneName().equals( "treX-like" ) ) {
4004 System.out.println( entry.getGeneName() );
4007 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
4008 System.out.println( entry.getTaxonomyIdentifier() );
4011 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
4012 System.out.println( entry.getAnnotations().first().getRefValue() );
4015 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
4016 System.out.println( entry.getAnnotations().first().getRefSource() );
4019 if ( entry.getCrossReferences().size() != 5 ) {
4022 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
4023 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
4026 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
4027 System.out.println( entry1.getTaxonomyScientificName() );
4030 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
4031 System.out.println( entry1.getSequenceName() );
4034 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
4035 System.out.println( entry1.getTaxonomyIdentifier() );
4038 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
4039 System.out.println( entry1.getGeneName() );
4042 if ( entry1.getCrossReferences().size() != 6 ) {
4045 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
4046 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
4049 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4050 System.out.println( entry2.getTaxonomyScientificName() );
4053 if ( !entry2.getSequenceName()
4054 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
4055 System.out.println( entry2.getSequenceName() );
4058 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
4059 System.out.println( entry2.getTaxonomyIdentifier() );
4062 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
4063 System.out.println( entry2.getGeneName() );
4066 if ( entry2.getCrossReferences().size() != 3 ) {
4070 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
4071 if ( !entry3.getAccession().equals( "HM043801" ) ) {
4074 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
4075 System.out.println( entry3.getTaxonomyScientificName() );
4078 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
4079 System.out.println( entry3.getSequenceName() );
4082 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
4083 System.out.println( entry3.getTaxonomyIdentifier() );
4086 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
4087 System.out.println( entry3.getSequenceSymbol() );
4090 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
4093 if ( entry3.getCrossReferences().size() < 7 ) {
4096 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
4097 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
4100 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
4101 System.out.println( entry4.getTaxonomyScientificName() );
4104 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
4105 System.out.println( entry4.getSequenceName() );
4108 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
4109 System.out.println( entry4.getTaxonomyIdentifier() );
4112 if ( !entry4.getGeneName().equals( "ras" ) ) {
4113 System.out.println( entry4.getGeneName() );
4116 // if ( !entry4.getChromosome().equals( "ras" ) ) {
4117 // System.out.println( entry4.getChromosome() );
4120 // if ( !entry4.getMap().equals( "ras" ) ) {
4121 // System.out.println( entry4.getMap() );
4127 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
4128 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
4131 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
4132 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
4135 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
4136 System.out.println( entry5.getTaxonomyScientificName() );
4139 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
4140 System.out.println( entry5.getSequenceName() );
4143 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
4144 System.out.println( entry5.getTaxonomyIdentifier() );
4148 catch ( final IOException e ) {
4149 System.out.println();
4150 System.out.println( "the following might be due to absence internet connection:" );
4151 e.printStackTrace( System.out );
4154 catch ( final Exception e ) {
4155 e.printStackTrace();
4161 private static boolean testExternalNodeRelatedMethods() {
4163 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4164 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4165 PhylogenyNode n = t1.getNode( "A" );
4166 n = n.getNextExternalNode();
4167 if ( !n.getName().equals( "B" ) ) {
4170 n = n.getNextExternalNode();
4171 if ( !n.getName().equals( "C" ) ) {
4174 n = n.getNextExternalNode();
4175 if ( !n.getName().equals( "D" ) ) {
4178 n = t1.getNode( "B" );
4179 while ( !n.isLastExternalNode() ) {
4180 n = n.getNextExternalNode();
4182 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
4183 n = t2.getNode( "A" );
4184 n = n.getNextExternalNode();
4185 if ( !n.getName().equals( "B" ) ) {
4188 n = n.getNextExternalNode();
4189 if ( !n.getName().equals( "C" ) ) {
4192 n = n.getNextExternalNode();
4193 if ( !n.getName().equals( "D" ) ) {
4196 n = t2.getNode( "B" );
4197 while ( !n.isLastExternalNode() ) {
4198 n = n.getNextExternalNode();
4200 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4201 n = t3.getNode( "A" );
4202 n = n.getNextExternalNode();
4203 if ( !n.getName().equals( "B" ) ) {
4206 n = n.getNextExternalNode();
4207 if ( !n.getName().equals( "C" ) ) {
4210 n = n.getNextExternalNode();
4211 if ( !n.getName().equals( "D" ) ) {
4214 n = n.getNextExternalNode();
4215 if ( !n.getName().equals( "E" ) ) {
4218 n = n.getNextExternalNode();
4219 if ( !n.getName().equals( "F" ) ) {
4222 n = n.getNextExternalNode();
4223 if ( !n.getName().equals( "G" ) ) {
4226 n = n.getNextExternalNode();
4227 if ( !n.getName().equals( "H" ) ) {
4230 n = t3.getNode( "B" );
4231 while ( !n.isLastExternalNode() ) {
4232 n = n.getNextExternalNode();
4234 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
4235 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
4236 final PhylogenyNode node = iter.next();
4238 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
4239 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
4240 final PhylogenyNode node = iter.next();
4242 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
4243 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
4244 if ( !iter.next().getName().equals( "A" ) ) {
4247 if ( !iter.next().getName().equals( "B" ) ) {
4250 if ( !iter.next().getName().equals( "C" ) ) {
4253 if ( !iter.next().getName().equals( "D" ) ) {
4256 if ( !iter.next().getName().equals( "E" ) ) {
4259 if ( !iter.next().getName().equals( "F" ) ) {
4262 if ( iter.hasNext() ) {
4266 catch ( final Exception e ) {
4267 e.printStackTrace( System.out );
4273 private static boolean testExtractSNFromNodeName() {
4275 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
4278 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
4281 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
4284 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
4285 .equals( "Mus musculus musculus" ) ) {
4288 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
4289 .equals( "Mus musculus musculus" ) ) {
4292 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
4293 .equals( "Mus musculus musculus" ) ) {
4296 if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
4297 .equals( "Mus musculus musculus" ) ) {
4300 if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
4303 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
4304 .equals( "Mus musculus musculus" ) ) {
4307 if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
4308 .equals( "Mus musculus musculus" ) ) {
4311 if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
4314 if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
4317 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
4320 if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
4323 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
4324 .equals( "Mus musculus musculus" ) ) {
4327 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
4330 if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
4333 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
4336 if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
4339 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
4342 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
4345 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
4348 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
4351 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
4352 .equals( "Mus musculus" ) ) {
4355 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
4356 .equals( "Mus musculus" ) ) {
4359 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
4362 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4363 .equals( "Mus musculus musculus" ) ) {
4366 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
4367 .equals( "Mus musculus musculus" ) ) {
4370 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
4371 .equals( "Mus musculus musculus" ) ) {
4374 if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
4377 if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
4378 .equals( "Pilostyles mexicana" ) ) {
4381 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
4382 .equals( "Escherichia coli strain K12/DH10B" ) ) {
4385 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
4386 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4389 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
4390 .equals( "Escherichia coli str. K12/DH10B" ) ) {
4393 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
4394 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4397 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
4398 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4401 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
4402 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4405 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
4406 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4409 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
4410 .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
4413 if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
4414 .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
4417 if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
4418 .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
4421 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
4422 .equals( "Escherichia coli (strain K12)" ) ) {
4425 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
4426 .equals( "Escherichia coli (strain K12)" ) ) {
4429 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
4430 .equals( "Escherichia coli (str. K12)" ) ) {
4433 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
4434 .equals( "Escherichia coli (str. K12)" ) ) {
4437 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
4438 .equals( "Escherichia coli (str. K12)" ) ) {
4441 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
4442 .equals( "Escherichia coli (var. K12)" ) ) {
4445 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
4446 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4449 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
4450 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4454 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
4455 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4458 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
4459 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4463 .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
4464 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4467 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4468 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4471 if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
4472 .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
4475 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
4478 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
4481 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
4484 if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
4485 .equals( "Macrocera sp." ) ) {
4488 if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
4491 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
4492 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4495 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
4496 .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
4499 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
4500 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4503 if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
4504 .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
4508 catch ( final Exception e ) {
4509 e.printStackTrace( System.out );
4515 private static boolean testExtractTaxonomyDataFromNodeName() {
4517 PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
4518 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4521 n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
4522 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4525 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
4526 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4529 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" );
4530 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4533 n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" );
4534 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4537 n = new PhylogenyNode( "HNRPR_HUMAN" );
4538 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4541 n = new PhylogenyNode( "HNRPR_HUMAN_X" );
4542 if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
4546 catch ( final Exception e ) {
4547 e.printStackTrace( System.out );
4553 private static boolean testExtractTaxonomyCodeFromNodeName() {
4555 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4558 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4559 .equals( "SOYBN" ) ) {
4562 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4563 .equals( "ARATH" ) ) {
4566 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
4567 .equals( "ARATH" ) ) {
4570 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4573 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
4576 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4579 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4580 .equals( "SOYBN" ) ) {
4583 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4584 .equals( "SOYBN" ) ) {
4587 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4588 .equals( "SOYBN" ) ) {
4591 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4592 .equals( "SOYBN" ) ) {
4595 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4596 .equals( "SOYBN" ) ) {
4599 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
4600 .equals( "SOYBN" ) ) {
4603 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
4604 .equals( "SOYBN" ) ) {
4607 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
4608 .equals( "SOYBN" ) ) {
4611 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
4614 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
4615 .equals( "SOYBN" ) ) {
4618 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
4619 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
4622 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
4623 .equals( "9YX45" ) ) {
4626 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4627 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4628 .equals( "MOUSE" ) ) {
4631 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4632 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4633 .equals( "MOUSE" ) ) {
4636 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4637 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4638 .equals( "MOUSE" ) ) {
4641 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4642 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4645 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4646 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4649 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4650 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4653 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4654 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4657 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4658 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4661 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4662 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4665 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4666 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4669 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4670 .equals( "RAT" ) ) {
4673 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4674 .equals( "PIG" ) ) {
4678 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4679 .equals( "MOUSE" ) ) {
4682 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4683 .equals( "MOUSE" ) ) {
4686 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4690 catch ( final Exception e ) {
4691 e.printStackTrace( System.out );
4697 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4699 PhylogenyNode n = new PhylogenyNode();
4700 n.setName( "tr|B3RJ64" );
4701 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4704 n.setName( "tr.B3RJ64" );
4705 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4708 n.setName( "tr=B3RJ64" );
4709 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4712 n.setName( "tr-B3RJ64" );
4713 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4716 n.setName( "tr/B3RJ64" );
4717 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4720 n.setName( "tr\\B3RJ64" );
4721 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4724 n.setName( "tr_B3RJ64" );
4725 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4728 n.setName( " tr|B3RJ64 " );
4729 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4732 n.setName( "-tr|B3RJ64-" );
4733 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4736 n.setName( "-tr=B3RJ64-" );
4737 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4740 n.setName( "_tr=B3RJ64_" );
4741 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4744 n.setName( " tr_tr|B3RJ64_sp|123 " );
4745 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4748 n.setName( "B3RJ64" );
4749 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4752 n.setName( "sp|B3RJ64" );
4753 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4756 n.setName( "sp|B3RJ64C" );
4757 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4760 n.setName( "sp B3RJ64" );
4761 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4764 n.setName( "sp|B3RJ6X" );
4765 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4768 n.setName( "sp|B3RJ6" );
4769 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4772 n.setName( "K1PYK7_CRAGI" );
4773 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4776 n.setName( "K1PYK7_PEA" );
4777 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4780 n.setName( "K1PYK7_RAT" );
4781 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4784 n.setName( "K1PYK7_PIG" );
4785 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4788 n.setName( "~K1PYK7_PIG~" );
4789 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4792 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4793 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4796 n.setName( "K1PYKX_CRAGI" );
4797 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4800 n.setName( "XXXXX_CRAGI" );
4801 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4804 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4805 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4808 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4809 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4812 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4813 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4816 n = new PhylogenyNode();
4817 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4818 seq.setSymbol( "K1PYK7_CRAGI" );
4819 n.getNodeData().addSequence( seq );
4820 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4823 seq.setSymbol( "tr|B3RJ64" );
4824 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4827 n = new PhylogenyNode();
4828 seq = new org.forester.phylogeny.data.Sequence();
4829 seq.setName( "K1PYK7_CRAGI" );
4830 n.getNodeData().addSequence( seq );
4831 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4834 seq.setName( "tr|B3RJ64" );
4835 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4838 n = new PhylogenyNode();
4839 seq = new org.forester.phylogeny.data.Sequence();
4840 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4841 n.getNodeData().addSequence( seq );
4842 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4845 n = new PhylogenyNode();
4846 seq = new org.forester.phylogeny.data.Sequence();
4847 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4848 n.getNodeData().addSequence( seq );
4849 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4853 n = new PhylogenyNode();
4854 n.setName( "ACP19736" );
4855 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4858 n = new PhylogenyNode();
4859 n.setName( "|ACP19736|" );
4860 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4864 catch ( final Exception e ) {
4865 e.printStackTrace( System.out );
4871 private static boolean testFastaParser() {
4873 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4876 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4879 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4880 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4883 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4886 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4889 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
4892 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4895 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4899 catch ( final Exception e ) {
4900 e.printStackTrace();
4906 private static boolean testGenbankAccessorParsing() {
4907 //The format for GenBank Accession numbers are:
4908 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
4909 //Protein: 3 letters + 5 numerals
4910 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
4911 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
4914 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
4917 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
4920 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
4923 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
4926 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
4929 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
4932 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
4935 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
4938 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
4941 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
4944 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
4947 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
4950 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
4956 private static boolean testGeneralMsaParser() {
4958 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4959 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4960 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4961 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4962 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4963 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4964 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4965 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4966 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4969 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4972 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4975 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4978 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4981 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4984 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4987 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4990 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4993 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4996 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4999 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
5002 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
5003 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5006 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5009 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5012 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
5013 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
5016 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
5019 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
5022 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
5023 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
5026 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
5029 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
5033 catch ( final Exception e ) {
5034 e.printStackTrace();
5040 private static boolean testGeneralTable() {
5042 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
5043 t0.setValue( 3, 2, "23" );
5044 t0.setValue( 10, 1, "error" );
5045 t0.setValue( 10, 1, "110" );
5046 t0.setValue( 9, 1, "19" );
5047 t0.setValue( 1, 10, "101" );
5048 t0.setValue( 10, 10, "1010" );
5049 t0.setValue( 100, 10, "10100" );
5050 t0.setValue( 0, 0, "00" );
5051 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
5054 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
5057 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
5060 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
5063 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
5066 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
5069 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
5072 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
5075 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
5078 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
5079 t1.setValue( "3", "2", "23" );
5080 t1.setValue( "10", "1", "error" );
