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;
33 import java.util.ArrayList;
34 import java.util.Date;
35 import java.util.HashSet;
36 import java.util.Iterator;
37 import java.util.List;
38 import java.util.Locale;
40 import java.util.SortedSet;
42 import org.forester.application.support_transfer;
43 import org.forester.archaeopteryx.TreePanelUtil;
44 import org.forester.development.DevelopmentTools;
45 import org.forester.evoinference.TestPhylogenyReconstruction;
46 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
47 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
48 import org.forester.go.TestGo;
49 import org.forester.io.parsers.FastaParser;
50 import org.forester.io.parsers.GeneralMsaParser;
51 import org.forester.io.parsers.HmmscanPerDomainTableParser;
52 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
53 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
54 import org.forester.io.parsers.nexus.NexusCharactersParser;
55 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
56 import org.forester.io.parsers.nhx.NHXParser;
57 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
58 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
59 import org.forester.io.parsers.tol.TolParser;
60 import org.forester.io.parsers.util.ParserUtils;
61 import org.forester.io.writers.PhylogenyWriter;
62 import org.forester.io.writers.SequenceWriter;
63 import org.forester.msa.BasicMsa;
64 import org.forester.msa.Mafft;
65 import org.forester.msa.Msa;
66 import org.forester.msa.MsaInferrer;
67 import org.forester.msa.MsaMethods;
68 import org.forester.pccx.TestPccx;
69 import org.forester.phylogeny.Phylogeny;
70 import org.forester.phylogeny.PhylogenyBranch;
71 import org.forester.phylogeny.PhylogenyMethods;
72 import org.forester.phylogeny.PhylogenyNode;
73 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
74 import org.forester.phylogeny.data.Accession;
75 import org.forester.phylogeny.data.Accession.Source;
76 import org.forester.phylogeny.data.BinaryCharacters;
77 import org.forester.phylogeny.data.BranchWidth;
78 import org.forester.phylogeny.data.Confidence;
79 import org.forester.phylogeny.data.Distribution;
80 import org.forester.phylogeny.data.DomainArchitecture;
81 import org.forester.phylogeny.data.Event;
82 import org.forester.phylogeny.data.Identifier;
83 import org.forester.phylogeny.data.PhylogenyData;
84 import org.forester.phylogeny.data.PhylogenyDataUtil;
85 import org.forester.phylogeny.data.Polygon;
86 import org.forester.phylogeny.data.PropertiesMap;
87 import org.forester.phylogeny.data.Property;
88 import org.forester.phylogeny.data.Property.AppliesTo;
89 import org.forester.phylogeny.data.ProteinDomain;
90 import org.forester.phylogeny.data.Taxonomy;
91 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
92 import org.forester.phylogeny.factories.PhylogenyFactory;
93 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
94 import org.forester.protein.BasicDomain;
95 import org.forester.protein.BasicProtein;
96 import org.forester.protein.Domain;
97 import org.forester.protein.Protein;
98 import org.forester.protein.ProteinId;
99 import org.forester.rio.TestRIO;
100 import org.forester.sdi.SDI;
101 import org.forester.sdi.SDIR;
102 import org.forester.sdi.TestGSDI;
103 import org.forester.sequence.BasicSequence;
104 import org.forester.sequence.Sequence;
105 import org.forester.species.BasicSpecies;
106 import org.forester.species.Species;
107 import org.forester.surfacing.TestSurfacing;
108 import org.forester.tools.ConfidenceAssessor;
109 import org.forester.tools.SupportCount;
110 import org.forester.tools.TreeSplitMatrix;
111 import org.forester.util.AsciiHistogram;
112 import org.forester.util.BasicDescriptiveStatistics;
113 import org.forester.util.BasicTable;
114 import org.forester.util.BasicTableParser;
115 import org.forester.util.DescriptiveStatistics;
116 import org.forester.util.ForesterConstants;
117 import org.forester.util.ForesterUtil;
118 import org.forester.util.GeneralTable;
119 import org.forester.util.SequenceAccessionTools;
120 import org.forester.ws.seqdb.SequenceDatabaseEntry;
121 import org.forester.ws.seqdb.SequenceDbWsTools;
122 import org.forester.ws.seqdb.UniProtTaxonomy;
123 import org.forester.ws.wabi.TxSearch;
124 import org.forester.ws.wabi.TxSearch.RANKS;
125 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
126 import org.forester.ws.wabi.TxSearch.TAX_RANK;
128 @SuppressWarnings( "unused")
129 public final class Test {
131 private final static boolean PERFORM_DB_TESTS = false;
132 private final static double ZERO_DIFF = 1.0E-9;
133 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
134 + ForesterUtil.getFileSeparator() + "test_data"
135 + ForesterUtil.getFileSeparator();
136 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
137 + ForesterUtil.getFileSeparator() + "resources"
138 + ForesterUtil.getFileSeparator();
139 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
140 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
141 + ForesterConstants.PHYLO_XML_VERSION + "/"
142 + ForesterConstants.PHYLO_XML_XSD;
143 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
144 + ForesterConstants.PHYLO_XML_VERSION + "/"
145 + ForesterConstants.PHYLO_XML_XSD;
147 public static boolean testOverlapRemoval() {
149 final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
150 final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
151 final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
152 final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
153 final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
154 final List<Boolean> covered = new ArrayList<Boolean>();
155 covered.add( true ); // 0
156 covered.add( false ); // 1
157 covered.add( true ); // 2
158 covered.add( false ); // 3
159 covered.add( true ); // 4
160 covered.add( true ); // 5
161 covered.add( false ); // 6
162 covered.add( true ); // 7
163 covered.add( true ); // 8
164 if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
167 if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
170 if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
173 if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
176 if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
179 final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
