2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
39 import java.util.SortedSet;
41 import org.forester.application.support_transfer;
42 import org.forester.archaeopteryx.TreePanelUtil;
43 import org.forester.development.DevelopmentTools;
44 import org.forester.evoinference.TestPhylogenyReconstruction;
45 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
46 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
47 import org.forester.go.TestGo;
48 import org.forester.io.parsers.FastaParser;
49 import org.forester.io.parsers.GeneralMsaParser;
50 import org.forester.io.parsers.HmmscanPerDomainTableParser;
51 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
52 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
53 import org.forester.io.parsers.nexus.NexusCharactersParser;
54 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
55 import org.forester.io.parsers.nhx.NHXParser;
56 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
57 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
58 import org.forester.io.parsers.tol.TolParser;
59 import org.forester.io.parsers.util.ParserUtils;
60 import org.forester.io.writers.PhylogenyWriter;
61 import org.forester.io.writers.SequenceWriter;
62 import org.forester.msa.BasicMsa;
63 import org.forester.msa.Mafft;
64 import org.forester.msa.Msa;
65 import org.forester.msa.MsaInferrer;
66 import org.forester.msa.MsaMethods;
67 import org.forester.pccx.TestPccx;
68 import org.forester.phylogeny.Phylogeny;
69 import org.forester.phylogeny.PhylogenyBranch;
70 import org.forester.phylogeny.PhylogenyMethods;
71 import org.forester.phylogeny.PhylogenyNode;
72 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
73 import org.forester.phylogeny.data.Accession;
74 import org.forester.phylogeny.data.Accession.Source;
75 import org.forester.phylogeny.data.BinaryCharacters;
76 import org.forester.phylogeny.data.BranchWidth;
77 import org.forester.phylogeny.data.Confidence;
78 import org.forester.phylogeny.data.Distribution;
79 import org.forester.phylogeny.data.DomainArchitecture;
80 import org.forester.phylogeny.data.Event;
81 import org.forester.phylogeny.data.Identifier;
82 import org.forester.phylogeny.data.PhylogenyData;
83 import org.forester.phylogeny.data.PhylogenyDataUtil;
84 import org.forester.phylogeny.data.Polygon;
85 import org.forester.phylogeny.data.PropertiesMap;
86 import org.forester.phylogeny.data.Property;
87 import org.forester.phylogeny.data.Property.AppliesTo;
88 import org.forester.phylogeny.data.ProteinDomain;
89 import org.forester.phylogeny.data.Taxonomy;
90 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
91 import org.forester.phylogeny.factories.PhylogenyFactory;
92 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
93 import org.forester.protein.BasicDomain;
94 import org.forester.protein.BasicProtein;
95 import org.forester.protein.Domain;
96 import org.forester.protein.Protein;
97 import org.forester.protein.ProteinId;
98 import org.forester.rio.TestRIO;
99 import org.forester.sdi.SDI;
100 import org.forester.sdi.SDIR;
101 import org.forester.sdi.TestGSDI;
102 import org.forester.sequence.BasicSequence;
103 import org.forester.sequence.Sequence;
104 import org.forester.species.BasicSpecies;
105 import org.forester.species.Species;
106 import org.forester.surfacing.TestSurfacing;
107 import org.forester.tools.ConfidenceAssessor;
108 import org.forester.tools.SupportCount;
109 import org.forester.tools.TreeSplitMatrix;
110 import org.forester.util.AsciiHistogram;
111 import org.forester.util.BasicDescriptiveStatistics;
112 import org.forester.util.BasicTable;
113 import org.forester.util.BasicTableParser;
114 import org.forester.util.DescriptiveStatistics;
115 import org.forester.util.ForesterConstants;
116 import org.forester.util.ForesterUtil;
117 import org.forester.util.GeneralTable;
118 import org.forester.util.SequenceAccessionTools;
119 import org.forester.ws.seqdb.SequenceDatabaseEntry;
120 import org.forester.ws.seqdb.SequenceDbWsTools;
121 import org.forester.ws.seqdb.UniProtTaxonomy;
122 import org.forester.ws.wabi.TxSearch;
123 import org.forester.ws.wabi.TxSearch.RANKS;
124 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
125 import org.forester.ws.wabi.TxSearch.TAX_RANK;
127 @SuppressWarnings( "unused")
128 public final class Test {
130 private final static boolean PERFORM_DB_TESTS = false;
131 private final static double ZERO_DIFF = 1.0E-9;
132 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
133 + ForesterUtil.getFileSeparator() + "test_data"
134 + ForesterUtil.getFileSeparator();
135 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
136 + ForesterUtil.getFileSeparator() + "resources"
137 + ForesterUtil.getFileSeparator();
138 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
139 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
140 + ForesterConstants.PHYLO_XML_VERSION + "/"
141 + ForesterConstants.PHYLO_XML_XSD;
142 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
143 + ForesterConstants.PHYLO_XML_VERSION + "/"
144 + ForesterConstants.PHYLO_XML_XSD;
146 public static boolean testOverlapRemoval() {
148 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
149 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
150 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
151 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
152 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
153 final List<Boolean> covered = new ArrayList<Boolean>();
154 covered.add( true ); // 0
155 covered.add( false ); // 1
156 covered.add( true ); // 2
157 covered.add( false ); // 3
158 covered.add( true ); // 4
159 covered.add( true ); // 5
160 covered.add( false ); // 6
161 covered.add( true ); // 7
162 covered.add( true ); // 8
163 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
166 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
169 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
172 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
175 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
178 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.01, 1 );
179 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
180 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
181 ab.addProteinDomain( a );
182 ab.addProteinDomain( b );
183 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
184 if ( ab.getNumberOfProteinDomains() != 2 ) {
187 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
190 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
193 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
194 if ( ab.getNumberOfProteinDomains() != 2 ) {
197 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
200 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
201 final Domain d = new BasicDomain( "d",
208 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
209 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
210 cde.addProteinDomain( c );
211 cde.addProteinDomain( d );
212 cde.addProteinDomain( e );
213 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
214 if ( cde.getNumberOfProteinDomains() != 3 ) {
217 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
220 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
221 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
222 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
223 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
224 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
225 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
226 fghi.addProteinDomain( f );
227 fghi.addProteinDomain( g );
228 fghi.addProteinDomain( h );
229 fghi.addProteinDomain( i );
230 fghi.addProteinDomain( i );
231 fghi.addProteinDomain( i );
232 fghi.addProteinDomain( i2 );
233 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
234 if ( fghi.getNumberOfProteinDomains() != 7 ) {
237 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
240 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
243 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
244 if ( fghi.getNumberOfProteinDomains() != 7 ) {
247 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
250 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
251 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
252 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
253 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
254 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
255 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
256 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
257 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
258 jklm.addProteinDomain( j );
259 jklm.addProteinDomain( k );
260 jklm.addProteinDomain( l );
261 jklm.addProteinDomain( m );
262 jklm.addProteinDomain( m0 );
263 jklm.addProteinDomain( m1 );
264 jklm.addProteinDomain( m2 );
265 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
266 if ( jklm.getNumberOfProteinDomains() != 7 ) {
269 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
272 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
275 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
276 if ( jklm.getNumberOfProteinDomains() != 7 ) {
279 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
282 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
283 final Protein od = new BasicProtein( "od", "varanus", 0 );
284 od.addProteinDomain( only );
285 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
286 if ( od.getNumberOfProteinDomains() != 1 ) {
289 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
293 catch ( final Exception e ) {
294 e.printStackTrace( System.out );
300 public static boolean testEngulfingOverlapRemoval() {
302 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
303 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
304 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
305 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
306 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
307 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
308 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
309 final List<Boolean> covered = new ArrayList<Boolean>();
310 covered.add( true ); // 0
311 covered.add( false ); // 1
312 covered.add( true ); // 2
313 covered.add( false ); // 3
314 covered.add( true ); // 4
315 covered.add( true ); // 5
316 covered.add( false ); // 6
317 covered.add( true ); // 7
318 covered.add( true ); // 8
319 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
322 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
325 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
328 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
331 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
334 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
337 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
340 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
341 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
342 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
343 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
344 abc.addProteinDomain( a );
345 abc.addProteinDomain( b );
346 abc.addProteinDomain( c );
347 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
348 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
349 if ( abc.getNumberOfProteinDomains() != 3 ) {
352 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
355 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
358 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
361 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
364 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
365 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
366 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
367 final Protein def = new BasicProtein( "def", "nemve", 0 );
368 def.addProteinDomain( d );
369 def.addProteinDomain( e );
370 def.addProteinDomain( f );
371 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
372 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
373 if ( def.getNumberOfProteinDomains() != 3 ) {
376 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
379 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
382 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
385 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
388 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
392 catch ( final Exception e ) {
393 e.printStackTrace( System.out );
399 public static boolean isEqual( final double a, final double b ) {
400 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
403 public static void main( final String[] args ) {
404 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
405 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
407 Locale.setDefault( Locale.US );
408 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
411 System.out.print( "[Test if directory with files for testing exists/is readable: " );
412 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
413 System.out.println( "OK.]" );
416 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
417 System.out.println( "Testing aborted." );
420 System.out.print( "[Test if resources directory exists/is readable: " );
421 if ( testDir( PATH_TO_RESOURCES ) ) {
422 System.out.println( "OK.]" );
425 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
426 System.out.println( "Testing aborted." );
429 final long start_time = new Date().getTime();
430 System.out.print( "Basic node methods: " );
431 if ( Test.testBasicNodeMethods() ) {
432 System.out.println( "OK." );
436 System.out.println( "failed." );
439 System.out.print( "Protein id: " );
440 if ( !testProteinId() ) {
441 System.out.println( "failed." );
447 System.out.println( "OK." );
448 System.out.print( "Species: " );
449 if ( !testSpecies() ) {
450 System.out.println( "failed." );
456 System.out.println( "OK." );
457 System.out.print( "Basic domain: " );
458 if ( !testBasicDomain() ) {
459 System.out.println( "failed." );
465 System.out.println( "OK." );
466 System.out.print( "Basic protein: " );
467 if ( !testBasicProtein() ) {
468 System.out.println( "failed." );
474 System.out.println( "OK." );
475 System.out.print( "Sequence writer: " );
476 if ( testSequenceWriter() ) {
477 System.out.println( "OK." );
481 System.out.println( "failed." );
484 System.out.print( "Sequence id parsing: " );
485 if ( testSequenceIdParsing() ) {
486 System.out.println( "OK." );
490 System.out.println( "failed." );
493 if ( PERFORM_DB_TESTS ) {
494 System.out.print( "Ebi Entry Retrieval: " );
495 if ( Test.testEbiEntryRetrieval() ) {
496 System.out.println( "OK." );
500 System.out.println( "failed." );
504 ///////////////////////////////////////// System.exit( 0 );
505 System.out.print( "UniProtKB id extraction: " );
506 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
507 System.out.println( "OK." );
511 System.out.println( "failed." );
514 System.out.print( "Sequence DB tools 1: " );
515 if ( testSequenceDbWsTools1() ) {
516 System.out.println( "OK." );
520 System.out.println( "failed." );
523 if ( PERFORM_DB_TESTS ) {
524 System.out.print( "Sequence DB tools 2: " );
525 if ( testSequenceDbWsTools2() ) {
526 System.out.println( "OK." );
530 System.out.println( "failed." );
535 System.out.print( "Hmmscan output parser: " );
536 if ( testHmmscanOutputParser() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
545 System.out.print( "Overlap removal: " );
546 if ( !org.forester.test.Test.testOverlapRemoval() ) {
547 System.out.println( "failed." );
553 System.out.println( "OK." );
554 System.out.print( "Engulfing overlap removal: " );
555 if ( !Test.testEngulfingOverlapRemoval() ) {
556 System.out.println( "failed." );
562 System.out.println( "OK." );
564 System.out.print( "Taxonomy code extraction: " );
565 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
566 System.out.println( "OK." );
570 System.out.println( "failed." );
573 System.out.print( "SN extraction: " );
574 if ( Test.testExtractSNFromNodeName() ) {
575 System.out.println( "OK." );
579 System.out.println( "failed." );
582 System.out.print( "Taxonomy extraction (general): " );
583 if ( Test.testTaxonomyExtraction() ) {
584 System.out.println( "OK." );
588 System.out.println( "failed." );
591 System.out.print( "Uri for Aptx web sequence accession: " );
592 if ( Test.testCreateUriForSeqWeb() ) {
593 System.out.println( "OK." );
597 System.out.println( "failed." );
600 System.out.print( "Basic node construction and parsing of NHX (node level): " );
601 if ( Test.testNHXNodeParsing() ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "NHX parsing iterating: " );
610 if ( Test.testNHParsingIter() ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "NH parsing: " );
619 if ( Test.testNHParsing() ) {
620 System.out.println( "OK." );
624 System.out.println( "failed." );
627 System.out.print( "Conversion to NHX (node level): " );
628 if ( Test.testNHXconversion() ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "NHX parsing: " );
637 if ( Test.testNHXParsing() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "NHX parsing with quotes: " );
646 if ( Test.testNHXParsingQuotes() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "NHX parsing (MrBayes): " );
655 if ( Test.testNHXParsingMB() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "Nexus characters parsing: " );
664 if ( Test.testNexusCharactersParsing() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Nexus tree parsing iterating: " );
673 if ( Test.testNexusTreeParsingIterating() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "Nexus tree parsing: " );
682 if ( Test.testNexusTreeParsing() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 System.out.print( "Nexus tree parsing (translating): " );
691 if ( Test.testNexusTreeParsingTranslating() ) {
692 System.out.println( "OK." );
696 System.out.println( "failed." );
699 System.out.print( "Nexus matrix parsing: " );
700 if ( Test.testNexusMatrixParsing() ) {
701 System.out.println( "OK." );
705 System.out.println( "failed." );
708 System.out.print( "Basic phyloXML parsing: " );
709 if ( Test.testBasicPhyloXMLparsing() ) {
710 System.out.println( "OK." );
714 System.out.println( "failed." );
717 System.out.print( "Basic phyloXML parsing (validating against schema): " );
718 if ( testBasicPhyloXMLparsingValidating() ) {
719 System.out.println( "OK." );
723 System.out.println( "failed." );
726 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
727 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
728 System.out.println( "OK." );
732 System.out.println( "failed." );
735 System.out.print( "phyloXML Distribution Element: " );
736 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
737 System.out.println( "OK." );
741 System.out.println( "failed." );
744 System.out.print( "Tol XML parsing: " );
745 if ( Test.testBasicTolXMLparsing() ) {
746 System.out.println( "OK." );
750 System.out.println( "failed." );
753 System.out.print( "Copying of node data: " );
754 if ( Test.testCopyOfNodeData() ) {
755 System.out.println( "OK." );
759 System.out.println( "failed." );
762 System.out.print( "Tree copy: " );
763 if ( Test.testTreeCopy() ) {
764 System.out.println( "OK." );
768 System.out.println( "failed." );
771 System.out.print( "Basic tree methods: " );
772 if ( Test.testBasicTreeMethods() ) {
773 System.out.println( "OK." );
777 System.out.println( "failed." );
780 System.out.print( "Tree methods: " );
781 if ( Test.testTreeMethods() ) {
782 System.out.println( "OK." );
786 System.out.println( "failed." );
789 System.out.print( "Postorder Iterator: " );
790 if ( Test.testPostOrderIterator() ) {
791 System.out.println( "OK." );
795 System.out.println( "failed." );
798 System.out.print( "Preorder Iterator: " );
799 if ( Test.testPreOrderIterator() ) {
800 System.out.println( "OK." );
804 System.out.println( "failed." );
807 System.out.print( "Levelorder Iterator: " );
808 if ( Test.testLevelOrderIterator() ) {
809 System.out.println( "OK." );
813 System.out.println( "failed." );
816 System.out.print( "Re-id methods: " );
817 if ( Test.testReIdMethods() ) {
818 System.out.println( "OK." );
822 System.out.println( "failed." );
825 System.out.print( "Methods on last external nodes: " );
826 if ( Test.testLastExternalNodeMethods() ) {
827 System.out.println( "OK." );
831 System.out.println( "failed." );
834 System.out.print( "Methods on external nodes: " );
835 if ( Test.testExternalNodeRelatedMethods() ) {
836 System.out.println( "OK." );
840 System.out.println( "failed." );
843 System.out.print( "Deletion of external nodes: " );
844 if ( Test.testDeletionOfExternalNodes() ) {
845 System.out.println( "OK." );
849 System.out.println( "failed." );
852 System.out.print( "Subtree deletion: " );
853 if ( Test.testSubtreeDeletion() ) {
854 System.out.println( "OK." );
858 System.out.println( "failed." );
861 System.out.print( "Phylogeny branch: " );
862 if ( Test.testPhylogenyBranch() ) {
863 System.out.println( "OK." );
867 System.out.println( "failed." );
870 System.out.print( "Rerooting: " );
871 if ( Test.testRerooting() ) {
872 System.out.println( "OK." );
876 System.out.println( "failed." );
879 System.out.print( "Mipoint rooting: " );
880 if ( Test.testMidpointrooting() ) {
881 System.out.println( "OK." );
885 System.out.println( "failed." );
888 System.out.print( "Node removal: " );
889 if ( Test.testNodeRemoval() ) {
890 System.out.println( "OK." );
894 System.out.println( "failed." );
897 System.out.print( "Support count: " );
898 if ( Test.testSupportCount() ) {
899 System.out.println( "OK." );
903 System.out.println( "failed." );
906 System.out.print( "Support transfer: " );
907 if ( Test.testSupportTransfer() ) {
908 System.out.println( "OK." );
912 System.out.println( "failed." );
915 System.out.print( "Finding of LCA: " );
916 if ( Test.testGetLCA() ) {
917 System.out.println( "OK." );
921 System.out.println( "failed." );
924 System.out.print( "Finding of LCA 2: " );
925 if ( Test.testGetLCA2() ) {
926 System.out.println( "OK." );
930 System.out.println( "failed." );
933 System.out.print( "Calculation of distance between nodes: " );
934 if ( Test.testGetDistance() ) {
935 System.out.println( "OK." );
939 System.out.println( "failed." );
942 System.out.print( "Descriptive statistics: " );
943 if ( Test.testDescriptiveStatistics() ) {
944 System.out.println( "OK." );
948 System.out.println( "failed." );
951 System.out.print( "Data objects and methods: " );
952 if ( Test.testDataObjects() ) {
953 System.out.println( "OK." );
957 System.out.println( "failed." );
960 System.out.print( "Properties map: " );
961 if ( Test.testPropertiesMap() ) {
962 System.out.println( "OK." );
966 System.out.println( "failed." );
969 System.out.print( "SDIse: " );
970 if ( Test.testSDIse() ) {
971 System.out.println( "OK." );
975 System.out.println( "failed." );
978 System.out.print( "SDIunrooted: " );
979 if ( Test.testSDIunrooted() ) {
980 System.out.println( "OK." );
984 System.out.println( "failed." );
987 System.out.print( "GSDI: " );
988 if ( TestGSDI.test() ) {
989 System.out.println( "OK." );
993 System.out.println( "failed." );
996 System.out.print( "RIO: " );
997 if ( TestRIO.test() ) {
998 System.out.println( "OK." );
1002 System.out.println( "failed." );
1005 System.out.print( "Phylogeny reconstruction:" );
1006 System.out.println();
1007 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
1008 System.out.println( "OK." );
1012 System.out.println( "failed." );
1015 System.out.print( "Analysis of domain architectures: " );
1016 System.out.println();
1017 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
1018 System.out.println( "OK." );
1022 System.out.println( "failed." );
1025 System.out.print( "GO: " );
1026 System.out.println();
1027 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
1028 System.out.println( "OK." );
1032 System.out.println( "failed." );
1035 System.out.print( "Modeling tools: " );
1036 if ( TestPccx.test() ) {
1037 System.out.println( "OK." );
1041 System.out.println( "failed." );
1044 System.out.print( "Split Matrix strict: " );
1045 if ( Test.testSplitStrict() ) {
1046 System.out.println( "OK." );
1050 System.out.println( "failed." );
1053 System.out.print( "Split Matrix: " );
1054 if ( Test.testSplit() ) {
1055 System.out.println( "OK." );
1059 System.out.println( "failed." );
1062 System.out.print( "Confidence Assessor: " );
1063 if ( Test.testConfidenceAssessor() ) {
1064 System.out.println( "OK." );
1068 System.out.println( "failed." );
1071 System.out.print( "Basic table: " );
1072 if ( Test.testBasicTable() ) {
1073 System.out.println( "OK." );
1077 System.out.println( "failed." );
1080 System.out.print( "General table: " );
1081 if ( Test.testGeneralTable() ) {
1082 System.out.println( "OK." );
1086 System.out.println( "failed." );
1089 System.out.print( "Amino acid sequence: " );
1090 if ( Test.testAminoAcidSequence() ) {
1091 System.out.println( "OK." );
1095 System.out.println( "failed." );
1098 System.out.print( "General MSA parser: " );
1099 if ( Test.testGeneralMsaParser() ) {
1100 System.out.println( "OK." );
1104 System.out.println( "failed." );
1107 System.out.print( "Fasta parser for msa: " );
1108 if ( Test.testFastaParser() ) {
1109 System.out.println( "OK." );
1113 System.out.println( "failed." );
1116 System.out.print( "Creation of balanced phylogeny: " );
1117 if ( Test.testCreateBalancedPhylogeny() ) {
1118 System.out.println( "OK." );
1122 System.out.println( "failed." );
1125 System.out.print( "Genbank accessor parsing: " );
1126 if ( Test.testGenbankAccessorParsing() ) {
1127 System.out.println( "OK." );
1131 System.out.println( "failed." );
1134 if ( PERFORM_DB_TESTS ) {
1135 System.out.print( "Uniprot Entry Retrieval: " );
1136 if ( Test.testUniprotEntryRetrieval() ) {
1137 System.out.println( "OK." );
1141 System.out.println( "failed." );
1145 if ( PERFORM_DB_TESTS ) {
1146 System.out.print( "Uniprot Taxonomy Search: " );
1147 if ( Test.testUniprotTaxonomySearch() ) {
1148 System.out.println( "OK." );
1152 System.out.println( "failed." );
1158 final String os = ForesterUtil.OS_NAME.toLowerCase();
1159 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
1160 path = "/usr/local/bin/mafft";
1162 else if ( os.indexOf( "win" ) >= 0 ) {
1163 path = "C:\\Program Files\\mafft-win\\mafft.bat";
1166 path = "/home/czmasek/bin/mafft";
1168 if ( !MsaInferrer.isInstalled( path ) ) {
1171 if ( !MsaInferrer.isInstalled( path ) ) {
1172 path = "/usr/local/bin/mafft";
1174 if ( MsaInferrer.isInstalled( path ) ) {
1175 System.out.print( "MAFFT (external program): " );
1176 if ( Test.testMafft( path ) ) {
1177 System.out.println( "OK." );
1181 System.out.println( "failed [will not count towards failed tests]" );
1185 System.out.print( "Next nodes with collapsed: " );
1186 if ( Test.testNextNodeWithCollapsing() ) {
1187 System.out.println( "OK." );
1191 System.out.println( "failed." );
1194 System.out.print( "Simple MSA quality: " );
1195 if ( Test.testMsaQualityMethod() ) {
1196 System.out.println( "OK." );
1200 System.out.println( "failed." );
1203 System.out.println();
1204 final Runtime rt = java.lang.Runtime.getRuntime();
1205 final long free_memory = rt.freeMemory() / 1000000;
1206 final long total_memory = rt.totalMemory() / 1000000;
1207 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1208 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1209 System.out.println();
1210 System.out.println( "Successful tests: " + succeeded );
1211 System.out.println( "Failed tests: " + failed );
1212 System.out.println();
1214 System.out.println( "OK." );
1217 System.out.println( "Not OK." );
1221 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1222 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1226 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1227 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1230 private static boolean testAminoAcidSequence() {
1232 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1233 if ( aa1.getLength() != 13 ) {
1236 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1239 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1242 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1245 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1246 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
1249 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1250 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1253 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1254 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1258 catch ( final Exception e ) {
1259 e.printStackTrace();
1265 private static boolean testBasicDomain() {
1267 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1268 if ( !pd.getDomainId().equals( "id" ) ) {
1271 if ( pd.getNumber() != 1 ) {
1274 if ( pd.getTotalCount() != 4 ) {
1277 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1280 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1281 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1282 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1283 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1284 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1285 if ( !a1.equals( a1 ) ) {
1288 if ( !a1.equals( a1_copy ) ) {
1291 if ( !a1.equals( a1_equal ) ) {
1294 if ( !a1.equals( a2 ) ) {
1297 if ( a1.equals( a3 ) ) {
1300 if ( a1.compareTo( a1 ) != 0 ) {
1303 if ( a1.compareTo( a1_copy ) != 0 ) {
1306 if ( a1.compareTo( a1_equal ) != 0 ) {
1309 if ( a1.compareTo( a2 ) != 0 ) {
1312 if ( a1.compareTo( a3 ) == 0 ) {
1316 catch ( final Exception e ) {
1317 e.printStackTrace( System.out );
1323 private static boolean testBasicNodeMethods() {
1325 if ( PhylogenyNode.getNodeCount() != 0 ) {
1328 final PhylogenyNode n1 = new PhylogenyNode();
1329 final PhylogenyNode n2 = PhylogenyNode
1330 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1331 final PhylogenyNode n3 = PhylogenyNode
1332 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1333 final PhylogenyNode n4 = PhylogenyNode
1334 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1335 if ( n1.isHasAssignedEvent() ) {
1338 if ( PhylogenyNode.getNodeCount() != 4 ) {
1341 if ( n3.getIndicator() != 0 ) {
1344 if ( n3.getNumberOfExternalNodes() != 1 ) {
1347 if ( !n3.isExternal() ) {
1350 if ( !n3.isRoot() ) {
1353 if ( !n4.getName().equals( "n4" ) ) {
1357 catch ( final Exception e ) {
1358 e.printStackTrace( System.out );
1364 private static boolean testBasicPhyloXMLparsing() {
1366 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1367 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1368 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1370 if ( xml_parser.getErrorCount() > 0 ) {
1371 System.out.println( xml_parser.getErrorMessages().toString() );
1374 if ( phylogenies_0.length != 4 ) {
1377 final Phylogeny t1 = phylogenies_0[ 0 ];
1378 final Phylogeny t2 = phylogenies_0[ 1 ];
1379 final Phylogeny t3 = phylogenies_0[ 2 ];
1380 final Phylogeny t4 = phylogenies_0[ 3 ];
1381 if ( t1.getNumberOfExternalNodes() != 1 ) {
1384 if ( !t1.isRooted() ) {
1387 if ( t1.isRerootable() ) {
1390 if ( !t1.getType().equals( "gene_tree" ) ) {
1393 if ( t2.getNumberOfExternalNodes() != 2 ) {
1396 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1399 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1402 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1405 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1408 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1411 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1414 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1415 .startsWith( "actgtgggggt" ) ) {
1418 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1419 .startsWith( "ctgtgatgcat" ) ) {
1422 if ( t3.getNumberOfExternalNodes() != 4 ) {
1425 if ( !t1.getName().equals( "t1" ) ) {
1428 if ( !t2.getName().equals( "t2" ) ) {
1431 if ( !t3.getName().equals( "t3" ) ) {
1434 if ( !t4.getName().equals( "t4" ) ) {
1437 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1440 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1443 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1446 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1447 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1450 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1453 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1456 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1459 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1460 .equals( "apoptosis" ) ) {
1463 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1464 .equals( "GO:0006915" ) ) {
1467 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1468 .equals( "UniProtKB" ) ) {
1471 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1472 .equals( "experimental" ) ) {
1475 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1476 .equals( "function" ) ) {
1479 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1480 .getValue() != 1 ) {
1483 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1484 .getType().equals( "ml" ) ) {
1487 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1488 .equals( "apoptosis" ) ) {
1491 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1492 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1495 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1496 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1499 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1500 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1503 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1504 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1507 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1508 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1511 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1512 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1515 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1516 .equals( "GO:0005829" ) ) {
1519 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1520 .equals( "intracellular organelle" ) ) {