5081 t1.setValue( "10", "1", "110" );
5082 t1.setValue( "9", "1", "19" );
5083 t1.setValue( "1", "10", "101" );
5084 t1.setValue( "10", "10", "1010" );
5085 t1.setValue( "100", "10", "10100" );
5086 t1.setValue( "0", "0", "00" );
5087 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
5088 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
5091 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
5094 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
5097 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
5100 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
5103 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
5106 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
5109 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
5112 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
5115 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
5119 catch ( final Exception e ) {
5120 e.printStackTrace( System.out );
5126 private static boolean testGetDistance() {
5128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5129 final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
5130 new NHXParser() )[ 0 ];
5131 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
5134 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
5137 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
5140 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
5143 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
5146 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
5149 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
5152 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
5155 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
5158 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
5161 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
5164 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
5167 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
5170 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
5173 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
5176 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
5179 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
5182 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
5185 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
5188 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
5191 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
5194 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
5197 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
5200 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
5203 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
5206 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
5209 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
5212 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
5215 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
5218 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
5221 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
5224 final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
5225 new NHXParser() )[ 0 ];
5226 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
5229 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
5232 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
5235 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
5238 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
5241 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
5244 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
5247 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
5250 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
5253 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
5256 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
5260 catch ( final Exception e ) {
5261 e.printStackTrace( System.out );
5267 private static boolean testGetLCA() {
5269 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5270 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5271 new NHXParser() )[ 0 ];
5272 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
5273 if ( !A.getName().equals( "A" ) ) {
5276 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
5277 if ( !gh.getName().equals( "gh" ) ) {
5280 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
5281 if ( !ab.getName().equals( "ab" ) ) {
5284 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
5285 if ( !ab2.getName().equals( "ab" ) ) {
5288 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
5289 if ( !gh2.getName().equals( "gh" ) ) {
5292 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
5293 if ( !gh3.getName().equals( "gh" ) ) {
5296 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
5297 if ( !abc.getName().equals( "abc" ) ) {
5300 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
5301 if ( !abc2.getName().equals( "abc" ) ) {
5304 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
5305 if ( !abcd.getName().equals( "abcd" ) ) {
5308 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
5309 if ( !abcd2.getName().equals( "abcd" ) ) {
5312 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
5313 if ( !abcdef.getName().equals( "abcdef" ) ) {
5316 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
5317 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5320 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
5321 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5324 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
5325 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5328 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
5329 if ( !abcde.getName().equals( "abcde" ) ) {
5332 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
5333 if ( !abcde2.getName().equals( "abcde" ) ) {
5336 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
5337 if ( !r.getName().equals( "abcdefgh" ) ) {
5340 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
5341 if ( !r2.getName().equals( "abcdefgh" ) ) {
5344 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
5345 if ( !r3.getName().equals( "abcdefgh" ) ) {
5348 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
5349 if ( !abcde3.getName().equals( "abcde" ) ) {
5352 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
5353 if ( !abcde4.getName().equals( "abcde" ) ) {
5356 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
5357 if ( !ab3.getName().equals( "ab" ) ) {
5360 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
5361 if ( !ab4.getName().equals( "ab" ) ) {
5364 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5365 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
5366 if ( !cd.getName().equals( "cd" ) ) {
5369 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
5370 if ( !cd2.getName().equals( "cd" ) ) {
5373 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
5374 if ( !cde.getName().equals( "cde" ) ) {
5377 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
5378 if ( !cde2.getName().equals( "cde" ) ) {
5381 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
5382 if ( !cdef.getName().equals( "cdef" ) ) {
5385 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
5386 if ( !cdef2.getName().equals( "cdef" ) ) {
5389 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
5390 if ( !cdef3.getName().equals( "cdef" ) ) {
5393 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
5394 if ( !rt.getName().equals( "r" ) ) {
5397 final Phylogeny p3 = factory
5398 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5399 new NHXParser() )[ 0 ];
5400 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
5401 if ( !bc_3.getName().equals( "bc" ) ) {
5404 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
5405 if ( !ac_3.getName().equals( "abc" ) ) {
5408 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
5409 if ( !ad_3.getName().equals( "abcde" ) ) {
5412 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
5413 if ( !af_3.getName().equals( "abcdef" ) ) {
5416 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
5417 if ( !ag_3.getName().equals( "" ) ) {
5420 if ( !ag_3.isRoot() ) {
5423 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
5424 if ( !al_3.getName().equals( "" ) ) {
5427 if ( !al_3.isRoot() ) {
5430 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
5431 if ( !kl_3.getName().equals( "" ) ) {
5434 if ( !kl_3.isRoot() ) {
5437 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
5438 if ( !fl_3.getName().equals( "" ) ) {
5441 if ( !fl_3.isRoot() ) {
5444 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
5445 if ( !gk_3.getName().equals( "ghijk" ) ) {
5448 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5449 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
5450 if ( !r_4.getName().equals( "r" ) ) {
5453 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5454 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
5455 if ( !r_5.getName().equals( "root" ) ) {
5458 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5459 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
5460 if ( !r_6.getName().equals( "rot" ) ) {
5463 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5464 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
5465 if ( !r_7.getName().equals( "rott" ) ) {
5469 catch ( final Exception e ) {
5470 e.printStackTrace( System.out );
5476 private static boolean testGetLCA2() {
5478 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5479 // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
5480 final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
5481 PhylogenyMethods.preOrderReId( p_a );
5482 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
5483 p_a.getNode( "a" ) );
5484 if ( !p_a_1.getName().equals( "a" ) ) {
5487 final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
5488 PhylogenyMethods.preOrderReId( p_b );
5489 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
5490 p_b.getNode( "a" ) );
5491 if ( !p_b_1.getName().equals( "b" ) ) {
5494 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
5495 p_b.getNode( "b" ) );
5496 if ( !p_b_2.getName().equals( "b" ) ) {
5499 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
5500 PhylogenyMethods.preOrderReId( p_c );
5501 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
5502 p_c.getNode( "a" ) );
5503 if ( !p_c_1.getName().equals( "b" ) ) {
5506 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5507 p_c.getNode( "c" ) );
5508 if ( !p_c_2.getName().equals( "c" ) ) {
5509 System.out.println( p_c_2.getName() );
5513 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
5514 p_c.getNode( "b" ) );
5515 if ( !p_c_3.getName().equals( "b" ) ) {
5518 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
5519 p_c.getNode( "a" ) );
5520 if ( !p_c_4.getName().equals( "c" ) ) {
5523 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
5524 new NHXParser() )[ 0 ];
5525 PhylogenyMethods.preOrderReId( p1 );
5526 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5527 p1.getNode( "A" ) );
5528 if ( !A.getName().equals( "A" ) ) {
5531 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
5532 p1.getNode( "gh" ) );
5533 if ( !gh.getName().equals( "gh" ) ) {
5536 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5537 p1.getNode( "B" ) );
5538 if ( !ab.getName().equals( "ab" ) ) {
5541 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5542 p1.getNode( "A" ) );
5543 if ( !ab2.getName().equals( "ab" ) ) {
5546 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5547 p1.getNode( "G" ) );
5548 if ( !gh2.getName().equals( "gh" ) ) {
5551 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
5552 p1.getNode( "H" ) );
5553 if ( !gh3.getName().equals( "gh" ) ) {
5556 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
5557 p1.getNode( "A" ) );
5558 if ( !abc.getName().equals( "abc" ) ) {
5561 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5562 p1.getNode( "C" ) );
5563 if ( !abc2.getName().equals( "abc" ) ) {
5566 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5567 p1.getNode( "D" ) );
5568 if ( !abcd.getName().equals( "abcd" ) ) {
5571 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
5572 p1.getNode( "A" ) );
5573 if ( !abcd2.getName().equals( "abcd" ) ) {
5576 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5577 p1.getNode( "F" ) );
5578 if ( !abcdef.getName().equals( "abcdef" ) ) {
5581 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5582 p1.getNode( "A" ) );
5583 if ( !abcdef2.getName().equals( "abcdef" ) ) {
5586 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5587 p1.getNode( "F" ) );
5588 if ( !abcdef3.getName().equals( "abcdef" ) ) {
5591 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
5592 p1.getNode( "ab" ) );
5593 if ( !abcdef4.getName().equals( "abcdef" ) ) {
5596 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5597 p1.getNode( "E" ) );
5598 if ( !abcde.getName().equals( "abcde" ) ) {
5601 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5602 p1.getNode( "A" ) );
5603 if ( !abcde2.getName().equals( "abcde" ) ) {
5606 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
5607 p1.getNode( "abcdefgh" ) );
5608 if ( !r.getName().equals( "abcdefgh" ) ) {
5611 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
5612 p1.getNode( "H" ) );
5613 if ( !r2.getName().equals( "abcdefgh" ) ) {
5616 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
5617 p1.getNode( "A" ) );
5618 if ( !r3.getName().equals( "abcdefgh" ) ) {
5621 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
5622 p1.getNode( "abcde" ) );
5623 if ( !abcde3.getName().equals( "abcde" ) ) {
5626 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
5627 p1.getNode( "E" ) );
5628 if ( !abcde4.getName().equals( "abcde" ) ) {
5631 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
5632 p1.getNode( "B" ) );
5633 if ( !ab3.getName().equals( "ab" ) ) {
5636 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
5637 p1.getNode( "ab" ) );
5638 if ( !ab4.getName().equals( "ab" ) ) {
5641 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
5642 PhylogenyMethods.preOrderReId( p2 );
5643 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5644 p2.getNode( "d" ) );
5645 if ( !cd.getName().equals( "cd" ) ) {
5648 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5649 p2.getNode( "c" ) );
5650 if ( !cd2.getName().equals( "cd" ) ) {
5653 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5654 p2.getNode( "e" ) );
5655 if ( !cde.getName().equals( "cde" ) ) {
5658 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
5659 p2.getNode( "c" ) );
5660 if ( !cde2.getName().equals( "cde" ) ) {
5663 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5664 p2.getNode( "f" ) );
5665 if ( !cdef.getName().equals( "cdef" ) ) {
5668 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
5669 p2.getNode( "f" ) );
5670 if ( !cdef2.getName().equals( "cdef" ) ) {
5673 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
5674 p2.getNode( "d" ) );
5675 if ( !cdef3.getName().equals( "cdef" ) ) {
5678 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5679 p2.getNode( "a" ) );
5680 if ( !rt.getName().equals( "r" ) ) {
5683 final Phylogeny p3 = factory
5684 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5685 new NHXParser() )[ 0 ];
5686 PhylogenyMethods.preOrderReId( p3 );
5687 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5688 p3.getNode( "c" ) );
5689 if ( !bc_3.getName().equals( "bc" ) ) {
5692 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5693 p3.getNode( "c" ) );
5694 if ( !ac_3.getName().equals( "abc" ) ) {
5697 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5698 p3.getNode( "d" ) );
5699 if ( !ad_3.getName().equals( "abcde" ) ) {
5702 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5703 p3.getNode( "f" ) );
5704 if ( !af_3.getName().equals( "abcdef" ) ) {
5707 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5708 p3.getNode( "g" ) );
5709 if ( !ag_3.getName().equals( "" ) ) {
5712 if ( !ag_3.isRoot() ) {
5715 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5716 p3.getNode( "l" ) );
5717 if ( !al_3.getName().equals( "" ) ) {
5720 if ( !al_3.isRoot() ) {
5723 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5724 p3.getNode( "l" ) );
5725 if ( !kl_3.getName().equals( "" ) ) {
5728 if ( !kl_3.isRoot() ) {
5731 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5732 p3.getNode( "l" ) );
5733 if ( !fl_3.getName().equals( "" ) ) {
5736 if ( !fl_3.isRoot() ) {
5739 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5740 p3.getNode( "k" ) );
5741 if ( !gk_3.getName().equals( "ghijk" ) ) {
5744 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5745 PhylogenyMethods.preOrderReId( p4 );
5746 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5747 p4.getNode( "c" ) );
5748 if ( !r_4.getName().equals( "r" ) ) {
5751 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5752 PhylogenyMethods.preOrderReId( p5 );
5753 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5754 p5.getNode( "c" ) );
5755 if ( !r_5.getName().equals( "root" ) ) {
5758 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5759 PhylogenyMethods.preOrderReId( p6 );
5760 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5761 p6.getNode( "a" ) );
5762 if ( !r_6.getName().equals( "rot" ) ) {
5765 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5766 PhylogenyMethods.preOrderReId( p7 );
5767 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5768 p7.getNode( "e" ) );
5769 if ( !r_7.getName().equals( "rott" ) ) {
5772 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5773 p7.getNode( "a" ) );
5774 if ( !r_71.getName().equals( "rott" ) ) {
5777 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5778 p7.getNode( "rott" ) );
5779 if ( !r_72.getName().equals( "rott" ) ) {
5782 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5783 p7.getNode( "a" ) );
5784 if ( !r_73.getName().equals( "rott" ) ) {
5787 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5788 p7.getNode( "rott" ) );
5789 if ( !r_74.getName().equals( "rott" ) ) {
5792 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5793 p7.getNode( "e" ) );
5794 if ( !r_75.getName().equals( "e" ) ) {
5798 catch ( final Exception e ) {
5799 e.printStackTrace( System.out );
5805 private static boolean testHmmscanOutputParser() {
5806 final String test_dir = Test.PATH_TO_TEST_DATA;
5808 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5809 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5811 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5812 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5813 final List<Protein> proteins = parser2.parse();
5814 if ( parser2.getProteinsEncountered() != 4 ) {
5817 if ( proteins.size() != 4 ) {
5820 if ( parser2.getDomainsEncountered() != 69 ) {
5823 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5826 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5829 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5832 final Protein p1 = proteins.get( 0 );
5833 if ( p1.getNumberOfProteinDomains() != 15 ) {
5836 if ( p1.getLength() != 850 ) {
5839 final Protein p2 = proteins.get( 1 );
5840 if ( p2.getNumberOfProteinDomains() != 51 ) {
5843 if ( p2.getLength() != 1291 ) {
5846 final Protein p3 = proteins.get( 2 );
5847 if ( p3.getNumberOfProteinDomains() != 2 ) {
5850 final Protein p4 = proteins.get( 3 );
5851 if ( p4.getNumberOfProteinDomains() != 1 ) {
5854 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5857 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5860 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5863 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5866 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5869 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5872 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5876 catch ( final Exception e ) {
5877 e.printStackTrace( System.out );
5883 private static boolean testLastExternalNodeMethods() {
5885 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5886 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5887 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5888 final PhylogenyNode n1 = t0.getNode( "A" );
5889 if ( n1.isLastExternalNode() ) {
5892 final PhylogenyNode n2 = t0.getNode( "B" );
5893 if ( n2.isLastExternalNode() ) {
5896 final PhylogenyNode n3 = t0.getNode( "C" );
5897 if ( n3.isLastExternalNode() ) {
5900 final PhylogenyNode n4 = t0.getNode( "D" );
5901 if ( !n4.isLastExternalNode() ) {
5905 catch ( final Exception e ) {
5906 e.printStackTrace( System.out );
5912 private static boolean testLevelOrderIterator() {
5914 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5915 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5916 PhylogenyNodeIterator it0;
5917 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5920 for( it0.reset(); it0.hasNext(); ) {
5923 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5924 if ( !it.next().getName().equals( "r" ) ) {
5927 if ( !it.next().getName().equals( "ab" ) ) {
5930 if ( !it.next().getName().equals( "cd" ) ) {
5933 if ( !it.next().getName().equals( "A" ) ) {
5936 if ( !it.next().getName().equals( "B" ) ) {
5939 if ( !it.next().getName().equals( "C" ) ) {
5942 if ( !it.next().getName().equals( "D" ) ) {
5945 if ( it.hasNext() ) {
5948 final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r",
5949 new NHXParser() )[ 0 ];
5950 PhylogenyNodeIterator it2;
5951 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5954 for( it2.reset(); it2.hasNext(); ) {
5957 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5958 if ( !it3.next().getName().equals( "r" ) ) {
5961 if ( !it3.next().getName().equals( "abc" ) ) {
5964 if ( !it3.next().getName().equals( "defg" ) ) {
5967 if ( !it3.next().getName().equals( "A" ) ) {
5970 if ( !it3.next().getName().equals( "B" ) ) {
5973 if ( !it3.next().getName().equals( "C" ) ) {
5976 if ( !it3.next().getName().equals( "D" ) ) {
5979 if ( !it3.next().getName().equals( "E" ) ) {
5982 if ( !it3.next().getName().equals( "F" ) ) {
5985 if ( !it3.next().getName().equals( "G" ) ) {
5988 if ( !it3.next().getName().equals( "1" ) ) {
5991 if ( !it3.next().getName().equals( "2" ) ) {
5994 if ( !it3.next().getName().equals( "3" ) ) {
5997 if ( !it3.next().getName().equals( "4" ) ) {
6000 if ( !it3.next().getName().equals( "5" ) ) {
6003 if ( !it3.next().getName().equals( "6" ) ) {
6006 if ( !it3.next().getName().equals( "f1" ) ) {
6009 if ( !it3.next().getName().equals( "f2" ) ) {
6012 if ( !it3.next().getName().equals( "f3" ) ) {
6015 if ( !it3.next().getName().equals( "a" ) ) {
6018 if ( !it3.next().getName().equals( "b" ) ) {
6021 if ( !it3.next().getName().equals( "f21" ) ) {
6024 if ( !it3.next().getName().equals( "X" ) ) {
6027 if ( !it3.next().getName().equals( "Y" ) ) {
6030 if ( !it3.next().getName().equals( "Z" ) ) {
6033 if ( it3.hasNext() ) {
6036 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
6037 PhylogenyNodeIterator it4;
6038 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
6041 for( it4.reset(); it4.hasNext(); ) {
6044 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
6045 if ( !it5.next().getName().equals( "r" ) ) {
6048 if ( !it5.next().getName().equals( "A" ) ) {
6051 if ( !it5.next().getName().equals( "B" ) ) {
6054 if ( !it5.next().getName().equals( "C" ) ) {
6057 if ( !it5.next().getName().equals( "D" ) ) {
6060 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
6061 PhylogenyNodeIterator it6;
6062 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
6065 for( it6.reset(); it6.hasNext(); ) {
6068 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
6069 if ( !it7.next().getName().equals( "A" ) ) {
6072 if ( it.hasNext() ) {
6076 catch ( final Exception e ) {
6077 e.printStackTrace( System.out );
6083 private static boolean testMafft( final String path ) {
6085 final List<String> opts = new ArrayList<String>();
6086 opts.add( "--maxiterate" );
6088 opts.add( "--localpair" );
6089 opts.add( "--quiet" );
6091 final MsaInferrer mafft = Mafft.createInstance( path );
6092 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
6093 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
6096 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
6100 catch ( final Exception e ) {
6101 e.printStackTrace( System.out );
6107 private static boolean testMidpointrooting() {
6109 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6110 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
6111 PhylogenyMethods.midpointRoot( t0 );
6112 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
6115 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
6118 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
6122 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
6123 new NHXParser() )[ 0 ];
6124 if ( !t1.isRooted() ) {
6127 PhylogenyMethods.midpointRoot( t1 );
6128 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6131 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6134 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6137 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6140 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6143 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6146 t1.reRoot( t1.getNode( "A" ) );
6147 PhylogenyMethods.midpointRoot( t1 );
6148 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6151 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6154 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6157 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
6160 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
6164 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
6168 catch ( final Exception e ) {
6169 e.printStackTrace( System.out );
6175 private static boolean testMsaQualityMethod() {
6177 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
6178 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
6179 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
6180 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
6181 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6186 final Msa msa = BasicMsa.createInstance( l );
6187 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