180 final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
181 final Protein ab = new BasicProtein( "ab", "varanus", 0 );
182 ab.addProteinDomain( a );
183 ab.addProteinDomain( b );
184 final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
185 if ( ab.getNumberOfProteinDomains() != 2 ) {
188 if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
191 if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
194 final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
195 if ( ab.getNumberOfProteinDomains() != 2 ) {
198 if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
201 final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
202 final Domain d = new BasicDomain( "d",
209 final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
210 final Protein cde = new BasicProtein( "cde", "varanus", 0 );
211 cde.addProteinDomain( c );
212 cde.addProteinDomain( d );
213 cde.addProteinDomain( e );
214 final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
215 if ( cde.getNumberOfProteinDomains() != 3 ) {
218 if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
221 final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
222 final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
223 final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
224 final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
225 final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
226 final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
227 fghi.addProteinDomain( f );
228 fghi.addProteinDomain( g );
229 fghi.addProteinDomain( h );
230 fghi.addProteinDomain( i );
231 fghi.addProteinDomain( i );
232 fghi.addProteinDomain( i );
233 fghi.addProteinDomain( i2 );
234 final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
235 if ( fghi.getNumberOfProteinDomains() != 7 ) {
238 if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
241 if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
244 final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
245 if ( fghi.getNumberOfProteinDomains() != 7 ) {
248 if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
251 final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
252 final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
253 final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
254 final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
255 final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
256 final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
257 final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
258 final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
259 jklm.addProteinDomain( j );
260 jklm.addProteinDomain( k );
261 jklm.addProteinDomain( l );
262 jklm.addProteinDomain( m );
263 jklm.addProteinDomain( m0 );
264 jklm.addProteinDomain( m1 );
265 jklm.addProteinDomain( m2 );
266 final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
267 if ( jklm.getNumberOfProteinDomains() != 7 ) {
270 if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
273 if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
276 final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
277 if ( jklm.getNumberOfProteinDomains() != 7 ) {
280 if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
283 final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
284 final Protein od = new BasicProtein( "od", "varanus", 0 );
285 od.addProteinDomain( only );
286 final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
287 if ( od.getNumberOfProteinDomains() != 1 ) {
290 if ( od_s0.getNumberOfProteinDomains() != 1 ) {
294 catch ( final Exception e ) {
295 e.printStackTrace( System.out );
301 public static boolean testEngulfingOverlapRemoval() {
303 final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
304 final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
305 final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
306 final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
307 final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
308 final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
309 final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
310 final List<Boolean> covered = new ArrayList<Boolean>();
311 covered.add( true ); // 0
312 covered.add( false ); // 1
313 covered.add( true ); // 2
314 covered.add( false ); // 3
315 covered.add( true ); // 4
316 covered.add( true ); // 5
317 covered.add( false ); // 6
318 covered.add( true ); // 7
319 covered.add( true ); // 8
320 if ( ForesterUtil.isEngulfed( d0, covered ) ) {
323 if ( ForesterUtil.isEngulfed( d1, covered ) ) {
326 if ( ForesterUtil.isEngulfed( d2, covered ) ) {
329 if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
332 if ( ForesterUtil.isEngulfed( d4, covered ) ) {
335 if ( ForesterUtil.isEngulfed( d5, covered ) ) {
338 if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
341 final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
342 final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
343 final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
344 final Protein abc = new BasicProtein( "abc", "nemve", 0 );
345 abc.addProteinDomain( a );
346 abc.addProteinDomain( b );
347 abc.addProteinDomain( c );
348 final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
349 final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
350 if ( abc.getNumberOfProteinDomains() != 3 ) {
353 if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
356 if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
359 if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
362 if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
365 final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
366 final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
367 final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
368 final Protein def = new BasicProtein( "def", "nemve", 0 );
369 def.addProteinDomain( d );
370 def.addProteinDomain( e );
371 def.addProteinDomain( f );
372 final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
373 final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
374 if ( def.getNumberOfProteinDomains() != 3 ) {
377 if ( def_r1.getNumberOfProteinDomains() != 3 ) {
380 if ( def_r2.getNumberOfProteinDomains() != 3 ) {
383 if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
386 if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