1523 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1526 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1527 .equals( "UniProt link" ) ) ) {
1530 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1533 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1534 if ( x.size() != 4 ) {
1538 for( final Accession acc : x ) {
1540 if ( !acc.getSource().equals( "KEGG" ) ) {
1543 if ( !acc.getValue().equals( "hsa:596" ) ) {
1550 catch ( final Exception e ) {
1551 e.printStackTrace( System.out );
1557 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1559 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1560 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1561 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1562 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1565 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1567 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1569 if ( xml_parser.getErrorCount() > 0 ) {
1570 System.out.println( xml_parser.getErrorMessages().toString() );
1573 if ( phylogenies_0.length != 4 ) {
1576 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1577 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1578 if ( phylogenies_t1.length != 1 ) {
1581 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1582 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1585 if ( !t1_rt.isRooted() ) {
1588 if ( t1_rt.isRerootable() ) {
1591 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1594 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1595 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1596 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1597 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1600 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1603 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1606 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1609 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1610 .startsWith( "actgtgggggt" ) ) {
1613 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1614 .startsWith( "ctgtgatgcat" ) ) {
1617 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1618 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1619 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1620 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1621 if ( phylogenies_1.length != 1 ) {
1624 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1625 if ( !t3_rt.getName().equals( "t3" ) ) {
1628 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1631 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1634 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1637 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1640 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1641 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1644 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1647 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1650 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1651 .equals( "UniProtKB" ) ) {
1654 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1655 .equals( "apoptosis" ) ) {
1658 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1659 .equals( "GO:0006915" ) ) {
1662 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1663 .equals( "UniProtKB" ) ) {
1666 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1667 .equals( "experimental" ) ) {
1670 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1671 .equals( "function" ) ) {
1674 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1675 .getValue() != 1 ) {
1678 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1679 .getType().equals( "ml" ) ) {
1682 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1683 .equals( "apoptosis" ) ) {
1686 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1687 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1690 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1691 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1694 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1695 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1698 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1699 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1702 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1703 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1706 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1707 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1710 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1711 .equals( "GO:0005829" ) ) {
1714 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1715 .equals( "intracellular organelle" ) ) {
1718 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1721 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1722 .equals( "UniProt link" ) ) ) {
1725 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1728 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1731 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1732 .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." ) ) ) {
1735 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1738 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1741 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1744 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1747 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1748 .equals( "ncbi" ) ) {
1751 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1754 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1755 .getName().equals( "B" ) ) {
1758 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1759 .getFrom() != 21 ) {
1762 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1765 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1766 .getLength() != 24 ) {
1769 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1770 .getConfidence() != 2144 ) {
1773 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1774 .equals( "pfam" ) ) {
1777 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1780 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1783 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1786 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1789 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1790 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1793 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1796 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1799 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1802 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1805 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1808 if ( taxbb.getSynonyms().size() != 2 ) {
1811 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1814 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1817 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1820 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1823 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1826 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1827 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1830 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1833 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1836 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1839 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1842 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1845 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1848 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1852 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1855 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1856 .equalsIgnoreCase( "435" ) ) {
1859 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1862 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1863 .equalsIgnoreCase( "443.7" ) ) {
1866 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1869 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1872 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1873 .equalsIgnoreCase( "433" ) ) {
1876 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
1877 .getCrossReferences();
1878 if ( x.size() != 4 ) {
1882 for( final Accession acc : x ) {
1884 if ( !acc.getSource().equals( "KEGG" ) ) {
1887 if ( !acc.getValue().equals( "hsa:596" ) ) {
1894 catch ( final Exception e ) {
1895 e.printStackTrace( System.out );
1901 private static boolean testBasicPhyloXMLparsingValidating() {
1903 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1904 PhyloXmlParser xml_parser = null;
1906 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1908 catch ( final Exception e ) {
1909 // Do nothing -- means were not running from jar.
1911 if ( xml_parser == null ) {
1912 xml_parser = new PhyloXmlParser();
1913 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1914 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1917 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1920 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1922 if ( xml_parser.getErrorCount() > 0 ) {
1923 System.out.println( xml_parser.getErrorMessages().toString() );
1926 if ( phylogenies_0.length != 4 ) {
1929 final Phylogeny t1 = phylogenies_0[ 0 ];
1930 final Phylogeny t2 = phylogenies_0[ 1 ];
1931 final Phylogeny t3 = phylogenies_0[ 2 ];
1932 final Phylogeny t4 = phylogenies_0[ 3 ];
1933 if ( !t1.getName().equals( "t1" ) ) {
1936 if ( !t2.getName().equals( "t2" ) ) {
1939 if ( !t3.getName().equals( "t3" ) ) {
1942 if ( !t4.getName().equals( "t4" ) ) {
1945 if ( t1.getNumberOfExternalNodes() != 1 ) {
1948 if ( t2.getNumberOfExternalNodes() != 2 ) {
1951 if ( t3.getNumberOfExternalNodes() != 4 ) {
1954 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1955 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1956 if ( xml_parser.getErrorCount() > 0 ) {
1957 System.out.println( "errors:" );
1958 System.out.println( xml_parser.getErrorMessages().toString() );
1961 if ( phylogenies_1.length != 4 ) {
1964 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1966 if ( xml_parser.getErrorCount() > 0 ) {
1967 System.out.println( "errors:" );
1968 System.out.println( xml_parser.getErrorMessages().toString() );
1971 if ( phylogenies_2.length != 1 ) {
1974 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1977 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1979 if ( xml_parser.getErrorCount() > 0 ) {
1980 System.out.println( xml_parser.getErrorMessages().toString() );
1983 if ( phylogenies_3.length != 2 ) {
1986 final Phylogeny a = phylogenies_3[ 0 ];
1987 if ( !a.getName().equals( "tree 4" ) ) {
1990 if ( a.getNumberOfExternalNodes() != 3 ) {
1993 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1996 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1999 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2001 if ( xml_parser.getErrorCount() > 0 ) {
2002 System.out.println( xml_parser.getErrorMessages().toString() );
2005 if ( phylogenies_4.length != 1 ) {
2008 final Phylogeny s = phylogenies_4[ 0 ];
2009 if ( s.getNumberOfExternalNodes() != 6 ) {
2012 s.getNode( "first" );
2014 s.getNode( "\"<a'b&c'd\">\"" );
2015 s.getNode( "'''\"" );
2016 s.getNode( "\"\"\"" );
2017 s.getNode( "dick & doof" );
2019 catch ( final Exception e ) {
2020 e.printStackTrace( System.out );
2026 private static boolean testBasicProtein() {
2028 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2029 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2030 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2031 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2032 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2033 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2034 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2035 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2036 p0.addProteinDomain( y );
2037 p0.addProteinDomain( e );
2038 p0.addProteinDomain( b );
2039 p0.addProteinDomain( c );
2040 p0.addProteinDomain( d );
2041 p0.addProteinDomain( a );
2042 p0.addProteinDomain( x );
2043 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2046 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2050 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2051 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2052 aa0.addProteinDomain( a1 );
2053 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2056 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2060 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2061 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2062 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2063 aa1.addProteinDomain( a11 );
2064 aa1.addProteinDomain( a12 );
2065 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2068 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2071 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2072 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2075 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2078 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2081 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2082 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2085 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2088 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2091 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2094 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2095 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2098 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2101 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2104 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2107 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2108 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2111 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2114 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2117 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2121 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2122 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2123 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2124 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2125 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2126 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2127 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2128 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2129 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2130 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2131 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2132 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2133 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2134 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2135 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2136 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2137 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2138 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2139 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2140 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2141 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2142 p00.addProteinDomain( y0 );
2143 p00.addProteinDomain( e0 );
2144 p00.addProteinDomain( b0 );
2145 p00.addProteinDomain( c0 );
2146 p00.addProteinDomain( d0 );
2147 p00.addProteinDomain( a0 );
2148 p00.addProteinDomain( x0 );
2149 p00.addProteinDomain( y1 );
2150 p00.addProteinDomain( y2 );
2151 p00.addProteinDomain( y3 );
2152 p00.addProteinDomain( e1 );
2153 p00.addProteinDomain( e2 );
2154 p00.addProteinDomain( e3 );
2155 p00.addProteinDomain( e4 );
2156 p00.addProteinDomain( e5 );
2157 p00.addProteinDomain( z0 );
2158 p00.addProteinDomain( z1 );
2159 p00.addProteinDomain( z2 );
2160 p00.addProteinDomain( zz0 );
2161 p00.addProteinDomain( zz1 );
2162 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2165 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2168 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2171 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2174 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" ) ) {
2177 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2178 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2179 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2180 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2181 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2182 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2183 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2184 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2185 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2186 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2187 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2188 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2189 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2190 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2191 p.addProteinDomain( B15 );
2192 p.addProteinDomain( C50 );
2193 p.addProteinDomain( A60 );
2194 p.addProteinDomain( A30 );
2195 p.addProteinDomain( C70 );
2196 p.addProteinDomain( B35 );
2197 p.addProteinDomain( B40 );
2198 p.addProteinDomain( A0 );
2199 p.addProteinDomain( A10 );
2200 p.addProteinDomain( A20 );
2201 p.addProteinDomain( B25 );
2202 p.addProteinDomain( D80 );
2203 List<String> domains_ids = new ArrayList<String>();
2204 domains_ids.add( "A" );
2205 domains_ids.add( "B" );
2206 domains_ids.add( "C" );
2207 if ( !p.contains( domains_ids, false ) ) {
2210 if ( !p.contains( domains_ids, true ) ) {
2213 domains_ids.add( "X" );
2214 if ( p.contains( domains_ids, false ) ) {
2217 if ( p.contains( domains_ids, true ) ) {
2220 domains_ids = new ArrayList<String>();
2221 domains_ids.add( "A" );
2222 domains_ids.add( "C" );
2223 domains_ids.add( "D" );
2224 if ( !p.contains( domains_ids, false ) ) {
2227 if ( !p.contains( domains_ids, true ) ) {
2230 domains_ids = new ArrayList<String>();
2231 domains_ids.add( "A" );
2232 domains_ids.add( "D" );
2233 domains_ids.add( "C" );
2234 if ( !p.contains( domains_ids, false ) ) {
2237 if ( p.contains( domains_ids, true ) ) {
2240 domains_ids = new ArrayList<String>();
2241 domains_ids.add( "A" );
2242 domains_ids.add( "A" );
2243 domains_ids.add( "B" );
2244 if ( !p.contains( domains_ids, false ) ) {
2247 if ( !p.contains( domains_ids, true ) ) {
2250 domains_ids = new ArrayList<String>();
2251 domains_ids.add( "A" );
2252 domains_ids.add( "A" );
2253 domains_ids.add( "A" );
2254 domains_ids.add( "B" );
2255 domains_ids.add( "B" );
2256 if ( !p.contains( domains_ids, false ) ) {
2259 if ( !p.contains( domains_ids, true ) ) {
2262 domains_ids = new ArrayList<String>();
2263 domains_ids.add( "A" );
2264 domains_ids.add( "A" );
2265 domains_ids.add( "B" );
2266 domains_ids.add( "A" );
2267 domains_ids.add( "B" );
2268 domains_ids.add( "B" );
2269 domains_ids.add( "A" );
2270 domains_ids.add( "B" );
2271 domains_ids.add( "C" );
2272 domains_ids.add( "A" );
2273 domains_ids.add( "C" );
2274 domains_ids.add( "D" );
2275 if ( !p.contains( domains_ids, false ) ) {
2278 if ( p.contains( domains_ids, true ) ) {
2282 catch ( final Exception e ) {
2283 e.printStackTrace( System.out );
2289 private static boolean testBasicTable() {
2291 final BasicTable<String> t0 = new BasicTable<String>();
2292 if ( t0.getNumberOfColumns() != 0 ) {
2295 if ( t0.getNumberOfRows() != 0 ) {
2298 t0.setValue( 3, 2, "23" );
2299 t0.setValue( 10, 1, "error" );
2300 t0.setValue( 10, 1, "110" );
2301 t0.setValue( 9, 1, "19" );
2302 t0.setValue( 1, 10, "101" );
2303 t0.setValue( 10, 10, "1010" );
2304 t0.setValue( 100, 10, "10100" );
2305 t0.setValue( 0, 0, "00" );
2306 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2309 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2312 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2315 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2318 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2321 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2324 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2327 if ( t0.getNumberOfColumns() != 101 ) {
2330 if ( t0.getNumberOfRows() != 11 ) {
2333 if ( t0.getValueAsString( 49, 4 ) != null ) {
2336 final String l = ForesterUtil.getLineSeparator();
2337 final StringBuffer source = new StringBuffer();
2338 source.append( "" + l );
2339 source.append( "# 1 1 1 1 1 1 1 1" + l );
2340 source.append( " 00 01 02 03" + l );
2341 source.append( " 10 11 12 13 " + l );
2342 source.append( "20 21 22 23 " + l );
2343 source.append( " 30 31 32 33" + l );
2344 source.append( "40 41 42 43" + l );
2345 source.append( " # 1 1 1 1 1 " + l );
2346 source.append( "50 51 52 53 54" + l );
2347 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2348 if ( t1.getNumberOfColumns() != 5 ) {
2351 if ( t1.getNumberOfRows() != 6 ) {
2354 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2357 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2360 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2363 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2366 final StringBuffer source1 = new StringBuffer();
2367 source1.append( "" + l );
2368 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2369 source1.append( " 00; 01 ;02;03" + l );
2370 source1.append( " 10; 11; 12; 13 " + l );
2371 source1.append( "20; 21; 22; 23 " + l );
2372 source1.append( " 30; 31; 32; 33" + l );
2373 source1.append( "40;41;42;43" + l );
2374 source1.append( " # 1 1 1 1 1 " + l );
2375 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2376 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2377 if ( t2.getNumberOfColumns() != 5 ) {
2380 if ( t2.getNumberOfRows() != 6 ) {
2383 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2386 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2389 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2392 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2395 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2398 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2401 final StringBuffer source2 = new StringBuffer();
2402 source2.append( "" + l );
2403 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2404 source2.append( " 00; 01 ;02;03" + l );
2405 source2.append( " 10; 11; 12; 13 " + l );
2406 source2.append( "20; 21; 22; 23 " + l );
2407 source2.append( " " + l );
2408 source2.append( " 30; 31; 32; 33" + l );
2409 source2.append( "40;41;42;43" + l );
2410 source2.append( " comment: 1 1 1 1 1 " + l );
2411 source2.append( ";;;50 ; 52; 53;;54 " + l );
2412 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2418 if ( tl.size() != 2 ) {
2421 final BasicTable<String> t3 = tl.get( 0 );
2422 final BasicTable<String> t4 = tl.get( 1 );
2423 if ( t3.getNumberOfColumns() != 4 ) {
2426 if ( t3.getNumberOfRows() != 3 ) {
2429 if ( t4.getNumberOfColumns() != 4 ) {
2432 if ( t4.getNumberOfRows() != 3 ) {
2435 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2438 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2442 catch ( final Exception e ) {
2443 e.printStackTrace( System.out );
2449 private static boolean testBasicTolXMLparsing() {
2451 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2452 final TolParser parser = new TolParser();
2453 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2454 if ( parser.getErrorCount() > 0 ) {
2455 System.out.println( parser.getErrorMessages().toString() );
2458 if ( phylogenies_0.length != 1 ) {
2461 final Phylogeny t1 = phylogenies_0[ 0 ];
2462 if ( t1.getNumberOfExternalNodes() != 5 ) {
2465 if ( !t1.isRooted() ) {
2468 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2471 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2474 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2477 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2480 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2481 if ( parser.getErrorCount() > 0 ) {
2482 System.out.println( parser.getErrorMessages().toString() );
2485 if ( phylogenies_1.length != 1 ) {
2488 final Phylogeny t2 = phylogenies_1[ 0 ];
2489 if ( t2.getNumberOfExternalNodes() != 664 ) {
2492 if ( !t2.isRooted() ) {
2495 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2498 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2501 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2504 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2507 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2510 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2511 .equals( "Aquifex" ) ) {
2514 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2515 if ( parser.getErrorCount() > 0 ) {
2516 System.out.println( parser.getErrorMessages().toString() );
2519 if ( phylogenies_2.length != 1 ) {
2522 final Phylogeny t3 = phylogenies_2[ 0 ];
2523 if ( t3.getNumberOfExternalNodes() != 184 ) {
2526 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2529 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2532 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2535 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2536 if ( parser.getErrorCount() > 0 ) {
2537 System.out.println( parser.getErrorMessages().toString() );
2540 if ( phylogenies_3.length != 1 ) {
2543 final Phylogeny t4 = phylogenies_3[ 0 ];
2544 if ( t4.getNumberOfExternalNodes() != 1 ) {
2547 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2550 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2553 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2556 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2557 if ( parser.getErrorCount() > 0 ) {
2558 System.out.println( parser.getErrorMessages().toString() );
2561 if ( phylogenies_4.length != 1 ) {
2564 final Phylogeny t5 = phylogenies_4[ 0 ];
2565 if ( t5.getNumberOfExternalNodes() != 13 ) {
2568 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2571 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2574 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2578 catch ( final Exception e ) {
2579 e.printStackTrace( System.out );
2585 private static boolean testBasicTreeMethods() {
2587 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2588 final Phylogeny t1 = factory.create();
2589 if ( !t1.isEmpty() ) {
2592 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2593 if ( t2.getNumberOfExternalNodes() != 4 ) {
2596 if ( t2.getHeight() != 8.5 ) {
2599 if ( !t2.isCompletelyBinary() ) {
2602 if ( t2.isEmpty() ) {
2605 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2606 if ( t3.getNumberOfExternalNodes() != 5 ) {
2609 if ( t3.getHeight() != 11 ) {
2612 if ( t3.isCompletelyBinary() ) {
2615 final PhylogenyNode n = t3.getNode( "ABC" );
2616 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 ];
2617 if ( t4.getNumberOfExternalNodes() != 9 ) {
2620 if ( t4.getHeight() != 11 ) {
2623 if ( t4.isCompletelyBinary() ) {
2626 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)" );
2627 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2628 if ( t5.getNumberOfExternalNodes() != 8 ) {
2631 if ( t5.getHeight() != 15 ) {
2634 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)" );
2635 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2636 if ( t6.getHeight() != 15 ) {
2639 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)" );
2640 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2641 if ( t7.getHeight() != 15 ) {
2644 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)" );
2645 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2646 if ( t8.getNumberOfExternalNodes() != 10 ) {
2649 if ( t8.getHeight() != 15 ) {
2652 final char[] a9 = new char[] { 'a' };
2653 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2654 if ( t9.getHeight() != 0 ) {
2657 final char[] a10 = new char[] { 'a', ':', '6' };
2658 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2659 if ( t10.getHeight() != 6 ) {
2663 catch ( final Exception e ) {
2664 e.printStackTrace( System.out );
2670 private static boolean testConfidenceAssessor() {
2672 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2673 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2674 final Phylogeny[] ev0 = factory
2675 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2677 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2678 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2681 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2684 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2685 final Phylogeny[] ev1 = factory
2686 .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)));",
2688 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2689 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2692 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2695 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2696 final Phylogeny[] ev_b = factory
2697 .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",
2699 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2700 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2703 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2707 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2708 final Phylogeny[] ev1x = factory
2709 .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)));",
2711 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2712 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2715 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2718 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2719 final Phylogeny[] ev_bx = factory
2720 .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",
2722 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2723 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2726 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2730 final Phylogeny[] t2 = factory
2731 .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);",
2733 final Phylogeny[] ev2 = factory
2734 .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);",
2736 for( final Phylogeny target : t2 ) {
2737 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2740 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2741 new NHXParser() )[ 0 ];
2742 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2743 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2744 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2747 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2750 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2754 catch ( final Exception e ) {
2755 e.printStackTrace();
2761 private static boolean testCopyOfNodeData() {
2763 final PhylogenyNode n1 = PhylogenyNode
2764 .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]" );
2765 final PhylogenyNode n2 = n1.copyNodeData();
2766 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2770 catch ( final Exception e ) {
2771 e.printStackTrace();
2777 private static boolean testTreeCopy() {
2779 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
2780 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
2781 final Phylogeny t1 = t0.copy();
2782 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
2785 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2788 t0.deleteSubtree( t0.getNode( "c" ), true );
2789 t0.deleteSubtree( t0.getNode( "a" ), true );
2790 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
2791 t0.getNode( "b" ).setName( "Bee" );
2792 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
2795 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2798 t0.deleteSubtree( t0.getNode( "e" ), true );
2799 t0.deleteSubtree( t0.getNode( "Bee" ), true );
2800 t0.deleteSubtree( t0.getNode( "d" ), true );
2801 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2805 catch ( final Exception e ) {
2806 e.printStackTrace();
2812 private static boolean testCreateBalancedPhylogeny() {
2814 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
2815 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
2818 if ( p0.getNumberOfExternalNodes() != 15625 ) {
2821 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
2822 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
2825 if ( p1.getNumberOfExternalNodes() != 100 ) {
2829 catch ( final Exception e ) {
2830 e.printStackTrace();
2836 private static boolean testCreateUriForSeqWeb() {
2838 final PhylogenyNode n = new PhylogenyNode();
2839 n.setName( "tr|B3RJ64" );
2840 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
2843 n.setName( "B0LM41_HUMAN" );
2844 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
2847 n.setName( "NP_001025424" );
2848 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
2851 n.setName( "_NM_001030253-" );
2852 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
2855 n.setName( "XM_002122186" );
2856 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
2859 n.setName( "dgh_AAA34956_gdg" );
2860 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2863 n.setName( "AAA34956" );
2864 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2867 n.setName( "GI:394892" );
2868 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2869 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2872 n.setName( "gi_394892" );
2873 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2874 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2877 n.setName( "gi6335_gi_394892_56635_Gi_43" );
2878 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2879 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2882 n.setName( "P12345" );
2883 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2884 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2887 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
2888 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2889 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2893 catch ( final Exception e ) {
2894 e.printStackTrace( System.out );
2900 private static boolean testDataObjects() {
2902 final Confidence s0 = new Confidence();
2903 final Confidence s1 = new Confidence();
2904 if ( !s0.isEqual( s1 ) ) {
2907 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2908 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2909 if ( s2.isEqual( s1 ) ) {
2912 if ( !s2.isEqual( s3 ) ) {
2915 final Confidence s4 = ( Confidence ) s3.copy();
2916 if ( !s4.isEqual( s3 ) ) {
2923 final Taxonomy t1 = new Taxonomy();