6190 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
6193 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
6196 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
6199 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
6202 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
6205 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
6209 catch ( final Exception e ) {
6210 e.printStackTrace( System.out );
6216 private static boolean testMsaEntropy() {
6218 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
6219 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
6220 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
6221 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
6222 final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
6227 final Msa msa = BasicMsa.createInstance( l );
6228 //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
6230 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
6231 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
6232 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
6233 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
6234 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
6235 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
6236 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
6237 // System.out.println();
6238 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
6239 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
6240 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
6241 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
6242 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
6243 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
6244 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
6245 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6246 l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
6247 l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
6248 l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
6249 l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
6250 l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
6251 l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
6252 l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
6253 l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
6254 l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
6255 l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
6256 l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
6257 l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
6258 l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
6259 l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
6260 l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
6261 l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
6262 l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
6263 l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
6264 l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
6265 l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
6266 l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
6267 l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
6268 final Msa msa2 = BasicMsa.createInstance( l2 );
6269 // System.out.println();
6270 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
6271 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
6272 // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
6274 catch ( final Exception e ) {
6275 e.printStackTrace( System.out );
6281 private static boolean testDeleteableMsa() {
6283 final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
6284 final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
6285 final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
6286 final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
6287 final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
6288 final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
6289 final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
6296 final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
6297 dmsa0.deleteRow( "b", false );
6298 if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
6301 dmsa0.deleteRow( "e", false );
6302 dmsa0.deleteRow( "a", false );
6303 dmsa0.deleteRow( "f", false );
6304 if ( dmsa0.getLength() != 4 ) {
6307 if ( dmsa0.getNumberOfSequences() != 2 ) {
6310 if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
6313 if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
6316 if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
6319 if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
6322 if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
6325 dmsa0.deleteRow( "c", false );
6326 dmsa0.deleteRow( "d", false );
6327 if ( dmsa0.getNumberOfSequences() != 0 ) {
6331 final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
6332 final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
6333 final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
6334 final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
6335 final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
6336 final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
6337 final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
6344 final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
6345 dmsa1.deleteGapOnlyColumns();
6346 dmsa1.deleteRow( "a", false );
6347 dmsa1.deleteRow( "f", false );
6348 dmsa1.deleteRow( "d", false );
6349 dmsa1.deleteGapOnlyColumns();
6350 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
6353 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
6356 if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
6359 dmsa1.deleteRow( "c", false );
6360 dmsa1.deleteGapOnlyColumns();
6361 final Writer w0 = new StringWriter();
6362 dmsa1.write( w0, MSA_FORMAT.FASTA );
6363 final Writer w1 = new StringWriter();
6364 dmsa1.write( w1, MSA_FORMAT.PHYLIP );
6365 if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
6368 if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
6371 final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
6372 final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
6373 final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
6374 final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
6375 final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
6376 final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
6377 final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
6384 final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
6385 dmsa2.deleteGapColumns( 0.5 );
6386 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
6389 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
6392 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
6395 dmsa2.deleteGapColumns( 0.2 );
6396 if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
6399 if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
6402 if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
6405 dmsa2.deleteGapColumns( 0 );
6406 dmsa2.deleteRow( "a", false );
6407 dmsa2.deleteRow( "b", false );
6408 dmsa2.deleteRow( "f", false );
6409 dmsa2.deleteRow( "e", false );
6410 dmsa2.setIdentifier( 0, "new_c" );
6411 dmsa2.setIdentifier( 1, "new_d" );
6412 dmsa2.setResidueAt( 0, 0, 'x' );
6413 final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
6414 if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
6417 final Writer w = new StringWriter();
6418 dmsa2.write( w, MSA_FORMAT.PHYLIP );
6419 final String phylip = w.toString();
6420 if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
6421 System.out.println( phylip );
6424 final Writer w2 = new StringWriter();
6425 dmsa2.write( w2, MSA_FORMAT.FASTA );
6426 final String fasta = w2.toString();
6427 if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
6428 System.out.println( fasta );
6432 catch ( final Exception e ) {
6433 e.printStackTrace( System.out );
6439 private static boolean testNextNodeWithCollapsing() {
6441 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6443 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
6444 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6445 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
6446 t0.getNode( "cd" ).setCollapse( true );
6447 t0.getNode( "cde" ).setCollapse( true );
6448 n = t0.getFirstExternalNode();
6449 while ( n != null ) {
6451 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6453 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6456 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6459 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
6462 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
6465 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
6468 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
6472 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6473 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
6474 t1.getNode( "ab" ).setCollapse( true );
6475 t1.getNode( "cd" ).setCollapse( true );
6476 t1.getNode( "cde" ).setCollapse( true );
6477 n = t1.getNode( "ab" );
6478 ext = new ArrayList<PhylogenyNode>();
6479 while ( n != null ) {
6481 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6483 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6486 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6489 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6492 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
6495 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
6499 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6500 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
6501 t2.getNode( "ab" ).setCollapse( true );
6502 t2.getNode( "cd" ).setCollapse( true );
6503 t2.getNode( "cde" ).setCollapse( true );
6504 t2.getNode( "c" ).setCollapse( true );
6505 t2.getNode( "d" ).setCollapse( true );
6506 t2.getNode( "e" ).setCollapse( true );
6507 t2.getNode( "gh" ).setCollapse( true );
6508 n = t2.getNode( "ab" );
6509 ext = new ArrayList<PhylogenyNode>();
6510 while ( n != null ) {
6512 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6514 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6517 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6520 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
6523 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
6527 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6528 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
6529 t3.getNode( "ab" ).setCollapse( true );
6530 t3.getNode( "cd" ).setCollapse( true );
6531 t3.getNode( "cde" ).setCollapse( true );
6532 t3.getNode( "c" ).setCollapse( true );
6533 t3.getNode( "d" ).setCollapse( true );
6534 t3.getNode( "e" ).setCollapse( true );
6535 t3.getNode( "gh" ).setCollapse( true );
6536 t3.getNode( "fgh" ).setCollapse( true );
6537 n = t3.getNode( "ab" );
6538 ext = new ArrayList<PhylogenyNode>();
6539 while ( n != null ) {
6541 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6543 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6546 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6549 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
6553 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6554 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
6555 t4.getNode( "ab" ).setCollapse( true );
6556 t4.getNode( "cd" ).setCollapse( true );
6557 t4.getNode( "cde" ).setCollapse( true );
6558 t4.getNode( "c" ).setCollapse( true );
6559 t4.getNode( "d" ).setCollapse( true );
6560 t4.getNode( "e" ).setCollapse( true );
6561 t4.getNode( "gh" ).setCollapse( true );
6562 t4.getNode( "fgh" ).setCollapse( true );
6563 t4.getNode( "abcdefgh" ).setCollapse( true );
6564 n = t4.getNode( "abcdefgh" );
6565 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
6568 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6569 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
6571 n = t5.getFirstExternalNode();
6572 while ( n != null ) {
6574 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6576 if ( ext.size() != 8 ) {
6579 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6582 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6585 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6588 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6591 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6594 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6597 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
6600 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
6603 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6604 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
6606 t6.getNode( "ab" ).setCollapse( true );
6607 n = t6.getNode( "ab" );
6608 while ( n != null ) {
6610 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6612 if ( ext.size() != 7 ) {
6615 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6618 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6621 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6624 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6627 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6630 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6633 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6636 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6637 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
6639 t7.getNode( "cd" ).setCollapse( true );
6640 n = t7.getNode( "a" );
6641 while ( n != null ) {
6643 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6645 if ( ext.size() != 7 ) {
6648 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6651 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6654 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6657 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6660 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6663 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6666 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6669 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
6670 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
6672 t8.getNode( "cd" ).setCollapse( true );
6673 t8.getNode( "c" ).setCollapse( true );
6674 t8.getNode( "d" ).setCollapse( true );
6675 n = t8.getNode( "a" );
6676 while ( n != null ) {
6678 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6680 if ( ext.size() != 7 ) {
6683 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6686 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6689 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
6690 System.out.println( "2 fail" );
6693 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6696 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
6699 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
6702 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
6705 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6706 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
6708 t9.getNode( "gh" ).setCollapse( true );
6709 n = t9.getNode( "a" );
6710 while ( n != null ) {
6712 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6714 if ( ext.size() != 7 ) {
6717 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6720 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6723 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6726 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6729 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6732 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6735 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6738 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6739 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
6741 t10.getNode( "gh" ).setCollapse( true );
6742 t10.getNode( "g" ).setCollapse( true );
6743 t10.getNode( "h" ).setCollapse( true );
6744 n = t10.getNode( "a" );
6745 while ( n != null ) {
6747 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6749 if ( ext.size() != 7 ) {
6752 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6755 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6758 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6761 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6764 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6767 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
6770 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
6773 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6774 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
6776 t11.getNode( "gh" ).setCollapse( true );
6777 t11.getNode( "fgh" ).setCollapse( true );
6778 n = t11.getNode( "a" );
6779 while ( n != null ) {
6781 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6783 if ( ext.size() != 6 ) {
6786 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6789 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6792 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6795 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6798 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6801 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6804 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6805 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
6807 t12.getNode( "gh" ).setCollapse( true );
6808 t12.getNode( "fgh" ).setCollapse( true );
6809 t12.getNode( "g" ).setCollapse( true );
6810 t12.getNode( "h" ).setCollapse( true );
6811 t12.getNode( "f" ).setCollapse( true );
6812 n = t12.getNode( "a" );
6813 while ( n != null ) {
6815 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6817 if ( ext.size() != 6 ) {
6820 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
6823 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
6826 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
6829 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
6832 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
6835 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6838 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
6839 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
6841 t13.getNode( "ab" ).setCollapse( true );
6842 t13.getNode( "b" ).setCollapse( true );
6843 t13.getNode( "fgh" ).setCollapse( true );
6844 t13.getNode( "gh" ).setCollapse( true );
6845 n = t13.getNode( "ab" );
6846 while ( n != null ) {
6848 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6850 if ( ext.size() != 5 ) {
6853 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6856 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6859 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6862 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6865 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6868 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
6869 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
6871 t14.getNode( "ab" ).setCollapse( true );
6872 t14.getNode( "a" ).setCollapse( true );
6873 t14.getNode( "fgh" ).setCollapse( true );
6874 t14.getNode( "gh" ).setCollapse( true );
6875 n = t14.getNode( "ab" );
6876 while ( n != null ) {
6878 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6880 if ( ext.size() != 5 ) {
6883 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6886 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6889 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6892 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6895 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6898 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" );
6899 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6901 t15.getNode( "ab" ).setCollapse( true );
6902 t15.getNode( "a" ).setCollapse( true );
6903 t15.getNode( "fgh" ).setCollapse( true );
6904 t15.getNode( "gh" ).setCollapse( true );
6905 n = t15.getNode( "ab" );
6906 while ( n != null ) {
6908 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6910 if ( ext.size() != 6 ) {
6913 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6916 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6919 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6922 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6925 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6928 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6933 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" );
6934 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6936 t16.getNode( "ab" ).setCollapse( true );
6937 t16.getNode( "a" ).setCollapse( true );
6938 t16.getNode( "fgh" ).setCollapse( true );
6939 t16.getNode( "gh" ).setCollapse( true );
6940 t16.getNode( "cd" ).setCollapse( true );
6941 t16.getNode( "cde" ).setCollapse( true );
6942 t16.getNode( "d" ).setCollapse( true );
6943 t16.getNode( "x" ).setCollapse( true );
6944 n = t16.getNode( "ab" );
6945 while ( n != null ) {
6947 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6949 if ( ext.size() != 4 ) {
6952 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6955 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6958 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6961 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6965 catch ( final Exception e ) {
6966 e.printStackTrace( System.out );
6972 private static boolean testNexusCharactersParsing() {
6974 final NexusCharactersParser parser = new NexusCharactersParser();
6975 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6977 String[] labels = parser.getCharStateLabels();
6978 if ( labels.length != 7 ) {
6981 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6984 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6987 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6990 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6993 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6996 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6999 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7002 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7004 labels = parser.getCharStateLabels();
7005 if ( labels.length != 7 ) {
7008 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7011 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7014 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7017 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7020 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7023 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7026 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7030 catch ( final Exception e ) {
7031 e.printStackTrace( System.out );
7037 private static boolean testNexusMatrixParsing() {
7039 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
7040 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
7042 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
7043 if ( m.getNumberOfCharacters() != 9 ) {
7046 if ( m.getNumberOfIdentifiers() != 5 ) {
7049 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
7052 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
7055 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
7058 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
7061 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
7064 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
7067 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
7070 // if ( labels.length != 7 ) {
7073 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7076 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7079 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7082 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7085 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7088 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7091 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7094 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
7096 // labels = parser.getCharStateLabels();
7097 // if ( labels.length != 7 ) {
7100 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
7103 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
7106 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
7109 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
7112 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
7115 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
7118 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
7122 catch ( final Exception e ) {
7123 e.printStackTrace( System.out );
7129 private static boolean testNexusTreeParsing() {
7131 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7132 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7133 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
7134 if ( phylogenies.length != 1 ) {
7137 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
7140 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7144 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
7145 if ( phylogenies.length != 1 ) {
7148 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7151 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
7155 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
7156 if ( phylogenies.length != 1 ) {
7159 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7162 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
7165 if ( phylogenies[ 0 ].isRooted() ) {
7169 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
7170 if ( phylogenies.length != 18 ) {
7173 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
7176 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
7179 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
7182 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
7185 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7188 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
7191 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
7194 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
7197 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
7200 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
7203 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
7206 if ( phylogenies[ 8 ].isRooted() ) {
7209 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
7212 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
7215 if ( !phylogenies[ 9 ].isRooted() ) {
7218 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
7221 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