389 if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
393 catch ( final Exception e ) {
394 e.printStackTrace( System.out );
400 public static boolean isEqual( final double a, final double b ) {
401 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
405 public static final boolean testNHXparsingFromURL() {
407 String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
408 final URL u = new URL( s );
409 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
410 final Phylogeny[] phys = factory.create( u.openStream(), new NHXParser() );
413 if ( phys == null || phys.length != 1 ) {
417 if ( !phys[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
418 System.out.println(phys[ 0 ].toNewHampshire() );
422 final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
423 if ( phys2 == null || phys2.length != 1 ) {
427 if ( !phys2[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
428 System.out.println(phys2[ 0 ].toNewHampshire() );
432 catch ( Exception e ) {
438 public static void main( final String[] args ) {
441 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
442 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
444 Locale.setDefault( Locale.US );
445 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
448 System.out.print( "[Test if directory with files for testing exists/is readable: " );
449 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
450 System.out.println( "OK.]" );
453 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
454 System.out.println( "Testing aborted." );
457 System.out.print( "[Test if resources directory exists/is readable: " );
458 if ( testDir( PATH_TO_RESOURCES ) ) {
459 System.out.println( "OK.]" );
462 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
463 System.out.println( "Testing aborted." );
466 final long start_time = new Date().getTime();
467 System.out.print( "Basic node methods: " );
468 if ( Test.testBasicNodeMethods() ) {
469 System.out.println( "OK." );
473 System.out.println( "failed." );
476 System.out.print( "Protein id: " );
477 if ( !testProteinId() ) {
478 System.out.println( "failed." );
484 System.out.println( "OK." );
485 System.out.print( "Species: " );
486 if ( !testSpecies() ) {
487 System.out.println( "failed." );
493 System.out.println( "OK." );
494 System.out.print( "Basic domain: " );
495 if ( !testBasicDomain() ) {
496 System.out.println( "failed." );
502 System.out.println( "OK." );
503 System.out.print( "Basic protein: " );
504 if ( !testBasicProtein() ) {
505 System.out.println( "failed." );
511 System.out.println( "OK." );
512 System.out.print( "Sequence writer: " );
513 if ( testSequenceWriter() ) {
514 System.out.println( "OK." );
518 System.out.println( "failed." );
521 System.out.print( "Sequence id parsing: " );
522 if ( testSequenceIdParsing() ) {
523 System.out.println( "OK." );
527 System.out.println( "failed." );
530 System.out.print( "UniProtKB id extraction: " );
531 if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
532 System.out.println( "OK." );
536 System.out.println( "failed." );
539 System.out.print( "Sequence DB tools 1: " );
540 if ( testSequenceDbWsTools1() ) {
541 System.out.println( "OK." );
545 System.out.println( "failed." );
548 if ( PERFORM_DB_TESTS ) {
549 System.out.print( "Ebi Entry Retrieval: " );
550 if ( Test.testEbiEntryRetrieval() ) {
551 System.out.println( "OK." );
555 System.out.println( "failed." );
560 if ( PERFORM_DB_TESTS ) {
561 System.out.print( "Sequence DB tools 2: " );
562 if ( testSequenceDbWsTools2() ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
573 System.out.print( "Hmmscan output parser: " );
574 if ( testHmmscanOutputParser() ) {
575 System.out.println( "OK." );
579 System.out.println( "failed." );
583 System.out.print( "Overlap removal: " );
584 if ( !org.forester.test.Test.testOverlapRemoval() ) {
585 System.out.println( "failed." );
591 System.out.println( "OK." );
592 System.out.print( "Engulfing overlap removal: " );
593 if ( !Test.testEngulfingOverlapRemoval() ) {
594 System.out.println( "failed." );
600 System.out.println( "OK." );
602 System.out.print( "Taxonomy code extraction: " );
603 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
604 System.out.println( "OK." );
608 System.out.println( "failed." );
611 System.out.print( "SN extraction: " );
612 if ( Test.testExtractSNFromNodeName() ) {
613 System.out.println( "OK." );
617 System.out.println( "failed." );
620 System.out.print( "Taxonomy extraction (general): " );
621 if ( Test.testTaxonomyExtraction() ) {
622 System.out.println( "OK." );
626 System.out.println( "failed." );
629 System.out.print( "Uri for Aptx web sequence accession: " );
630 if ( Test.testCreateUriForSeqWeb() ) {
631 System.out.println( "OK." );
635 System.out.println( "failed." );
638 System.out.print( "Basic node construction and parsing of NHX (node level): " );
639 if ( Test.testNHXNodeParsing() ) {
640 System.out.println( "OK." );
644 System.out.println( "failed." );
647 System.out.print( "NHX parsing iterating: " );
648 if ( Test.testNHParsingIter() ) {
649 System.out.println( "OK." );
653 System.out.println( "failed." );
656 System.out.print( "NH parsing: " );
657 if ( Test.testNHParsing() ) {
658 System.out.println( "OK." );
662 System.out.println( "failed." );
665 System.out.print( "Conversion to NHX (node level): " );
666 if ( Test.testNHXconversion() ) {
667 System.out.println( "OK." );
671 System.out.println( "failed." );
674 System.out.print( "NHX parsing: " );
675 if ( Test.testNHXParsing() ) {
676 System.out.println( "OK." );
680 System.out.println( "failed." );
683 System.out.print( "NHX parsing with quotes: " );
684 if ( Test.testNHXParsingQuotes() ) {
685 System.out.println( "OK." );
689 System.out.println( "failed." );
692 System.out.print( "NHX parsing (MrBayes): " );
693 if ( Test.testNHXParsingMB() ) {
694 System.out.println( "OK." );
698 System.out.println( "failed." );
701 System.out.print( "Nexus characters parsing: " );
702 if ( Test.testNexusCharactersParsing() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed." );
710 System.out.print( "Nexus tree parsing iterating: " );
711 if ( Test.testNexusTreeParsingIterating() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
719 System.out.print( "Nexus tree parsing: " );