2924 final Taxonomy t2 = new Taxonomy();
2925 final Taxonomy t3 = new Taxonomy();
2926 final Taxonomy t4 = new Taxonomy();
2927 final Taxonomy t5 = new Taxonomy();
2928 t1.setIdentifier( new Identifier( "ecoli" ) );
2929 t1.setTaxonomyCode( "ECOLI" );
2930 t1.setScientificName( "E. coli" );
2931 t1.setCommonName( "coli" );
2932 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2933 if ( !t1.isEqual( t0 ) ) {
2936 t2.setIdentifier( new Identifier( "ecoli" ) );
2937 t2.setTaxonomyCode( "OTHER" );
2938 t2.setScientificName( "what" );
2939 t2.setCommonName( "something" );
2940 if ( !t1.isEqual( t2 ) ) {
2943 t2.setIdentifier( new Identifier( "nemve" ) );
2944 if ( t1.isEqual( t2 ) ) {
2947 t1.setIdentifier( null );
2948 t3.setTaxonomyCode( "ECOLI" );
2949 t3.setScientificName( "what" );
2950 t3.setCommonName( "something" );
2951 if ( !t1.isEqual( t3 ) ) {
2954 t1.setIdentifier( null );
2955 t1.setTaxonomyCode( "" );
2956 t4.setScientificName( "E. ColI" );
2957 t4.setCommonName( "something" );
2958 if ( !t1.isEqual( t4 ) ) {
2961 t4.setScientificName( "B. subtilis" );
2962 t4.setCommonName( "something" );
2963 if ( t1.isEqual( t4 ) ) {
2966 t1.setIdentifier( null );
2967 t1.setTaxonomyCode( "" );
2968 t1.setScientificName( "" );
2969 t5.setCommonName( "COLI" );
2970 if ( !t1.isEqual( t5 ) ) {
2973 t5.setCommonName( "vibrio" );
2974 if ( t1.isEqual( t5 ) ) {
2979 final Identifier id0 = new Identifier( "123", "pfam" );
2980 final Identifier id1 = ( Identifier ) id0.copy();
2981 if ( !id1.isEqual( id1 ) ) {
2984 if ( !id1.isEqual( id0 ) ) {
2987 if ( !id0.isEqual( id1 ) ) {
2994 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2995 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2996 if ( !pd1.isEqual( pd1 ) ) {
2999 if ( !pd1.isEqual( pd0 ) ) {
3004 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3005 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3006 if ( !pd3.isEqual( pd3 ) ) {
3009 if ( !pd2.isEqual( pd3 ) ) {
3012 if ( !pd0.isEqual( pd3 ) ) {
3017 // DomainArchitecture
3018 // ------------------
3019 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3020 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3021 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3022 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3023 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3024 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3029 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3030 if ( ds0.getNumberOfDomains() != 4 ) {
3033 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3034 if ( !ds0.isEqual( ds0 ) ) {
3037 if ( !ds0.isEqual( ds1 ) ) {
3040 if ( ds1.getNumberOfDomains() != 4 ) {
3043 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3048 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3049 if ( ds0.isEqual( ds2 ) ) {
3055 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3056 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3057 System.out.println( ds3.toNHX() );
3060 if ( ds3.getNumberOfDomains() != 3 ) {
3065 final Event e1 = new Event( Event.EventType.fusion );
3066 if ( e1.isDuplication() ) {
3069 if ( !e1.isFusion() ) {
3072 if ( !e1.asText().toString().equals( "fusion" ) ) {
3075 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3078 final Event e11 = new Event( Event.EventType.fusion );
3079 if ( !e11.isEqual( e1 ) ) {
3082 if ( !e11.toNHX().toString().equals( "" ) ) {
3085 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3086 if ( e2.isDuplication() ) {
3089 if ( !e2.isSpeciationOrDuplication() ) {
3092 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3095 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3098 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3101 if ( e11.isEqual( e2 ) ) {
3104 final Event e2c = ( Event ) e2.copy();
3105 if ( !e2c.isEqual( e2 ) ) {
3108 Event e3 = new Event( 1, 2, 3 );
3109 if ( e3.isDuplication() ) {
3112 if ( e3.isSpeciation() ) {
3115 if ( e3.isGeneLoss() ) {
3118 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3121 final Event e3c = ( Event ) e3.copy();
3122 final Event e3cc = ( Event ) e3c.copy();
3123 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3127 if ( !e3c.isEqual( e3cc ) ) {
3130 Event e4 = new Event( 1, 2, 3 );
3131 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3134 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3137 final Event e4c = ( Event ) e4.copy();
3139 final Event e4cc = ( Event ) e4c.copy();
3140 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3143 if ( !e4c.isEqual( e4cc ) ) {
3146 final Event e5 = new Event();
3147 if ( !e5.isUnassigned() ) {
3150 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3153 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3156 final Event e6 = new Event( 1, 0, 0 );
3157 if ( !e6.asText().toString().equals( "duplication" ) ) {
3160 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3163 final Event e7 = new Event( 0, 1, 0 );
3164 if ( !e7.asText().toString().equals( "speciation" ) ) {
3167 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3170 final Event e8 = new Event( 0, 0, 1 );
3171 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3174 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3178 catch ( final Exception e ) {
3179 e.printStackTrace( System.out );
3185 private static boolean testDeletionOfExternalNodes() {
3187 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3188 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3189 final PhylogenyWriter w = new PhylogenyWriter();
3190 if ( t0.isEmpty() ) {
3193 if ( t0.getNumberOfExternalNodes() != 1 ) {
3196 t0.deleteSubtree( t0.getNode( "A" ), false );
3197 if ( t0.getNumberOfExternalNodes() != 0 ) {
3200 if ( !t0.isEmpty() ) {
3203 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3204 if ( t1.getNumberOfExternalNodes() != 2 ) {
3207 t1.deleteSubtree( t1.getNode( "A" ), false );
3208 if ( t1.getNumberOfExternalNodes() != 1 ) {
3211 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3214 t1.deleteSubtree( t1.getNode( "B" ), false );
3215 if ( t1.getNumberOfExternalNodes() != 1 ) {
3218 t1.deleteSubtree( t1.getNode( "r" ), false );
3219 if ( !t1.isEmpty() ) {
3222 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3223 if ( t2.getNumberOfExternalNodes() != 3 ) {
3226 t2.deleteSubtree( t2.getNode( "B" ), false );
3227 if ( t2.getNumberOfExternalNodes() != 2 ) {
3230 t2.toNewHampshireX();
3231 PhylogenyNode n = t2.getNode( "A" );
3232 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3235 t2.deleteSubtree( t2.getNode( "A" ), false );
3236 if ( t2.getNumberOfExternalNodes() != 2 ) {
3239 t2.deleteSubtree( t2.getNode( "C" ), true );
3240 if ( t2.getNumberOfExternalNodes() != 1 ) {
3243 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3244 if ( t3.getNumberOfExternalNodes() != 4 ) {
3247 t3.deleteSubtree( t3.getNode( "B" ), true );
3248 if ( t3.getNumberOfExternalNodes() != 3 ) {
3251 n = t3.getNode( "A" );
3252 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3255 n = n.getNextExternalNode();
3256 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3259 t3.deleteSubtree( t3.getNode( "A" ), true );
3260 if ( t3.getNumberOfExternalNodes() != 2 ) {
3263 n = t3.getNode( "C" );
3264 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3267 t3.deleteSubtree( t3.getNode( "C" ), true );
3268 if ( t3.getNumberOfExternalNodes() != 1 ) {
3271 t3.deleteSubtree( t3.getNode( "D" ), true );
3272 if ( t3.getNumberOfExternalNodes() != 0 ) {
3275 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3276 if ( t4.getNumberOfExternalNodes() != 6 ) {
3279 t4.deleteSubtree( t4.getNode( "B2" ), true );
3280 if ( t4.getNumberOfExternalNodes() != 5 ) {
3283 String s = w.toNewHampshire( t4, false, true ).toString();
3284 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3287 t4.deleteSubtree( t4.getNode( "B11" ), true );
3288 if ( t4.getNumberOfExternalNodes() != 4 ) {
3291 t4.deleteSubtree( t4.getNode( "C" ), true );
3292 if ( t4.getNumberOfExternalNodes() != 3 ) {
3295 n = t4.getNode( "A" );
3296 n = n.getNextExternalNode();
3297 if ( !n.getName().equals( "B12" ) ) {
3300 n = n.getNextExternalNode();
3301 if ( !n.getName().equals( "D" ) ) {
3304 s = w.toNewHampshire( t4, false, true ).toString();
3305 if ( !s.equals( "((A,B12),D);" ) ) {
3308 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3309 t5.deleteSubtree( t5.getNode( "A" ), true );
3310 if ( t5.getNumberOfExternalNodes() != 5 ) {
3313 s = w.toNewHampshire( t5, false, true ).toString();
3314 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3317 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3318 t6.deleteSubtree( t6.getNode( "B11" ), true );
3319 if ( t6.getNumberOfExternalNodes() != 5 ) {
3322 s = w.toNewHampshire( t6, false, false ).toString();
3323 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3326 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3327 t7.deleteSubtree( t7.getNode( "B12" ), true );
3328 if ( t7.getNumberOfExternalNodes() != 5 ) {
3331 s = w.toNewHampshire( t7, false, true ).toString();
3332 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3335 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3336 t8.deleteSubtree( t8.getNode( "B2" ), true );
3337 if ( t8.getNumberOfExternalNodes() != 5 ) {
3340 s = w.toNewHampshire( t8, false, false ).toString();
3341 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3344 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3345 t9.deleteSubtree( t9.getNode( "C" ), true );
3346 if ( t9.getNumberOfExternalNodes() != 5 ) {
3349 s = w.toNewHampshire( t9, false, true ).toString();
3350 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3353 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3354 t10.deleteSubtree( t10.getNode( "D" ), true );
3355 if ( t10.getNumberOfExternalNodes() != 5 ) {
3358 s = w.toNewHampshire( t10, false, true ).toString();
3359 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3362 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3363 t11.deleteSubtree( t11.getNode( "A" ), true );
3364 if ( t11.getNumberOfExternalNodes() != 2 ) {
3367 s = w.toNewHampshire( t11, false, true ).toString();
3368 if ( !s.equals( "(B,C);" ) ) {
3371 t11.deleteSubtree( t11.getNode( "C" ), true );
3372 if ( t11.getNumberOfExternalNodes() != 1 ) {
3375 s = w.toNewHampshire( t11, false, false ).toString();
3376 if ( !s.equals( "B;" ) ) {
3379 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3380 t12.deleteSubtree( t12.getNode( "B2" ), true );
3381 if ( t12.getNumberOfExternalNodes() != 8 ) {
3384 s = w.toNewHampshire( t12, false, true ).toString();
3385 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3388 t12.deleteSubtree( t12.getNode( "B3" ), true );
3389 if ( t12.getNumberOfExternalNodes() != 7 ) {
3392 s = w.toNewHampshire( t12, false, true ).toString();
3393 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3396 t12.deleteSubtree( t12.getNode( "C3" ), true );
3397 if ( t12.getNumberOfExternalNodes() != 6 ) {
3400 s = w.toNewHampshire( t12, false, true ).toString();
3401 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3404 t12.deleteSubtree( t12.getNode( "A1" ), true );
3405 if ( t12.getNumberOfExternalNodes() != 5 ) {
3408 s = w.toNewHampshire( t12, false, true ).toString();
3409 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3412 t12.deleteSubtree( t12.getNode( "B1" ), true );
3413 if ( t12.getNumberOfExternalNodes() != 4 ) {
3416 s = w.toNewHampshire( t12, false, true ).toString();
3417 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3420 t12.deleteSubtree( t12.getNode( "A3" ), true );
3421 if ( t12.getNumberOfExternalNodes() != 3 ) {
3424 s = w.toNewHampshire( t12, false, true ).toString();
3425 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3428 t12.deleteSubtree( t12.getNode( "A2" ), true );
3429 if ( t12.getNumberOfExternalNodes() != 2 ) {
3432 s = w.toNewHampshire( t12, false, true ).toString();
3433 if ( !s.equals( "(C1,C2);" ) ) {
3436 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3437 t13.deleteSubtree( t13.getNode( "D" ), true );
3438 if ( t13.getNumberOfExternalNodes() != 4 ) {
3441 s = w.toNewHampshire( t13, false, true ).toString();
3442 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3445 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3446 t14.deleteSubtree( t14.getNode( "E" ), true );
3447 if ( t14.getNumberOfExternalNodes() != 5 ) {
3450 s = w.toNewHampshire( t14, false, true ).toString();
3451 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3454 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3455 t15.deleteSubtree( t15.getNode( "B2" ), true );
3456 if ( t15.getNumberOfExternalNodes() != 11 ) {
3459 t15.deleteSubtree( t15.getNode( "B1" ), true );
3460 if ( t15.getNumberOfExternalNodes() != 10 ) {
3463 t15.deleteSubtree( t15.getNode( "B3" ), true );
3464 if ( t15.getNumberOfExternalNodes() != 9 ) {
3467 t15.deleteSubtree( t15.getNode( "B4" ), true );
3468 if ( t15.getNumberOfExternalNodes() != 8 ) {
3471 t15.deleteSubtree( t15.getNode( "A1" ), true );
3472 if ( t15.getNumberOfExternalNodes() != 7 ) {
3475 t15.deleteSubtree( t15.getNode( "C4" ), true );
3476 if ( t15.getNumberOfExternalNodes() != 6 ) {
3480 catch ( final Exception e ) {
3481 e.printStackTrace( System.out );
3487 private static boolean testDescriptiveStatistics() {
3489 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3490 dss1.addValue( 82 );
3491 dss1.addValue( 78 );
3492 dss1.addValue( 70 );
3493 dss1.addValue( 58 );
3494 dss1.addValue( 42 );
3495 if ( dss1.getN() != 5 ) {
3498 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3501 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3504 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3507 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3510 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3513 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3516 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3519 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3522 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3525 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3528 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3531 dss1.addValue( 123 );
3532 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3535 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3538 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3541 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3542 dss2.addValue( -1.85 );
3543 dss2.addValue( 57.5 );
3544 dss2.addValue( 92.78 );
3545 dss2.addValue( 57.78 );
3546 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3549 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3552 final double[] a = dss2.getDataAsDoubleArray();
3553 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3556 dss2.addValue( -100 );
3557 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3560 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3563 final double[] ds = new double[ 14 ];
3578 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3579 if ( bins.length != 4 ) {
3582 if ( bins[ 0 ] != 2 ) {
3585 if ( bins[ 1 ] != 3 ) {
3588 if ( bins[ 2 ] != 4 ) {
3591 if ( bins[ 3 ] != 5 ) {
3594 final double[] ds1 = new double[ 9 ];
3604 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3605 if ( bins1.length != 4 ) {
3608 if ( bins1[ 0 ] != 2 ) {
3611 if ( bins1[ 1 ] != 3 ) {
3614 if ( bins1[ 2 ] != 0 ) {
3617 if ( bins1[ 3 ] != 4 ) {
3620 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3621 if ( bins1_1.length != 3 ) {
3624 if ( bins1_1[ 0 ] != 3 ) {
3627 if ( bins1_1[ 1 ] != 2 ) {
3630 if ( bins1_1[ 2 ] != 4 ) {
3633 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3634 if ( bins1_2.length != 3 ) {
3637 if ( bins1_2[ 0 ] != 2 ) {
3640 if ( bins1_2[ 1 ] != 2 ) {
3643 if ( bins1_2[ 2 ] != 2 ) {
3646 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3660 dss3.addValue( 10 );
3661 dss3.addValue( 10 );
3662 dss3.addValue( 10 );
3663 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3664 histo.toStringBuffer( 10, '=', 40, 5 );
3665 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3667 catch ( final Exception e ) {
3668 e.printStackTrace( System.out );
3674 private static boolean testDir( final String file ) {
3676 final File f = new File( file );
3677 if ( !f.exists() ) {
3680 if ( !f.isDirectory() ) {
3683 if ( !f.canRead() ) {
3687 catch ( final Exception e ) {
3693 private static boolean testGenbankAccessorParsing() {
3694 //The format for GenBank Accession numbers are:
3695 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
3696 //Protein: 3 letters + 5 numerals
3697 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
3698 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
3701 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
3704 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
3707 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
3710 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
3713 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
3716 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
3719 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
3722 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
3725 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
3728 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
3731 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
3734 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
3737 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
3743 private static boolean testExternalNodeRelatedMethods() {
3745 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3746 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3747 PhylogenyNode n = t1.getNode( "A" );
3748 n = n.getNextExternalNode();
3749 if ( !n.getName().equals( "B" ) ) {
3752 n = n.getNextExternalNode();
3753 if ( !n.getName().equals( "C" ) ) {
3756 n = n.getNextExternalNode();
3757 if ( !n.getName().equals( "D" ) ) {
3760 n = t1.getNode( "B" );
3761 while ( !n.isLastExternalNode() ) {
3762 n = n.getNextExternalNode();
3764 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
3765 n = t2.getNode( "A" );
3766 n = n.getNextExternalNode();
3767 if ( !n.getName().equals( "B" ) ) {
3770 n = n.getNextExternalNode();
3771 if ( !n.getName().equals( "C" ) ) {
3774 n = n.getNextExternalNode();
3775 if ( !n.getName().equals( "D" ) ) {
3778 n = t2.getNode( "B" );
3779 while ( !n.isLastExternalNode() ) {
3780 n = n.getNextExternalNode();
3782 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
3783 n = t3.getNode( "A" );
3784 n = n.getNextExternalNode();
3785 if ( !n.getName().equals( "B" ) ) {
3788 n = n.getNextExternalNode();
3789 if ( !n.getName().equals( "C" ) ) {
3792 n = n.getNextExternalNode();
3793 if ( !n.getName().equals( "D" ) ) {
3796 n = n.getNextExternalNode();
3797 if ( !n.getName().equals( "E" ) ) {
3800 n = n.getNextExternalNode();
3801 if ( !n.getName().equals( "F" ) ) {
3804 n = n.getNextExternalNode();
3805 if ( !n.getName().equals( "G" ) ) {
3808 n = n.getNextExternalNode();
3809 if ( !n.getName().equals( "H" ) ) {
3812 n = t3.getNode( "B" );
3813 while ( !n.isLastExternalNode() ) {
3814 n = n.getNextExternalNode();
3816 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3817 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
3818 final PhylogenyNode node = iter.next();
3820 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
3821 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
3822 final PhylogenyNode node = iter.next();
3824 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
3825 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
3826 if ( !iter.next().getName().equals( "A" ) ) {
3829 if ( !iter.next().getName().equals( "B" ) ) {
3832 if ( !iter.next().getName().equals( "C" ) ) {
3835 if ( !iter.next().getName().equals( "D" ) ) {
3838 if ( !iter.next().getName().equals( "E" ) ) {
3841 if ( !iter.next().getName().equals( "F" ) ) {
3844 if ( iter.hasNext() ) {
3848 catch ( final Exception e ) {
3849 e.printStackTrace( System.out );
3855 private static boolean testExtractSNFromNodeName() {
3857 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
3860 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
3861 .equals( "Mus musculus musculus" ) ) {
3864 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
3865 .equals( "Mus musculus musculus" ) ) {
3868 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
3871 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
3872 .equals( "Mus musculus" ) ) {
3876 catch ( final Exception e ) {
3877 e.printStackTrace( System.out );
3883 private static boolean testExtractTaxonomyCodeFromNodeName() {
3885 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3888 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3889 .equals( "SOYBN" ) ) {
3892 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
3893 .equals( "ARATH" ) ) {
3896 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
3897 .equals( "ARATH" ) ) {
3900 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
3903 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
3906 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3909 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3910 .equals( "SOYBN" ) ) {
3913 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3914 .equals( "SOYBN" ) ) {
3917 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3918 .equals( "SOYBN" ) ) {
3921 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3922 .equals( "SOYBN" ) ) {
3925 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
3926 .equals( "SOYBN" ) ) {
3929 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3930 .equals( "SOYBN" ) ) {
3933 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
3934 .equals( "SOYBN" ) ) {
3937 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
3938 .equals( "SOYBN" ) ) {
3941 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
3944 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
3945 .equals( "SOYBN" ) ) {
3948 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
3949 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
3952 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
3953 .equals( "9YX45" ) ) {
3956 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
3957 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
3958 .equals( "MOUSE" ) ) {
3961 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
3962 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
3963 .equals( "MOUSE" ) ) {
3966 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
3967 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
3968 .equals( "MOUSE" ) ) {
3971 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
3972 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3975 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
3976 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3979 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
3980 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
3983 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
3984 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
3987 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
3988 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
3991 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
3992 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3995 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
3996 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3999 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4000 .equals( "RAT" ) ) {
4003 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4004 .equals( "PIG" ) ) {
4008 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4009 .equals( "MOUSE" ) ) {
4012 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4013 .equals( "MOUSE" ) ) {
4016 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4020 catch ( final Exception e ) {
4021 e.printStackTrace( System.out );
4027 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4029 PhylogenyNode n = new PhylogenyNode();
4030 n.setName( "tr|B3RJ64" );
4031 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4034 n.setName( "tr.B3RJ64" );
4035 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4038 n.setName( "tr=B3RJ64" );
4039 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4042 n.setName( "tr-B3RJ64" );
4043 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4046 n.setName( "tr/B3RJ64" );
4047 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4050 n.setName( "tr\\B3RJ64" );
4051 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4054 n.setName( "tr_B3RJ64" );
4055 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4058 n.setName( " tr|B3RJ64 " );
4059 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4062 n.setName( "-tr|B3RJ64-" );
4063 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4066 n.setName( "-tr=B3RJ64-" );
4067 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4070 n.setName( "_tr=B3RJ64_" );
4071 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4074 n.setName( " tr_tr|B3RJ64_sp|123 " );
4075 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4078 n.setName( "B3RJ64" );
4079 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4082 n.setName( "sp|B3RJ64" );
4083 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4086 n.setName( "sp|B3RJ64C" );
4087 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4090 n.setName( "sp B3RJ64" );
4091 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4094 n.setName( "sp|B3RJ6X" );
4095 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4098 n.setName( "sp|B3RJ6" );
4099 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4102 n.setName( "K1PYK7_CRAGI" );
4103 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4106 n.setName( "K1PYK7_PEA" );
4107 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4110 n.setName( "K1PYK7_RAT" );
4111 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4114 n.setName( "K1PYK7_PIG" );
4115 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4118 n.setName( "~K1PYK7_PIG~" );
4119 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4122 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4123 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4126 n.setName( "K1PYKX_CRAGI" );
4127 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4130 n.setName( "XXXXX_CRAGI" );
4131 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4134 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4135 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4138 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4139 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4142 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4143 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4146 n = new PhylogenyNode();
4147 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4148 seq.setSymbol( "K1PYK7_CRAGI" );
4149 n.getNodeData().addSequence( seq );
4150 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4153 seq.setSymbol( "tr|B3RJ64" );
4154 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4157 n = new PhylogenyNode();
4158 seq = new org.forester.phylogeny.data.Sequence();
4159 seq.setName( "K1PYK7_CRAGI" );
4160 n.getNodeData().addSequence( seq );
4161 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4164 seq.setName( "tr|B3RJ64" );
4165 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4168 n = new PhylogenyNode();
4169 seq = new org.forester.phylogeny.data.Sequence();
4170 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4171 n.getNodeData().addSequence( seq );
4172 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4175 n = new PhylogenyNode();
4176 seq = new org.forester.phylogeny.data.Sequence();
4177 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4178 n.getNodeData().addSequence( seq );
4179 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4183 n = new PhylogenyNode();
4184 n.setName( "ACP19736" );
4185 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4188 n = new PhylogenyNode();
4189 n.setName( "|ACP19736|" );
4190 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4194 catch ( final Exception e ) {
4195 e.printStackTrace( System.out );
4201 private static boolean testFastaParser() {
4203 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4206 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4209 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4210 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4213 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4216 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4219 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
4222 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4225 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4229 catch ( final Exception e ) {
4230 e.printStackTrace();
4236 private static boolean testGeneralMsaParser() {
4238 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4239 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4240 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4241 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4242 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4243 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4244 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4245 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4246 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4249 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4252 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4255 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4258 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4261 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4264 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4267 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4270 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4273 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4276 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4279 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4282 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
4283 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4286 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4289 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4292 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
4293 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
4296 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
4299 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
4302 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
4303 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4306 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4309 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4313 catch ( final Exception e ) {
4314 e.printStackTrace();
4320 private static boolean testGeneralTable() {
4322 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
4323 t0.setValue( 3, 2, "23" );
4324 t0.setValue( 10, 1, "error" );
4325 t0.setValue( 10, 1, "110" );
4326 t0.setValue( 9, 1, "19" );
4327 t0.setValue( 1, 10, "101" );
4328 t0.setValue( 10, 10, "1010" );
4329 t0.setValue( 100, 10, "10100" );
4330 t0.setValue( 0, 0, "00" );
4331 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
4334 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
4337 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
4340 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
4343 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
4346 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
4349 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
4352 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
4355 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
4358 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
4359 t1.setValue( "3", "2", "23" );
4360 t1.setValue( "10", "1", "error" );
4361 t1.setValue( "10", "1", "110" );
4362 t1.setValue( "9", "1", "19" );
4363 t1.setValue( "1", "10", "101" );
4364 t1.setValue( "10", "10", "1010" );
4365 t1.setValue( "100", "10", "10100" );
4366 t1.setValue( "0", "0", "00" );
4367 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
4368 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
4371 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
4374 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
4377 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
4380 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
4383 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
4386 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
4389 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
4392 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
4395 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
4399 catch ( final Exception e ) {
4400 e.printStackTrace( System.out );
4406 private static boolean testGetDistance() {
4408 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4409 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",
4410 new NHXParser() )[ 0 ];
4411 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
4414 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
4417 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
4420 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
4423 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
4426 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
4429 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
4432 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
4435 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
4438 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
4441 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
4444 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
4447 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
4450 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
4453 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
4456 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
4459 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