7224 if ( !phylogenies[ 10 ].isRooted() ) {
7227 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
7230 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
7233 if ( phylogenies[ 11 ].isRooted() ) {
7236 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
7239 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
7242 if ( !phylogenies[ 12 ].isRooted() ) {
7245 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
7248 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
7251 if ( !phylogenies[ 13 ].isRooted() ) {
7254 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
7257 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
7260 if ( !phylogenies[ 14 ].isRooted() ) {
7263 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
7266 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
7269 if ( phylogenies[ 15 ].isRooted() ) {
7272 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
7275 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
7278 if ( !phylogenies[ 16 ].isRooted() ) {
7281 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
7284 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
7287 if ( phylogenies[ 17 ].isRooted() ) {
7290 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
7293 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7295 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
7296 if ( phylogenies.length != 9 ) {
7299 if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
7300 .getDistanceToParent() ) ) {
7303 if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
7304 .getDistanceToParent() ) ) {
7307 if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
7310 if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7313 if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
7316 if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7319 if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7323 catch ( final Exception e ) {
7324 e.printStackTrace( System.out );
7330 private static boolean testNexusTreeParsingIterating() {
7332 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
7333 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
7334 if ( !p.hasNext() ) {
7337 Phylogeny phy = p.next();
7338 if ( phy == null ) {
7341 if ( phy.getNumberOfExternalNodes() != 25 ) {
7344 if ( !phy.getName().equals( "" ) ) {
7347 if ( p.hasNext() ) {
7351 if ( phy != null ) {
7355 if ( !p.hasNext() ) {
7359 if ( phy == null ) {
7362 if ( phy.getNumberOfExternalNodes() != 25 ) {
7365 if ( !phy.getName().equals( "" ) ) {
7368 if ( p.hasNext() ) {
7372 if ( phy != null ) {
7375 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
7376 if ( !p.hasNext() ) {
7380 if ( phy == null ) {
7383 if ( phy.getNumberOfExternalNodes() != 10 ) {
7386 if ( !phy.getName().equals( "name" ) ) {
7389 if ( p.hasNext() ) {
7393 if ( phy != null ) {
7397 if ( !p.hasNext() ) {
7401 if ( phy == null ) {
7404 if ( phy.getNumberOfExternalNodes() != 10 ) {
7407 if ( !phy.getName().equals( "name" ) ) {
7410 if ( p.hasNext() ) {
7414 if ( phy != null ) {
7417 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
7418 if ( !p.hasNext() ) {
7422 if ( phy == null ) {
7425 if ( phy.getNumberOfExternalNodes() != 3 ) {
7428 if ( !phy.getName().equals( "" ) ) {
7431 if ( phy.isRooted() ) {
7434 if ( p.hasNext() ) {
7438 if ( phy != null ) {
7443 if ( !p.hasNext() ) {
7447 if ( phy == null ) {
7450 if ( phy.getNumberOfExternalNodes() != 3 ) {
7453 if ( !phy.getName().equals( "" ) ) {
7456 if ( p.hasNext() ) {
7460 if ( phy != null ) {
7464 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
7465 if ( !p.hasNext() ) {
7470 if ( phy == null ) {
7473 if ( phy.getNumberOfExternalNodes() != 10 ) {
7476 if ( !phy.getName().equals( "tree 0" ) ) {
7480 if ( !p.hasNext() ) {
7484 if ( phy == null ) {
7487 if ( phy.getNumberOfExternalNodes() != 10 ) {
7490 if ( !phy.getName().equals( "tree 1" ) ) {
7494 if ( !p.hasNext() ) {
7498 if ( phy == null ) {
7501 if ( phy.getNumberOfExternalNodes() != 3 ) {
7502 System.out.println( phy.toString() );
7505 if ( !phy.getName().equals( "" ) ) {
7508 if ( phy.isRooted() ) {
7512 if ( !p.hasNext() ) {
7516 if ( phy == null ) {
7519 if ( phy.getNumberOfExternalNodes() != 4 ) {
7522 if ( !phy.getName().equals( "" ) ) {
7525 if ( !phy.isRooted() ) {
7529 if ( !p.hasNext() ) {
7533 if ( phy == null ) {
7536 if ( phy.getNumberOfExternalNodes() != 5 ) {
7537 System.out.println( phy.getNumberOfExternalNodes() );
7540 if ( !phy.getName().equals( "" ) ) {
7543 if ( !phy.isRooted() ) {
7547 if ( !p.hasNext() ) {
7551 if ( phy == null ) {
7554 if ( phy.getNumberOfExternalNodes() != 3 ) {
7557 if ( !phy.getName().equals( "" ) ) {
7560 if ( phy.isRooted() ) {
7564 if ( !p.hasNext() ) {
7568 if ( phy == null ) {
7571 if ( phy.getNumberOfExternalNodes() != 2 ) {
7574 if ( !phy.getName().equals( "" ) ) {
7577 if ( !phy.isRooted() ) {
7581 if ( !p.hasNext() ) {
7585 if ( phy.getNumberOfExternalNodes() != 3 ) {
7588 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7591 if ( !phy.isRooted() ) {
7595 if ( !p.hasNext() ) {
7599 if ( phy.getNumberOfExternalNodes() != 3 ) {
7602 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
7605 if ( !phy.getName().equals( "tree 8" ) ) {
7609 if ( !p.hasNext() ) {
7613 if ( phy.getNumberOfExternalNodes() != 3 ) {
7616 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
7619 if ( !phy.getName().equals( "tree 9" ) ) {
7623 if ( !p.hasNext() ) {
7627 if ( phy.getNumberOfExternalNodes() != 3 ) {
7630 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7633 if ( !phy.getName().equals( "tree 10" ) ) {
7636 if ( !phy.isRooted() ) {
7640 if ( !p.hasNext() ) {
7644 if ( phy.getNumberOfExternalNodes() != 3 ) {
7647 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
7650 if ( !phy.getName().equals( "tree 11" ) ) {
7653 if ( phy.isRooted() ) {
7657 if ( !p.hasNext() ) {
7661 if ( phy.getNumberOfExternalNodes() != 3 ) {
7664 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
7667 if ( !phy.getName().equals( "tree 12" ) ) {
7670 if ( !phy.isRooted() ) {
7674 if ( !p.hasNext() ) {
7678 if ( phy.getNumberOfExternalNodes() != 3 ) {
7681 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
7684 if ( !phy.getName().equals( "tree 13" ) ) {
7687 if ( !phy.isRooted() ) {
7691 if ( !p.hasNext() ) {
7695 if ( phy.getNumberOfExternalNodes() != 10 ) {
7696 System.out.println( phy.getNumberOfExternalNodes() );
7701 .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;" ) ) {
7702 System.out.println( phy.toNewHampshire() );
7705 if ( !phy.getName().equals( "tree 14" ) ) {
7708 if ( !phy.isRooted() ) {
7712 if ( !p.hasNext() ) {
7716 if ( phy.getNumberOfExternalNodes() != 10 ) {
7717 System.out.println( phy.getNumberOfExternalNodes() );
7722 .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;" ) ) {
7723 System.out.println( phy.toNewHampshire() );
7726 if ( !phy.getName().equals( "tree 15" ) ) {
7729 if ( phy.isRooted() ) {
7733 if ( !p.hasNext() ) {
7737 if ( phy.getNumberOfExternalNodes() != 10 ) {
7738 System.out.println( phy.getNumberOfExternalNodes() );
7743 .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;" ) ) {
7744 System.out.println( phy.toNewHampshire() );
7747 if ( !phy.getName().equals( "tree 16" ) ) {
7750 if ( !phy.isRooted() ) {
7754 if ( !p.hasNext() ) {
7758 if ( phy.getNumberOfExternalNodes() != 10 ) {
7759 System.out.println( phy.getNumberOfExternalNodes() );
7764 .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;" ) ) {
7765 System.out.println( phy.toNewHampshire() );
7768 if ( !phy.getName().equals( "tree 17" ) ) {
7771 if ( phy.isRooted() ) {
7775 if ( p.hasNext() ) {
7779 if ( phy != null ) {
7784 if ( !p.hasNext() ) {
7788 if ( phy == null ) {
7791 if ( phy.getNumberOfExternalNodes() != 10 ) {
7794 if ( !phy.getName().equals( "tree 0" ) ) {
7798 if ( !p.hasNext() ) {
7802 if ( phy == null ) {
7805 if ( phy.getNumberOfExternalNodes() != 10 ) {
7808 if ( !phy.getName().equals( "tree 1" ) ) {
7812 if ( !p.hasNext() ) {
7816 if ( phy == null ) {
7819 if ( phy.getNumberOfExternalNodes() != 3 ) {
7822 if ( !phy.getName().equals( "" ) ) {
7825 if ( phy.isRooted() ) {
7829 if ( !p.hasNext() ) {
7833 if ( phy == null ) {
7836 if ( phy.getNumberOfExternalNodes() != 4 ) {
7839 if ( !phy.getName().equals( "" ) ) {
7842 if ( !phy.isRooted() ) {
7846 if ( !p.hasNext() ) {
7850 if ( phy == null ) {
7853 if ( phy.getNumberOfExternalNodes() != 5 ) {
7854 System.out.println( phy.getNumberOfExternalNodes() );
7857 if ( !phy.getName().equals( "" ) ) {
7860 if ( !phy.isRooted() ) {
7864 if ( !p.hasNext() ) {
7868 if ( phy == null ) {
7871 if ( phy.getNumberOfExternalNodes() != 3 ) {
7874 if ( !phy.getName().equals( "" ) ) {
7877 if ( phy.isRooted() ) {
7881 final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
7882 p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
7884 if ( !p2.hasNext() ) {
7888 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7891 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7895 if ( !p2.hasNext() ) {
7900 if ( !p2.hasNext() ) {
7905 if ( !p2.hasNext() ) {
7910 if ( !p2.hasNext() ) {
7915 if ( !p2.hasNext() ) {
7920 if ( !p2.hasNext() ) {
7925 if ( !p2.hasNext() ) {
7930 if ( !p2.hasNext() ) {
7934 if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
7937 if ( p2.hasNext() ) {
7941 if ( phy != null ) {
7946 if ( !p2.hasNext() ) {
7950 if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
7953 if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
7957 catch ( final Exception e ) {
7958 e.printStackTrace( System.out );
7964 private static boolean testNexusTreeParsingTranslating() {
7966 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7967 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
7968 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
7969 if ( phylogenies.length != 1 ) {
7972 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7975 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7978 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7981 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7984 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7985 .equals( "Aranaeus" ) ) {
7989 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7990 if ( phylogenies.length != 3 ) {
7993 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7996 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7999 if ( phylogenies[ 0 ].isRooted() ) {
8002 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8005 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8008 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8009 .equals( "Aranaeus" ) ) {
8012 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8015 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8018 if ( phylogenies[ 1 ].isRooted() ) {
8021 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8024 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8027 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8028 .equals( "Aranaeus" ) ) {
8031 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8034 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8037 if ( !phylogenies[ 2 ].isRooted() ) {
8040 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8043 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8046 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8047 .equals( "Aranaeus" ) ) {
8051 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
8052 if ( phylogenies.length != 3 ) {
8055 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
8058 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
8061 if ( phylogenies[ 0 ].isRooted() ) {
8064 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8067 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8070 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8071 .equals( "Aranaeus" ) ) {
8074 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
8077 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
8080 if ( phylogenies[ 1 ].isRooted() ) {
8083 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8086 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8089 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8090 .equals( "Aranaeus" ) ) {
8093 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
8096 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
8099 if ( !phylogenies[ 2 ].isRooted() ) {
8102 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
8105 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
8108 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
8109 .equals( "Aranaeus" ) ) {
8112 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
8113 if ( phylogenies.length != 3 ) {
8116 if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
8121 catch ( final Exception e ) {
8122 e.printStackTrace( System.out );
8128 private static boolean testNHParsing() {
8130 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8131 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
8132 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
8135 final NHXParser nhxp = new NHXParser();
8136 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
8137 nhxp.setReplaceUnderscores( true );
8138 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
8139 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
8142 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
8145 final Phylogeny p1b = factory
8146 .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 ",
8147 new NHXParser() )[ 0 ];
8148 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
8151 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
8154 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
8155 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
8156 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
8157 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
8158 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
8159 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
8160 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
8161 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
8162 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
8163 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
8164 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
8165 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
8166 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
8168 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
8171 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
8174 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
8177 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
8180 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
8181 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
8182 final String p16_S = "((A,B),C)";
8183 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
8184 if ( p16.length != 1 ) {
8187 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
8190 final String p17_S = "(C,(A,B))";
8191 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
8192 if ( p17.length != 1 ) {
8195 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
8198 final String p18_S = "((A,B),(C,D))";
8199 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
8200 if ( p18.length != 1 ) {
8203 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
8206 final String p19_S = "(((A,B),C),D)";
8207 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
8208 if ( p19.length != 1 ) {
8211 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
8214 final String p20_S = "(A,(B,(C,D)))";
8215 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
8216 if ( p20.length != 1 ) {
8219 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
8222 final String p21_S = "(A,(B,(C,(D,E))))";
8223 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
8224 if ( p21.length != 1 ) {
8227 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
8230 final String p22_S = "((((A,B),C),D),E)";
8231 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
8232 if ( p22.length != 1 ) {
8235 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
8238 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8239 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
8240 if ( p23.length != 1 ) {
8241 System.out.println( "xl=" + p23.length );
8245 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
8248 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8249 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
8250 if ( p24.length != 1 ) {
8253 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
8256 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8257 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8258 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
8259 if ( p241.length != 2 ) {
8262 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
8265 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
8268 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
8269 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
8270 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
8271 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
8272 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
8273 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
8274 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
8275 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
8276 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
8277 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
8280 final String p26_S = "(A,B)ab";
8281 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
8282 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
8285 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8286 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
8287 if ( p27s.length != 1 ) {
8288 System.out.println( "xxl=" + p27s.length );
8292 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8293 System.out.println( p27s[ 0 ].toNewHampshireX() );
8297 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
8299 if ( p27.length != 1 ) {
8300 System.out.println( "yl=" + p27.length );
8304 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
8305 System.out.println( p27[ 0 ].toNewHampshireX() );
8309 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8310 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8311 final String p28_S3 = "(A,B)ab";
8312 final String p28_S4 = "((((A,B),C),D),;E;)";
8313 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
8315 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
8318 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
8321 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
8324 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
8327 if ( p28.length != 4 ) {
8330 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";
8331 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
8332 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
8335 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";
8336 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
8337 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
8340 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
8341 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
8342 if ( ( p32.length != 0 ) ) {
8345 final String p33_S = "A";
8346 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
8347 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
8350 final String p34_S = "B;";
8351 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
8352 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
8355 final String p35_S = "B:0.2";
8356 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
8357 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
8360 final String p36_S = "(A)";
8361 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
8362 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
8365 final String p37_S = "((A))";
8366 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
8367 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
8370 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8371 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
8372 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
8375 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
8376 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
8377 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
8380 final String p40_S = "(A,B,C)";
8381 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
8382 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
8385 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
8386 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
8387 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
8390 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
8391 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
8392 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
8395 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)";
8396 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
8397 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
8400 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)))";
8401 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
8402 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
8405 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
8406 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
8407 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
8410 final String p46_S = "";
8411 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
8412 if ( p46.length != 0 ) {
8415 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
8416 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8419 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8420 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8423 final Phylogeny p49 = factory
8424 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
8425 new NHXParser() )[ 0 ];
8426 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
8429 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8430 if ( p50.getNode( "A" ) == null ) {
8433 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
8434 .equals( "((A,B)ab:2.0[88],C);" ) ) {
8437 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
8440 if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
8441 .equals( "((A,B)88:2.0,C);" ) ) {
8444 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8445 if ( p51.getNode( "A(A" ) == null ) {
8448 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
8449 if ( p52.getNode( "A(A" ) == null ) {
8452 final Phylogeny p53 = factory
8453 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
8454 new NHXParser() )[ 0 ];
8455 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
8458 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
8459 if ( p54.getNode( "A" ) == null ) {
8462 if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
8465 final Phylogeny p55 = factory
8466 .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);" ),
8467 new NHXParser() )[ 0 ];
8470 .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);" ) ) {
8471 System.out.println( p55.toNewHampshire() );
8474 final Phylogeny p56 = factory
8475 .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);" ),
8476 new NHXParser() )[ 0 ];
8479 .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);" ) ) {
8480 System.out.println( p56.toNewHampshire() );
8483 final Phylogeny p57 = factory
8484 .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);" ),
8485 new NHXParser() )[ 0 ];
8488 .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);" ) ) {
8489 System.out.println( p56.toNewHampshire() );
8492 final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
8493 final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
8494 if ( !p58.toNewHampshire().equals( s58 ) ) {
8495 System.out.println( p58.toNewHampshire() );
8498 final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
8499 final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
8500 if ( !p59.toNewHampshire().equals( s59 ) ) {
8501 System.out.println( p59.toNewHampshire() );
8504 final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
8505 final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
8506 if ( !p60.toNewHampshire().equals( s60 ) ) {
8507 System.out.println( p60.toNewHampshire() );
8510 final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
8511 final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
8512 if ( !p61.toNewHampshire()
8513 .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
8514 System.out.println( p61.toNewHampshire() );
8518 catch ( final Exception e ) {
8519 e.printStackTrace( System.out );
8525 private static boolean testNHParsingIter() {
8527 final String p0_str = "(A,B);";
8528 final NHXParser p = new NHXParser();
8529 p.setSource( p0_str );
8530 if ( !p.hasNext() ) {
8533 final Phylogeny p0 = p.next();
8534 if ( !p0.toNewHampshire().equals( p0_str ) ) {
8535 System.out.println( p0.toNewHampshire() );
8538 if ( p.hasNext() ) {
8541 if ( p.next() != null ) {
8545 final String p00_str = "(A,B)root;";
8546 p.setSource( p00_str );
8547 final Phylogeny p00 = p.next();
8548 if ( !p00.toNewHampshire().equals( p00_str ) ) {
8549 System.out.println( p00.toNewHampshire() );
8553 final String p000_str = "A;";
8554 p.setSource( p000_str );
8555 final Phylogeny p000 = p.next();
8556 if ( !p000.toNewHampshire().equals( p000_str ) ) {
8557 System.out.println( p000.toNewHampshire() );
8561 final String p0000_str = "A";
8562 p.setSource( p0000_str );
8563 final Phylogeny p0000 = p.next();
8564 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
8565 System.out.println( p0000.toNewHampshire() );
8569 p.setSource( "(A)" );
8570 final Phylogeny p00000 = p.next();
8571 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
8572 System.out.println( p00000.toNewHampshire() );
8576 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
8577 p.setSource( p1_str );
8578 if ( !p.hasNext() ) {
8581 final Phylogeny p1_0 = p.next();
8582 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
8583 System.out.println( p1_0.toNewHampshire() );
8586 if ( !p.hasNext() ) {