720 if ( Test.testNexusTreeParsing() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 System.out.print( "Nexus tree parsing (translating): " );
729 if ( Test.testNexusTreeParsingTranslating() ) {
730 System.out.println( "OK." );
734 System.out.println( "failed." );
737 System.out.print( "Nexus matrix parsing: " );
738 if ( Test.testNexusMatrixParsing() ) {
739 System.out.println( "OK." );
743 System.out.println( "failed." );
746 System.out.print( "Basic phyloXML parsing: " );
747 if ( Test.testBasicPhyloXMLparsing() ) {
748 System.out.println( "OK." );
752 System.out.println( "failed." );
755 System.out.print( "Basic phyloXML parsing (validating against schema): " );
756 if ( testBasicPhyloXMLparsingValidating() ) {
757 System.out.println( "OK." );
761 System.out.println( "failed." );
764 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
765 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
766 System.out.println( "OK." );
770 System.out.println( "failed." );
773 System.out.print( "phyloXML Distribution Element: " );
774 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
775 System.out.println( "OK." );
779 System.out.println( "failed." );
782 System.out.print( "Tol XML parsing: " );
783 if ( Test.testBasicTolXMLparsing() ) {
784 System.out.println( "OK." );
788 System.out.println( "failed." );
791 System.out.print( "Copying of node data: " );
792 if ( Test.testCopyOfNodeData() ) {
793 System.out.println( "OK." );
797 System.out.println( "failed." );
800 System.out.print( "Tree copy: " );
801 if ( Test.testTreeCopy() ) {
802 System.out.println( "OK." );
806 System.out.println( "failed." );
809 System.out.print( "Basic tree methods: " );
810 if ( Test.testBasicTreeMethods() ) {
811 System.out.println( "OK." );
815 System.out.println( "failed." );
818 System.out.print( "Tree methods: " );
819 if ( Test.testTreeMethods() ) {
820 System.out.println( "OK." );
824 System.out.println( "failed." );
827 System.out.print( "Postorder Iterator: " );
828 if ( Test.testPostOrderIterator() ) {
829 System.out.println( "OK." );
833 System.out.println( "failed." );
836 System.out.print( "Preorder Iterator: " );
837 if ( Test.testPreOrderIterator() ) {
838 System.out.println( "OK." );
842 System.out.println( "failed." );
845 System.out.print( "Levelorder Iterator: " );
846 if ( Test.testLevelOrderIterator() ) {
847 System.out.println( "OK." );
851 System.out.println( "failed." );
854 System.out.print( "Re-id methods: " );
855 if ( Test.testReIdMethods() ) {
856 System.out.println( "OK." );
860 System.out.println( "failed." );
863 System.out.print( "Methods on last external nodes: " );
864 if ( Test.testLastExternalNodeMethods() ) {
865 System.out.println( "OK." );
869 System.out.println( "failed." );
872 System.out.print( "Methods on external nodes: " );
873 if ( Test.testExternalNodeRelatedMethods() ) {
874 System.out.println( "OK." );
878 System.out.println( "failed." );
881 System.out.print( "Deletion of external nodes: " );
882 if ( Test.testDeletionOfExternalNodes() ) {
883 System.out.println( "OK." );
887 System.out.println( "failed." );
890 System.out.print( "Subtree deletion: " );
891 if ( Test.testSubtreeDeletion() ) {
892 System.out.println( "OK." );
896 System.out.println( "failed." );
899 System.out.print( "Phylogeny branch: " );
900 if ( Test.testPhylogenyBranch() ) {
901 System.out.println( "OK." );
905 System.out.println( "failed." );
908 System.out.print( "Rerooting: " );
909 if ( Test.testRerooting() ) {
910 System.out.println( "OK." );
914 System.out.println( "failed." );
917 System.out.print( "Mipoint rooting: " );
918 if ( Test.testMidpointrooting() ) {
919 System.out.println( "OK." );
923 System.out.println( "failed." );
926 System.out.print( "Node removal: " );
927 if ( Test.testNodeRemoval() ) {
928 System.out.println( "OK." );
932 System.out.println( "failed." );
935 System.out.print( "Support count: " );
936 if ( Test.testSupportCount() ) {
937 System.out.println( "OK." );
941 System.out.println( "failed." );
944 System.out.print( "Support transfer: " );
945 if ( Test.testSupportTransfer() ) {
946 System.out.println( "OK." );
950 System.out.println( "failed." );
953 System.out.print( "Finding of LCA: " );
954 if ( Test.testGetLCA() ) {
955 System.out.println( "OK." );
959 System.out.println( "failed." );
962 System.out.print( "Finding of LCA 2: " );
963 if ( Test.testGetLCA2() ) {
964 System.out.println( "OK." );
968 System.out.println( "failed." );
971 System.out.print( "Calculation of distance between nodes: " );
972 if ( Test.testGetDistance() ) {
973 System.out.println( "OK." );
977 System.out.println( "failed." );
980 System.out.print( "Descriptive statistics: " );
981 if ( Test.testDescriptiveStatistics() ) {
982 System.out.println( "OK." );
986 System.out.println( "failed." );
989 System.out.print( "Data objects and methods: " );
990 if ( Test.testDataObjects() ) {
991 System.out.println( "OK." );
995 System.out.println( "failed." );
998 System.out.print( "Properties map: " );
999 if ( Test.testPropertiesMap() ) {
1000 System.out.println( "OK." );
1004 System.out.println( "failed." );
1007 System.out.print( "SDIse: " );
1008 if ( Test.testSDIse() ) {
1009 System.out.println( "OK." );
1013 System.out.println( "failed." );
1016 System.out.print( "SDIunrooted: " );
1017 if ( Test.testSDIunrooted() ) {
1018 System.out.println( "OK." );
1022 System.out.println( "failed." );
1025 System.out.print( "GSDI: " );
1026 if ( TestGSDI.test() ) {
1027 System.out.println( "OK." );
1031 System.out.println( "failed." );
1034 System.out.print( "RIO: " );
1035 if ( TestRIO.test() ) {
1036 System.out.println( "OK." );
1040 System.out.println( "failed." );
1043 System.out.print( "Phylogeny reconstruction:" );
1044 System.out.println();
1045 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
1046 System.out.println( "OK." );
1050 System.out.println( "failed." );
1053 System.out.print( "Analysis of domain architectures: " );
1054 System.out.println();
1055 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
1056 System.out.println( "OK." );
1060 System.out.println( "failed." );
1063 System.out.print( "GO: " );
1064 System.out.println();
1065 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
1066 System.out.println( "OK." );
1070 System.out.println( "failed." );
1073 System.out.print( "Modeling tools: " );
1074 if ( TestPccx.test() ) {