4462 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
4465 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
4468 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
4471 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
4474 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
4477 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
4480 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
4483 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
4486 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
4489 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
4492 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
4495 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
4498 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
4501 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
4504 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",
4505 new NHXParser() )[ 0 ];
4506 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
4509 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
4512 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
4515 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
4518 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
4521 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
4524 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
4527 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
4530 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
4533 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
4536 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
4540 catch ( final Exception e ) {
4541 e.printStackTrace( System.out );
4547 private static boolean testGetLCA() {
4549 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4550 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
4551 new NHXParser() )[ 0 ];
4552 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
4553 if ( !A.getName().equals( "A" ) ) {
4556 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
4557 if ( !gh.getName().equals( "gh" ) ) {
4560 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
4561 if ( !ab.getName().equals( "ab" ) ) {
4564 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
4565 if ( !ab2.getName().equals( "ab" ) ) {
4568 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
4569 if ( !gh2.getName().equals( "gh" ) ) {
4572 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
4573 if ( !gh3.getName().equals( "gh" ) ) {
4576 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
4577 if ( !abc.getName().equals( "abc" ) ) {
4580 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
4581 if ( !abc2.getName().equals( "abc" ) ) {
4584 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
4585 if ( !abcd.getName().equals( "abcd" ) ) {
4588 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
4589 if ( !abcd2.getName().equals( "abcd" ) ) {
4592 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
4593 if ( !abcdef.getName().equals( "abcdef" ) ) {
4596 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
4597 if ( !abcdef2.getName().equals( "abcdef" ) ) {
4600 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
4601 if ( !abcdef3.getName().equals( "abcdef" ) ) {
4604 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
4605 if ( !abcdef4.getName().equals( "abcdef" ) ) {
4608 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
4609 if ( !abcde.getName().equals( "abcde" ) ) {
4612 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
4613 if ( !abcde2.getName().equals( "abcde" ) ) {
4616 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
4617 if ( !r.getName().equals( "abcdefgh" ) ) {
4620 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
4621 if ( !r2.getName().equals( "abcdefgh" ) ) {
4624 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
4625 if ( !r3.getName().equals( "abcdefgh" ) ) {
4628 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
4629 if ( !abcde3.getName().equals( "abcde" ) ) {
4632 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
4633 if ( !abcde4.getName().equals( "abcde" ) ) {
4636 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
4637 if ( !ab3.getName().equals( "ab" ) ) {
4640 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
4641 if ( !ab4.getName().equals( "ab" ) ) {
4644 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
4645 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
4646 if ( !cd.getName().equals( "cd" ) ) {
4649 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
4650 if ( !cd2.getName().equals( "cd" ) ) {
4653 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
4654 if ( !cde.getName().equals( "cde" ) ) {
4657 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
4658 if ( !cde2.getName().equals( "cde" ) ) {
4661 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
4662 if ( !cdef.getName().equals( "cdef" ) ) {
4665 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
4666 if ( !cdef2.getName().equals( "cdef" ) ) {
4669 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
4670 if ( !cdef3.getName().equals( "cdef" ) ) {
4673 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
4674 if ( !rt.getName().equals( "r" ) ) {
4677 final Phylogeny p3 = factory
4678 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
4679 new NHXParser() )[ 0 ];
4680 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
4681 if ( !bc_3.getName().equals( "bc" ) ) {
4684 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
4685 if ( !ac_3.getName().equals( "abc" ) ) {
4688 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
4689 if ( !ad_3.getName().equals( "abcde" ) ) {
4692 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
4693 if ( !af_3.getName().equals( "abcdef" ) ) {
4696 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
4697 if ( !ag_3.getName().equals( "" ) ) {
4700 if ( !ag_3.isRoot() ) {
4703 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
4704 if ( !al_3.getName().equals( "" ) ) {
4707 if ( !al_3.isRoot() ) {
4710 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
4711 if ( !kl_3.getName().equals( "" ) ) {
4714 if ( !kl_3.isRoot() ) {
4717 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
4718 if ( !fl_3.getName().equals( "" ) ) {
4721 if ( !fl_3.isRoot() ) {
4724 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
4725 if ( !gk_3.getName().equals( "ghijk" ) ) {
4728 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
4729 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
4730 if ( !r_4.getName().equals( "r" ) ) {
4733 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
4734 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
4735 if ( !r_5.getName().equals( "root" ) ) {
4738 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
4739 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
4740 if ( !r_6.getName().equals( "rot" ) ) {
4743 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
4744 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
4745 if ( !r_7.getName().equals( "rott" ) ) {
4749 catch ( final Exception e ) {
4750 e.printStackTrace( System.out );
4756 private static boolean testGetLCA2() {
4758 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4759 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
4760 PhylogenyMethods.preOrderReId( p_a );
4761 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
4762 p_a.getNode( "a" ) );
4763 if ( !p_a_1.getName().equals( "a" ) ) {
4766 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
4767 PhylogenyMethods.preOrderReId( p_b );
4768 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
4769 p_b.getNode( "a" ) );
4770 if ( !p_b_1.getName().equals( "b" ) ) {
4773 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
4774 p_b.getNode( "b" ) );
4775 if ( !p_b_2.getName().equals( "b" ) ) {
4778 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
4779 PhylogenyMethods.preOrderReId( p_c );
4780 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
4781 p_c.getNode( "a" ) );
4782 if ( !p_c_1.getName().equals( "b" ) ) {
4785 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
4786 p_c.getNode( "c" ) );
4787 if ( !p_c_2.getName().equals( "c" ) ) {
4788 System.out.println( p_c_2.getName() );
4792 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
4793 p_c.getNode( "b" ) );
4794 if ( !p_c_3.getName().equals( "b" ) ) {
4797 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
4798 p_c.getNode( "a" ) );
4799 if ( !p_c_4.getName().equals( "c" ) ) {
4802 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
4803 new NHXParser() )[ 0 ];
4804 PhylogenyMethods.preOrderReId( p1 );
4805 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4806 p1.getNode( "A" ) );
4807 if ( !A.getName().equals( "A" ) ) {
4810 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
4811 p1.getNode( "gh" ) );
4812 if ( !gh.getName().equals( "gh" ) ) {
4815 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4816 p1.getNode( "B" ) );
4817 if ( !ab.getName().equals( "ab" ) ) {
4820 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
4821 p1.getNode( "A" ) );
4822 if ( !ab2.getName().equals( "ab" ) ) {
4825 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
4826 p1.getNode( "G" ) );
4827 if ( !gh2.getName().equals( "gh" ) ) {
4830 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
4831 p1.getNode( "H" ) );
4832 if ( !gh3.getName().equals( "gh" ) ) {
4835 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
4836 p1.getNode( "A" ) );
4837 if ( !abc.getName().equals( "abc" ) ) {
4840 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4841 p1.getNode( "C" ) );
4842 if ( !abc2.getName().equals( "abc" ) ) {
4845 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4846 p1.getNode( "D" ) );
4847 if ( !abcd.getName().equals( "abcd" ) ) {
4850 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
4851 p1.getNode( "A" ) );
4852 if ( !abcd2.getName().equals( "abcd" ) ) {
4855 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4856 p1.getNode( "F" ) );
4857 if ( !abcdef.getName().equals( "abcdef" ) ) {
4860 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
4861 p1.getNode( "A" ) );
4862 if ( !abcdef2.getName().equals( "abcdef" ) ) {
4865 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
4866 p1.getNode( "F" ) );
4867 if ( !abcdef3.getName().equals( "abcdef" ) ) {
4870 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
4871 p1.getNode( "ab" ) );
4872 if ( !abcdef4.getName().equals( "abcdef" ) ) {
4875 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4876 p1.getNode( "E" ) );
4877 if ( !abcde.getName().equals( "abcde" ) ) {
4880 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
4881 p1.getNode( "A" ) );
4882 if ( !abcde2.getName().equals( "abcde" ) ) {
4885 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
4886 p1.getNode( "abcdefgh" ) );
4887 if ( !r.getName().equals( "abcdefgh" ) ) {
4890 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4891 p1.getNode( "H" ) );
4892 if ( !r2.getName().equals( "abcdefgh" ) ) {
4895 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
4896 p1.getNode( "A" ) );
4897 if ( !r3.getName().equals( "abcdefgh" ) ) {
4900 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
4901 p1.getNode( "abcde" ) );
4902 if ( !abcde3.getName().equals( "abcde" ) ) {
4905 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
4906 p1.getNode( "E" ) );
4907 if ( !abcde4.getName().equals( "abcde" ) ) {
4910 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
4911 p1.getNode( "B" ) );
4912 if ( !ab3.getName().equals( "ab" ) ) {
4915 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
4916 p1.getNode( "ab" ) );
4917 if ( !ab4.getName().equals( "ab" ) ) {
4920 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
4921 PhylogenyMethods.preOrderReId( p2 );
4922 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4923 p2.getNode( "d" ) );
4924 if ( !cd.getName().equals( "cd" ) ) {
4927 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
4928 p2.getNode( "c" ) );
4929 if ( !cd2.getName().equals( "cd" ) ) {
4932 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4933 p2.getNode( "e" ) );
4934 if ( !cde.getName().equals( "cde" ) ) {
4937 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
4938 p2.getNode( "c" ) );
4939 if ( !cde2.getName().equals( "cde" ) ) {
4942 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4943 p2.getNode( "f" ) );
4944 if ( !cdef.getName().equals( "cdef" ) ) {
4947 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
4948 p2.getNode( "f" ) );
4949 if ( !cdef2.getName().equals( "cdef" ) ) {
4952 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
4953 p2.getNode( "d" ) );
4954 if ( !cdef3.getName().equals( "cdef" ) ) {
4957 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4958 p2.getNode( "a" ) );
4959 if ( !rt.getName().equals( "r" ) ) {
4962 final Phylogeny p3 = factory
4963 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
4964 new NHXParser() )[ 0 ];
4965 PhylogenyMethods.preOrderReId( p3 );
4966 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
4967 p3.getNode( "c" ) );
4968 if ( !bc_3.getName().equals( "bc" ) ) {
4971 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
4972 p3.getNode( "c" ) );
4973 if ( !ac_3.getName().equals( "abc" ) ) {
4976 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
4977 p3.getNode( "d" ) );
4978 if ( !ad_3.getName().equals( "abcde" ) ) {
4981 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
4982 p3.getNode( "f" ) );
4983 if ( !af_3.getName().equals( "abcdef" ) ) {
4986 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
4987 p3.getNode( "g" ) );
4988 if ( !ag_3.getName().equals( "" ) ) {
4991 if ( !ag_3.isRoot() ) {
4994 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
4995 p3.getNode( "l" ) );
4996 if ( !al_3.getName().equals( "" ) ) {
4999 if ( !al_3.isRoot() ) {
5002 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5003 p3.getNode( "l" ) );
5004 if ( !kl_3.getName().equals( "" ) ) {
5007 if ( !kl_3.isRoot() ) {
5010 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5011 p3.getNode( "l" ) );
5012 if ( !fl_3.getName().equals( "" ) ) {
5015 if ( !fl_3.isRoot() ) {
5018 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5019 p3.getNode( "k" ) );
5020 if ( !gk_3.getName().equals( "ghijk" ) ) {
5023 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5024 PhylogenyMethods.preOrderReId( p4 );
5025 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5026 p4.getNode( "c" ) );
5027 if ( !r_4.getName().equals( "r" ) ) {
5030 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5031 PhylogenyMethods.preOrderReId( p5 );
5032 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5033 p5.getNode( "c" ) );
5034 if ( !r_5.getName().equals( "root" ) ) {
5037 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5038 PhylogenyMethods.preOrderReId( p6 );
5039 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5040 p6.getNode( "a" ) );
5041 if ( !r_6.getName().equals( "rot" ) ) {
5044 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5045 PhylogenyMethods.preOrderReId( p7 );
5046 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5047 p7.getNode( "e" ) );
5048 if ( !r_7.getName().equals( "rott" ) ) {
5051 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5052 p7.getNode( "a" ) );
5053 if ( !r_71.getName().equals( "rott" ) ) {
5056 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5057 p7.getNode( "rott" ) );
5058 if ( !r_72.getName().equals( "rott" ) ) {
5061 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5062 p7.getNode( "a" ) );
5063 if ( !r_73.getName().equals( "rott" ) ) {
5066 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5067 p7.getNode( "rott" ) );
5068 if ( !r_74.getName().equals( "rott" ) ) {
5071 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5072 p7.getNode( "e" ) );
5073 if ( !r_75.getName().equals( "e" ) ) {
5077 catch ( final Exception e ) {
5078 e.printStackTrace( System.out );
5084 private static boolean testHmmscanOutputParser() {
5085 final String test_dir = Test.PATH_TO_TEST_DATA;
5087 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5088 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5090 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5091 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5092 final List<Protein> proteins = parser2.parse();
5093 if ( parser2.getProteinsEncountered() != 4 ) {
5096 if ( proteins.size() != 4 ) {
5099 if ( parser2.getDomainsEncountered() != 69 ) {
5102 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5105 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
5108 final Protein p1 = proteins.get( 0 );
5109 if ( p1.getNumberOfProteinDomains() != 15 ) {
5112 if ( p1.getLength() != 850 ) {
5115 final Protein p2 = proteins.get( 1 );
5116 if ( p2.getNumberOfProteinDomains() != 51 ) {
5119 if ( p2.getLength() != 1291 ) {
5122 final Protein p3 = proteins.get( 2 );
5123 if ( p3.getNumberOfProteinDomains() != 2 ) {
5126 final Protein p4 = proteins.get( 3 );
5127 if ( p4.getNumberOfProteinDomains() != 1 ) {
5130 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5133 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5136 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5139 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5142 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5145 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
5148 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
5151 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5154 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5158 catch ( final Exception e ) {
5159 e.printStackTrace( System.out );
5165 private static boolean testLastExternalNodeMethods() {
5167 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5168 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5169 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5170 final PhylogenyNode n1 = t0.getNode( "A" );
5171 if ( n1.isLastExternalNode() ) {
5174 final PhylogenyNode n2 = t0.getNode( "B" );
5175 if ( n2.isLastExternalNode() ) {
5178 final PhylogenyNode n3 = t0.getNode( "C" );
5179 if ( n3.isLastExternalNode() ) {
5182 final PhylogenyNode n4 = t0.getNode( "D" );
5183 if ( !n4.isLastExternalNode() ) {
5187 catch ( final Exception e ) {
5188 e.printStackTrace( System.out );
5194 private static boolean testLevelOrderIterator() {
5196 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5197 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5198 PhylogenyNodeIterator it0;
5199 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5202 for( it0.reset(); it0.hasNext(); ) {
5205 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5206 if ( !it.next().getName().equals( "r" ) ) {
5209 if ( !it.next().getName().equals( "ab" ) ) {
5212 if ( !it.next().getName().equals( "cd" ) ) {
5215 if ( !it.next().getName().equals( "A" ) ) {
5218 if ( !it.next().getName().equals( "B" ) ) {
5221 if ( !it.next().getName().equals( "C" ) ) {
5224 if ( !it.next().getName().equals( "D" ) ) {
5227 if ( it.hasNext() ) {
5230 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",
5231 new NHXParser() )[ 0 ];
5232 PhylogenyNodeIterator it2;
5233 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5236 for( it2.reset(); it2.hasNext(); ) {
5239 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5240 if ( !it3.next().getName().equals( "r" ) ) {
5243 if ( !it3.next().getName().equals( "abc" ) ) {
5246 if ( !it3.next().getName().equals( "defg" ) ) {
5249 if ( !it3.next().getName().equals( "A" ) ) {
5252 if ( !it3.next().getName().equals( "B" ) ) {
5255 if ( !it3.next().getName().equals( "C" ) ) {
5258 if ( !it3.next().getName().equals( "D" ) ) {
5261 if ( !it3.next().getName().equals( "E" ) ) {
5264 if ( !it3.next().getName().equals( "F" ) ) {
5267 if ( !it3.next().getName().equals( "G" ) ) {
5270 if ( !it3.next().getName().equals( "1" ) ) {
5273 if ( !it3.next().getName().equals( "2" ) ) {
5276 if ( !it3.next().getName().equals( "3" ) ) {
5279 if ( !it3.next().getName().equals( "4" ) ) {
5282 if ( !it3.next().getName().equals( "5" ) ) {
5285 if ( !it3.next().getName().equals( "6" ) ) {
5288 if ( !it3.next().getName().equals( "f1" ) ) {
5291 if ( !it3.next().getName().equals( "f2" ) ) {
5294 if ( !it3.next().getName().equals( "f3" ) ) {
5297 if ( !it3.next().getName().equals( "a" ) ) {
5300 if ( !it3.next().getName().equals( "b" ) ) {
5303 if ( !it3.next().getName().equals( "f21" ) ) {
5306 if ( !it3.next().getName().equals( "X" ) ) {
5309 if ( !it3.next().getName().equals( "Y" ) ) {
5312 if ( !it3.next().getName().equals( "Z" ) ) {
5315 if ( it3.hasNext() ) {
5318 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
5319 PhylogenyNodeIterator it4;
5320 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
5323 for( it4.reset(); it4.hasNext(); ) {
5326 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
5327 if ( !it5.next().getName().equals( "r" ) ) {
5330 if ( !it5.next().getName().equals( "A" ) ) {
5333 if ( !it5.next().getName().equals( "B" ) ) {
5336 if ( !it5.next().getName().equals( "C" ) ) {
5339 if ( !it5.next().getName().equals( "D" ) ) {
5342 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
5343 PhylogenyNodeIterator it6;
5344 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
5347 for( it6.reset(); it6.hasNext(); ) {
5350 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
5351 if ( !it7.next().getName().equals( "A" ) ) {
5354 if ( it.hasNext() ) {
5358 catch ( final Exception e ) {
5359 e.printStackTrace( System.out );
5365 private static boolean testMafft( final String path ) {
5367 final List<String> opts = new ArrayList<String>();
5368 opts.add( "--maxiterate" );
5370 opts.add( "--localpair" );
5371 opts.add( "--quiet" );
5373 final MsaInferrer mafft = Mafft.createInstance( path );
5374 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
5375 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
5378 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
5382 catch ( final Exception e ) {
5383 e.printStackTrace( System.out );
5389 private static boolean testMidpointrooting() {
5391 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5392 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
5393 PhylogenyMethods.midpointRoot( t0 );
5394 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
5397 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
5400 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
5404 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",
5405 new NHXParser() )[ 0 ];
5406 if ( !t1.isRooted() ) {
5409 PhylogenyMethods.midpointRoot( t1 );
5410 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5413 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5416 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5419 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5422 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5425 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5428 t1.reRoot( t1.getNode( "A" ) );
5429 PhylogenyMethods.midpointRoot( t1 );
5430 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5433 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5436 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5439 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5442 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5446 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5450 catch ( final Exception e ) {
5451 e.printStackTrace( System.out );
5457 private static boolean testMsaQualityMethod() {
5459 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
5460 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
5461 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
5462 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
5463 final List<Sequence> l = new ArrayList<Sequence>();
5468 final Msa msa = BasicMsa.createInstance( l );
5469 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
5472 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
5475 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
5478 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
5482 catch ( final Exception e ) {
5483 e.printStackTrace( System.out );
5489 private static boolean testNextNodeWithCollapsing() {
5491 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5493 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
5494 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5495 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
5496 t0.getNode( "cd" ).setCollapse( true );
5497 t0.getNode( "cde" ).setCollapse( true );
5498 n = t0.getFirstExternalNode();
5499 while ( n != null ) {
5501 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5503 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5506 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5509 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
5512 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
5515 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
5518 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
5522 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5523 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
5524 t1.getNode( "ab" ).setCollapse( true );
5525 t1.getNode( "cd" ).setCollapse( true );
5526 t1.getNode( "cde" ).setCollapse( true );
5527 n = t1.getNode( "ab" );
5528 ext = new ArrayList<PhylogenyNode>();
5529 while ( n != null ) {
5531 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5533 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5536 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5539 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5542 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
5545 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
5551 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5552 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
5553 t2.getNode( "ab" ).setCollapse( true );
5554 t2.getNode( "cd" ).setCollapse( true );
5555 t2.getNode( "cde" ).setCollapse( true );
5556 t2.getNode( "c" ).setCollapse( true );
5557 t2.getNode( "d" ).setCollapse( true );
5558 t2.getNode( "e" ).setCollapse( true );
5559 t2.getNode( "gh" ).setCollapse( true );
5560 n = t2.getNode( "ab" );
5561 ext = new ArrayList<PhylogenyNode>();
5562 while ( n != null ) {
5564 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5566 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5569 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5572 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5575 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
5581 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5582 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
5583 t3.getNode( "ab" ).setCollapse( true );
5584 t3.getNode( "cd" ).setCollapse( true );
5585 t3.getNode( "cde" ).setCollapse( true );
5586 t3.getNode( "c" ).setCollapse( true );
5587 t3.getNode( "d" ).setCollapse( true );
5588 t3.getNode( "e" ).setCollapse( true );
5589 t3.getNode( "gh" ).setCollapse( true );
5590 t3.getNode( "fgh" ).setCollapse( true );
5591 n = t3.getNode( "ab" );
5592 ext = new ArrayList<PhylogenyNode>();
5593 while ( n != null ) {
5595 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5597 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5600 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5603 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
5609 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5610 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
5611 t4.getNode( "ab" ).setCollapse( true );
5612 t4.getNode( "cd" ).setCollapse( true );
5613 t4.getNode( "cde" ).setCollapse( true );
5614 t4.getNode( "c" ).setCollapse( true );
5615 t4.getNode( "d" ).setCollapse( true );
5616 t4.getNode( "e" ).setCollapse( true );
5617 t4.getNode( "gh" ).setCollapse( true );
5618 t4.getNode( "fgh" ).setCollapse( true );
5619 t4.getNode( "abcdefgh" ).setCollapse( true );
5620 n = t4.getNode( "abcdefgh" );
5621 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
5626 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5627 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
5629 n = t5.getFirstExternalNode();
5630 while ( n != null ) {
5632 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5634 if ( ext.size() != 8 ) {
5637 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5640 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5643 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5646 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5649 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5652 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5655 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
5658 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
5663 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5664 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
5666 t6.getNode( "ab" ).setCollapse( true );
5667 n = t6.getNode( "ab" );
5668 while ( n != null ) {
5670 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5672 if ( ext.size() != 7 ) {
5675 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5678 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5681 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5684 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5687 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5690 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5693 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5698 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5699 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
5701 t7.getNode( "cd" ).setCollapse( true );
5702 n = t7.getNode( "a" );
5703 while ( n != null ) {
5705 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5707 if ( ext.size() != 7 ) {
5710 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5713 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5716 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
5719 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5722 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5725 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5728 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5733 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5734 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
5736 t8.getNode( "cd" ).setCollapse( true );
5737 t8.getNode( "c" ).setCollapse( true );
5738 t8.getNode( "d" ).setCollapse( true );
5739 n = t8.getNode( "a" );
5740 while ( n != null ) {
5742 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5744 if ( ext.size() != 7 ) {
5747 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5750 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5753 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
5754 System.out.println( "2 fail" );
5757 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5760 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5763 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5766 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5771 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5772 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
5774 t9.getNode( "gh" ).setCollapse( true );
5775 n = t9.getNode( "a" );
5776 while ( n != null ) {
5778 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5780 if ( ext.size() != 7 ) {
5783 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5786 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5789 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5792 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5795 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5798 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5801 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
5806 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5807 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
5809 t10.getNode( "gh" ).setCollapse( true );
5810 t10.getNode( "g" ).setCollapse( true );
5811 t10.getNode( "h" ).setCollapse( true );
5812 n = t10.getNode( "a" );
5813 while ( n != null ) {
5815 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5817 if ( ext.size() != 7 ) {
5820 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5823 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5826 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5829 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5832 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5835 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5838 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
5843 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5844 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
5846 t11.getNode( "gh" ).setCollapse( true );
5847 t11.getNode( "fgh" ).setCollapse( true );
5848 n = t11.getNode( "a" );
5849 while ( n != null ) {
5851 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5853 if ( ext.size() != 6 ) {
5856 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5859 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5862 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5865 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5868 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5871 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
5876 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5877 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
5879 t12.getNode( "gh" ).setCollapse( true );
5880 t12.getNode( "fgh" ).setCollapse( true );
5881 t12.getNode( "g" ).setCollapse( true );
5882 t12.getNode( "h" ).setCollapse( true );
5883 t12.getNode( "f" ).setCollapse( true );
5884 n = t12.getNode( "a" );
5885 while ( n != null ) {
5887 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5889 if ( ext.size() != 6 ) {
5892 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5895 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5898 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5901 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5904 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5907 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