8589 final Phylogeny p1_1 = p.next();
8590 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
8591 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
8594 if ( !p.hasNext() ) {
8597 final Phylogeny p1_2 = p.next();
8598 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
8599 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
8602 if ( !p.hasNext() ) {
8605 final Phylogeny p1_3 = p.next();
8606 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
8607 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
8610 if ( p.hasNext() ) {
8613 if ( p.next() != null ) {
8617 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
8618 p.setSource( p2_str );
8619 if ( !p.hasNext() ) {
8622 Phylogeny p2_0 = p.next();
8623 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8624 System.out.println( p2_0.toNewHampshire() );
8627 if ( !p.hasNext() ) {
8630 Phylogeny p2_1 = p.next();
8631 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8632 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8635 if ( !p.hasNext() ) {
8638 Phylogeny p2_2 = p.next();
8639 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8640 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8643 if ( !p.hasNext() ) {
8646 Phylogeny p2_3 = p.next();
8647 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8648 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8651 if ( !p.hasNext() ) {
8654 Phylogeny p2_4 = p.next();
8655 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8656 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8659 if ( p.hasNext() ) {
8662 if ( p.next() != null ) {
8667 if ( !p.hasNext() ) {
8671 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
8672 System.out.println( p2_0.toNewHampshire() );
8675 if ( !p.hasNext() ) {
8679 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
8680 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
8683 if ( !p.hasNext() ) {
8687 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
8688 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
8691 if ( !p.hasNext() ) {
8695 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
8696 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
8699 if ( !p.hasNext() ) {
8703 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
8704 System.out.println( "(X) != " + p2_4.toNewHampshire() );
8707 if ( p.hasNext() ) {
8710 if ( p.next() != null ) {
8714 final String p3_str = "((A,B),C)abc";
8715 p.setSource( p3_str );
8716 if ( !p.hasNext() ) {
8719 final Phylogeny p3_0 = p.next();
8720 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
8723 if ( p.hasNext() ) {
8726 if ( p.next() != null ) {
8730 final String p4_str = "((A,B)ab,C)abc";
8731 p.setSource( p4_str );
8732 if ( !p.hasNext() ) {
8735 final Phylogeny p4_0 = p.next();
8736 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
8739 if ( p.hasNext() ) {
8742 if ( p.next() != null ) {
8746 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
8747 p.setSource( p5_str );
8748 if ( !p.hasNext() ) {
8751 final Phylogeny p5_0 = p.next();
8752 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
8755 if ( p.hasNext() ) {
8758 if ( p.next() != null ) {
8762 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
8763 p.setSource( p6_str );
8764 if ( !p.hasNext() ) {
8767 Phylogeny p6_0 = p.next();
8768 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8771 if ( p.hasNext() ) {
8774 if ( p.next() != null ) {
8778 if ( !p.hasNext() ) {
8782 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
8785 if ( p.hasNext() ) {
8788 if ( p.next() != null ) {
8792 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
8793 p.setSource( p7_str );
8794 if ( !p.hasNext() ) {
8797 Phylogeny p7_0 = p.next();
8798 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8801 if ( p.hasNext() ) {
8804 if ( p.next() != null ) {
8808 if ( !p.hasNext() ) {
8812 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8815 if ( p.hasNext() ) {
8818 if ( p.next() != null ) {
8822 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
8823 p.setSource( p8_str );
8824 if ( !p.hasNext() ) {
8827 Phylogeny p8_0 = p.next();
8828 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8831 if ( !p.hasNext() ) {
8834 if ( !p.hasNext() ) {
8837 Phylogeny p8_1 = p.next();
8838 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8841 if ( p.hasNext() ) {
8844 if ( p.next() != null ) {
8848 if ( !p.hasNext() ) {
8852 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
8855 if ( !p.hasNext() ) {
8859 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
8862 if ( p.hasNext() ) {
8865 if ( p.next() != null ) {
8871 if ( p.hasNext() ) {
8875 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
8876 if ( !p.hasNext() ) {
8879 Phylogeny p_27 = p.next();
8880 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8881 System.out.println( p_27.toNewHampshireX() );
8885 if ( p.hasNext() ) {
8888 if ( p.next() != null ) {
8892 if ( !p.hasNext() ) {
8896 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
8897 System.out.println( p_27.toNewHampshireX() );
8901 if ( p.hasNext() ) {
8904 if ( p.next() != null ) {
8908 final String p30_str = "(A,B);(C,D)";
8909 final NHXParser p30 = new NHXParser();
8910 p30.setSource( p30_str );
8911 if ( !p30.hasNext() ) {
8914 Phylogeny phy30 = p30.next();
8915 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8916 System.out.println( phy30.toNewHampshire() );
8919 if ( !p30.hasNext() ) {
8922 Phylogeny phy301 = p30.next();
8923 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8924 System.out.println( phy301.toNewHampshire() );
8927 if ( p30.hasNext() ) {
8930 if ( p30.hasNext() ) {
8933 if ( p30.next() != null ) {
8936 if ( p30.next() != null ) {
8940 if ( !p30.hasNext() ) {
8944 if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
8945 System.out.println( phy30.toNewHampshire() );
8948 if ( !p30.hasNext() ) {
8951 phy301 = p30.next();
8952 if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
8953 System.out.println( phy301.toNewHampshire() );
8956 if ( p30.hasNext() ) {
8959 if ( p30.hasNext() ) {
8962 if ( p30.next() != null ) {
8965 if ( p30.next() != null ) {
8969 catch ( final Exception e ) {
8970 e.printStackTrace( System.out );
8976 private static boolean testNHXconversion() {
8978 final PhylogenyNode n1 = new PhylogenyNode();
8979 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
8980 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
8981 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
8982 final PhylogenyNode n5 = PhylogenyNode
8983 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
8984 final PhylogenyNode n6 = PhylogenyNode
8985 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
8986 if ( !n1.toNewHampshireX().equals( "" ) ) {
8989 if ( !n2.toNewHampshireX().equals( "" ) ) {
8992 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
8995 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
8998 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
9001 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
9002 System.out.println( n6.toNewHampshireX() );
9005 final PhylogenyNode n7 = new PhylogenyNode();
9006 n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
9007 if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
9008 .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
9009 System.out.println( n7
9010 .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
9014 catch ( final Exception e ) {
9015 e.printStackTrace( System.out );
9021 private static boolean testNHXNodeParsing() {
9023 final PhylogenyNode n1 = new PhylogenyNode();
9024 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
9025 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
9026 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
9027 final PhylogenyNode n5 = PhylogenyNode
9028 .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]" );
9029 if ( !n3.getName().equals( "n3" ) ) {
9032 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9035 if ( n3.isDuplication() ) {
9038 if ( n3.isHasAssignedEvent() ) {
9041 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
9044 if ( !n4.getName().equals( "n4" ) ) {
9047 if ( n4.getDistanceToParent() != 0.01 ) {
9050 if ( !n5.getName().equals( "n5" ) ) {
9053 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
9056 if ( n5.getDistanceToParent() != 0.1 ) {
9059 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
9062 if ( !n5.isDuplication() ) {
9065 if ( !n5.isHasAssignedEvent() ) {
9068 final PhylogenyNode n8 = PhylogenyNode
9069 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
9070 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9071 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9074 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
9077 final PhylogenyNode n9 = PhylogenyNode
9078 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
9079 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9080 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
9083 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
9086 final PhylogenyNode n10 = PhylogenyNode
9087 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9088 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
9091 final PhylogenyNode n20 = PhylogenyNode
9092 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9093 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9096 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
9099 final PhylogenyNode n20x = PhylogenyNode
9100 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9101 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
9104 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
9107 final PhylogenyNode n20xx = PhylogenyNode
9108 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9109 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
9112 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
9115 final PhylogenyNode n20xxx = PhylogenyNode
9116 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9117 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
9120 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
9123 final PhylogenyNode n20xxxx = PhylogenyNode
9124 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9125 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
9128 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
9131 final PhylogenyNode n21 = PhylogenyNode
9132 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9133 if ( !n21.getName().equals( "N21_PIG" ) ) {
9136 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
9139 final PhylogenyNode n21x = PhylogenyNode
9140 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9141 if ( !n21x.getName().equals( "n21_PIG" ) ) {
9144 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
9147 final PhylogenyNode n22 = PhylogenyNode
9148 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9149 if ( !n22.getName().equals( "n22/PIG" ) ) {
9152 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
9155 final PhylogenyNode n23 = PhylogenyNode
9156 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9157 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
9160 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
9163 final PhylogenyNode a = PhylogenyNode
9164 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9165 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
9168 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
9171 final PhylogenyNode c1 = PhylogenyNode
9172 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
9173 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9174 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
9177 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
9180 final PhylogenyNode c2 = PhylogenyNode
9181 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
9182 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9183 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
9186 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
9189 final PhylogenyNode e3 = PhylogenyNode
9190 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9191 if ( !e3.getName().equals( "n10_RAT~" ) ) {
9194 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
9197 final PhylogenyNode n11 = PhylogenyNode
9198 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
9199 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9200 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
9203 if ( n11.getDistanceToParent() != 0.4 ) {
9206 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
9209 final PhylogenyNode n12 = PhylogenyNode
9210 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
9211 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9212 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
9215 if ( n12.getDistanceToParent() != 0.4 ) {
9218 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
9221 final PhylogenyNode o = PhylogenyNode
9222 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9223 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
9226 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
9229 if ( n1.getName().compareTo( "" ) != 0 ) {
9232 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9235 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9238 if ( n2.getName().compareTo( "" ) != 0 ) {
9241 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
9244 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
9247 final PhylogenyNode n00 = PhylogenyNode
9248 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
9249 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
9252 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
9255 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
9256 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
9259 final PhylogenyNode n13 = PhylogenyNode
9260 .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9261 if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
9264 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
9267 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9270 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9273 final PhylogenyNode n14 = PhylogenyNode
9274 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9275 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
9278 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
9281 final PhylogenyNode n15 = PhylogenyNode
9282 .createInstanceFromNhxString( "something_wicked[123]",
9283 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9284 if ( !n15.getName().equals( "something_wicked" ) ) {
9287 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
9290 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
9293 final PhylogenyNode n16 = PhylogenyNode
9294 .createInstanceFromNhxString( "something_wicked2[9]",
9295 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9296 if ( !n16.getName().equals( "something_wicked2" ) ) {
9299 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
9302 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
9305 final PhylogenyNode n17 = PhylogenyNode
9306 .createInstanceFromNhxString( "something_wicked3[a]",
9307 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9308 if ( !n17.getName().equals( "something_wicked3" ) ) {
9311 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
9314 final PhylogenyNode n18 = PhylogenyNode
9315 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9316 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
9319 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
9322 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
9325 final PhylogenyNode n19 = PhylogenyNode
9326 .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9327 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
9330 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9333 final PhylogenyNode n30 = PhylogenyNode
9334 .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
9335 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9336 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
9339 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
9342 final PhylogenyNode n31 = PhylogenyNode
9343 .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
9344 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9345 if ( n31.getNodeData().isHasTaxonomy() ) {
9348 final PhylogenyNode n32 = PhylogenyNode
9349 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9350 if ( n32.getNodeData().isHasTaxonomy() ) {
9353 final PhylogenyNode n40 = PhylogenyNode
9354 .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9355 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
9358 final PhylogenyNode n41 = PhylogenyNode
9359 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9360 if ( n41.getNodeData().isHasTaxonomy() ) {
9363 final PhylogenyNode n42 = PhylogenyNode
9364 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
9365 if ( n42.getNodeData().isHasTaxonomy() ) {
9368 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
9369 NHXParser.TAXONOMY_EXTRACTION.NO );
9370 if ( n43.getNodeData().isHasTaxonomy() ) {
9373 final PhylogenyNode n44 = PhylogenyNode
9374 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
9375 if ( n44.getNodeData().isHasTaxonomy() ) {
9379 catch ( final Exception e ) {
9380 e.printStackTrace( System.out );
9386 private static boolean testNHXParsing() {
9388 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9389 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
9390 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
9393 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]";
9394 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
9395 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9398 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]";
9399 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
9400 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
9403 final Phylogeny[] p3 = factory
9404 .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]",
9406 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9409 final Phylogeny[] p4 = factory
9410 .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(]",
9412 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9415 final Phylogeny[] p5 = factory
9416 .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(((]",
9418 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
9421 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)";
9422 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)";
9423 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
9424 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
9427 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)))";
9428 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)))";
9429 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
9430 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
9433 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]) ))[,,, ])))))))";
9434 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
9435 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
9436 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
9439 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
9440 if ( !p9.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 p10 = 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 ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9449 final Phylogeny p11 = factory
9450 .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]",
9451 new NHXParser() )[ 0 ];
9452 if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9455 final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
9456 new NHXParser() )[ 0 ];
9457 if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
9461 catch ( final Exception e ) {
9462 e.printStackTrace( System.out );
9468 private static boolean testNHXParsingMB() {
9470 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9471 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
9472 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9473 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9474 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9475 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9476 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9477 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9478 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9479 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
9480 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
9483 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
9486 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
9487 0.1100000000000000e+00 ) ) {
9490 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
9493 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
9496 final Phylogeny p2 = factory
9497 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
9498 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9499 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
9500 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
9501 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
9502 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
9503 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
9504 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
9505 + "7.369400000000000e-02}])",
9506 new NHXParser() )[ 0 ];
9507 if ( p2.getNode( "1" ) == null ) {
9510 if ( p2.getNode( "2" ) == null ) {
9514 catch ( final Exception e ) {
9515 e.printStackTrace( System.out );
9522 private static boolean testNHXParsingQuotes() {
9524 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9525 final NHXParser p = new NHXParser();
9526 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
9527 if ( phylogenies_0.length != 5 ) {
9530 final Phylogeny phy = phylogenies_0[ 4 ];
9531 if ( phy.getNumberOfExternalNodes() != 7 ) {
9534 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
9537 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
9540 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
9541 .getScientificName().equals( "hsapiens" ) ) {
9544 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
9547 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
9550 if ( phy.getNodes( "\"double quotes\" inside single quotes" ).size() != 1 ) {
9553 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
9556 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
9559 final NHXParser p1p = new NHXParser();
9560 p1p.setIgnoreQuotes( true );
9561 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
9562 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
9565 final NHXParser p2p = new NHXParser();
9566 p1p.setIgnoreQuotes( false );
9567 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
9568 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
9571 final NHXParser p3p = new NHXParser();
9572 p3p.setIgnoreQuotes( false );
9573 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
9574 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
9577 final NHXParser p4p = new NHXParser();
9578 p4p.setIgnoreQuotes( false );
9579 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
9580 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
9583 final Phylogeny p10 = factory
9584 .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]",
9585 new NHXParser() )[ 0 ];
9586 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]";
9587 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
9590 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
9591 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
9594 final Phylogeny p12 = factory
9595 .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]",
9596 new NHXParser() )[ 0 ];
9597 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]";
9598 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
9601 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
9602 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
9605 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;";
9606 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
9609 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
9610 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
9614 catch ( final Exception e ) {
9615 e.printStackTrace( System.out );
9621 private static boolean testNodeRemoval() {
9623 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9624 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
9625 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
9626 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
9629 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
9630 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
9631 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
9634 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
9635 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
9636 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
9640 catch ( final Exception e ) {
9641 e.printStackTrace( System.out );
9647 private static boolean testPhylogenyBranch() {
9649 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
9650 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
9651 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
9652 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
9653 if ( !a1b1.equals( a1b1 ) ) {
9656 if ( !a1b1.equals( b1a1 ) ) {
9659 if ( !b1a1.equals( a1b1 ) ) {
9662 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
9663 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
9664 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
9665 if ( a1_b1.equals( b1_a1 ) ) {
9668 if ( a1_b1.equals( a1_b1_ ) ) {
9671 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
9672 if ( !a1_b1.equals( b1_a1_ ) ) {
9675 if ( a1_b1_.equals( b1_a1_ ) ) {
9678 if ( !a1_b1_.equals( b1_a1 ) ) {
9682 catch ( final Exception e ) {
9683 e.printStackTrace( System.out );
9689 private static boolean testPhyloXMLparsingOfDistributionElement() {
9691 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9692 PhyloXmlParser xml_parser = null;
9694 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
9696 catch ( final Exception e ) {
9697 // Do nothing -- means were not running from jar.