1075 System.out.println( "OK." );
1079 System.out.println( "failed." );
1082 System.out.print( "Split Matrix strict: " );
1083 if ( Test.testSplitStrict() ) {
1084 System.out.println( "OK." );
1088 System.out.println( "failed." );
1091 System.out.print( "Split Matrix: " );
1092 if ( Test.testSplit() ) {
1093 System.out.println( "OK." );
1097 System.out.println( "failed." );
1100 System.out.print( "Confidence Assessor: " );
1101 if ( Test.testConfidenceAssessor() ) {
1102 System.out.println( "OK." );
1106 System.out.println( "failed." );
1109 System.out.print( "Basic table: " );
1110 if ( Test.testBasicTable() ) {
1111 System.out.println( "OK." );
1115 System.out.println( "failed." );
1118 System.out.print( "General table: " );
1119 if ( Test.testGeneralTable() ) {
1120 System.out.println( "OK." );
1124 System.out.println( "failed." );
1127 System.out.print( "Amino acid sequence: " );
1128 if ( Test.testAminoAcidSequence() ) {
1129 System.out.println( "OK." );
1133 System.out.println( "failed." );
1136 System.out.print( "General MSA parser: " );
1137 if ( Test.testGeneralMsaParser() ) {
1138 System.out.println( "OK." );
1142 System.out.println( "failed." );
1145 System.out.print( "Fasta parser for msa: " );
1146 if ( Test.testFastaParser() ) {
1147 System.out.println( "OK." );
1151 System.out.println( "failed." );
1154 System.out.print( "Creation of balanced phylogeny: " );
1155 if ( Test.testCreateBalancedPhylogeny() ) {
1156 System.out.println( "OK." );
1160 System.out.println( "failed." );
1163 System.out.print( "Genbank accessor parsing: " );
1164 if ( Test.testGenbankAccessorParsing() ) {
1165 System.out.println( "OK." );
1169 System.out.println( "failed." );
1172 if ( PERFORM_DB_TESTS ) {
1173 System.out.print( "Uniprot Entry Retrieval: " );
1174 if ( Test.testUniprotEntryRetrieval() ) {
1175 System.out.println( "OK." );
1179 System.out.println( "failed." );
1183 if ( PERFORM_DB_TESTS ) {
1184 System.out.print( "Uniprot Taxonomy Search: " );
1185 if ( Test.testUniprotTaxonomySearch() ) {
1186 System.out.println( "OK." );
1190 System.out.println( "failed." );
1196 final String os = ForesterUtil.OS_NAME.toLowerCase();
1197 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
1198 path = "/usr/local/bin/mafft";
1200 else if ( os.indexOf( "win" ) >= 0 ) {
1201 path = "C:\\Program Files\\mafft-win\\mafft.bat";
1204 path = "/home/czmasek/bin/mafft";
1206 if ( !MsaInferrer.isInstalled( path ) ) {
1209 if ( !MsaInferrer.isInstalled( path ) ) {
1210 path = "/usr/local/bin/mafft";
1212 if ( MsaInferrer.isInstalled( path ) ) {
1213 System.out.print( "MAFFT (external program): " );
1214 if ( Test.testMafft( path ) ) {
1215 System.out.println( "OK." );
1219 System.out.println( "failed [will not count towards failed tests]" );
1223 System.out.print( "Next nodes with collapsed: " );
1224 if ( Test.testNextNodeWithCollapsing() ) {
1225 System.out.println( "OK." );
1229 System.out.println( "failed." );
1232 System.out.print( "Simple MSA quality: " );
1233 if ( Test.testMsaQualityMethod() ) {
1234 System.out.println( "OK." );
1238 System.out.println( "failed." );
1243 System.out.print( "NHX parsing from URL: " );
1244 if ( Test.testNHXparsingFromURL() ) {
1245 System.out.println( "OK." );
1249 System.out.println( "failed." );
1253 System.out.println();
1254 final Runtime rt = java.lang.Runtime.getRuntime();
1255 final long free_memory = rt.freeMemory() / 1000000;
1256 final long total_memory = rt.totalMemory() / 1000000;
1257 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
1258 + free_memory + "MB, total memory: " + total_memory + "MB)" );
1259 System.out.println();
1260 System.out.println( "Successful tests: " + succeeded );
1261 System.out.println( "Failed tests: " + failed );
1262 System.out.println();
1264 System.out.println( "OK." );
1267 System.out.println( "Not OK." );
1271 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
1272 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
1276 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
1277 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
1280 private static boolean testAminoAcidSequence() {
1282 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
1283 if ( aa1.getLength() != 13 ) {
1286 if ( aa1.getResidueAt( 0 ) != 'A' ) {
1289 if ( aa1.getResidueAt( 2 ) != 'K' ) {
1292 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
1295 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
1296 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
1299 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
1300 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
1303 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
1304 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
1308 catch ( final Exception e ) {
1309 e.printStackTrace();
1315 private static boolean testBasicDomain() {
1317 final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
1318 if ( !pd.getDomainId().equals( "id" ) ) {
1321 if ( pd.getNumber() != 1 ) {
1324 if ( pd.getTotalCount() != 4 ) {
1327 if ( !pd.equals( new BasicDomain( "id", 22, 111, ( short ) 1, ( short ) 4, 0.2, -12 ) ) ) {
1330 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1331 final BasicDomain a1_copy = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1332 final BasicDomain a1_equal = new BasicDomain( "a", 524, 743994, ( short ) 1, ( short ) 300, 3.0005, 230 );
1333 final BasicDomain a2 = new BasicDomain( "a", 1, 10, ( short ) 2, ( short ) 4, 0.1, -12 );
1334 final BasicDomain a3 = new BasicDomain( "A", 1, 10, ( short ) 1, ( short ) 4, 0.1, -12 );
1335 if ( !a1.equals( a1 ) ) {
1338 if ( !a1.equals( a1_copy ) ) {
1341 if ( !a1.equals( a1_equal ) ) {
1344 if ( !a1.equals( a2 ) ) {
1347 if ( a1.equals( a3 ) ) {
1350 if ( a1.compareTo( a1 ) != 0 ) {
1353 if ( a1.compareTo( a1_copy ) != 0 ) {
1356 if ( a1.compareTo( a1_equal ) != 0 ) {
1359 if ( a1.compareTo( a2 ) != 0 ) {
1362 if ( a1.compareTo( a3 ) == 0 ) {
1366 catch ( final Exception e ) {
1367 e.printStackTrace( System.out );
1373 private static boolean testBasicNodeMethods() {
1375 if ( PhylogenyNode.getNodeCount() != 0 ) {
1378 final PhylogenyNode n1 = new PhylogenyNode();
1379 final PhylogenyNode n2 = PhylogenyNode
1380 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1381 final PhylogenyNode n3 = PhylogenyNode