5912 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5913 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
5915 t13.getNode( "ab" ).setCollapse( true );
5916 t13.getNode( "b" ).setCollapse( true );
5917 t13.getNode( "fgh" ).setCollapse( true );
5918 t13.getNode( "gh" ).setCollapse( true );
5919 n = t13.getNode( "ab" );
5920 while ( n != null ) {
5922 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5924 if ( ext.size() != 5 ) {
5927 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5930 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5933 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5936 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5939 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
5944 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
5945 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
5947 t14.getNode( "ab" ).setCollapse( true );
5948 t14.getNode( "a" ).setCollapse( true );
5949 t14.getNode( "fgh" ).setCollapse( true );
5950 t14.getNode( "gh" ).setCollapse( true );
5951 n = t14.getNode( "ab" );
5952 while ( n != null ) {
5954 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5956 if ( ext.size() != 5 ) {
5959 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5962 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5965 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5968 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5971 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
5976 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" );
5977 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
5979 t15.getNode( "ab" ).setCollapse( true );
5980 t15.getNode( "a" ).setCollapse( true );
5981 t15.getNode( "fgh" ).setCollapse( true );
5982 t15.getNode( "gh" ).setCollapse( true );
5983 n = t15.getNode( "ab" );
5984 while ( n != null ) {
5986 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5988 if ( ext.size() != 6 ) {
5991 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5994 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5997 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6000 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6003 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6006 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6011 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" );
6012 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6014 t16.getNode( "ab" ).setCollapse( true );
6015 t16.getNode( "a" ).setCollapse( true );
6016 t16.getNode( "fgh" ).setCollapse( true );
6017 t16.getNode( "gh" ).setCollapse( true );
6018 t16.getNode( "cd" ).setCollapse( true );
6019 t16.getNode( "cde" ).setCollapse( true );
6020 t16.getNode( "d" ).setCollapse( true );
6021 t16.getNode( "x" ).setCollapse( true );
6022 n = t16.getNode( "ab" );
6023 while ( n != null ) {
6025 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6027 if ( ext.size() != 4 ) {
6030 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6033 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6036 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6039 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6043 catch ( final Exception e ) {
6044 e.printStackTrace( System.out );
6050 private static boolean testNexusCharactersParsing() {
6052 final NexusCharactersParser parser = new NexusCharactersParser();
6053 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6055 String[] labels = parser.getCharStateLabels();
6056 if ( labels.length != 7 ) {
6059 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6062 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6065 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6068 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6071 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6074 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6077 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6080 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6082 labels = parser.getCharStateLabels();
6083 if ( labels.length != 7 ) {
6086 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6089 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6092 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6095 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6098 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6101 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6104 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6108 catch ( final Exception e ) {
6109 e.printStackTrace( System.out );
6115 private static boolean testNexusMatrixParsing() {
6117 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
6118 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
6120 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
6121 if ( m.getNumberOfCharacters() != 9 ) {
6124 if ( m.getNumberOfIdentifiers() != 5 ) {
6127 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
6130 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
6133 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
6136 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
6139 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
6142 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
6145 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
6148 // if ( labels.length != 7 ) {
6151 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6154 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6157 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6160 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6163 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6166 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6169 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6172 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6174 // labels = parser.getCharStateLabels();
6175 // if ( labels.length != 7 ) {
6178 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6181 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6184 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6187 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6190 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6193 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6196 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6200 catch ( final Exception e ) {
6201 e.printStackTrace( System.out );
6207 private static boolean testNexusTreeParsing() {
6209 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6210 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6211 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
6212 if ( phylogenies.length != 1 ) {
6215 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
6218 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6222 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
6223 if ( phylogenies.length != 1 ) {
6226 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6229 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
6233 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
6234 if ( phylogenies.length != 1 ) {
6237 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6240 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6243 if ( phylogenies[ 0 ].isRooted() ) {
6247 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
6248 if ( phylogenies.length != 18 ) {
6251 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6254 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
6257 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
6260 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
6263 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
6266 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
6269 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
6272 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
6275 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
6278 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
6281 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
6284 if ( phylogenies[ 8 ].isRooted() ) {
6287 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
6290 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
6293 if ( !phylogenies[ 9 ].isRooted() ) {
6296 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
6299 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
6302 if ( !phylogenies[ 10 ].isRooted() ) {
6305 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
6308 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
6311 if ( phylogenies[ 11 ].isRooted() ) {
6314 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
6317 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
6320 if ( !phylogenies[ 12 ].isRooted() ) {
6323 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
6326 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
6329 if ( !phylogenies[ 13 ].isRooted() ) {
6332 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
6335 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
6338 if ( !phylogenies[ 14 ].isRooted() ) {
6341 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
6344 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
6347 if ( phylogenies[ 15 ].isRooted() ) {
6350 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
6353 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
6356 if ( !phylogenies[ 16 ].isRooted() ) {
6359 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
6362 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
6365 if ( phylogenies[ 17 ].isRooted() ) {
6368 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
6372 catch ( final Exception e ) {
6373 e.printStackTrace( System.out );
6379 private static boolean testNexusTreeParsingIterating() {
6381 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
6382 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
6383 if ( !p.hasNext() ) {
6386 Phylogeny phy = p.next();
6387 if ( phy == null ) {
6390 if ( phy.getNumberOfExternalNodes() != 25 ) {
6393 if ( !phy.getName().equals( "" ) ) {
6396 if ( p.hasNext() ) {
6400 if ( phy != null ) {
6405 if ( !p.hasNext() ) {
6409 if ( phy == null ) {
6412 if ( phy.getNumberOfExternalNodes() != 25 ) {
6415 if ( !phy.getName().equals( "" ) ) {
6418 if ( p.hasNext() ) {
6422 if ( phy != null ) {
6426 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
6427 if ( !p.hasNext() ) {
6431 if ( phy == null ) {
6434 if ( phy.getNumberOfExternalNodes() != 10 ) {
6437 if ( !phy.getName().equals( "name" ) ) {
6440 if ( p.hasNext() ) {
6444 if ( phy != null ) {
6449 if ( !p.hasNext() ) {
6453 if ( phy == null ) {
6456 if ( phy.getNumberOfExternalNodes() != 10 ) {
6459 if ( !phy.getName().equals( "name" ) ) {
6462 if ( p.hasNext() ) {
6466 if ( phy != null ) {
6470 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
6471 if ( !p.hasNext() ) {
6475 if ( phy == null ) {
6478 if ( phy.getNumberOfExternalNodes() != 3 ) {
6481 if ( !phy.getName().equals( "" ) ) {
6484 if ( phy.isRooted() ) {
6487 if ( p.hasNext() ) {
6491 if ( phy != null ) {
6496 if ( !p.hasNext() ) {
6500 if ( phy == null ) {
6503 if ( phy.getNumberOfExternalNodes() != 3 ) {
6506 if ( !phy.getName().equals( "" ) ) {
6509 if ( p.hasNext() ) {
6513 if ( phy != null ) {
6517 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
6518 // if ( phylogenies.length != 18 ) {
6522 if ( !p.hasNext() ) {
6526 if ( phy == null ) {
6529 if ( phy.getNumberOfExternalNodes() != 10 ) {
6532 if ( !phy.getName().equals( "tree 0" ) ) {
6536 if ( !p.hasNext() ) {
6540 if ( phy == null ) {
6543 if ( phy.getNumberOfExternalNodes() != 10 ) {
6546 if ( !phy.getName().equals( "tree 1" ) ) {
6550 if ( !p.hasNext() ) {
6554 if ( phy == null ) {
6557 if ( phy.getNumberOfExternalNodes() != 3 ) {
6560 if ( !phy.getName().equals( "" ) ) {
6563 if ( phy.isRooted() ) {
6567 if ( !p.hasNext() ) {
6571 if ( phy == null ) {
6574 if ( phy.getNumberOfExternalNodes() != 4 ) {
6577 if ( !phy.getName().equals( "" ) ) {
6580 if ( !phy.isRooted() ) {
6584 if ( !p.hasNext() ) {
6588 if ( phy == null ) {
6591 if ( phy.getNumberOfExternalNodes() != 5 ) {
6592 System.out.println( phy.getNumberOfExternalNodes() );
6595 if ( !phy.getName().equals( "" ) ) {
6598 if ( !phy.isRooted() ) {
6602 if ( !p.hasNext() ) {
6606 if ( phy == null ) {
6609 if ( phy.getNumberOfExternalNodes() != 3 ) {
6612 if ( !phy.getName().equals( "" ) ) {
6615 if ( phy.isRooted() ) {
6619 if ( !p.hasNext() ) {
6623 if ( phy == null ) {
6626 if ( phy.getNumberOfExternalNodes() != 2 ) {
6629 if ( !phy.getName().equals( "" ) ) {
6632 if ( !phy.isRooted() ) {
6636 if ( !p.hasNext() ) {
6640 if ( phy.getNumberOfExternalNodes() != 3 ) {
6643 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6646 if ( !phy.isRooted() ) {
6650 if ( !p.hasNext() ) {
6654 if ( phy.getNumberOfExternalNodes() != 3 ) {
6657 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
6660 if ( !phy.getName().equals( "tree 8" ) ) {
6664 if ( !p.hasNext() ) {
6668 if ( phy.getNumberOfExternalNodes() != 3 ) {
6671 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
6674 if ( !phy.getName().equals( "tree 9" ) ) {
6678 if ( !p.hasNext() ) {
6682 if ( phy.getNumberOfExternalNodes() != 3 ) {
6685 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6688 if ( !phy.getName().equals( "tree 10" ) ) {
6691 if ( !phy.isRooted() ) {
6695 if ( !p.hasNext() ) {
6699 if ( phy.getNumberOfExternalNodes() != 3 ) {
6702 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
6705 if ( !phy.getName().equals( "tree 11" ) ) {
6708 if ( phy.isRooted() ) {
6712 if ( !p.hasNext() ) {
6716 if ( phy.getNumberOfExternalNodes() != 3 ) {
6719 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
6722 if ( !phy.getName().equals( "tree 12" ) ) {
6725 if ( !phy.isRooted() ) {
6729 if ( !p.hasNext() ) {
6733 if ( phy.getNumberOfExternalNodes() != 3 ) {
6736 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6739 if ( !phy.getName().equals( "tree 13" ) ) {
6742 if ( !phy.isRooted() ) {
6746 if ( !p.hasNext() ) {
6750 if ( phy.getNumberOfExternalNodes() != 10 ) {
6751 System.out.println( phy.getNumberOfExternalNodes() );
6756 .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;" ) ) {
6757 System.out.println( phy.toNewHampshire() );
6760 if ( !phy.getName().equals( "tree 14" ) ) {
6763 if ( !phy.isRooted() ) {
6767 if ( !p.hasNext() ) {
6771 if ( phy.getNumberOfExternalNodes() != 10 ) {
6772 System.out.println( phy.getNumberOfExternalNodes() );
6777 .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;" ) ) {
6778 System.out.println( phy.toNewHampshire() );
6781 if ( !phy.getName().equals( "tree 15" ) ) {
6784 if ( phy.isRooted() ) {
6788 if ( !p.hasNext() ) {
6792 if ( phy.getNumberOfExternalNodes() != 10 ) {
6793 System.out.println( phy.getNumberOfExternalNodes() );
6798 .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;" ) ) {
6799 System.out.println( phy.toNewHampshire() );
6802 if ( !phy.getName().equals( "tree 16" ) ) {
6805 if ( !phy.isRooted() ) {
6809 if ( !p.hasNext() ) {
6813 if ( phy.getNumberOfExternalNodes() != 10 ) {
6814 System.out.println( phy.getNumberOfExternalNodes() );
6819 .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;" ) ) {
6820 System.out.println( phy.toNewHampshire() );
6823 if ( !phy.getName().equals( "tree 17" ) ) {
6826 if ( phy.isRooted() ) {
6830 if ( p.hasNext() ) {
6834 if ( phy != null ) {
6839 if ( !p.hasNext() ) {
6843 if ( phy == null ) {
6846 if ( phy.getNumberOfExternalNodes() != 10 ) {
6849 if ( !phy.getName().equals( "tree 0" ) ) {
6853 if ( !p.hasNext() ) {
6857 if ( phy == null ) {
6860 if ( phy.getNumberOfExternalNodes() != 10 ) {
6863 if ( !phy.getName().equals( "tree 1" ) ) {
6867 if ( !p.hasNext() ) {
6871 if ( phy == null ) {
6874 if ( phy.getNumberOfExternalNodes() != 3 ) {
6877 if ( !phy.getName().equals( "" ) ) {
6880 if ( phy.isRooted() ) {
6884 if ( !p.hasNext() ) {
6888 if ( phy == null ) {
6891 if ( phy.getNumberOfExternalNodes() != 4 ) {
6894 if ( !phy.getName().equals( "" ) ) {
6897 if ( !phy.isRooted() ) {
6901 if ( !p.hasNext() ) {
6905 if ( phy == null ) {
6908 if ( phy.getNumberOfExternalNodes() != 5 ) {
6909 System.out.println( phy.getNumberOfExternalNodes() );
6912 if ( !phy.getName().equals( "" ) ) {
6915 if ( !phy.isRooted() ) {
6919 if ( !p.hasNext() ) {
6923 if ( phy == null ) {
6926 if ( phy.getNumberOfExternalNodes() != 3 ) {
6929 if ( !phy.getName().equals( "" ) ) {
6932 if ( phy.isRooted() ) {
6936 catch ( final Exception e ) {
6937 e.printStackTrace( System.out );
6943 private static boolean testNexusTreeParsingTranslating() {
6945 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6946 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6947 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
6948 if ( phylogenies.length != 1 ) {
6951 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6954 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
6957 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
6960 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
6963 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
6964 .equals( "Aranaeus" ) ) {
6968 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
6969 if ( phylogenies.length != 3 ) {
6972 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6975 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
6978 if ( phylogenies[ 0 ].isRooted() ) {
6981 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
6984 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
6987 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
6988 .equals( "Aranaeus" ) ) {
6991 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
6994 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
6997 if ( phylogenies[ 1 ].isRooted() ) {
7000 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7003 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7006 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7007 .equals( "Aranaeus" ) ) {
7010 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7013 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7016 if ( !phylogenies[ 2 ].isRooted() ) {
7019 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7022 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7025 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7026 .equals( "Aranaeus" ) ) {
7030 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
7031 if ( phylogenies.length != 3 ) {
7034 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7037 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7040 if ( phylogenies[ 0 ].isRooted() ) {
7043 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7046 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7049 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7050 .equals( "Aranaeus" ) ) {
7053 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7056 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7059 if ( phylogenies[ 1 ].isRooted() ) {
7062 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7065 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7068 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7069 .equals( "Aranaeus" ) ) {
7072 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7075 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7078 if ( !phylogenies[ 2 ].isRooted() ) {
7081 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7084 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7087 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7088 .equals( "Aranaeus" ) ) {
7092 catch ( final Exception e ) {
7093 e.printStackTrace( System.out );
7099 private static boolean testNHParsing() {
7101 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7102 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
7103 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
7106 final NHXParser nhxp = new NHXParser();
7107 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
7108 nhxp.setReplaceUnderscores( true );
7109 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
7110 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
7113 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
7116 final Phylogeny p1b = factory
7117 .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 ",
7118 new NHXParser() )[ 0 ];
7119 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
7122 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
7125 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
7126 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
7127 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
7128 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
7129 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
7130 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
7131 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
7132 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
7133 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
7134 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
7135 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
7136 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
7137 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
7139 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
7142 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
7145 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
7148 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
7151 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
7152 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
7153 final String p16_S = "((A,B),C)";
7154 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
7155 if ( p16.length != 1 ) {
7158 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
7161 final String p17_S = "(C,(A,B))";
7162 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
7163 if ( p17.length != 1 ) {
7166 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
7169 final String p18_S = "((A,B),(C,D))";
7170 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
7171 if ( p18.length != 1 ) {
7174 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
7177 final String p19_S = "(((A,B),C),D)";
7178 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
7179 if ( p19.length != 1 ) {
7182 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
7185 final String p20_S = "(A,(B,(C,D)))";
7186 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
7187 if ( p20.length != 1 ) {
7190 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
7193 final String p21_S = "(A,(B,(C,(D,E))))";
7194 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
7195 if ( p21.length != 1 ) {
7198 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
7201 final String p22_S = "((((A,B),C),D),E)";
7202 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
7203 if ( p22.length != 1 ) {
7206 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
7209 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7210 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
7211 if ( p23.length != 1 ) {
7212 System.out.println( "xl=" + p23.length );
7216 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
7219 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7220 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
7221 if ( p24.length != 1 ) {
7224 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
7227 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7228 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7229 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
7230 if ( p241.length != 2 ) {
7233 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
7236 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
7239 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
7240 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
7241 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
7242 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
7243 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
7244 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
7245 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
7246 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
7247 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
7248 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
7251 final String p26_S = "(A,B)ab";
7252 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
7253 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
7256 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7257 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
7258 if ( p27s.length != 1 ) {
7259 System.out.println( "xxl=" + p27s.length );
7263 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7264 System.out.println( p27s[ 0 ].toNewHampshireX() );
7268 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
7270 if ( p27.length != 1 ) {
7271 System.out.println( "yl=" + p27.length );
7275 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7276 System.out.println( p27[ 0 ].toNewHampshireX() );
7280 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7281 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7282 final String p28_S3 = "(A,B)ab";
7283 final String p28_S4 = "((((A,B),C),D),;E;)";
7284 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
7286 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
7289 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
7292 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
7295 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
7298 if ( p28.length != 4 ) {
7301 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";
7302 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
7303 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
7306 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";
7307 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
7308 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
7311 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
7312 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
7313 if ( ( p32.length != 0 ) ) {
7316 final String p33_S = "A";
7317 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
7318 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
7321 final String p34_S = "B;";
7322 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
7323 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
7326 final String p35_S = "B:0.2";
7327 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
7328 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
7331 final String p36_S = "(A)";
7332 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
7333 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
7336 final String p37_S = "((A))";
7337 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
7338 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
7341 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7342 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
7343 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
7346 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7347 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
7348 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
7351 final String p40_S = "(A,B,C)";
7352 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
7353 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
7356 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
7357 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
7358 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
7361 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
7362 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
7363 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
7366 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)";
7367 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
7368 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
7371 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)))";
7372 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
7373 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
7376 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
7377 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
7378 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
7381 final String p46_S = "";
7382 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
7383 if ( p46.length != 0 ) {
7386 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
7387 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7390 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7391 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7394 final Phylogeny p49 = factory
7395 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
7396 new NHXParser() )[ 0 ];
7397 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7400 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7401 if ( p50.getNode( "A" ) == null ) {
7404 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7405 .equals( "((A,B)ab:2.0[88],C);" ) ) {
7408 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
7411 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
7412 .equals( "((A,B)88:2.0,C);" ) ) {
7415 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7416 if ( p51.getNode( "A(A" ) == null ) {
7419 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7420 if ( p52.getNode( "A(A" ) == null ) {
7423 final Phylogeny p53 = factory
7424 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
7425 new NHXParser() )[ 0 ];
7426 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
7430 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
7431 if ( p54.getNode( "A" ) == null ) {
7434 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7435 .equals( "((A,B)[88],C);" ) ) {
7439 catch ( final Exception e ) {
7440 e.printStackTrace( System.out );
7446 private static boolean testNHParsingIter() {
7448 final String p0_str = "(A,B);";
7449 final NHXParser p = new NHXParser();
7450 p.setSource( p0_str );
7451 if ( !p.hasNext() ) {
7454 final Phylogeny p0 = p.next();
7455 if ( !p0.toNewHampshire().equals( p0_str ) ) {
7456 System.out.println( p0.toNewHampshire() );
7459 if ( p.hasNext() ) {
7462 if ( p.next() != null ) {
7466 final String p00_str = "(A,B)root;";
7467 p.setSource( p00_str );
7468 final Phylogeny p00 = p.next();
7469 if ( !p00.toNewHampshire().equals( p00_str ) ) {
7470 System.out.println( p00.toNewHampshire() );
7474 final String p000_str = "A;";
7475 p.setSource( p000_str );
7476 final Phylogeny p000 = p.next();
7477 if ( !p000.toNewHampshire().equals( p000_str ) ) {
7478 System.out.println( p000.toNewHampshire() );
7482 final String p0000_str = "A";
7483 p.setSource( p0000_str );
7484 final Phylogeny p0000 = p.next();
7485 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
7486 System.out.println( p0000.toNewHampshire() );
7490 p.setSource( "(A)" );
7491 final Phylogeny p00000 = p.next();
7492 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
7493 System.out.println( p00000.toNewHampshire() );
7497 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
7498 p.setSource( p1_str );
7499 if ( !p.hasNext() ) {
7502 final Phylogeny p1_0 = p.next();
7503 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
7504 System.out.println( p1_0.toNewHampshire() );
7507 if ( !p.hasNext() ) {
7510 final Phylogeny p1_1 = p.next();
7511 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
7512 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
7515 if ( !p.hasNext() ) {
7518 final Phylogeny p1_2 = p.next();
7519 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
7520 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
7523 if ( !p.hasNext() ) {
7526 final Phylogeny p1_3 = p.next();
7527 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
7528 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
7531 if ( p.hasNext() ) {
7534 if ( p.next() != null ) {
7538 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
7539 p.setSource( p2_str );
7540 if ( !p.hasNext() ) {
7543 Phylogeny p2_0 = p.next();
7544 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7545 System.out.println( p2_0.toNewHampshire() );
7548 if ( !p.hasNext() ) {
7551 Phylogeny p2_1 = p.next();
7552 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7553 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7556 if ( !p.hasNext() ) {
7559 Phylogeny p2_2 = p.next();
7560 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
7561 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
7564 if ( !p.hasNext() ) {
7567 Phylogeny p2_3 = p.next();
7568 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
7569 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
7572 if ( !p.hasNext() ) {
7575 Phylogeny p2_4 = p.next();
7576 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
7577 System.out.println( "(X) != " + p2_4.toNewHampshire() );
7580 if ( p.hasNext() ) {
7583 if ( p.next() != null ) {
7588 if ( !p.hasNext() ) {
7592 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7593 System.out.println( p2_0.toNewHampshire() );
7596 if ( !p.hasNext() ) {
7600 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7601 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7604 if ( !p.hasNext() ) {
7608 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
7609 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
7612 if ( !p.hasNext() ) {
7616 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
7617 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
7620 if ( !p.hasNext() ) {
7624 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
7625 System.out.println( "(X) != " + p2_4.toNewHampshire() );
7628 if ( p.hasNext() ) {
7631 if ( p.next() != null ) {
7635 final String p3_str = "((A,B),C)abc";
7636 p.setSource( p3_str );
7637 if ( !p.hasNext() ) {
7640 final Phylogeny p3_0 = p.next();
7641 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
7644 if ( p.hasNext() ) {
7647 if ( p.next() != null ) {
7651 final String p4_str = "((A,B)ab,C)abc";
7652 p.setSource( p4_str );
7653 if ( !p.hasNext() ) {
7656 final Phylogeny p4_0 = p.next();
7657 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
7660 if ( p.hasNext() ) {
7663 if ( p.next() != null ) {
7667 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
7668 p.setSource( p5_str );
7669 if ( !p.hasNext() ) {