9699 if ( xml_parser == null ) {
9700 xml_parser = PhyloXmlParser.createPhyloXmlParser();
9701 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
9702 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
9705 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
9708 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
9710 if ( xml_parser.getErrorCount() > 0 ) {
9711 System.out.println( xml_parser.getErrorMessages().toString() );
9714 if ( phylogenies_0.length != 1 ) {
9717 final Phylogeny t1 = phylogenies_0[ 0 ];
9718 PhylogenyNode n = null;
9719 Distribution d = null;
9720 n = t1.getNode( "root node" );
9721 if ( !n.getNodeData().isHasDistribution() ) {
9724 if ( n.getNodeData().getDistributions().size() != 1 ) {
9727 d = n.getNodeData().getDistribution();
9728 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9731 if ( d.getPoints().size() != 1 ) {
9734 if ( d.getPolygons() != null ) {
9737 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9740 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9743 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9746 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9749 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9752 n = t1.getNode( "node a" );
9753 if ( !n.getNodeData().isHasDistribution() ) {
9756 if ( n.getNodeData().getDistributions().size() != 2 ) {
9759 d = n.getNodeData().getDistribution( 1 );
9760 if ( !d.getDesc().equals( "San Diego" ) ) {
9763 if ( d.getPoints().size() != 1 ) {
9766 if ( d.getPolygons() != null ) {
9769 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9772 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9775 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9778 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9781 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9784 n = t1.getNode( "node bb" );
9785 if ( !n.getNodeData().isHasDistribution() ) {
9788 if ( n.getNodeData().getDistributions().size() != 1 ) {
9791 d = n.getNodeData().getDistribution( 0 );
9792 if ( d.getPoints().size() != 3 ) {
9795 if ( d.getPolygons().size() != 2 ) {
9798 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9801 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9804 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9807 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9810 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9813 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9816 Polygon p = d.getPolygons().get( 0 );
9817 if ( p.getPoints().size() != 3 ) {
9820 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9823 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9826 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9829 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9832 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9835 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9838 p = d.getPolygons().get( 1 );
9839 if ( p.getPoints().size() != 3 ) {
9842 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9845 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9848 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9852 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
9853 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
9854 if ( rt.length != 1 ) {
9857 final Phylogeny t1_rt = rt[ 0 ];
9858 n = t1_rt.getNode( "root node" );
9859 if ( !n.getNodeData().isHasDistribution() ) {
9862 if ( n.getNodeData().getDistributions().size() != 1 ) {
9865 d = n.getNodeData().getDistribution();
9866 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
9869 if ( d.getPoints().size() != 1 ) {
9872 if ( d.getPolygons() != null ) {
9875 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
9878 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9881 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9884 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
9887 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
9890 n = t1_rt.getNode( "node a" );
9891 if ( !n.getNodeData().isHasDistribution() ) {
9894 if ( n.getNodeData().getDistributions().size() != 2 ) {
9897 d = n.getNodeData().getDistribution( 1 );
9898 if ( !d.getDesc().equals( "San Diego" ) ) {
9901 if ( d.getPoints().size() != 1 ) {
9904 if ( d.getPolygons() != null ) {
9907 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
9910 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
9913 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
9916 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
9919 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
9922 n = t1_rt.getNode( "node bb" );
9923 if ( !n.getNodeData().isHasDistribution() ) {
9926 if ( n.getNodeData().getDistributions().size() != 1 ) {
9929 d = n.getNodeData().getDistribution( 0 );
9930 if ( d.getPoints().size() != 3 ) {
9933 if ( d.getPolygons().size() != 2 ) {
9936 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
9939 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
9942 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
9945 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
9948 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
9951 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
9954 p = d.getPolygons().get( 0 );
9955 if ( p.getPoints().size() != 3 ) {
9958 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
9961 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
9964 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9967 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
9970 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
9973 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
9976 p = d.getPolygons().get( 1 );
9977 if ( p.getPoints().size() != 3 ) {
9980 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
9983 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
9986 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
9990 catch ( final Exception e ) {
9991 e.printStackTrace( System.out );
9997 private static boolean testPostOrderIterator() {
9999 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10000 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10001 PhylogenyNodeIterator it0;
10002 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
10005 for( it0.reset(); it0.hasNext(); ) {
10008 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10009 final PhylogenyNodeIterator it = t1.iteratorPostorder();
10010 if ( !it.next().getName().equals( "A" ) ) {
10013 if ( !it.next().getName().equals( "B" ) ) {
10016 if ( !it.next().getName().equals( "ab" ) ) {
10019 if ( !it.next().getName().equals( "C" ) ) {
10022 if ( !it.next().getName().equals( "D" ) ) {
10025 if ( !it.next().getName().equals( "cd" ) ) {
10028 if ( !it.next().getName().equals( "abcd" ) ) {
10031 if ( !it.next().getName().equals( "E" ) ) {
10034 if ( !it.next().getName().equals( "F" ) ) {
10037 if ( !it.next().getName().equals( "ef" ) ) {
10040 if ( !it.next().getName().equals( "G" ) ) {
10043 if ( !it.next().getName().equals( "H" ) ) {
10046 if ( !it.next().getName().equals( "gh" ) ) {
10049 if ( !it.next().getName().equals( "efgh" ) ) {
10052 if ( !it.next().getName().equals( "r" ) ) {
10055 if ( it.hasNext() ) {
10059 catch ( final Exception e ) {
10060 e.printStackTrace( System.out );
10066 private static boolean testPreOrderIterator() {
10068 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10069 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
10070 PhylogenyNodeIterator it0;
10071 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
10074 for( it0.reset(); it0.hasNext(); ) {
10077 PhylogenyNodeIterator it = t0.iteratorPreorder();
10078 if ( !it.next().getName().equals( "r" ) ) {
10081 if ( !it.next().getName().equals( "ab" ) ) {
10084 if ( !it.next().getName().equals( "A" ) ) {
10087 if ( !it.next().getName().equals( "B" ) ) {
10090 if ( !it.next().getName().equals( "cd" ) ) {
10093 if ( !it.next().getName().equals( "C" ) ) {
10096 if ( !it.next().getName().equals( "D" ) ) {
10099 if ( it.hasNext() ) {
10102 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
10103 it = t1.iteratorPreorder();
10104 if ( !it.next().getName().equals( "r" ) ) {
10107 if ( !it.next().getName().equals( "abcd" ) ) {
10110 if ( !it.next().getName().equals( "ab" ) ) {
10113 if ( !it.next().getName().equals( "A" ) ) {
10116 if ( !it.next().getName().equals( "B" ) ) {
10119 if ( !it.next().getName().equals( "cd" ) ) {
10122 if ( !it.next().getName().equals( "C" ) ) {
10125 if ( !it.next().getName().equals( "D" ) ) {
10128 if ( !it.next().getName().equals( "efgh" ) ) {
10131 if ( !it.next().getName().equals( "ef" ) ) {
10134 if ( !it.next().getName().equals( "E" ) ) {
10137 if ( !it.next().getName().equals( "F" ) ) {
10140 if ( !it.next().getName().equals( "gh" ) ) {
10143 if ( !it.next().getName().equals( "G" ) ) {
10146 if ( !it.next().getName().equals( "H" ) ) {
10149 if ( it.hasNext() ) {
10153 catch ( final Exception e ) {
10154 e.printStackTrace( System.out );
10160 private static boolean testPropertiesMap() {
10162 final PropertiesMap pm = new PropertiesMap();
10163 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10164 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
10165 final Property p2 = new Property( "something:else",
10167 "improbable:research",
10170 pm.addProperty( p0 );
10171 pm.addProperty( p1 );
10172 pm.addProperty( p2 );
10173 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
10176 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
10179 if ( pm.getProperties().size() != 3 ) {
10182 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
10185 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10188 if ( pm.getProperties().size() != 3 ) {
10191 pm.removeProperty( "dimensions:diameter" );
10192 if ( pm.getProperties().size() != 2 ) {
10195 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
10198 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
10202 catch ( final Exception e ) {
10203 e.printStackTrace( System.out );
10209 private static boolean testProteinId() {
10211 final ProteinId id1 = new ProteinId( "a" );
10212 final ProteinId id2 = new ProteinId( "a" );
10213 final ProteinId id3 = new ProteinId( "A" );
10214 final ProteinId id4 = new ProteinId( "b" );
10215 if ( !id1.equals( id1 ) ) {
10218 if ( id1.getId().equals( "x" ) ) {
10221 if ( id1.getId().equals( null ) ) {
10224 if ( !id1.equals( id2 ) ) {
10227 if ( id1.equals( id3 ) ) {
10230 if ( id1.hashCode() != id1.hashCode() ) {
10233 if ( id1.hashCode() != id2.hashCode() ) {
10236 if ( id1.hashCode() == id3.hashCode() ) {
10239 if ( id1.compareTo( id1 ) != 0 ) {
10242 if ( id1.compareTo( id2 ) != 0 ) {
10245 if ( id1.compareTo( id3 ) != 0 ) {
10248 if ( id1.compareTo( id4 ) >= 0 ) {
10251 if ( id4.compareTo( id1 ) <= 0 ) {
10254 if ( !id4.getId().equals( "b" ) ) {
10257 final ProteinId id5 = new ProteinId( " C " );
10258 if ( !id5.getId().equals( "C" ) ) {
10261 if ( id5.equals( id1 ) ) {
10265 catch ( final Exception e ) {
10266 e.printStackTrace( System.out );
10272 private static boolean testReIdMethods() {
10274 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10275 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
10276 final long count = PhylogenyNode.getNodeCount();
10277 p.levelOrderReID();
10278 if ( p.getNode( "r" ).getId() != count ) {
10281 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
10284 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
10287 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
10290 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
10293 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
10296 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
10299 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
10302 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
10305 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
10308 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
10311 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
10314 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
10317 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
10320 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
10324 catch ( final Exception e ) {
10325 e.printStackTrace( System.out );
10331 private static boolean testRerooting() {
10333 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10334 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",
10335 new NHXParser() )[ 0 ];
10336 if ( !t1.isRooted() ) {
10339 t1.reRoot( t1.getNode( "D" ) );
10340 t1.reRoot( t1.getNode( "CD" ) );
10341 t1.reRoot( t1.getNode( "A" ) );
10342 t1.reRoot( t1.getNode( "B" ) );
10343 t1.reRoot( t1.getNode( "AB" ) );
10344 t1.reRoot( t1.getNode( "D" ) );
10345 t1.reRoot( t1.getNode( "C" ) );
10346 t1.reRoot( t1.getNode( "CD" ) );
10347 t1.reRoot( t1.getNode( "A" ) );
10348 t1.reRoot( t1.getNode( "B" ) );
10349 t1.reRoot( t1.getNode( "AB" ) );
10350 t1.reRoot( t1.getNode( "D" ) );
10351 t1.reRoot( t1.getNode( "D" ) );
10352 t1.reRoot( t1.getNode( "C" ) );
10353 t1.reRoot( t1.getNode( "A" ) );
10354 t1.reRoot( t1.getNode( "B" ) );
10355 t1.reRoot( t1.getNode( "AB" ) );
10356 t1.reRoot( t1.getNode( "C" ) );
10357 t1.reRoot( t1.getNode( "D" ) );
10358 t1.reRoot( t1.getNode( "CD" ) );
10359 t1.reRoot( t1.getNode( "D" ) );
10360 t1.reRoot( t1.getNode( "A" ) );
10361 t1.reRoot( t1.getNode( "B" ) );
10362 t1.reRoot( t1.getNode( "AB" ) );
10363 t1.reRoot( t1.getNode( "C" ) );
10364 t1.reRoot( t1.getNode( "D" ) );
10365 t1.reRoot( t1.getNode( "CD" ) );
10366 t1.reRoot( t1.getNode( "D" ) );
10367 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
10370 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
10373 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
10376 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
10379 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
10382 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
10385 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",
10386 new NHXParser() )[ 0 ];
10387 t2.reRoot( t2.getNode( "A" ) );
10388 t2.reRoot( t2.getNode( "D" ) );
10389 t2.reRoot( t2.getNode( "ABC" ) );
10390 t2.reRoot( t2.getNode( "A" ) );
10391 t2.reRoot( t2.getNode( "B" ) );
10392 t2.reRoot( t2.getNode( "D" ) );
10393 t2.reRoot( t2.getNode( "C" ) );
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( "AB" ) );
10399 t2.reRoot( t2.getNode( "D" ) );
10400 t2.reRoot( t2.getNode( "C" ) );
10401 t2.reRoot( t2.getNode( "B" ) );
10402 t2.reRoot( t2.getNode( "AB" ) );
10403 t2.reRoot( t2.getNode( "D" ) );
10404 t2.reRoot( t2.getNode( "D" ) );
10405 t2.reRoot( t2.getNode( "ABC" ) );
10406 t2.reRoot( t2.getNode( "A" ) );
10407 t2.reRoot( t2.getNode( "B" ) );
10408 t2.reRoot( t2.getNode( "AB" ) );
10409 t2.reRoot( t2.getNode( "D" ) );
10410 t2.reRoot( t2.getNode( "C" ) );
10411 t2.reRoot( t2.getNode( "ABC" ) );
10412 t2.reRoot( t2.getNode( "A" ) );
10413 t2.reRoot( t2.getNode( "B" ) );
10414 t2.reRoot( t2.getNode( "AB" ) );
10415 t2.reRoot( t2.getNode( "D" ) );
10416 t2.reRoot( t2.getNode( "D" ) );
10417 t2.reRoot( t2.getNode( "C" ) );
10418 t2.reRoot( t2.getNode( "A" ) );
10419 t2.reRoot( t2.getNode( "B" ) );
10420 t2.reRoot( t2.getNode( "AB" ) );
10421 t2.reRoot( t2.getNode( "C" ) );
10422 t2.reRoot( t2.getNode( "D" ) );
10423 t2.reRoot( t2.getNode( "ABC" ) );
10424 t2.reRoot( t2.getNode( "D" ) );
10425 t2.reRoot( t2.getNode( "A" ) );
10426 t2.reRoot( t2.getNode( "B" ) );
10427 t2.reRoot( t2.getNode( "AB" ) );
10428 t2.reRoot( t2.getNode( "C" ) );
10429 t2.reRoot( t2.getNode( "D" ) );
10430 t2.reRoot( t2.getNode( "ABC" ) );
10431 t2.reRoot( t2.getNode( "D" ) );
10432 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10435 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10438 t2.reRoot( t2.getNode( "ABC" ) );
10439 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10442 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10445 t2.reRoot( t2.getNode( "AB" ) );
10446 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10449 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10452 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10455 t2.reRoot( t2.getNode( "AB" ) );
10456 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10459 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10462 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10465 t2.reRoot( t2.getNode( "D" ) );
10466 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10469 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10472 t2.reRoot( t2.getNode( "ABC" ) );
10473 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
10476 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
10479 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
10480 new NHXParser() )[ 0 ];
10481 t3.reRoot( t3.getNode( "B" ) );
10482 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10485 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10488 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10491 t3.reRoot( t3.getNode( "B" ) );
10492 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10495 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10498 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10501 t3.reRoot( t3.getRoot() );
10502 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10505 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
10508 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
10512 catch ( final Exception e ) {
10513 e.printStackTrace( System.out );
10519 private static boolean testSDIse() {
10521 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10522 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
10523 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
10524 gene1.setRooted( true );
10525 species1.setRooted( true );
10526 final SDI sdi = new SDI( gene1, species1 );
10527 if ( !gene1.getRoot().isDuplication() ) {
10530 final Phylogeny species2 = factory
10531 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10532 new NHXParser() )[ 0 ];
10533 final Phylogeny gene2 = factory
10534 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10535 new NHXParser() )[ 0 ];
10536 species2.setRooted( true );
10537 gene2.setRooted( true );
10538 final SDI sdi2 = new SDI( gene2, species2 );
10539 if ( sdi2.getDuplicationsSum() != 0 ) {
10542 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
10545 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
10548 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
10551 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
10554 if ( !gene2.getNode( "r" ).isSpeciation() ) {
10557 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
10560 final Phylogeny species3 = factory
10561 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10562 new NHXParser() )[ 0 ];
10563 final Phylogeny gene3 = factory
10564 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10565 new NHXParser() )[ 0 ];
10566 species3.setRooted( true );
10567 gene3.setRooted( true );
10568 final SDI sdi3 = new SDI( gene3, species3 );
10569 if ( sdi3.getDuplicationsSum() != 1 ) {
10572 if ( !gene3.getNode( "aa" ).isDuplication() ) {
10575 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
10578 final Phylogeny species4 = factory
10579 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10580 new NHXParser() )[ 0 ];
10581 final Phylogeny gene4 = factory
10582 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10583 new NHXParser() )[ 0 ];
10584 species4.setRooted( true );
10585 gene4.setRooted( true );
10586 final SDI sdi4 = new SDI( gene4, species4 );
10587 if ( sdi4.getDuplicationsSum() != 1 ) {
10590 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
10593 if ( !gene4.getNode( "abc" ).isDuplication() ) {
10596 if ( gene4.getNode( "abcd" ).isDuplication() ) {
10599 if ( species4.getNumberOfExternalNodes() != 6 ) {
10602 if ( gene4.getNumberOfExternalNodes() != 6 ) {
10605 final Phylogeny species5 = factory
10606 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10607 new NHXParser() )[ 0 ];
10608 final Phylogeny gene5 = factory
10609 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
10610 new NHXParser() )[ 0 ];
10611 species5.setRooted( true );
10612 gene5.setRooted( true );
10613 final SDI sdi5 = new SDI( gene5, species5 );
10614 if ( sdi5.getDuplicationsSum() != 2 ) {
10617 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
10620 if ( !gene5.getNode( "adc" ).isDuplication() ) {
10623 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
10626 if ( species5.getNumberOfExternalNodes() != 6 ) {
10629 if ( gene5.getNumberOfExternalNodes() != 6 ) {
10632 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
10633 // Conjecture for Comparing Molecular Phylogenies"
10634 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
10635 final Phylogeny species6 = factory
10636 .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,"
10637 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10638 new NHXParser() )[ 0 ];
10639 final Phylogeny gene6 = factory
10640 .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,"
10641 + "((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,"
10642 + "(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;",
10643 new NHXParser() )[ 0 ];
10644 species6.setRooted( true );
10645 gene6.setRooted( true );
10646 final SDI sdi6 = new SDI( gene6, species6 );
10647 if ( sdi6.getDuplicationsSum() != 3 ) {
10650 if ( !gene6.getNode( "r" ).isDuplication() ) {
10653 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
10656 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
10659 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
10662 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
10665 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
10668 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
10671 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
10674 sdi6.computeMappingCostL();
10675 if ( sdi6.computeMappingCostL() != 17 ) {
10678 if ( species6.getNumberOfExternalNodes() != 9 ) {
10681 if ( gene6.getNumberOfExternalNodes() != 9 ) {
10684 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
10685 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
10686 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
10687 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
10688 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
10689 species7.setRooted( true );
10690 final Phylogeny gene7_1 = Test
10691 .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])" );
10692 gene7_1.setRooted( true );
10693 final SDI sdi7 = new SDI( gene7_1, species7 );
10694 if ( sdi7.getDuplicationsSum() != 0 ) {
10697 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
10700 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
10703 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
10706 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
10709 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
10712 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
10715 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
10718 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
10721 final Phylogeny gene7_2 = Test
10722 .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])" );
10723 gene7_2.setRooted( true );
10724 final SDI sdi7_2 = new SDI( gene7_2, species7 );
10725 if ( sdi7_2.getDuplicationsSum() != 1 ) {
10728 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
10731 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
10734 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
10737 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
10740 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
10743 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
10746 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
10749 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
10752 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
10756 catch ( final Exception e ) {
10762 private static boolean testSDIunrooted() {
10764 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10765 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
10766 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
10767 final Iterator<PhylogenyBranch> iter = l.iterator();
10768 PhylogenyBranch br = iter.next();
10769 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
10772 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
10776 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10779 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10783 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
10786 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
10790 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10793 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10797 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10800 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10804 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
10807 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
10811 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10814 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10818 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10821 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10825 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10828 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10832 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
10835 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
10839 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10842 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10846 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
10849 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
10853 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
10856 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
10860 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
10863 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
10867 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
10870 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
10873 if ( iter.hasNext() ) {
10876 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
10877 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
10878 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
10880 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10883 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10887 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10890 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10894 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10897 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10900 if ( iter1.hasNext() ) {
10903 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
10904 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
10905 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
10907 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