1382 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1383 final PhylogenyNode n4 = PhylogenyNode
1384 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1385 if ( n1.isHasAssignedEvent() ) {
1388 if ( PhylogenyNode.getNodeCount() != 4 ) {
1391 if ( n3.getIndicator() != 0 ) {
1394 if ( n3.getNumberOfExternalNodes() != 1 ) {
1397 if ( !n3.isExternal() ) {
1400 if ( !n3.isRoot() ) {
1403 if ( !n4.getName().equals( "n4" ) ) {
1407 catch ( final Exception e ) {
1408 e.printStackTrace( System.out );
1414 private static boolean testBasicPhyloXMLparsing() {
1416 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1417 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1418 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1420 if ( xml_parser.getErrorCount() > 0 ) {
1421 System.out.println( xml_parser.getErrorMessages().toString() );
1424 if ( phylogenies_0.length != 4 ) {
1427 final Phylogeny t1 = phylogenies_0[ 0 ];
1428 final Phylogeny t2 = phylogenies_0[ 1 ];
1429 final Phylogeny t3 = phylogenies_0[ 2 ];
1430 final Phylogeny t4 = phylogenies_0[ 3 ];
1431 if ( t1.getNumberOfExternalNodes() != 1 ) {
1434 if ( !t1.isRooted() ) {
1437 if ( t1.isRerootable() ) {
1440 if ( !t1.getType().equals( "gene_tree" ) ) {
1443 if ( t2.getNumberOfExternalNodes() != 2 ) {
1446 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
1449 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
1452 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1455 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1458 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1461 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1464 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1465 .startsWith( "actgtgggggt" ) ) {
1468 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1469 .startsWith( "ctgtgatgcat" ) ) {
1472 if ( t3.getNumberOfExternalNodes() != 4 ) {
1475 if ( !t1.getName().equals( "t1" ) ) {
1478 if ( !t2.getName().equals( "t2" ) ) {
1481 if ( !t3.getName().equals( "t3" ) ) {
1484 if ( !t4.getName().equals( "t4" ) ) {
1487 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1490 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1493 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1496 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1497 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1500 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1503 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1506 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1509 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1510 .equals( "apoptosis" ) ) {
1513 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1514 .equals( "GO:0006915" ) ) {
1517 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1518 .equals( "UniProtKB" ) ) {
1521 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1522 .equals( "experimental" ) ) {
1525 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1526 .equals( "function" ) ) {
1529 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1530 .getValue() != 1 ) {
1533 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1534 .getType().equals( "ml" ) ) {
1537 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1538 .equals( "apoptosis" ) ) {
1541 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1542 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1545 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1546 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1549 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1550 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1553 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1554 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1557 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1558 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1561 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1562 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1565 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1566 .equals( "GO:0005829" ) ) {
1569 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1570 .equals( "intracellular organelle" ) ) {
1573 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1576 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1577 .equals( "UniProt link" ) ) ) {
1580 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1583 final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
1584 if ( x.size() != 4 ) {
1588 for( final Accession acc : x ) {
1590 if ( !acc.getSource().equals( "KEGG" ) ) {
1593 if ( !acc.getValue().equals( "hsa:596" ) ) {
1600 catch ( final Exception e ) {
1601 e.printStackTrace( System.out );
1607 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1609 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1610 final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
1611 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1612 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1615 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1617 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1619 if ( xml_parser.getErrorCount() > 0 ) {
1620 System.out.println( xml_parser.getErrorMessages().toString() );
1623 if ( phylogenies_0.length != 4 ) {
1626 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1627 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1628 if ( phylogenies_t1.length != 1 ) {
1631 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1632 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1635 if ( !t1_rt.isRooted() ) {
1638 if ( t1_rt.isRerootable() ) {
1641 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1644 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1645 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1646 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1647 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1650 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1653 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1656 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1659 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1660 .startsWith( "actgtgggggt" ) ) {
1663 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1664 .startsWith( "ctgtgatgcat" ) ) {
1667 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1668 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1669 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1670 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1671 if ( phylogenies_1.length != 1 ) {