7672 final Phylogeny p5_0 = p.next();
7673 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
7676 if ( p.hasNext() ) {
7679 if ( p.next() != null ) {
7683 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7684 p.setSource( p6_str );
7685 if ( !p.hasNext() ) {
7688 Phylogeny p6_0 = p.next();
7689 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
7692 if ( p.hasNext() ) {
7695 if ( p.next() != null ) {
7699 if ( !p.hasNext() ) {
7703 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
7706 if ( p.hasNext() ) {
7709 if ( p.next() != null ) {
7713 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7714 p.setSource( p7_str );
7715 if ( !p.hasNext() ) {
7718 Phylogeny p7_0 = p.next();
7719 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7722 if ( p.hasNext() ) {
7725 if ( p.next() != null ) {
7729 if ( !p.hasNext() ) {
7733 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7736 if ( p.hasNext() ) {
7739 if ( p.next() != null ) {
7743 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
7744 p.setSource( p8_str );
7745 if ( !p.hasNext() ) {
7748 Phylogeny p8_0 = p.next();
7749 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7752 if ( !p.hasNext() ) {
7755 if ( !p.hasNext() ) {
7758 Phylogeny p8_1 = p.next();
7759 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
7762 if ( p.hasNext() ) {
7765 if ( p.next() != null ) {
7769 if ( !p.hasNext() ) {
7773 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7776 if ( !p.hasNext() ) {
7780 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
7783 if ( p.hasNext() ) {
7786 if ( p.next() != null ) {
7792 if ( p.hasNext() ) {
7796 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
7797 if ( !p.hasNext() ) {
7800 Phylogeny p_27 = p.next();
7801 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
7802 System.out.println( p_27.toNewHampshireX() );
7806 if ( p.hasNext() ) {
7809 if ( p.next() != null ) {
7813 if ( !p.hasNext() ) {
7817 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
7818 System.out.println( p_27.toNewHampshireX() );
7822 if ( p.hasNext() ) {
7825 if ( p.next() != null ) {
7829 catch ( final Exception e ) {
7830 e.printStackTrace( System.out );
7836 private static boolean testNHXconversion() {
7838 final PhylogenyNode n1 = new PhylogenyNode();
7839 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
7840 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
7841 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
7842 final PhylogenyNode n5 = PhylogenyNode
7843 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
7844 final PhylogenyNode n6 = PhylogenyNode
7845 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
7846 if ( !n1.toNewHampshireX().equals( "" ) ) {
7849 if ( !n2.toNewHampshireX().equals( "" ) ) {
7852 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
7855 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
7858 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
7861 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
7862 System.out.println( n6.toNewHampshireX() );
7866 catch ( final Exception e ) {
7867 e.printStackTrace( System.out );
7873 private static boolean testNHXNodeParsing() {
7875 final PhylogenyNode n1 = new PhylogenyNode();
7876 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
7877 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
7878 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
7879 final PhylogenyNode n5 = PhylogenyNode
7880 .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]" );
7881 if ( !n3.getName().equals( "n3" ) ) {
7884 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
7887 if ( n3.isDuplication() ) {
7890 if ( n3.isHasAssignedEvent() ) {
7893 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
7896 if ( !n4.getName().equals( "n4" ) ) {
7899 if ( n4.getDistanceToParent() != 0.01 ) {
7902 if ( !n5.getName().equals( "n5" ) ) {
7905 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
7908 if ( n5.getDistanceToParent() != 0.1 ) {
7911 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
7914 if ( !n5.isDuplication() ) {
7917 if ( !n5.isHasAssignedEvent() ) {
7920 final PhylogenyNode n8 = PhylogenyNode
7921 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
7922 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7923 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
7926 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
7929 final PhylogenyNode n9 = PhylogenyNode
7930 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
7931 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7932 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
7935 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
7938 final PhylogenyNode n10 = PhylogenyNode
7939 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7940 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
7943 final PhylogenyNode n20 = PhylogenyNode
7944 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7945 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
7948 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
7951 final PhylogenyNode n20x = PhylogenyNode
7952 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
7953 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
7956 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
7959 final PhylogenyNode n20xx = PhylogenyNode
7960 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7961 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
7964 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
7967 final PhylogenyNode n20xxx = PhylogenyNode
7968 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7969 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
7972 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
7975 final PhylogenyNode n20xxxx = PhylogenyNode
7976 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7977 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
7980 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
7983 final PhylogenyNode n21 = PhylogenyNode
7984 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
7985 if ( !n21.getName().equals( "N21_PIG" ) ) {
7988 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
7991 final PhylogenyNode n21x = PhylogenyNode
7992 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7993 if ( !n21x.getName().equals( "n21_PIG" ) ) {
7996 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
7999 final PhylogenyNode n22 = PhylogenyNode
8000 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8001 if ( !n22.getName().equals( "n22/PIG" ) ) {
8004 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
8007 final PhylogenyNode n23 = PhylogenyNode
8008 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8009 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
8012 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
8015 final PhylogenyNode a = PhylogenyNode
8016 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8017 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8020 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
8023 final PhylogenyNode c1 = PhylogenyNode
8024 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
8025 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8026 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
8029 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
8032 final PhylogenyNode c2 = PhylogenyNode
8033 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
8034 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8035 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
8038 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
8041 final PhylogenyNode e3 = PhylogenyNode
8042 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8043 if ( !e3.getName().equals( "n10_RAT~" ) ) {
8046 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
8049 final PhylogenyNode n11 = PhylogenyNode
8050 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
8051 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8052 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
8055 if ( n11.getDistanceToParent() != 0.4 ) {
8058 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
8061 final PhylogenyNode n12 = PhylogenyNode
8062 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
8063 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8064 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
8067 if ( n12.getDistanceToParent() != 0.4 ) {
8070 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
8073 final PhylogenyNode o = PhylogenyNode
8074 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8075 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
8078 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
8081 if ( n1.getName().compareTo( "" ) != 0 ) {
8084 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8087 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8090 if ( n2.getName().compareTo( "" ) != 0 ) {
8093 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8096 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8099 final PhylogenyNode n00 = PhylogenyNode
8100 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
8101 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
8104 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
8107 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
8108 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
8111 final PhylogenyNode n13 = PhylogenyNode
8112 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8113 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
8116 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
8119 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8122 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8125 final PhylogenyNode n14 = PhylogenyNode
8126 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8127 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
8130 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
8133 final PhylogenyNode n15 = PhylogenyNode
8134 .createInstanceFromNhxString( "something_wicked[123]",
8135 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8136 if ( !n15.getName().equals( "something_wicked" ) ) {
8139 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
8142 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
8145 final PhylogenyNode n16 = PhylogenyNode
8146 .createInstanceFromNhxString( "something_wicked2[9]",
8147 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8148 if ( !n16.getName().equals( "something_wicked2" ) ) {
8151 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
8154 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
8157 final PhylogenyNode n17 = PhylogenyNode
8158 .createInstanceFromNhxString( "something_wicked3[a]",
8159 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8160 if ( !n17.getName().equals( "something_wicked3" ) ) {
8163 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
8166 final PhylogenyNode n18 = PhylogenyNode
8167 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8168 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
8171 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
8174 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
8177 final PhylogenyNode n19 = PhylogenyNode
8178 .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8179 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
8182 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8185 final PhylogenyNode n30 = PhylogenyNode
8186 .createInstanceFromNhxString( "blah_1234567-roejojoej",
8187 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8188 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
8191 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8194 final PhylogenyNode n31 = PhylogenyNode
8195 .createInstanceFromNhxString( "blah_12345678-roejojoej",
8196 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8197 if ( n31.getNodeData().isHasTaxonomy() ) {
8200 final PhylogenyNode n32 = PhylogenyNode
8201 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8202 if ( n32.getNodeData().isHasTaxonomy() ) {
8205 final PhylogenyNode n40 = PhylogenyNode
8206 .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8207 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8210 final PhylogenyNode n41 = PhylogenyNode
8211 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8212 if ( n41.getNodeData().isHasTaxonomy() ) {
8215 final PhylogenyNode n42 = PhylogenyNode
8216 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8217 if ( n42.getNodeData().isHasTaxonomy() ) {
8220 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
8221 NHXParser.TAXONOMY_EXTRACTION.NO );
8222 if ( n43.getNodeData().isHasTaxonomy() ) {
8225 final PhylogenyNode n44 = PhylogenyNode
8226 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8227 if ( n44.getNodeData().isHasTaxonomy() ) {
8231 catch ( final Exception e ) {
8232 e.printStackTrace( System.out );
8238 private static boolean testNHXParsing() {
8240 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8241 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
8242 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
8245 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]";
8246 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
8247 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8250 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]";
8251 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
8252 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
8255 final Phylogeny[] p3 = factory
8256 .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]",
8258 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8261 final Phylogeny[] p4 = factory
8262 .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(]",
8264 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8267 final Phylogeny[] p5 = factory
8268 .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(((]",
8270 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8273 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)";
8274 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)";
8275 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
8276 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
8279 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)))";
8280 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)))";
8281 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
8282 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
8285 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]) ))[,,, ])))))))";
8286 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
8287 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
8288 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
8291 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
8292 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8295 final Phylogeny p10 = factory
8296 .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]",
8297 new NHXParser() )[ 0 ];
8298 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8302 catch ( final Exception e ) {
8303 e.printStackTrace( System.out );
8309 private static boolean testNHXParsingMB() {
8311 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8312 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
8313 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8314 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8315 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8316 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8317 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8318 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8319 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8320 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
8321 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
8324 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
8327 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
8328 0.1100000000000000e+00 ) ) {
8331 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
8334 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
8337 final Phylogeny p2 = factory
8338 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
8339 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8340 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8341 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8342 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8343 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8344 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8345 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8346 + "7.369400000000000e-02}])",
8347 new NHXParser() )[ 0 ];
8348 if ( p2.getNode( "1" ) == null ) {
8351 if ( p2.getNode( "2" ) == null ) {
8355 catch ( final Exception e ) {
8356 e.printStackTrace( System.out );
8363 private static boolean testNHXParsingQuotes() {
8365 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8366 final NHXParser p = new NHXParser();
8367 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
8368 if ( phylogenies_0.length != 5 ) {
8371 final Phylogeny phy = phylogenies_0[ 4 ];
8372 if ( phy.getNumberOfExternalNodes() != 7 ) {
8375 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
8378 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
8381 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
8382 .getScientificName().equals( "hsapiens" ) ) {
8385 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
8388 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
8391 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
8394 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
8397 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
8400 final NHXParser p1p = new NHXParser();
8401 p1p.setIgnoreQuotes( true );
8402 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
8403 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
8406 final NHXParser p2p = new NHXParser();
8407 p1p.setIgnoreQuotes( false );
8408 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
8409 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
8412 final NHXParser p3p = new NHXParser();
8413 p3p.setIgnoreQuotes( false );
8414 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
8415 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
8418 final NHXParser p4p = new NHXParser();
8419 p4p.setIgnoreQuotes( false );
8420 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
8421 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
8424 final Phylogeny p10 = factory
8425 .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]",
8426 new NHXParser() )[ 0 ];
8427 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]";
8428 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
8431 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
8432 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
8436 final Phylogeny p12 = factory
8437 .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]",
8438 new NHXParser() )[ 0 ];
8439 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]";
8440 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
8443 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
8444 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
8447 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;";
8448 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
8451 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
8452 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
8456 catch ( final Exception e ) {
8457 e.printStackTrace( System.out );
8463 private static boolean testNodeRemoval() {
8465 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8466 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
8467 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
8468 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
8471 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
8472 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
8473 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
8476 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
8477 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
8478 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
8482 catch ( final Exception e ) {
8483 e.printStackTrace( System.out );
8489 private static boolean testPhylogenyBranch() {
8491 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
8492 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
8493 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
8494 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
8495 if ( !a1b1.equals( a1b1 ) ) {
8498 if ( !a1b1.equals( b1a1 ) ) {
8501 if ( !b1a1.equals( a1b1 ) ) {
8504 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
8505 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
8506 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
8507 if ( a1_b1.equals( b1_a1 ) ) {
8510 if ( a1_b1.equals( a1_b1_ ) ) {
8513 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
8514 if ( !a1_b1.equals( b1_a1_ ) ) {
8517 if ( a1_b1_.equals( b1_a1_ ) ) {
8520 if ( !a1_b1_.equals( b1_a1 ) ) {
8524 catch ( final Exception e ) {
8525 e.printStackTrace( System.out );
8531 private static boolean testPhyloXMLparsingOfDistributionElement() {
8533 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8534 PhyloXmlParser xml_parser = null;
8536 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
8538 catch ( final Exception e ) {
8539 // Do nothing -- means were not running from jar.
8541 if ( xml_parser == null ) {
8542 xml_parser = new PhyloXmlParser();
8543 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
8544 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
8547 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
8550 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
8552 if ( xml_parser.getErrorCount() > 0 ) {
8553 System.out.println( xml_parser.getErrorMessages().toString() );
8556 if ( phylogenies_0.length != 1 ) {
8559 final Phylogeny t1 = phylogenies_0[ 0 ];
8560 PhylogenyNode n = null;
8561 Distribution d = null;
8562 n = t1.getNode( "root node" );
8563 if ( !n.getNodeData().isHasDistribution() ) {
8566 if ( n.getNodeData().getDistributions().size() != 1 ) {
8569 d = n.getNodeData().getDistribution();
8570 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
8573 if ( d.getPoints().size() != 1 ) {
8576 if ( d.getPolygons() != null ) {
8579 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
8582 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8585 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8588 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
8591 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
8594 n = t1.getNode( "node a" );
8595 if ( !n.getNodeData().isHasDistribution() ) {
8598 if ( n.getNodeData().getDistributions().size() != 2 ) {
8601 d = n.getNodeData().getDistribution( 1 );
8602 if ( !d.getDesc().equals( "San Diego" ) ) {
8605 if ( d.getPoints().size() != 1 ) {
8608 if ( d.getPolygons() != null ) {
8611 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
8614 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8617 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8620 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
8623 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
8626 n = t1.getNode( "node bb" );
8627 if ( !n.getNodeData().isHasDistribution() ) {
8630 if ( n.getNodeData().getDistributions().size() != 1 ) {
8633 d = n.getNodeData().getDistribution( 0 );
8634 if ( d.getPoints().size() != 3 ) {
8637 if ( d.getPolygons().size() != 2 ) {
8640 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
8643 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
8646 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
8649 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
8652 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
8655 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
8658 Polygon p = d.getPolygons().get( 0 );
8659 if ( p.getPoints().size() != 3 ) {
8662 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
8665 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
8668 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8671 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
8674 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
8677 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
8680 p = d.getPolygons().get( 1 );
8681 if ( p.getPoints().size() != 3 ) {
8684 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
8687 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
8690 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8694 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
8695 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
8696 if ( rt.length != 1 ) {
8699 final Phylogeny t1_rt = rt[ 0 ];
8700 n = t1_rt.getNode( "root node" );
8701 if ( !n.getNodeData().isHasDistribution() ) {
8704 if ( n.getNodeData().getDistributions().size() != 1 ) {
8707 d = n.getNodeData().getDistribution();
8708 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
8711 if ( d.getPoints().size() != 1 ) {
8714 if ( d.getPolygons() != null ) {
8717 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
8720 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8723 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8726 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
8729 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
8732 n = t1_rt.getNode( "node a" );
8733 if ( !n.getNodeData().isHasDistribution() ) {
8736 if ( n.getNodeData().getDistributions().size() != 2 ) {
8739 d = n.getNodeData().getDistribution( 1 );
8740 if ( !d.getDesc().equals( "San Diego" ) ) {
8743 if ( d.getPoints().size() != 1 ) {
8746 if ( d.getPolygons() != null ) {
8749 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
8752 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8755 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8758 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
8761 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
8764 n = t1_rt.getNode( "node bb" );
8765 if ( !n.getNodeData().isHasDistribution() ) {
8768 if ( n.getNodeData().getDistributions().size() != 1 ) {
8771 d = n.getNodeData().getDistribution( 0 );
8772 if ( d.getPoints().size() != 3 ) {
8775 if ( d.getPolygons().size() != 2 ) {
8778 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
8781 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
8784 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
8787 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
8790 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
8793 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
8796 p = d.getPolygons().get( 0 );
8797 if ( p.getPoints().size() != 3 ) {
8800 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
8803 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
8806 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8809 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
8812 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
8815 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
8818 p = d.getPolygons().get( 1 );
8819 if ( p.getPoints().size() != 3 ) {
8822 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
8825 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
8828 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8832 catch ( final Exception e ) {
8833 e.printStackTrace( System.out );
8839 private static boolean testPostOrderIterator() {
8841 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8842 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
8843 PhylogenyNodeIterator it0;
8844 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
8847 for( it0.reset(); it0.hasNext(); ) {
8850 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
8851 final PhylogenyNodeIterator it = t1.iteratorPostorder();
8852 if ( !it.next().getName().equals( "A" ) ) {
8855 if ( !it.next().getName().equals( "B" ) ) {
8858 if ( !it.next().getName().equals( "ab" ) ) {
8861 if ( !it.next().getName().equals( "C" ) ) {
8864 if ( !it.next().getName().equals( "D" ) ) {
8867 if ( !it.next().getName().equals( "cd" ) ) {
8870 if ( !it.next().getName().equals( "abcd" ) ) {
8873 if ( !it.next().getName().equals( "E" ) ) {
8876 if ( !it.next().getName().equals( "F" ) ) {
8879 if ( !it.next().getName().equals( "ef" ) ) {
8882 if ( !it.next().getName().equals( "G" ) ) {
8885 if ( !it.next().getName().equals( "H" ) ) {
8888 if ( !it.next().getName().equals( "gh" ) ) {
8891 if ( !it.next().getName().equals( "efgh" ) ) {
8894 if ( !it.next().getName().equals( "r" ) ) {
8897 if ( it.hasNext() ) {
8901 catch ( final Exception e ) {
8902 e.printStackTrace( System.out );
8908 private static boolean testPreOrderIterator() {
8910 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8911 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
8912 PhylogenyNodeIterator it0;
8913 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
8916 for( it0.reset(); it0.hasNext(); ) {
8919 PhylogenyNodeIterator it = t0.iteratorPreorder();
8920 if ( !it.next().getName().equals( "r" ) ) {
8923 if ( !it.next().getName().equals( "ab" ) ) {
8926 if ( !it.next().getName().equals( "A" ) ) {
8929 if ( !it.next().getName().equals( "B" ) ) {
8932 if ( !it.next().getName().equals( "cd" ) ) {
8935 if ( !it.next().getName().equals( "C" ) ) {
8938 if ( !it.next().getName().equals( "D" ) ) {
8941 if ( it.hasNext() ) {
8944 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
8945 it = t1.iteratorPreorder();
8946 if ( !it.next().getName().equals( "r" ) ) {
8949 if ( !it.next().getName().equals( "abcd" ) ) {
8952 if ( !it.next().getName().equals( "ab" ) ) {
8955 if ( !it.next().getName().equals( "A" ) ) {
8958 if ( !it.next().getName().equals( "B" ) ) {
8961 if ( !it.next().getName().equals( "cd" ) ) {
8964 if ( !it.next().getName().equals( "C" ) ) {
8967 if ( !it.next().getName().equals( "D" ) ) {
8970 if ( !it.next().getName().equals( "efgh" ) ) {
8973 if ( !it.next().getName().equals( "ef" ) ) {
8976 if ( !it.next().getName().equals( "E" ) ) {
8979 if ( !it.next().getName().equals( "F" ) ) {
8982 if ( !it.next().getName().equals( "gh" ) ) {
8985 if ( !it.next().getName().equals( "G" ) ) {
8988 if ( !it.next().getName().equals( "H" ) ) {
8991 if ( it.hasNext() ) {
8995 catch ( final Exception e ) {
8996 e.printStackTrace( System.out );
9002 private static boolean testPropertiesMap() {
9004 final PropertiesMap pm = new PropertiesMap();
9005 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9006 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9007 final Property p2 = new Property( "something:else",
9009 "improbable:research",
9012 pm.addProperty( p0 );
9013 pm.addProperty( p1 );
9014 pm.addProperty( p2 );
9015 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
9018 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
9021 if ( pm.getProperties().size() != 3 ) {
9024 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
9027 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9030 if ( pm.getProperties().size() != 3 ) {
9033 pm.removeProperty( "dimensions:diameter" );
9034 if ( pm.getProperties().size() != 2 ) {
9037 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
9040 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9044 catch ( final Exception e ) {
9045 e.printStackTrace( System.out );
9051 private static boolean testProteinId() {
9053 final ProteinId id1 = new ProteinId( "a" );
9054 final ProteinId id2 = new ProteinId( "a" );
9055 final ProteinId id3 = new ProteinId( "A" );
9056 final ProteinId id4 = new ProteinId( "b" );
9057 if ( !id1.equals( id1 ) ) {
9060 if ( id1.getId().equals( "x" ) ) {
9063 if ( id1.getId().equals( null ) ) {
9066 if ( !id1.equals( id2 ) ) {
9069 if ( id1.equals( id3 ) ) {
9072 if ( id1.hashCode() != id1.hashCode() ) {
9075 if ( id1.hashCode() != id2.hashCode() ) {
9078 if ( id1.hashCode() == id3.hashCode() ) {
9081 if ( id1.compareTo( id1 ) != 0 ) {
9084 if ( id1.compareTo( id2 ) != 0 ) {
9087 if ( id1.compareTo( id3 ) != 0 ) {
9090 if ( id1.compareTo( id4 ) >= 0 ) {
9093 if ( id4.compareTo( id1 ) <= 0 ) {
9096 if ( !id4.getId().equals( "b" ) ) {
9099 final ProteinId id5 = new ProteinId( " C " );
9100 if ( !id5.getId().equals( "C" ) ) {
9103 if ( id5.equals( id1 ) ) {
9107 catch ( final Exception e ) {
9108 e.printStackTrace( System.out );
9114 private static boolean testReIdMethods() {
9116 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9117 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
9118 final long count = PhylogenyNode.getNodeCount();
9120 if ( p.getNode( "r" ).getId() != count ) {
9123 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
9126 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
9129 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
9132 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
9135 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
9138 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
9141 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
9144 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
9147 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
9150 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
9153 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
9156 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
9159 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
9162 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
9166 catch ( final Exception e ) {
9167 e.printStackTrace( System.out );
9173 private static boolean testRerooting() {
9175 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9176 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",
9177 new NHXParser() )[ 0 ];
9178 if ( !t1.isRooted() ) {
9181 t1.reRoot( t1.getNode( "D" ) );
9182 t1.reRoot( t1.getNode( "CD" ) );
9183 t1.reRoot( t1.getNode( "A" ) );
9184 t1.reRoot( t1.getNode( "B" ) );
9185 t1.reRoot( t1.getNode( "AB" ) );
9186 t1.reRoot( t1.getNode( "D" ) );
9187 t1.reRoot( t1.getNode( "C" ) );
9188 t1.reRoot( t1.getNode( "CD" ) );
9189 t1.reRoot( t1.getNode( "A" ) );
9190 t1.reRoot( t1.getNode( "B" ) );