10910 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
10914 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
10917 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
10921 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
10924 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
10927 if ( iter2.hasNext() ) {
10930 final Phylogeny species0 = factory
10931 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
10932 new NHXParser() )[ 0 ];
10933 final Phylogeny gene1 = factory
10934 .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])",
10935 new NHXParser() )[ 0 ];
10936 species0.setRooted( true );
10937 gene1.setRooted( true );
10938 final SDIR sdi_unrooted = new SDIR();
10939 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
10940 if ( sdi_unrooted.getCount() != 1 ) {
10943 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
10946 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
10949 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
10952 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10955 final Phylogeny gene2 = factory
10956 .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])",
10957 new NHXParser() )[ 0 ];
10958 gene2.setRooted( true );
10959 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
10960 if ( sdi_unrooted.getCount() != 1 ) {
10963 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
10966 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10969 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
10972 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
10975 final Phylogeny species6 = factory
10976 .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,"
10977 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
10978 new NHXParser() )[ 0 ];
10979 final Phylogeny gene6 = factory
10980 .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],"
10981 + "(((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],"
10982 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
10983 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
10984 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
10985 new NHXParser() )[ 0 ];
10986 species6.setRooted( true );
10987 gene6.setRooted( true );
10988 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
10989 if ( sdi_unrooted.getCount() != 1 ) {
10992 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
10995 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
10998 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11001 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11004 if ( !p6[ 0 ].getRoot().isDuplication() ) {
11007 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11010 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11013 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
11016 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11019 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
11022 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
11025 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11029 final Phylogeny species7 = factory
11030 .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,"
11031 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11032 new NHXParser() )[ 0 ];
11033 final Phylogeny gene7 = factory
11034 .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],"
11035 + "(((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],"
11036 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11037 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11038 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11039 new NHXParser() )[ 0 ];
11040 species7.setRooted( true );
11041 gene7.setRooted( true );
11042 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
11043 if ( sdi_unrooted.getCount() != 1 ) {
11046 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11049 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11052 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11055 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
11058 if ( !p7[ 0 ].getRoot().isDuplication() ) {
11061 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11064 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11067 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
11070 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11073 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
11076 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
11079 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11083 final Phylogeny species8 = factory
11084 .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,"
11085 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
11086 new NHXParser() )[ 0 ];
11087 final Phylogeny gene8 = factory
11088 .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],"
11089 + "(((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],"
11090 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
11091 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
11092 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
11093 new NHXParser() )[ 0 ];
11094 species8.setRooted( true );
11095 gene8.setRooted( true );
11096 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
11097 if ( sdi_unrooted.getCount() != 1 ) {
11100 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
11103 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
11106 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
11109 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
11112 if ( !p8[ 0 ].getRoot().isDuplication() ) {
11115 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
11118 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
11121 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
11124 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
11127 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
11130 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
11133 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
11138 catch ( final Exception e ) {
11139 e.printStackTrace( System.out );
11145 private static boolean testSequenceDbWsTools1() {
11147 final PhylogenyNode n = new PhylogenyNode();
11148 n.setName( "NP_001025424" );
11149 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11150 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11151 || !acc.getValue().equals( "NP_001025424" ) ) {
11154 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11155 acc = SequenceDbWsTools.obtainSeqAccession( n );
11156 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11157 || !acc.getValue().equals( "NP_001025424" ) ) {
11160 n.setName( "NP_001025424.1" );
11161 acc = SequenceDbWsTools.obtainSeqAccession( n );
11162 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11163 || !acc.getValue().equals( "NP_001025424" ) ) {
11166 n.setName( "NM_001030253" );
11167 acc = SequenceDbWsTools.obtainSeqAccession( n );
11168 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11169 || !acc.getValue().equals( "NM_001030253" ) ) {
11172 n.setName( "BCL2_HUMAN" );
11173 acc = SequenceDbWsTools.obtainSeqAccession( n );
11174 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11175 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11176 System.out.println( acc.toString() );
11179 n.setName( "P10415" );
11180 acc = SequenceDbWsTools.obtainSeqAccession( n );
11181 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11182 || !acc.getValue().equals( "P10415" ) ) {
11183 System.out.println( acc.toString() );
11186 n.setName( " P10415 " );
11187 acc = SequenceDbWsTools.obtainSeqAccession( n );
11188 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11189 || !acc.getValue().equals( "P10415" ) ) {
11190 System.out.println( acc.toString() );
11193 n.setName( "_P10415|" );
11194 acc = SequenceDbWsTools.obtainSeqAccession( n );
11195 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11196 || !acc.getValue().equals( "P10415" ) ) {
11197 System.out.println( acc.toString() );
11200 n.setName( "AY695820" );
11201 acc = SequenceDbWsTools.obtainSeqAccession( n );
11202 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11203 || !acc.getValue().equals( "AY695820" ) ) {
11204 System.out.println( acc.toString() );
11207 n.setName( "_AY695820_" );
11208 acc = SequenceDbWsTools.obtainSeqAccession( n );
11209 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11210 || !acc.getValue().equals( "AY695820" ) ) {
11211 System.out.println( acc.toString() );
11214 n.setName( "AAA59452" );
11215 acc = SequenceDbWsTools.obtainSeqAccession( n );
11216 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11217 || !acc.getValue().equals( "AAA59452" ) ) {
11218 System.out.println( acc.toString() );
11221 n.setName( "_AAA59452_" );
11222 acc = SequenceDbWsTools.obtainSeqAccession( n );
11223 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11224 || !acc.getValue().equals( "AAA59452" ) ) {
11225 System.out.println( acc.toString() );
11228 n.setName( "AAA59452.1" );
11229 acc = SequenceDbWsTools.obtainSeqAccession( n );
11230 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11231 || !acc.getValue().equals( "AAA59452.1" ) ) {
11232 System.out.println( acc.toString() );
11235 n.setName( "_AAA59452.1_" );
11236 acc = SequenceDbWsTools.obtainSeqAccession( n );
11237 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11238 || !acc.getValue().equals( "AAA59452.1" ) ) {
11239 System.out.println( acc.toString() );
11242 n.setName( "GI:94894583" );
11243 acc = SequenceDbWsTools.obtainSeqAccession( n );
11244 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11245 || !acc.getValue().equals( "94894583" ) ) {
11246 System.out.println( acc.toString() );
11249 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11250 acc = SequenceDbWsTools.obtainSeqAccession( n );
11251 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11252 || !acc.getValue().equals( "71845847" ) ) {
11253 System.out.println( acc.toString() );
11256 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11257 acc = SequenceDbWsTools.obtainSeqAccession( n );
11258 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11259 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11260 System.out.println( acc.toString() );
11264 catch ( final Exception e ) {
11270 private static boolean testSequenceDbWsTools2() {
11272 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11273 SequenceDbWsTools.obtainSeqInformation( n1 );
11274 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11277 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11280 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11283 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11286 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11287 SequenceDbWsTools.obtainSeqInformation( n2 );
11288 if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
11291 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11294 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11297 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11300 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11301 SequenceDbWsTools.obtainSeqInformation( n3 );
11302 if ( !n3.getNodeData().getSequence().getName()
11303 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11306 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11309 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11312 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11316 catch ( final IOException e ) {
11317 System.out.println();
11318 System.out.println( "the following might be due to absence internet connection:" );
11319 e.printStackTrace( System.out );
11322 catch ( final Exception e ) {
11323 e.printStackTrace();
11329 private static boolean testSequenceIdParsing() {
11331 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
11332 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11333 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11334 if ( id != null ) {
11335 System.out.println( "value =" + id.getValue() );
11336 System.out.println( "provider=" + id.getSource() );
11340 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
11341 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11342 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11343 if ( id != null ) {
11344 System.out.println( "value =" + id.getValue() );
11345 System.out.println( "provider=" + id.getSource() );
11349 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
11350 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11351 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
11352 if ( id != null ) {
11353 System.out.println( "value =" + id.getValue() );
11354 System.out.println( "provider=" + id.getSource() );
11358 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
11359 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11360 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
11361 if ( id != null ) {
11362 System.out.println( "value =" + id.getValue() );
11363 System.out.println( "provider=" + id.getSource() );
11367 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
11368 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11369 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
11370 if ( id != null ) {
11371 System.out.println( "value =" + id.getValue() );
11372 System.out.println( "provider=" + id.getSource() );
11376 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
11377 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11378 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
11379 if ( id != null ) {
11380 System.out.println( "value =" + id.getValue() );
11381 System.out.println( "provider=" + id.getSource() );
11385 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
11386 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11387 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
11388 if ( id != null ) {
11389 System.out.println( "value =" + id.getValue() );
11390 System.out.println( "provider=" + id.getSource() );
11394 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
11395 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11396 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11397 if ( id != null ) {
11398 System.out.println( "value =" + id.getValue() );
11399 System.out.println( "provider=" + id.getSource() );
11403 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
11404 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11405 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
11406 if ( id != null ) {
11407 System.out.println( "value =" + id.getValue() );
11408 System.out.println( "provider=" + id.getSource() );
11412 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
11413 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11414 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
11415 if ( id != null ) {
11416 System.out.println( "value =" + id.getValue() );
11417 System.out.println( "provider=" + id.getSource() );
11421 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
11422 if ( id != null ) {
11423 System.out.println( "value =" + id.getValue() );
11424 System.out.println( "provider=" + id.getSource() );
11427 id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
11428 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11429 || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
11430 if ( id != null ) {
11431 System.out.println( "value =" + id.getValue() );
11432 System.out.println( "provider=" + id.getSource() );
11436 id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
11437 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11438 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11439 if ( id != null ) {
11440 System.out.println( "value =" + id.getValue() );
11441 System.out.println( "provider=" + id.getSource() );
11445 id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
11446 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
11447 || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
11448 if ( id != null ) {
11449 System.out.println( "value =" + id.getValue() );
11450 System.out.println( "provider=" + id.getSource() );
11454 id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
11455 if ( id != null ) {
11456 System.out.println( "value =" + id.getValue() );
11457 System.out.println( "provider=" + id.getSource() );
11461 catch ( final Exception e ) {
11462 e.printStackTrace( System.out );
11468 private static boolean testSequenceWriter() {
11470 final String n = ForesterUtil.LINE_SEPARATOR;
11471 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
11474 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
11477 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
11480 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
11483 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
11484 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
11487 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
11488 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
11492 catch ( final Exception e ) {
11493 e.printStackTrace();
11499 private static boolean testSpecies() {
11501 final Species s1 = new BasicSpecies( "a" );
11502 final Species s2 = new BasicSpecies( "a" );
11503 final Species s3 = new BasicSpecies( "A" );
11504 final Species s4 = new BasicSpecies( "b" );
11505 if ( !s1.equals( s1 ) ) {
11508 if ( s1.getSpeciesId().equals( "x" ) ) {
11511 if ( s1.getSpeciesId().equals( null ) ) {
11514 if ( !s1.equals( s2 ) ) {
11517 if ( s1.equals( s3 ) ) {
11520 if ( s1.hashCode() != s1.hashCode() ) {
11523 if ( s1.hashCode() != s2.hashCode() ) {
11526 if ( s1.hashCode() == s3.hashCode() ) {
11529 if ( s1.compareTo( s1 ) != 0 ) {
11532 if ( s1.compareTo( s2 ) != 0 ) {
11535 if ( s1.compareTo( s3 ) != 0 ) {
11538 if ( s1.compareTo( s4 ) >= 0 ) {
11541 if ( s4.compareTo( s1 ) <= 0 ) {
11544 if ( !s4.getSpeciesId().equals( "b" ) ) {
11547 final Species s5 = new BasicSpecies( " C " );
11548 if ( !s5.getSpeciesId().equals( "C" ) ) {
11551 if ( s5.equals( s1 ) ) {
11555 catch ( final Exception e ) {
11556 e.printStackTrace( System.out );
11562 private static boolean testSplit() {
11564 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11565 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11566 //Archaeopteryx.createApplication( p0 );
11567 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11568 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11569 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11570 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11571 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11572 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11573 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11574 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11575 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11576 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11577 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
11578 // System.out.println( s0.toString() );
11580 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11583 if ( s0.match( query_nodes ) ) {
11586 query_nodes = new HashSet<PhylogenyNode>();
11587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11594 if ( !s0.match( query_nodes ) ) {
11598 query_nodes = new HashSet<PhylogenyNode>();
11599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11602 if ( !s0.match( query_nodes ) ) {
11606 query_nodes = new HashSet<PhylogenyNode>();
11607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11611 if ( !s0.match( query_nodes ) ) {
11615 query_nodes = new HashSet<PhylogenyNode>();
11616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11620 if ( !s0.match( query_nodes ) ) {
11624 query_nodes = new HashSet<PhylogenyNode>();
11625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11628 if ( !s0.match( query_nodes ) ) {
11631 query_nodes = new HashSet<PhylogenyNode>();
11632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11634 if ( !s0.match( query_nodes ) ) {
11637 query_nodes = new HashSet<PhylogenyNode>();
11638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11643 if ( !s0.match( query_nodes ) ) {
11646 query_nodes = new HashSet<PhylogenyNode>();
11647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11650 if ( !s0.match( query_nodes ) ) {
11653 query_nodes = new HashSet<PhylogenyNode>();
11654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11658 if ( !s0.match( query_nodes ) ) {
11661 query_nodes = new HashSet<PhylogenyNode>();
11662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11664 if ( s0.match( query_nodes ) ) {
11667 query_nodes = new HashSet<PhylogenyNode>();
11668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11672 if ( s0.match( query_nodes ) ) {
11675 query_nodes = new HashSet<PhylogenyNode>();
11676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11681 if ( s0.match( query_nodes ) ) {
11684 query_nodes = new HashSet<PhylogenyNode>();
11685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11688 if ( s0.match( query_nodes ) ) {
11691 query_nodes = new HashSet<PhylogenyNode>();
11692 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11694 if ( s0.match( query_nodes ) ) {
11697 query_nodes = new HashSet<PhylogenyNode>();
11698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11700 if ( s0.match( query_nodes ) ) {
11703 query_nodes = new HashSet<PhylogenyNode>();
11704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11706 if ( s0.match( query_nodes ) ) {
11709 query_nodes = new HashSet<PhylogenyNode>();
11710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11712 if ( s0.match( query_nodes ) ) {
11715 query_nodes = new HashSet<PhylogenyNode>();
11716 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11718 if ( s0.match( query_nodes ) ) {
11721 query_nodes = new HashSet<PhylogenyNode>();
11722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11724 if ( s0.match( query_nodes ) ) {
11727 query_nodes = new HashSet<PhylogenyNode>();
11728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11731 if ( s0.match( query_nodes ) ) {
11734 query_nodes = new HashSet<PhylogenyNode>();
11735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11738 if ( s0.match( query_nodes ) ) {
11741 query_nodes = new HashSet<PhylogenyNode>();
11742 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11743 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11745 if ( s0.match( query_nodes ) ) {
11748 query_nodes = new HashSet<PhylogenyNode>();
11749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11753 if ( s0.match( query_nodes ) ) {
11757 // query_nodes = new HashSet<PhylogenyNode>();
11758 // query_nodes.add( new PhylogenyNode( "X" ) );
11759 // query_nodes.add( new PhylogenyNode( "Y" ) );
11760 // query_nodes.add( new PhylogenyNode( "A" ) );
11761 // query_nodes.add( new PhylogenyNode( "B" ) );
11762 // query_nodes.add( new PhylogenyNode( "C" ) );
11763 // query_nodes.add( new PhylogenyNode( "D" ) );
11764 // query_nodes.add( new PhylogenyNode( "E" ) );
11765 // query_nodes.add( new PhylogenyNode( "F" ) );
11766 // query_nodes.add( new PhylogenyNode( "G" ) );
11767 // if ( !s0.match( query_nodes ) ) {
11770 // query_nodes = new HashSet<PhylogenyNode>();
11771 // query_nodes.add( new PhylogenyNode( "X" ) );
11772 // query_nodes.add( new PhylogenyNode( "Y" ) );
11773 // query_nodes.add( new PhylogenyNode( "A" ) );
11774 // query_nodes.add( new PhylogenyNode( "B" ) );
11775 // query_nodes.add( new PhylogenyNode( "C" ) );
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( "D" ) );
11784 // query_nodes.add( new PhylogenyNode( "E" ) );
11785 // query_nodes.add( new PhylogenyNode( "F" ) );
11786 // query_nodes.add( new PhylogenyNode( "G" ) );
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( "A" ) );
11795 // query_nodes.add( new PhylogenyNode( "B" ) );
11796 // query_nodes.add( new PhylogenyNode( "C" ) );
11797 // query_nodes.add( new PhylogenyNode( "D" ) );
11798 // if ( !s0.match( query_nodes ) ) {
11802 // query_nodes = new HashSet<PhylogenyNode>();
11803 // query_nodes.add( new PhylogenyNode( "X" ) );
11804 // query_nodes.add( new PhylogenyNode( "Y" ) );
11805 // query_nodes.add( new PhylogenyNode( "E" ) );
11806 // query_nodes.add( new PhylogenyNode( "F" ) );
11807 // query_nodes.add( new PhylogenyNode( "G" ) );
11808 // if ( !s0.match( query_nodes ) ) {
11812 // query_nodes = new HashSet<PhylogenyNode>();
11813 // query_nodes.add( new PhylogenyNode( "X" ) );
11814 // query_nodes.add( new PhylogenyNode( "Y" ) );
11815 // query_nodes.add( new PhylogenyNode( "F" ) );
11816 // query_nodes.add( new PhylogenyNode( "G" ) );
11817 // if ( !s0.match( query_nodes ) ) {
11821 query_nodes = new HashSet<PhylogenyNode>();
11822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11826 if ( s0.match( query_nodes ) ) {
11830 query_nodes = new HashSet<PhylogenyNode>();
11831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11835 if ( s0.match( query_nodes ) ) {
11838 ///////////////////////////
11840 query_nodes = new HashSet<PhylogenyNode>();
11841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11843 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11844 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11845 if ( s0.match( query_nodes ) ) {
11849 query_nodes = new HashSet<PhylogenyNode>();
11850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11854 if ( s0.match( query_nodes ) ) {
11858 query_nodes = new HashSet<PhylogenyNode>();
11859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11863 if ( s0.match( query_nodes ) ) {
11867 query_nodes = new HashSet<PhylogenyNode>();
11868 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11872 if ( s0.match( query_nodes ) ) {
11876 query_nodes = new HashSet<PhylogenyNode>();
11877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11881 if ( s0.match( query_nodes ) ) {
11885 query_nodes = new HashSet<PhylogenyNode>();
11886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11889 if ( s0.match( query_nodes ) ) {
11893 query_nodes = new HashSet<PhylogenyNode>();
11894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11899 if ( s0.match( query_nodes ) ) {
11903 query_nodes = new HashSet<PhylogenyNode>();
11904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11909 if ( s0.match( query_nodes ) ) {
11913 query_nodes = new HashSet<PhylogenyNode>();
11914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11919 if ( s0.match( query_nodes ) ) {
11923 query_nodes = new HashSet<PhylogenyNode>();
11924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
11925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
11926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11930 if ( s0.match( query_nodes ) ) {
11934 catch ( final Exception e ) {
11935 e.printStackTrace();
11941 private static boolean testSplitStrict() {
11943 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11944 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