1674 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1675 if ( !t3_rt.getName().equals( "t3" ) ) {
1678 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1681 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1684 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1687 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1690 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1691 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1694 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1697 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1700 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1701 .equals( "UniProtKB" ) ) {
1704 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1705 .equals( "apoptosis" ) ) {
1708 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1709 .equals( "GO:0006915" ) ) {
1712 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1713 .equals( "UniProtKB" ) ) {
1716 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1717 .equals( "experimental" ) ) {
1720 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1721 .equals( "function" ) ) {
1724 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1725 .getValue() != 1 ) {
1728 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1729 .getType().equals( "ml" ) ) {
1732 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1733 .equals( "apoptosis" ) ) {
1736 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1737 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1740 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1741 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1744 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1745 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1748 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1749 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1752 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1753 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1756 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1757 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1760 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1761 .equals( "GO:0005829" ) ) {
1764 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1765 .equals( "intracellular organelle" ) ) {
1768 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1771 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1772 .equals( "UniProt link" ) ) ) {
1775 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1778 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1781 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1782 .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." ) ) ) {
1785 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1788 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1791 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1794 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1797 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1798 .equals( "ncbi" ) ) {
1801 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1804 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1805 .getName().equals( "B" ) ) {
1808 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1809 .getFrom() != 21 ) {
1812 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1815 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1816 .getLength() != 24 ) {
1819 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1820 .getConfidence() != 2144 ) {
1823 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1824 .equals( "pfam" ) ) {
1827 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1830 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1833 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1836 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1839 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1840 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1843 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1846 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1849 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1852 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1855 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1858 if ( taxbb.getSynonyms().size() != 2 ) {
1861 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1864 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1867 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1870 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1873 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1876 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1877 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1880 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1883 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1886 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1889 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1892 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1895 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1898 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1902 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1905 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1906 .equalsIgnoreCase( "435" ) ) {
1909 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1912 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1913 .equalsIgnoreCase( "443.7" ) ) {
1916 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1919 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1922 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1923 .equalsIgnoreCase( "433" ) ) {
1926 final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
1927 .getCrossReferences();
1928 if ( x.size() != 4 ) {
1932 for( final Accession acc : x ) {
1934 if ( !acc.getSource().equals( "KEGG" ) ) {
1937 if ( !acc.getValue().equals( "hsa:596" ) ) {
1944 catch ( final Exception e ) {
1945 e.printStackTrace( System.out );
1951 private static boolean testBasicPhyloXMLparsingValidating() {
1953 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1954 PhyloXmlParser xml_parser = null;
1956 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1958 catch ( final Exception e ) {
1959 // Do nothing -- means were not running from jar.