9191 t1.reRoot( t1.getNode( "AB" ) );
9192 t1.reRoot( t1.getNode( "D" ) );
9193 t1.reRoot( t1.getNode( "D" ) );
9194 t1.reRoot( t1.getNode( "C" ) );
9195 t1.reRoot( t1.getNode( "A" ) );
9196 t1.reRoot( t1.getNode( "B" ) );
9197 t1.reRoot( t1.getNode( "AB" ) );
9198 t1.reRoot( t1.getNode( "C" ) );
9199 t1.reRoot( t1.getNode( "D" ) );
9200 t1.reRoot( t1.getNode( "CD" ) );
9201 t1.reRoot( t1.getNode( "D" ) );
9202 t1.reRoot( t1.getNode( "A" ) );
9203 t1.reRoot( t1.getNode( "B" ) );
9204 t1.reRoot( t1.getNode( "AB" ) );
9205 t1.reRoot( t1.getNode( "C" ) );
9206 t1.reRoot( t1.getNode( "D" ) );
9207 t1.reRoot( t1.getNode( "CD" ) );
9208 t1.reRoot( t1.getNode( "D" ) );
9209 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
9212 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
9215 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
9218 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
9221 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
9224 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
9227 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",
9228 new NHXParser() )[ 0 ];
9229 t2.reRoot( t2.getNode( "A" ) );
9230 t2.reRoot( t2.getNode( "D" ) );
9231 t2.reRoot( t2.getNode( "ABC" ) );
9232 t2.reRoot( t2.getNode( "A" ) );
9233 t2.reRoot( t2.getNode( "B" ) );
9234 t2.reRoot( t2.getNode( "D" ) );
9235 t2.reRoot( t2.getNode( "C" ) );
9236 t2.reRoot( t2.getNode( "ABC" ) );
9237 t2.reRoot( t2.getNode( "A" ) );
9238 t2.reRoot( t2.getNode( "B" ) );
9239 t2.reRoot( t2.getNode( "AB" ) );
9240 t2.reRoot( t2.getNode( "AB" ) );
9241 t2.reRoot( t2.getNode( "D" ) );
9242 t2.reRoot( t2.getNode( "C" ) );
9243 t2.reRoot( t2.getNode( "B" ) );
9244 t2.reRoot( t2.getNode( "AB" ) );
9245 t2.reRoot( t2.getNode( "D" ) );
9246 t2.reRoot( t2.getNode( "D" ) );
9247 t2.reRoot( t2.getNode( "ABC" ) );
9248 t2.reRoot( t2.getNode( "A" ) );
9249 t2.reRoot( t2.getNode( "B" ) );
9250 t2.reRoot( t2.getNode( "AB" ) );
9251 t2.reRoot( t2.getNode( "D" ) );
9252 t2.reRoot( t2.getNode( "C" ) );
9253 t2.reRoot( t2.getNode( "ABC" ) );
9254 t2.reRoot( t2.getNode( "A" ) );
9255 t2.reRoot( t2.getNode( "B" ) );
9256 t2.reRoot( t2.getNode( "AB" ) );
9257 t2.reRoot( t2.getNode( "D" ) );
9258 t2.reRoot( t2.getNode( "D" ) );
9259 t2.reRoot( t2.getNode( "C" ) );
9260 t2.reRoot( t2.getNode( "A" ) );
9261 t2.reRoot( t2.getNode( "B" ) );
9262 t2.reRoot( t2.getNode( "AB" ) );
9263 t2.reRoot( t2.getNode( "C" ) );
9264 t2.reRoot( t2.getNode( "D" ) );
9265 t2.reRoot( t2.getNode( "ABC" ) );
9266 t2.reRoot( t2.getNode( "D" ) );
9267 t2.reRoot( t2.getNode( "A" ) );
9268 t2.reRoot( t2.getNode( "B" ) );
9269 t2.reRoot( t2.getNode( "AB" ) );
9270 t2.reRoot( t2.getNode( "C" ) );
9271 t2.reRoot( t2.getNode( "D" ) );
9272 t2.reRoot( t2.getNode( "ABC" ) );
9273 t2.reRoot( t2.getNode( "D" ) );
9274 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9277 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9280 t2.reRoot( t2.getNode( "ABC" ) );
9281 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9284 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9287 t2.reRoot( t2.getNode( "AB" ) );
9288 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9291 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9294 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9297 t2.reRoot( t2.getNode( "AB" ) );
9298 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9301 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9304 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9307 t2.reRoot( t2.getNode( "D" ) );
9308 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9311 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9314 t2.reRoot( t2.getNode( "ABC" ) );
9315 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9318 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9321 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
9322 new NHXParser() )[ 0 ];
9323 t3.reRoot( t3.getNode( "B" ) );
9324 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9327 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9330 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9333 t3.reRoot( t3.getNode( "B" ) );
9334 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9337 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9340 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9343 t3.reRoot( t3.getRoot() );
9344 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9347 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9350 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9354 catch ( final Exception e ) {
9355 e.printStackTrace( System.out );
9361 private static boolean testSDIse() {
9363 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9364 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
9365 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
9366 gene1.setRooted( true );
9367 species1.setRooted( true );
9368 final SDI sdi = new SDI( gene1, species1 );
9369 if ( !gene1.getRoot().isDuplication() ) {
9372 final Phylogeny species2 = factory
9373 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9374 new NHXParser() )[ 0 ];
9375 final Phylogeny gene2 = factory
9376 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9377 new NHXParser() )[ 0 ];
9378 species2.setRooted( true );
9379 gene2.setRooted( true );
9380 final SDI sdi2 = new SDI( gene2, species2 );
9381 if ( sdi2.getDuplicationsSum() != 0 ) {
9384 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
9387 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
9390 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
9393 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
9396 if ( !gene2.getNode( "r" ).isSpeciation() ) {
9399 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
9402 final Phylogeny species3 = factory
9403 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9404 new NHXParser() )[ 0 ];
9405 final Phylogeny gene3 = factory
9406 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9407 new NHXParser() )[ 0 ];
9408 species3.setRooted( true );
9409 gene3.setRooted( true );
9410 final SDI sdi3 = new SDI( gene3, species3 );
9411 if ( sdi3.getDuplicationsSum() != 1 ) {
9414 if ( !gene3.getNode( "aa" ).isDuplication() ) {
9417 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
9420 final Phylogeny species4 = factory
9421 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9422 new NHXParser() )[ 0 ];
9423 final Phylogeny gene4 = factory
9424 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9425 new NHXParser() )[ 0 ];
9426 species4.setRooted( true );
9427 gene4.setRooted( true );
9428 final SDI sdi4 = new SDI( gene4, species4 );
9429 if ( sdi4.getDuplicationsSum() != 1 ) {
9432 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
9435 if ( !gene4.getNode( "abc" ).isDuplication() ) {
9438 if ( gene4.getNode( "abcd" ).isDuplication() ) {
9441 if ( species4.getNumberOfExternalNodes() != 6 ) {
9444 if ( gene4.getNumberOfExternalNodes() != 6 ) {
9447 final Phylogeny species5 = factory
9448 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9449 new NHXParser() )[ 0 ];
9450 final Phylogeny gene5 = factory
9451 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9452 new NHXParser() )[ 0 ];
9453 species5.setRooted( true );
9454 gene5.setRooted( true );
9455 final SDI sdi5 = new SDI( gene5, species5 );
9456 if ( sdi5.getDuplicationsSum() != 2 ) {
9459 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
9462 if ( !gene5.getNode( "adc" ).isDuplication() ) {
9465 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
9468 if ( species5.getNumberOfExternalNodes() != 6 ) {
9471 if ( gene5.getNumberOfExternalNodes() != 6 ) {
9474 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
9475 // Conjecture for Comparing Molecular Phylogenies"
9476 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
9477 final Phylogeny species6 = factory
9478 .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,"
9479 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9480 new NHXParser() )[ 0 ];
9481 final Phylogeny gene6 = factory
9482 .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,"
9483 + "((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,"
9484 + "(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;",
9485 new NHXParser() )[ 0 ];
9486 species6.setRooted( true );
9487 gene6.setRooted( true );
9488 final SDI sdi6 = new SDI( gene6, species6 );
9489 if ( sdi6.getDuplicationsSum() != 3 ) {
9492 if ( !gene6.getNode( "r" ).isDuplication() ) {
9495 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
9498 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
9501 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
9504 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
9507 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
9510 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
9513 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
9516 sdi6.computeMappingCostL();
9517 if ( sdi6.computeMappingCostL() != 17 ) {
9520 if ( species6.getNumberOfExternalNodes() != 9 ) {
9523 if ( gene6.getNumberOfExternalNodes() != 9 ) {
9526 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
9527 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
9528 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
9529 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
9530 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
9531 species7.setRooted( true );
9532 final Phylogeny gene7_1 = Test
9533 .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])" );
9534 gene7_1.setRooted( true );
9535 final SDI sdi7 = new SDI( gene7_1, species7 );
9536 if ( sdi7.getDuplicationsSum() != 0 ) {
9539 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
9542 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
9545 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
9548 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
9551 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
9554 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
9557 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
9560 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
9563 final Phylogeny gene7_2 = Test
9564 .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])" );
9565 gene7_2.setRooted( true );
9566 final SDI sdi7_2 = new SDI( gene7_2, species7 );
9567 if ( sdi7_2.getDuplicationsSum() != 1 ) {
9570 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
9573 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
9576 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
9579 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
9582 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
9585 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
9588 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
9591 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
9594 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
9598 catch ( final Exception e ) {
9604 private static boolean testSDIunrooted() {
9606 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9607 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
9608 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
9609 final Iterator<PhylogenyBranch> iter = l.iterator();
9610 PhylogenyBranch br = iter.next();
9611 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
9614 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
9618 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
9621 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
9625 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
9628 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
9632 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9635 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9639 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9642 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9646 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
9649 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
9653 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9656 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9660 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9663 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9667 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9670 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9674 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9677 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9681 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
9684 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
9688 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
9691 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
9695 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
9698 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
9702 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
9705 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
9709 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
9712 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
9715 if ( iter.hasNext() ) {
9718 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
9719 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
9720 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
9722 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
9725 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
9729 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9732 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9736 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9739 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9742 if ( iter1.hasNext() ) {
9745 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
9746 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
9747 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
9749 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
9752 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
9756 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9759 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9763 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9766 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9769 if ( iter2.hasNext() ) {
9772 final Phylogeny species0 = factory
9773 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9774 new NHXParser() )[ 0 ];
9775 final Phylogeny gene1 = factory
9776 .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])",
9777 new NHXParser() )[ 0 ];
9778 species0.setRooted( true );
9779 gene1.setRooted( true );
9780 final SDIR sdi_unrooted = new SDIR();
9781 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
9782 if ( sdi_unrooted.getCount() != 1 ) {
9785 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
9788 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
9791 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
9794 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9797 final Phylogeny gene2 = factory
9798 .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])",
9799 new NHXParser() )[ 0 ];
9800 gene2.setRooted( true );
9801 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
9802 if ( sdi_unrooted.getCount() != 1 ) {
9805 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9808 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9811 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
9814 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9817 final Phylogeny species6 = factory
9818 .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,"
9819 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9820 new NHXParser() )[ 0 ];
9821 final Phylogeny gene6 = factory
9822 .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],"
9823 + "(((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],"
9824 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9825 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9826 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9827 new NHXParser() )[ 0 ];
9828 species6.setRooted( true );
9829 gene6.setRooted( true );
9830 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
9831 if ( sdi_unrooted.getCount() != 1 ) {
9834 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9837 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9840 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9843 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9846 if ( !p6[ 0 ].getRoot().isDuplication() ) {
9849 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
9852 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
9855 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
9858 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
9861 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
9864 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
9867 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
9871 final Phylogeny species7 = factory
9872 .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,"
9873 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9874 new NHXParser() )[ 0 ];
9875 final Phylogeny gene7 = factory
9876 .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],"
9877 + "(((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],"
9878 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9879 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9880 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9881 new NHXParser() )[ 0 ];
9882 species7.setRooted( true );
9883 gene7.setRooted( true );
9884 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
9885 if ( sdi_unrooted.getCount() != 1 ) {
9888 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9891 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9894 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9897 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
9900 if ( !p7[ 0 ].getRoot().isDuplication() ) {
9903 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
9906 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
9909 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
9912 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
9915 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
9918 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
9921 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
9925 final Phylogeny species8 = factory
9926 .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,"
9927 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9928 new NHXParser() )[ 0 ];
9929 final Phylogeny gene8 = factory
9930 .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],"
9931 + "(((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],"
9932 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9933 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9934 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9935 new NHXParser() )[ 0 ];
9936 species8.setRooted( true );
9937 gene8.setRooted( true );
9938 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
9939 if ( sdi_unrooted.getCount() != 1 ) {
9942 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9945 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9948 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9951 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9954 if ( !p8[ 0 ].getRoot().isDuplication() ) {
9957 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
9960 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
9963 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
9966 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
9969 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
9972 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
9975 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
9980 catch ( final Exception e ) {
9981 e.printStackTrace( System.out );
9987 private static boolean testSequenceIdParsing() {
9989 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
9990 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
9991 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
9993 System.out.println( "value =" + id.getValue() );
9994 System.out.println( "provider=" + id.getSource() );
9999 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
10000 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10001 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10002 if ( id != null ) {
10003 System.out.println( "value =" + id.getValue() );
10004 System.out.println( "provider=" + id.getSource() );
10009 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
10010 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10011 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10012 if ( id != null ) {
10013 System.out.println( "value =" + id.getValue() );
10014 System.out.println( "provider=" + id.getSource() );
10019 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
10020 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10021 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
10022 if ( id != null ) {
10023 System.out.println( "value =" + id.getValue() );
10024 System.out.println( "provider=" + id.getSource() );
10029 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
10030 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10031 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
10032 if ( id != null ) {
10033 System.out.println( "value =" + id.getValue() );
10034 System.out.println( "provider=" + id.getSource() );
10039 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
10040 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10041 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
10042 if ( id != null ) {
10043 System.out.println( "value =" + id.getValue() );
10044 System.out.println( "provider=" + id.getSource() );
10049 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
10050 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10051 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
10052 if ( id != null ) {
10053 System.out.println( "value =" + id.getValue() );
10054 System.out.println( "provider=" + id.getSource() );
10059 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
10060 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10061 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10062 if ( id != null ) {
10063 System.out.println( "value =" + id.getValue() );
10064 System.out.println( "provider=" + id.getSource() );
10069 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
10070 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10071 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10072 if ( id != null ) {
10073 System.out.println( "value =" + id.getValue() );
10074 System.out.println( "provider=" + id.getSource() );
10079 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
10080 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10081 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
10082 if ( id != null ) {
10083 System.out.println( "value =" + id.getValue() );
10084 System.out.println( "provider=" + id.getSource() );
10088 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
10089 if ( id != null ) {
10090 System.out.println( "value =" + id.getValue() );
10091 System.out.println( "provider=" + id.getSource() );
10095 catch ( final Exception e ) {
10096 e.printStackTrace( System.out );
10102 private static boolean testSequenceWriter() {
10104 final String n = ForesterUtil.LINE_SEPARATOR;
10105 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
10108 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
10111 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
10114 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
10117 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
10118 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
10121 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
10122 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
10126 catch ( final Exception e ) {
10127 e.printStackTrace();
10133 private static boolean testSpecies() {
10135 final Species s1 = new BasicSpecies( "a" );
10136 final Species s2 = new BasicSpecies( "a" );
10137 final Species s3 = new BasicSpecies( "A" );
10138 final Species s4 = new BasicSpecies( "b" );
10139 if ( !s1.equals( s1 ) ) {
10142 if ( s1.getSpeciesId().equals( "x" ) ) {
10145 if ( s1.getSpeciesId().equals( null ) ) {
10148 if ( !s1.equals( s2 ) ) {
10151 if ( s1.equals( s3 ) ) {
10154 if ( s1.hashCode() != s1.hashCode() ) {
10157 if ( s1.hashCode() != s2.hashCode() ) {
10160 if ( s1.hashCode() == s3.hashCode() ) {
10163 if ( s1.compareTo( s1 ) != 0 ) {
10166 if ( s1.compareTo( s2 ) != 0 ) {
10169 if ( s1.compareTo( s3 ) != 0 ) {
10172 if ( s1.compareTo( s4 ) >= 0 ) {
10175 if ( s4.compareTo( s1 ) <= 0 ) {
10178 if ( !s4.getSpeciesId().equals( "b" ) ) {
10181 final Species s5 = new BasicSpecies( " C " );
10182 if ( !s5.getSpeciesId().equals( "C" ) ) {
10185 if ( s5.equals( s1 ) ) {
10189 catch ( final Exception e ) {
10190 e.printStackTrace( System.out );
10196 private static boolean testSplit() {
10198 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10199 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
10200 //Archaeopteryx.createApplication( p0 );
10201 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
10202 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10203 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10204 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10205 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10206 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10207 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10208 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10209 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10210 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10211 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
10212 // System.out.println( s0.toString() );
10214 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
10215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10217 if ( s0.match( query_nodes ) ) {
10220 query_nodes = new HashSet<PhylogenyNode>();
10221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10224 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10225 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10228 if ( !s0.match( query_nodes ) ) {
10232 query_nodes = new HashSet<PhylogenyNode>();
10233 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10234 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10236 if ( !s0.match( query_nodes ) ) {
10240 query_nodes = new HashSet<PhylogenyNode>();
10241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10242 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10245 if ( !s0.match( query_nodes ) ) {
10249 query_nodes = new HashSet<PhylogenyNode>();
10250 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10254 if ( !s0.match( query_nodes ) ) {
10258 query_nodes = new HashSet<PhylogenyNode>();
10259 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10260 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10261 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10262 if ( !s0.match( query_nodes ) ) {
10266 query_nodes = new HashSet<PhylogenyNode>();
10267 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10268 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10269 if ( !s0.match( query_nodes ) ) {
10273 query_nodes = new HashSet<PhylogenyNode>();
10274 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10275 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10276 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10277 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10279 if ( !s0.match( query_nodes ) ) {
10283 query_nodes = new HashSet<PhylogenyNode>();
10284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10287 if ( !s0.match( query_nodes ) ) {
10291 query_nodes = new HashSet<PhylogenyNode>();
10292 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10293 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10294 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10296 if ( !s0.match( query_nodes ) ) {
10300 query_nodes = new HashSet<PhylogenyNode>();
10301 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10302 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10303 if ( s0.match( query_nodes ) ) {
10307 query_nodes = new HashSet<PhylogenyNode>();
10308 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10309 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10310 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10311 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10312 if ( s0.match( query_nodes ) ) {
10316 query_nodes = new HashSet<PhylogenyNode>();
10317 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10318 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10319 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10322 if ( s0.match( query_nodes ) ) {
10326 query_nodes = new HashSet<PhylogenyNode>();
10327 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10328 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10329 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10330 if ( s0.match( query_nodes ) ) {
10334 query_nodes = new HashSet<PhylogenyNode>();
10335 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10336 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10337 if ( s0.match( query_nodes ) ) {
10341 query_nodes = new HashSet<PhylogenyNode>();
10342 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10343 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10344 if ( s0.match( query_nodes ) ) {
10348 query_nodes = new HashSet<PhylogenyNode>();
10349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10351 if ( s0.match( query_nodes ) ) {
10355 query_nodes = new HashSet<PhylogenyNode>();
10356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10358 if ( s0.match( query_nodes ) ) {
10362 query_nodes = new HashSet<PhylogenyNode>();
10363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10365 if ( s0.match( query_nodes ) ) {
10369 query_nodes = new HashSet<PhylogenyNode>();
10370 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10372 if ( s0.match( query_nodes ) ) {
10376 query_nodes = new HashSet<PhylogenyNode>();
10377 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10378 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10380 if ( s0.match( query_nodes ) ) {
10384 query_nodes = new HashSet<PhylogenyNode>();
10385 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10386 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10387 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10388 if ( s0.match( query_nodes ) ) {
10392 query_nodes = new HashSet<PhylogenyNode>();
10393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10394 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10395 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10396 if ( s0.match( query_nodes ) ) {
10400 query_nodes = new HashSet<PhylogenyNode>();
10401 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10402 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10403 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10404 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10405 if ( s0.match( query_nodes ) ) {
10409 // query_nodes = new HashSet<PhylogenyNode>();
10410 // query_nodes.add( new PhylogenyNode( "X" ) );
10411 // query_nodes.add( new PhylogenyNode( "Y" ) );
10412 // query_nodes.add( new PhylogenyNode( "A" ) );
10413 // query_nodes.add( new PhylogenyNode( "B" ) );
10414 // query_nodes.add( new PhylogenyNode( "C" ) );
10415 // query_nodes.add( new PhylogenyNode( "D" ) );
10416 // query_nodes.add( new PhylogenyNode( "E" ) );
10417 // query_nodes.add( new PhylogenyNode( "F" ) );
10418 // query_nodes.add( new PhylogenyNode( "G" ) );
10419 // if ( !s0.match( query_nodes ) ) {
10422 // query_nodes = new HashSet<PhylogenyNode>();
10423 // query_nodes.add( new PhylogenyNode( "X" ) );
10424 // query_nodes.add( new PhylogenyNode( "Y" ) );
10425 // query_nodes.add( new PhylogenyNode( "A" ) );
10426 // query_nodes.add( new PhylogenyNode( "B" ) );
10427 // query_nodes.add( new PhylogenyNode( "C" ) );
10428 // if ( !s0.match( query_nodes ) ) {
10432 // query_nodes = new HashSet<PhylogenyNode>();
10433 // query_nodes.add( new PhylogenyNode( "X" ) );
10434 // query_nodes.add( new PhylogenyNode( "Y" ) );
10435 // query_nodes.add( new PhylogenyNode( "D" ) );
10436 // query_nodes.add( new PhylogenyNode( "E" ) );
10437 // query_nodes.add( new PhylogenyNode( "F" ) );
10438 // query_nodes.add( new PhylogenyNode( "G" ) );
10439 // if ( !s0.match( query_nodes ) ) {
10443 // query_nodes = new HashSet<PhylogenyNode>();
10444 // query_nodes.add( new PhylogenyNode( "X" ) );
10445 // query_nodes.add( new PhylogenyNode( "Y" ) );
10446 // query_nodes.add( new PhylogenyNode( "A" ) );
10447 // query_nodes.add( new PhylogenyNode( "B" ) );
10448 // query_nodes.add( new PhylogenyNode( "C" ) );
10449 // query_nodes.add( new PhylogenyNode( "D" ) );
10450 // if ( !s0.match( query_nodes ) ) {
10454 // query_nodes = new HashSet<PhylogenyNode>();
10455 // query_nodes.add( new PhylogenyNode( "X" ) );
10456 // query_nodes.add( new PhylogenyNode( "Y" ) );
10457 // query_nodes.add( new PhylogenyNode( "E" ) );
10458 // query_nodes.add( new PhylogenyNode( "F" ) );
10459 // query_nodes.add( new PhylogenyNode( "G" ) );
10460 // if ( !s0.match( query_nodes ) ) {
10464 // query_nodes = new HashSet<PhylogenyNode>();
10465 // query_nodes.add( new PhylogenyNode( "X" ) );
10466 // query_nodes.add( new PhylogenyNode( "Y" ) );
10467 // query_nodes.add( new PhylogenyNode( "F" ) );
10468 // query_nodes.add( new PhylogenyNode( "G" ) );
10469 // if ( !s0.match( query_nodes ) ) {
10473 query_nodes = new HashSet<PhylogenyNode>();
10474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10475 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10476 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10477 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10478 if ( s0.match( query_nodes ) ) {
10482 query_nodes = new HashSet<PhylogenyNode>();