11945 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
11946 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11947 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11948 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11949 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11950 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11951 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11952 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11953 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
11954 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
11955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11957 if ( s0.match( query_nodes ) ) {
11960 query_nodes = new HashSet<PhylogenyNode>();
11961 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11962 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11968 if ( !s0.match( query_nodes ) ) {
11972 query_nodes = new HashSet<PhylogenyNode>();
11973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11976 if ( !s0.match( query_nodes ) ) {
11980 query_nodes = new HashSet<PhylogenyNode>();
11981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
11983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
11984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
11985 if ( !s0.match( query_nodes ) ) {
11989 query_nodes = new HashSet<PhylogenyNode>();
11990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
11991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
11992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
11993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
11994 if ( !s0.match( query_nodes ) ) {
11998 query_nodes = new HashSet<PhylogenyNode>();
11999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12002 if ( !s0.match( query_nodes ) ) {
12006 query_nodes = new HashSet<PhylogenyNode>();
12007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12009 if ( !s0.match( query_nodes ) ) {
12013 query_nodes = new HashSet<PhylogenyNode>();
12014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12019 if ( !s0.match( query_nodes ) ) {
12023 query_nodes = new HashSet<PhylogenyNode>();
12024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12027 if ( !s0.match( query_nodes ) ) {
12031 query_nodes = new HashSet<PhylogenyNode>();
12032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12036 if ( !s0.match( query_nodes ) ) {
12040 query_nodes = new HashSet<PhylogenyNode>();
12041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12043 if ( s0.match( query_nodes ) ) {
12047 query_nodes = new HashSet<PhylogenyNode>();
12048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12052 if ( s0.match( query_nodes ) ) {
12056 query_nodes = new HashSet<PhylogenyNode>();
12057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12062 if ( s0.match( query_nodes ) ) {
12066 query_nodes = new HashSet<PhylogenyNode>();
12067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12070 if ( s0.match( query_nodes ) ) {
12074 query_nodes = new HashSet<PhylogenyNode>();
12075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12077 if ( s0.match( query_nodes ) ) {
12081 query_nodes = new HashSet<PhylogenyNode>();
12082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12084 if ( s0.match( query_nodes ) ) {
12088 query_nodes = new HashSet<PhylogenyNode>();
12089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
12091 if ( s0.match( query_nodes ) ) {
12095 query_nodes = new HashSet<PhylogenyNode>();
12096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12098 if ( s0.match( query_nodes ) ) {
12102 query_nodes = new HashSet<PhylogenyNode>();
12103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12105 if ( s0.match( query_nodes ) ) {
12109 query_nodes = new HashSet<PhylogenyNode>();
12110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12112 if ( s0.match( query_nodes ) ) {
12116 query_nodes = new HashSet<PhylogenyNode>();
12117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
12119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12120 if ( s0.match( query_nodes ) ) {
12124 query_nodes = new HashSet<PhylogenyNode>();
12125 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12126 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
12127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12128 if ( s0.match( query_nodes ) ) {
12132 query_nodes = new HashSet<PhylogenyNode>();
12133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12134 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12135 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12136 if ( s0.match( query_nodes ) ) {
12140 query_nodes = new HashSet<PhylogenyNode>();
12141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
12142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
12143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
12144 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
12145 if ( s0.match( query_nodes ) ) {
12149 catch ( final Exception e ) {
12150 e.printStackTrace();
12156 private static boolean testSubtreeDeletion() {
12158 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12159 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12160 t1.deleteSubtree( t1.getNode( "A" ), false );
12161 if ( t1.getNumberOfExternalNodes() != 5 ) {
12164 t1.toNewHampshireX();
12165 t1.deleteSubtree( t1.getNode( "E" ), false );
12166 if ( t1.getNumberOfExternalNodes() != 4 ) {
12169 t1.toNewHampshireX();
12170 t1.deleteSubtree( t1.getNode( "F" ), false );
12171 if ( t1.getNumberOfExternalNodes() != 3 ) {
12174 t1.toNewHampshireX();
12175 t1.deleteSubtree( t1.getNode( "D" ), false );
12176 t1.toNewHampshireX();
12177 if ( t1.getNumberOfExternalNodes() != 3 ) {
12180 t1.deleteSubtree( t1.getNode( "def" ), false );
12181 t1.toNewHampshireX();
12182 if ( t1.getNumberOfExternalNodes() != 2 ) {
12185 t1.deleteSubtree( t1.getNode( "B" ), false );
12186 t1.toNewHampshireX();
12187 if ( t1.getNumberOfExternalNodes() != 1 ) {
12190 t1.deleteSubtree( t1.getNode( "C" ), false );
12191 t1.toNewHampshireX();
12192 if ( t1.getNumberOfExternalNodes() != 1 ) {
12195 t1.deleteSubtree( t1.getNode( "abc" ), false );
12196 t1.toNewHampshireX();
12197 if ( t1.getNumberOfExternalNodes() != 1 ) {
12200 t1.deleteSubtree( t1.getNode( "r" ), false );
12201 if ( t1.getNumberOfExternalNodes() != 0 ) {
12204 if ( !t1.isEmpty() ) {
12207 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
12208 t2.deleteSubtree( t2.getNode( "A" ), false );
12209 t2.toNewHampshireX();
12210 if ( t2.getNumberOfExternalNodes() != 5 ) {
12213 t2.deleteSubtree( t2.getNode( "abc" ), false );
12214 t2.toNewHampshireX();
12215 if ( t2.getNumberOfExternalNodes() != 3 ) {
12218 t2.deleteSubtree( t2.getNode( "def" ), false );
12219 t2.toNewHampshireX();
12220 if ( t2.getNumberOfExternalNodes() != 1 ) {
12224 catch ( final Exception e ) {
12225 e.printStackTrace( System.out );
12231 private static boolean testSupportCount() {
12233 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12234 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
12235 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
12236 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
12237 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
12238 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
12239 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
12241 SupportCount.count( t0_1, phylogenies_1, true, false );
12242 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
12243 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
12244 + "(((((A,B),C),D),E),((F,G),X))"
12245 + "(((((A,Y),B),C),D),((F,G),E))"
12246 + "(((((A,B),C),D),E),(F,G))"
12247 + "(((((A,B),C),D),E),(F,G))"
12248 + "(((((A,B),C),D),E),(F,G))"
12249 + "(((((A,B),C),D),E),(F,G),Z)"
12250 + "(((((A,B),C),D),E),(F,G))"
12251 + "((((((A,B),C),D),E),F),G)"
12252 + "(((((X,Y),F,G),E),((A,B),C)),D)",
12254 SupportCount.count( t0_2, phylogenies_2, true, false );
12255 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
12256 while ( it.hasNext() ) {
12257 final PhylogenyNode n = it.next();
12258 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
12262 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
12263 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
12264 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
12265 SupportCount.count( t0_3, phylogenies_3, true, false );
12266 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
12267 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
12270 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
12273 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
12276 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
12279 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
12282 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
12285 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
12288 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
12291 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
12294 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
12297 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12298 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
12299 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
12300 SupportCount.count( t0_4, phylogenies_4, true, false );
12301 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
12302 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
12305 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
12308 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
12311 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
12314 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
12317 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
12320 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
12323 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
12326 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
12329 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
12332 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12333 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12334 double d = SupportCount.compare( b1, a, true, true, true );
12335 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
12338 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12339 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12340 d = SupportCount.compare( b2, a, true, true, true );
12341 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
12344 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
12345 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
12346 d = SupportCount.compare( b3, a, true, true, true );
12347 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
12350 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
12351 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
12352 d = SupportCount.compare( b4, a, true, true, false );
12353 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
12357 catch ( final Exception e ) {
12358 e.printStackTrace( System.out );
12364 private static boolean testSupportTransfer() {
12366 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12367 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)",
12368 new NHXParser() )[ 0 ];
12369 final Phylogeny p2 = factory
12370 .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 ];
12371 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
12374 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
12377 support_transfer.moveBranchLengthsToBootstrap( p1 );
12378 support_transfer.transferSupportValues( p1, p2 );
12379 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
12382 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
12385 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
12388 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
12391 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
12394 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
12397 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
12400 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
12404 catch ( final Exception e ) {
12405 e.printStackTrace( System.out );
12411 private static boolean testTaxonomyExtraction() {
12413 final PhylogenyNode n0 = PhylogenyNode
12414 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12415 if ( n0.getNodeData().isHasTaxonomy() ) {
12418 final PhylogenyNode n1 = PhylogenyNode
12419 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12420 if ( n1.getNodeData().isHasTaxonomy() ) {
12421 System.out.println( n1.toString() );
12424 final PhylogenyNode n2x = PhylogenyNode
12425 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12426 if ( n2x.getNodeData().isHasTaxonomy() ) {
12429 final PhylogenyNode n3 = PhylogenyNode
12430 .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12431 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12432 System.out.println( n3.toString() );
12435 final PhylogenyNode n4 = PhylogenyNode
12436 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12437 if ( n4.getNodeData().isHasTaxonomy() ) {
12438 System.out.println( n4.toString() );
12441 final PhylogenyNode n5 = PhylogenyNode
12442 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12443 if ( n5.getNodeData().isHasTaxonomy() ) {
12444 System.out.println( n5.toString() );
12447 final PhylogenyNode n6 = PhylogenyNode
12448 .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12449 if ( n6.getNodeData().isHasTaxonomy() ) {
12450 System.out.println( n6.toString() );
12453 final PhylogenyNode n7 = PhylogenyNode
12454 .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12455 if ( n7.getNodeData().isHasTaxonomy() ) {
12456 System.out.println( n7.toString() );
12459 final PhylogenyNode n8 = PhylogenyNode
12460 .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12461 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12462 System.out.println( n8.toString() );
12465 final PhylogenyNode n9 = PhylogenyNode
12466 .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12467 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
12468 System.out.println( n9.toString() );
12471 final PhylogenyNode n10x = PhylogenyNode
12472 .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12473 if ( n10x.getNodeData().isHasTaxonomy() ) {
12474 System.out.println( n10x.toString() );
12477 final PhylogenyNode n10xx = PhylogenyNode
12478 .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12479 if ( n10xx.getNodeData().isHasTaxonomy() ) {
12480 System.out.println( n10xx.toString() );
12483 final PhylogenyNode n10 = PhylogenyNode
12484 .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
12485 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
12486 System.out.println( n10.toString() );
12489 final PhylogenyNode n11 = PhylogenyNode
12490 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12491 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12492 System.out.println( n11.toString() );
12495 final PhylogenyNode n12 = PhylogenyNode
12496 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
12497 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12498 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12499 System.out.println( n12.toString() );
12502 final PhylogenyNode n13 = PhylogenyNode
12503 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12504 if ( n13.getNodeData().isHasTaxonomy() ) {
12505 System.out.println( n13.toString() );
12508 final PhylogenyNode n14 = PhylogenyNode
12509 .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12510 if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12511 System.out.println( n14.toString() );
12514 final PhylogenyNode n15 = PhylogenyNode
12515 .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12516 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12517 System.out.println( n15.toString() );
12520 final PhylogenyNode n16 = PhylogenyNode
12521 .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12522 if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12523 System.out.println( n16.toString() );
12526 final PhylogenyNode n17 = PhylogenyNode
12527 .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12528 if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
12529 System.out.println( n17.toString() );
12532 final PhylogenyNode n18 = PhylogenyNode
12533 .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12534 if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12535 System.out.println( n18.toString() );
12538 final PhylogenyNode n19 = PhylogenyNode
12539 .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
12540 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12541 if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12542 System.out.println( n19.toString() );
12545 final PhylogenyNode n20 = PhylogenyNode
12546 .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12547 if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12548 System.out.println( n20.toString() );
12551 final PhylogenyNode n21 = PhylogenyNode
12552 .createInstanceFromNhxString( "Mus musculus musculus K392",
12553 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12554 if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
12555 System.out.println( n21.toString() );
12558 final PhylogenyNode n23 = PhylogenyNode
12559 .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
12560 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12561 if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12562 System.out.println( n23.toString() );
12565 final PhylogenyNode n24 = PhylogenyNode
12566 .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12567 if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12568 System.out.println( n24.toString() );
12572 final PhylogenyNode n25 = PhylogenyNode
12573 .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
12574 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12575 if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
12576 System.out.println( n25.toString() );
12579 final PhylogenyNode n26 = PhylogenyNode
12580 .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
12581 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12582 if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
12583 System.out.println( n26.toString() );
12586 final PhylogenyNode n27 = PhylogenyNode
12587 .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
12588 if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
12589 System.out.println( n27.toString() );
12593 catch ( final Exception e ) {
12594 e.printStackTrace( System.out );
12600 private static boolean testTreeCopy() {
12602 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
12603 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
12604 final Phylogeny t1 = t0.copy();
12605 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
12608 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12611 t0.deleteSubtree( t0.getNode( "c" ), true );
12612 t0.deleteSubtree( t0.getNode( "a" ), true );
12613 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
12614 t0.getNode( "b" ).setName( "Bee" );
12615 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
12618 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12621 t0.deleteSubtree( t0.getNode( "e" ), true );
12622 t0.deleteSubtree( t0.getNode( "Bee" ), true );
12623 t0.deleteSubtree( t0.getNode( "d" ), true );
12624 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
12628 catch ( final Exception e ) {
12629 e.printStackTrace();
12635 private static boolean testTreeMethods() {
12637 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
12638 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
12639 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
12640 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
12641 System.out.println( t0.toNewHampshireX() );
12644 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
12645 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
12646 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
12649 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
12652 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
12656 catch ( final Exception e ) {
12657 e.printStackTrace( System.out );
12663 private static boolean testUniprotEntryRetrieval() {
12665 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
12666 if ( !entry.getAccession().equals( "P12345" ) ) {
12669 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
12672 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
12675 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
12678 if ( !entry.getGeneName().equals( "GOT2" ) ) {
12681 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
12684 if ( entry.getMolecularSequence() == null ) {
12688 .getMolecularSequence()
12689 .getMolecularSequenceAsString()
12690 .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
12691 || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
12692 System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() );
12693 System.out.println( "expected something else." );
12697 catch ( final IOException e ) {
12698 System.out.println();
12699 System.out.println( "the following might be due to absence internet connection:" );
12700 e.printStackTrace( System.out );
12703 catch ( final NullPointerException f ) {
12704 f.printStackTrace( System.out );
12707 catch ( final Exception e ) {
12713 private static boolean testUniprotTaxonomySearch() {
12715 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
12717 if ( results.size() != 1 ) {
12720 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12723 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12726 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12729 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12732 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12736 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
12737 if ( results.size() != 1 ) {
12740 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12743 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12746 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12749 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12752 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12756 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
12757 if ( results.size() != 1 ) {
12760 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12763 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12766 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12769 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12772 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12776 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
12777 if ( results.size() != 1 ) {
12780 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
12783 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
12786 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
12789 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12792 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
12795 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
12798 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
12801 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12802 .equals( "Nematostella vectensis" ) ) {
12803 System.out.println( results.get( 0 ).getLineage() );
12808 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
12809 if ( results.size() != 1 ) {
12812 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12815 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12818 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12821 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12824 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12827 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12828 .equals( "Xenopus tropicalis" ) ) {
12829 System.out.println( results.get( 0 ).getLineage() );
12834 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
12835 if ( results.size() != 1 ) {
12838 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12841 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12844 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12847 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12850 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12853 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12854 .equals( "Xenopus tropicalis" ) ) {
12855 System.out.println( results.get( 0 ).getLineage() );
12860 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
12861 if ( results.size() != 1 ) {
12864 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
12867 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
12870 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
12873 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
12876 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
12879 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
12880 .equals( "Xenopus tropicalis" ) ) {
12881 System.out.println( results.get( 0 ).getLineage() );
12885 catch ( final IOException e ) {
12886 System.out.println();
12887 System.out.println( "the following might be due to absence internet connection:" );
12888 e.printStackTrace( System.out );
12891 catch ( final Exception e ) {
12897 private static boolean testWabiTxSearch() {
12899 String result = "";
12900 result = TxSearch.searchSimple( "nematostella" );
12901 result = TxSearch.getTxId( "nematostella" );
12902 if ( !result.equals( "45350" ) ) {
12905 result = TxSearch.getTxName( "45350" );
12906 if ( !result.equals( "Nematostella" ) ) {
12909 result = TxSearch.getTxId( "nematostella vectensis" );
12910 if ( !result.equals( "45351" ) ) {
12913 result = TxSearch.getTxName( "45351" );
12914 if ( !result.equals( "Nematostella vectensis" ) ) {
12917 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
12918 if ( !result.equals( "536089" ) ) {
12921 result = TxSearch.getTxName( "536089" );
12922 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
12925 final List<String> queries = new ArrayList<String>();
12926 queries.add( "Campylobacter coli" );
12927 queries.add( "Escherichia coli" );
12928 queries.add( "Arabidopsis" );
12929 queries.add( "Trichoplax" );
12930 queries.add( "Samanea saman" );
12931 queries.add( "Kluyveromyces marxianus" );
12932 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
12933 queries.add( "Bornavirus parrot/PDD/2008" );
12934 final List<RANKS> ranks = new ArrayList<RANKS>();
12935 ranks.add( RANKS.SUPERKINGDOM );
12936 ranks.add( RANKS.KINGDOM );
12937 ranks.add( RANKS.FAMILY );
12938 ranks.add( RANKS.GENUS );
12939 ranks.add( RANKS.TRIBE );
12940 result = TxSearch.searchLineage( queries, ranks );
12941 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
12942 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
12944 catch ( final Exception e ) {
12945 System.out.println();
12946 System.out.println( "the following might be due to absence internet connection:" );
12947 e.printStackTrace( System.out );