10483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10486 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10487 if ( s0.match( query_nodes ) ) {
10490 ///////////////////////////
10492 query_nodes = new HashSet<PhylogenyNode>();
10493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10494 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10495 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10496 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10497 if ( s0.match( query_nodes ) ) {
10501 query_nodes = new HashSet<PhylogenyNode>();
10502 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10503 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10504 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10505 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10506 if ( s0.match( query_nodes ) ) {
10510 query_nodes = new HashSet<PhylogenyNode>();
10511 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10512 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10514 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10515 if ( s0.match( query_nodes ) ) {
10519 query_nodes = new HashSet<PhylogenyNode>();
10520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10523 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10524 if ( s0.match( query_nodes ) ) {
10528 query_nodes = new HashSet<PhylogenyNode>();
10529 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10533 if ( s0.match( query_nodes ) ) {
10537 query_nodes = new HashSet<PhylogenyNode>();
10538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10540 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10541 if ( s0.match( query_nodes ) ) {
10545 query_nodes = new HashSet<PhylogenyNode>();
10546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10551 if ( s0.match( query_nodes ) ) {
10555 query_nodes = new HashSet<PhylogenyNode>();
10556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10560 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10561 if ( s0.match( query_nodes ) ) {
10565 query_nodes = new HashSet<PhylogenyNode>();
10566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10569 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10571 if ( s0.match( query_nodes ) ) {
10575 query_nodes = new HashSet<PhylogenyNode>();
10576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10582 if ( s0.match( query_nodes ) ) {
10586 catch ( final Exception e ) {
10587 e.printStackTrace();
10593 private static boolean testSplitStrict() {
10595 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10596 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
10597 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
10598 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10599 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10600 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10601 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10602 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10603 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10604 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10605 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
10606 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
10607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10609 if ( s0.match( query_nodes ) ) {
10612 query_nodes = new HashSet<PhylogenyNode>();
10613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10620 if ( !s0.match( query_nodes ) ) {
10624 query_nodes = new HashSet<PhylogenyNode>();
10625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10628 if ( !s0.match( query_nodes ) ) {
10632 query_nodes = new HashSet<PhylogenyNode>();
10633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10637 if ( !s0.match( query_nodes ) ) {
10641 query_nodes = new HashSet<PhylogenyNode>();
10642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10646 if ( !s0.match( query_nodes ) ) {
10650 query_nodes = new HashSet<PhylogenyNode>();
10651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10654 if ( !s0.match( query_nodes ) ) {
10658 query_nodes = new HashSet<PhylogenyNode>();
10659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10661 if ( !s0.match( query_nodes ) ) {
10665 query_nodes = new HashSet<PhylogenyNode>();
10666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10671 if ( !s0.match( query_nodes ) ) {
10675 query_nodes = new HashSet<PhylogenyNode>();
10676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10679 if ( !s0.match( query_nodes ) ) {
10683 query_nodes = new HashSet<PhylogenyNode>();
10684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10688 if ( !s0.match( query_nodes ) ) {
10692 query_nodes = new HashSet<PhylogenyNode>();
10693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10695 if ( s0.match( query_nodes ) ) {
10699 query_nodes = new HashSet<PhylogenyNode>();
10700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10704 if ( s0.match( query_nodes ) ) {
10708 query_nodes = new HashSet<PhylogenyNode>();
10709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10714 if ( s0.match( query_nodes ) ) {
10718 query_nodes = new HashSet<PhylogenyNode>();
10719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10722 if ( s0.match( query_nodes ) ) {
10726 query_nodes = new HashSet<PhylogenyNode>();
10727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10729 if ( s0.match( query_nodes ) ) {
10733 query_nodes = new HashSet<PhylogenyNode>();
10734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10736 if ( s0.match( query_nodes ) ) {
10740 query_nodes = new HashSet<PhylogenyNode>();
10741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10742 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10743 if ( s0.match( query_nodes ) ) {
10747 query_nodes = new HashSet<PhylogenyNode>();
10748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10750 if ( s0.match( query_nodes ) ) {
10754 query_nodes = new HashSet<PhylogenyNode>();
10755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10757 if ( s0.match( query_nodes ) ) {
10761 query_nodes = new HashSet<PhylogenyNode>();
10762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10764 if ( s0.match( query_nodes ) ) {
10768 query_nodes = new HashSet<PhylogenyNode>();
10769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10770 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10772 if ( s0.match( query_nodes ) ) {
10776 query_nodes = new HashSet<PhylogenyNode>();
10777 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10780 if ( s0.match( query_nodes ) ) {
10784 query_nodes = new HashSet<PhylogenyNode>();
10785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10786 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10787 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10788 if ( s0.match( query_nodes ) ) {
10792 query_nodes = new HashSet<PhylogenyNode>();
10793 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10794 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10796 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10797 if ( s0.match( query_nodes ) ) {
10801 catch ( final Exception e ) {
10802 e.printStackTrace();
10808 private static boolean testSubtreeDeletion() {
10810 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10811 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
10812 t1.deleteSubtree( t1.getNode( "A" ), false );
10813 if ( t1.getNumberOfExternalNodes() != 5 ) {
10816 t1.toNewHampshireX();
10817 t1.deleteSubtree( t1.getNode( "E" ), false );
10818 if ( t1.getNumberOfExternalNodes() != 4 ) {
10821 t1.toNewHampshireX();
10822 t1.deleteSubtree( t1.getNode( "F" ), false );
10823 if ( t1.getNumberOfExternalNodes() != 3 ) {
10826 t1.toNewHampshireX();
10827 t1.deleteSubtree( t1.getNode( "D" ), false );
10828 t1.toNewHampshireX();
10829 if ( t1.getNumberOfExternalNodes() != 3 ) {
10832 t1.deleteSubtree( t1.getNode( "def" ), false );
10833 t1.toNewHampshireX();
10834 if ( t1.getNumberOfExternalNodes() != 2 ) {
10837 t1.deleteSubtree( t1.getNode( "B" ), false );
10838 t1.toNewHampshireX();
10839 if ( t1.getNumberOfExternalNodes() != 1 ) {
10842 t1.deleteSubtree( t1.getNode( "C" ), false );
10843 t1.toNewHampshireX();
10844 if ( t1.getNumberOfExternalNodes() != 1 ) {
10847 t1.deleteSubtree( t1.getNode( "abc" ), false );
10848 t1.toNewHampshireX();
10849 if ( t1.getNumberOfExternalNodes() != 1 ) {
10852 t1.deleteSubtree( t1.getNode( "r" ), false );
10853 if ( t1.getNumberOfExternalNodes() != 0 ) {
10856 if ( !t1.isEmpty() ) {
10859 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
10860 t2.deleteSubtree( t2.getNode( "A" ), false );
10861 t2.toNewHampshireX();
10862 if ( t2.getNumberOfExternalNodes() != 5 ) {
10865 t2.deleteSubtree( t2.getNode( "abc" ), false );
10866 t2.toNewHampshireX();
10867 if ( t2.getNumberOfExternalNodes() != 3 ) {
10870 t2.deleteSubtree( t2.getNode( "def" ), false );
10871 t2.toNewHampshireX();
10872 if ( t2.getNumberOfExternalNodes() != 1 ) {
10876 catch ( final Exception e ) {
10877 e.printStackTrace( System.out );
10883 private static boolean testSupportCount() {
10885 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10886 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
10887 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
10888 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
10889 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
10890 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
10891 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
10893 SupportCount.count( t0_1, phylogenies_1, true, false );
10894 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
10895 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
10896 + "(((((A,B),C),D),E),((F,G),X))"
10897 + "(((((A,Y),B),C),D),((F,G),E))"
10898 + "(((((A,B),C),D),E),(F,G))"
10899 + "(((((A,B),C),D),E),(F,G))"
10900 + "(((((A,B),C),D),E),(F,G))"
10901 + "(((((A,B),C),D),E),(F,G),Z)"
10902 + "(((((A,B),C),D),E),(F,G))"
10903 + "((((((A,B),C),D),E),F),G)"
10904 + "(((((X,Y),F,G),E),((A,B),C)),D)",
10906 SupportCount.count( t0_2, phylogenies_2, true, false );
10907 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
10908 while ( it.hasNext() ) {
10909 final PhylogenyNode n = it.next();
10910 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
10914 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
10915 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
10916 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
10917 SupportCount.count( t0_3, phylogenies_3, true, false );
10918 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
10919 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
10922 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
10925 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
10928 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
10931 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
10934 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
10937 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
10940 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
10943 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
10946 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
10949 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10950 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
10951 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
10952 SupportCount.count( t0_4, phylogenies_4, true, false );
10953 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
10954 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
10957 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
10960 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
10963 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
10966 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
10969 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
10972 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
10975 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
10978 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
10981 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
10984 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10985 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10986 double d = SupportCount.compare( b1, a, true, true, true );
10987 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
10990 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10991 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10992 d = SupportCount.compare( b2, a, true, true, true );
10993 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
10996 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10997 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
10998 d = SupportCount.compare( b3, a, true, true, true );
10999 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
11002 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
11003 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
11004 d = SupportCount.compare( b4, a, true, true, false );
11005 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
11009 catch ( final Exception e ) {
11010 e.printStackTrace( System.out );
11016 private static boolean testSupportTransfer() {
11018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11019 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)",
11020 new NHXParser() )[ 0 ];
11021 final Phylogeny p2 = factory
11022 .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 ];
11023 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
11026 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
11029 support_transfer.moveBranchLengthsToBootstrap( p1 );
11030 support_transfer.transferSupportValues( p1, p2 );
11031 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
11034 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
11037 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
11040 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
11043 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
11046 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
11049 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
11052 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
11056 catch ( final Exception e ) {
11057 e.printStackTrace( System.out );
11063 private static boolean testTaxonomyExtraction() {
11065 final PhylogenyNode n0 = PhylogenyNode
11066 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11067 if ( n0.getNodeData().isHasTaxonomy() ) {
11070 final PhylogenyNode n1 = PhylogenyNode
11071 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11072 if ( n1.getNodeData().isHasTaxonomy() ) {
11073 System.out.println( n1.toString() );
11076 final PhylogenyNode n2x = PhylogenyNode
11077 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11078 if ( n2x.getNodeData().isHasTaxonomy() ) {
11081 final PhylogenyNode n3 = PhylogenyNode
11082 .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11083 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11084 System.out.println( n3.toString() );
11087 final PhylogenyNode n4 = PhylogenyNode
11088 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11089 if ( n4.getNodeData().isHasTaxonomy() ) {
11090 System.out.println( n4.toString() );
11093 final PhylogenyNode n5 = PhylogenyNode
11094 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11095 if ( n5.getNodeData().isHasTaxonomy() ) {
11096 System.out.println( n5.toString() );
11099 final PhylogenyNode n6 = PhylogenyNode
11100 .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11101 if ( n6.getNodeData().isHasTaxonomy() ) {
11102 System.out.println( n6.toString() );
11105 final PhylogenyNode n7 = PhylogenyNode
11106 .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11107 if ( n7.getNodeData().isHasTaxonomy() ) {
11108 System.out.println( n7.toString() );
11111 final PhylogenyNode n8 = PhylogenyNode
11112 .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11113 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11114 System.out.println( n8.toString() );
11117 final PhylogenyNode n9 = PhylogenyNode
11118 .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11119 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11120 System.out.println( n9.toString() );
11123 final PhylogenyNode n10x = PhylogenyNode
11124 .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11125 if ( n10x.getNodeData().isHasTaxonomy() ) {
11126 System.out.println( n10x.toString() );
11129 final PhylogenyNode n10xx = PhylogenyNode
11130 .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11131 if ( n10xx.getNodeData().isHasTaxonomy() ) {
11132 System.out.println( n10xx.toString() );
11135 final PhylogenyNode n10 = PhylogenyNode
11136 .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11137 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
11138 System.out.println( n10.toString() );
11141 final PhylogenyNode n11 = PhylogenyNode
11142 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11143 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
11144 System.out.println( n11.toString() );
11147 final PhylogenyNode n12 = PhylogenyNode
11148 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
11149 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11150 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
11151 System.out.println( n12.toString() );
11154 final PhylogenyNode n13 = PhylogenyNode
11155 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11156 if ( n13.getNodeData().isHasTaxonomy() ) {
11157 System.out.println( n13.toString() );
11161 catch ( final Exception e ) {
11162 e.printStackTrace( System.out );
11168 private static boolean testTreeMethods() {
11170 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11171 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
11172 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
11173 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
11174 System.out.println( t0.toNewHampshireX() );
11177 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
11178 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
11179 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
11182 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
11185 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
11189 catch ( final Exception e ) {
11190 e.printStackTrace( System.out );
11196 private static boolean testSequenceDbWsTools1() {
11198 final PhylogenyNode n = new PhylogenyNode();
11199 n.setName( "NP_001025424" );
11200 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11201 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11202 || !acc.getValue().equals( "NP_001025424" ) ) {
11205 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11206 acc = SequenceDbWsTools.obtainSeqAccession( n );
11207 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11208 || !acc.getValue().equals( "NP_001025424" ) ) {
11211 n.setName( "NP_001025424.1" );
11212 acc = SequenceDbWsTools.obtainSeqAccession( n );
11213 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11214 || !acc.getValue().equals( "NP_001025424" ) ) {
11217 n.setName( "NM_001030253" );
11218 acc = SequenceDbWsTools.obtainSeqAccession( n );
11219 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11220 || !acc.getValue().equals( "NM_001030253" ) ) {
11223 n.setName( "BCL2_HUMAN" );
11224 acc = SequenceDbWsTools.obtainSeqAccession( n );
11225 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11226 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11227 System.out.println( acc.toString() );
11230 n.setName( "P10415" );
11231 acc = SequenceDbWsTools.obtainSeqAccession( n );
11232 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11233 || !acc.getValue().equals( "P10415" ) ) {
11234 System.out.println( acc.toString() );
11237 n.setName( " P10415 " );
11238 acc = SequenceDbWsTools.obtainSeqAccession( n );
11239 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11240 || !acc.getValue().equals( "P10415" ) ) {
11241 System.out.println( acc.toString() );
11244 n.setName( "_P10415|" );
11245 acc = SequenceDbWsTools.obtainSeqAccession( n );
11246 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11247 || !acc.getValue().equals( "P10415" ) ) {
11248 System.out.println( acc.toString() );
11251 n.setName( "AY695820" );
11252 acc = SequenceDbWsTools.obtainSeqAccession( n );
11253 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11254 || !acc.getValue().equals( "AY695820" ) ) {
11255 System.out.println( acc.toString() );
11258 n.setName( "_AY695820_" );
11259 acc = SequenceDbWsTools.obtainSeqAccession( n );
11260 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11261 || !acc.getValue().equals( "AY695820" ) ) {
11262 System.out.println( acc.toString() );
11265 n.setName( "AAA59452" );
11266 acc = SequenceDbWsTools.obtainSeqAccession( n );
11267 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11268 || !acc.getValue().equals( "AAA59452" ) ) {
11269 System.out.println( acc.toString() );
11272 n.setName( "_AAA59452_" );
11273 acc = SequenceDbWsTools.obtainSeqAccession( n );
11274 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11275 || !acc.getValue().equals( "AAA59452" ) ) {
11276 System.out.println( acc.toString() );
11279 n.setName( "AAA59452.1" );
11280 acc = SequenceDbWsTools.obtainSeqAccession( n );
11281 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11282 || !acc.getValue().equals( "AAA59452.1" ) ) {
11283 System.out.println( acc.toString() );
11286 n.setName( "_AAA59452.1_" );
11287 acc = SequenceDbWsTools.obtainSeqAccession( n );
11288 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11289 || !acc.getValue().equals( "AAA59452.1" ) ) {
11290 System.out.println( acc.toString() );
11293 n.setName( "GI:94894583" );
11294 acc = SequenceDbWsTools.obtainSeqAccession( n );
11295 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11296 || !acc.getValue().equals( "94894583" ) ) {
11297 System.out.println( acc.toString() );
11301 catch ( final Exception e ) {
11307 private static boolean testSequenceDbWsTools2() {
11309 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11310 SequenceDbWsTools.obtainSeqInformation( n1 );
11311 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11314 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11317 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11320 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11323 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11324 SequenceDbWsTools.obtainSeqInformation( n2 );
11325 System.out.println( n2.toString() );
11326 if ( !n2.getNodeData().getSequence().getName()
11327 .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
11330 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11333 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11336 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11339 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11340 SequenceDbWsTools.obtainSeqInformation( n3 );
11341 System.out.println( "n=" + n3.toString() );
11342 if ( !n3.getNodeData().getSequence().getName()
11343 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11346 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11349 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11352 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11356 catch ( final IOException e ) {
11357 System.out.println();
11358 System.out.println( "the following might be due to absence internet connection:" );
11359 e.printStackTrace( System.out );
11362 catch ( final Exception e ) {
11363 e.printStackTrace();
11369 private static boolean testEbiEntryRetrieval() {
11371 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
11372 if ( !entry.getAccession().equals( "AAK41263" ) ) {
11373 System.out.println( entry.getAccession() );
11376 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
11377 System.out.println( entry.getTaxonomyScientificName() );
11380 if ( !entry.getSequenceName()
11381 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
11382 System.out.println( entry.getSequenceName() );
11385 // if ( !entry.getSequenceSymbol().equals( "" ) ) {
11386 // System.out.println( entry.getSequenceSymbol() );
11389 if ( !entry.getGeneName().equals( "treX-like" ) ) {
11390 System.out.println( entry.getGeneName() );
11393 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
11394 System.out.println( entry.getTaxonomyIdentifier() );
11397 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
11398 System.out.println( entry.getAnnotations().first().getRefValue() );
11401 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
11402 System.out.println( entry.getAnnotations().first().getRefSource() );
11405 if ( entry.getCrossReferences().size() != 5 ) {
11409 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
11410 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
11413 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
11414 System.out.println( entry1.getTaxonomyScientificName() );
11417 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
11418 System.out.println( entry1.getSequenceName() );
11421 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
11422 System.out.println( entry1.getTaxonomyIdentifier() );
11425 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
11426 System.out.println( entry1.getGeneName() );
11429 if ( entry1.getCrossReferences().size() != 6 ) {
11433 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
11434 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
11437 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
11438 System.out.println( entry2.getTaxonomyScientificName() );
11441 if ( !entry2.getSequenceName()
11442 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11443 System.out.println( entry2.getSequenceName() );
11446 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
11447 System.out.println( entry2.getTaxonomyIdentifier() );
11450 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
11451 System.out.println( entry2.getGeneName() );
11454 if ( entry2.getCrossReferences().size() != 3 ) {
11458 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
11459 if ( !entry3.getAccession().equals( "HM043801" ) ) {
11462 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
11463 System.out.println( entry3.getTaxonomyScientificName() );
11466 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
11467 System.out.println( entry3.getSequenceName() );
11470 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
11471 System.out.println( entry3.getTaxonomyIdentifier() );
11474 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
11475 System.out.println( entry3.getSequenceSymbol() );
11478 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
11481 if ( entry3.getCrossReferences().size() != 8 ) {
11486 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
11487 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
11490 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
11491 System.out.println( entry4.getTaxonomyScientificName() );
11494 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
11495 System.out.println( entry4.getSequenceName() );
11498 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
11499 System.out.println( entry4.getTaxonomyIdentifier() );
11502 if ( !entry4.getGeneName().equals( "ras" ) ) {
11503 System.out.println( entry4.getGeneName() );
11506 // if ( !entry4.getChromosome().equals( "ras" ) ) {
11507 // System.out.println( entry4.getChromosome() );
11510 // if ( !entry4.getMap().equals( "ras" ) ) {
11511 // System.out.println( entry4.getMap() );
11516 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
11517 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
11521 catch ( final IOException e ) {
11522 System.out.println();
11523 System.out.println( "the following might be due to absence internet connection:" );
11524 e.printStackTrace( System.out );
11527 catch ( final Exception e ) {
11528 e.printStackTrace();
11534 private static boolean testUniprotEntryRetrieval() {
11536 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
11537 if ( !entry.getAccession().equals( "P12345" ) ) {
11540 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
11543 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
11546 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
11549 if ( !entry.getGeneName().equals( "GOT2" ) ) {
11552 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
11556 catch ( final IOException e ) {
11557 System.out.println();
11558 System.out.println( "the following might be due to absence internet connection:" );
11559 e.printStackTrace( System.out );
11562 catch ( final Exception e ) {
11568 private static boolean testUniprotTaxonomySearch() {
11570 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
11572 if ( results.size() != 1 ) {
11575 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11578 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11581 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11584 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11587 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11591 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
11592 if ( results.size() != 1 ) {
11595 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11598 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11601 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11604 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11607 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11611 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
11612 if ( results.size() != 1 ) {
11615 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11618 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11621 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11624 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11627 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11631 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
11632 if ( results.size() != 1 ) {
11635 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11638 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11641 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11644 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11647 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11650 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
11653 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
11656 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11657 .equals( "Nematostella vectensis" ) ) {
11658 System.out.println( results.get( 0 ).getLineage() );
11663 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
11664 if ( results.size() != 1 ) {
11667 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11670 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11673 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11676 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11679 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11682 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11683 .equals( "Xenopus tropicalis" ) ) {
11684 System.out.println( results.get( 0 ).getLineage() );
11689 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
11690 if ( results.size() != 1 ) {
11693 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11696 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11699 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11702 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11705 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11708 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11709 .equals( "Xenopus tropicalis" ) ) {
11710 System.out.println( results.get( 0 ).getLineage() );
11715 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
11716 if ( results.size() != 1 ) {
11719 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11722 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11725 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11728 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11731 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11734 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11735 .equals( "Xenopus tropicalis" ) ) {
11736 System.out.println( results.get( 0 ).getLineage() );
11740 catch ( final IOException e ) {
11741 System.out.println();
11742 System.out.println( "the following might be due to absence internet connection:" );
11743 e.printStackTrace( System.out );
11746 catch ( final Exception e ) {
11752 private static boolean testWabiTxSearch() {
11754 String result = "";
11755 result = TxSearch.searchSimple( "nematostella" );
11756 result = TxSearch.getTxId( "nematostella" );
11757 if ( !result.equals( "45350" ) ) {
11760 result = TxSearch.getTxName( "45350" );
11761 if ( !result.equals( "Nematostella" ) ) {
11764 result = TxSearch.getTxId( "nematostella vectensis" );
11765 if ( !result.equals( "45351" ) ) {
11768 result = TxSearch.getTxName( "45351" );
11769 if ( !result.equals( "Nematostella vectensis" ) ) {
11772 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
11773 if ( !result.equals( "536089" ) ) {
11776 result = TxSearch.getTxName( "536089" );
11777 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
11780 final List<String> queries = new ArrayList<String>();
11781 queries.add( "Campylobacter coli" );
11782 queries.add( "Escherichia coli" );
11783 queries.add( "Arabidopsis" );
11784 queries.add( "Trichoplax" );
11785 queries.add( "Samanea saman" );
11786 queries.add( "Kluyveromyces marxianus" );
11787 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
11788 queries.add( "Bornavirus parrot/PDD/2008" );
11789 final List<RANKS> ranks = new ArrayList<RANKS>();
11790 ranks.add( RANKS.SUPERKINGDOM );
11791 ranks.add( RANKS.KINGDOM );
11792 ranks.add( RANKS.FAMILY );
11793 ranks.add( RANKS.GENUS );
11794 ranks.add( RANKS.TRIBE );
11795 result = TxSearch.searchLineage( queries, ranks );
11796 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
11797 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
11799 catch ( final Exception e ) {
11800 System.out.println();
11801 System.out.println( "the following might be due to absence internet connection:" );
11802 e.printStackTrace( System.out );