1961 if ( xml_parser == null ) {
1962 xml_parser = PhyloXmlParser.createPhyloXmlParser();
1963 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1964 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1967 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1970 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1972 if ( xml_parser.getErrorCount() > 0 ) {
1973 System.out.println( xml_parser.getErrorMessages().toString() );
1976 if ( phylogenies_0.length != 4 ) {
1979 final Phylogeny t1 = phylogenies_0[ 0 ];
1980 final Phylogeny t2 = phylogenies_0[ 1 ];
1981 final Phylogeny t3 = phylogenies_0[ 2 ];
1982 final Phylogeny t4 = phylogenies_0[ 3 ];
1983 if ( !t1.getName().equals( "t1" ) ) {
1986 if ( !t2.getName().equals( "t2" ) ) {
1989 if ( !t3.getName().equals( "t3" ) ) {
1992 if ( !t4.getName().equals( "t4" ) ) {
1995 if ( t1.getNumberOfExternalNodes() != 1 ) {
1998 if ( t2.getNumberOfExternalNodes() != 2 ) {
2001 if ( t3.getNumberOfExternalNodes() != 4 ) {
2004 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
2005 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
2006 if ( xml_parser.getErrorCount() > 0 ) {
2007 System.out.println( "errors:" );
2008 System.out.println( xml_parser.getErrorMessages().toString() );
2011 if ( phylogenies_1.length != 4 ) {
2014 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
2016 if ( xml_parser.getErrorCount() > 0 ) {
2017 System.out.println( "errors:" );
2018 System.out.println( xml_parser.getErrorMessages().toString() );
2021 if ( phylogenies_2.length != 1 ) {
2024 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
2027 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
2029 if ( xml_parser.getErrorCount() > 0 ) {
2030 System.out.println( xml_parser.getErrorMessages().toString() );
2033 if ( phylogenies_3.length != 2 ) {
2036 final Phylogeny a = phylogenies_3[ 0 ];
2037 if ( !a.getName().equals( "tree 4" ) ) {
2040 if ( a.getNumberOfExternalNodes() != 3 ) {
2043 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
2046 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
2049 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
2051 if ( xml_parser.getErrorCount() > 0 ) {
2052 System.out.println( xml_parser.getErrorMessages().toString() );
2055 if ( phylogenies_4.length != 1 ) {
2058 final Phylogeny s = phylogenies_4[ 0 ];
2059 if ( s.getNumberOfExternalNodes() != 6 ) {
2062 s.getNode( "first" );
2064 s.getNode( "\"<a'b&c'd\">\"" );
2065 s.getNode( "'''\"" );
2066 s.getNode( "\"\"\"" );
2067 s.getNode( "dick & doof" );
2069 catch ( final Exception e ) {
2070 e.printStackTrace( System.out );
2076 private static boolean testBasicProtein() {
2078 final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
2079 final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2080 final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2081 final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2082 final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2083 final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2084 final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2085 final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2086 p0.addProteinDomain( y );
2087 p0.addProteinDomain( e );
2088 p0.addProteinDomain( b );
2089 p0.addProteinDomain( c );
2090 p0.addProteinDomain( d );
2091 p0.addProteinDomain( a );
2092 p0.addProteinDomain( x );
2093 if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
2096 if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
2100 final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
2101 final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2102 aa0.addProteinDomain( a1 );
2103 if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
2106 if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
2110 final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
2111 final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2112 final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2113 aa1.addProteinDomain( a11 );
2114 aa1.addProteinDomain( a12 );
2115 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
2118 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
2121 aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2122 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
2125 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2128 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
2131 aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2132 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
2135 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
2138 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
2141 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
2144 aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2145 if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
2148 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
2151 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
2154 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
2157 aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
2158 if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
2161 if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
2164 if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
2167 if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
2171 final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
2172 final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
2173 final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
2174 final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
2175 final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
2176 final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
2177 final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
2178 final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
2179 final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
2180 final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
2181 final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
2182 final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2183 final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
2184 final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
2185 final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
2186 final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
2187 final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
2188 final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
2189 final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
2190 final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
2191 final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
2192 p00.addProteinDomain( y0 );
2193 p00.addProteinDomain( e0 );
2194 p00.addProteinDomain( b0 );
2195 p00.addProteinDomain( c0 );
2196 p00.addProteinDomain( d0 );
2197 p00.addProteinDomain( a0 );
2198 p00.addProteinDomain( x0 );
2199 p00.addProteinDomain( y1 );
2200 p00.addProteinDomain( y2 );
2201 p00.addProteinDomain( y3 );
2202 p00.addProteinDomain( e1 );
2203 p00.addProteinDomain( e2 );
2204 p00.addProteinDomain( e3 );
2205 p00.addProteinDomain( e4 );
2206 p00.addProteinDomain( e5 );
2207 p00.addProteinDomain( z0 );
2208 p00.addProteinDomain( z1 );
2209 p00.addProteinDomain( z2 );
2210 p00.addProteinDomain( zz0 );
2211 p00.addProteinDomain( zz1 );
2212 if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
2215 if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
2218 if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2221 if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
2224 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" ) ) {
2227 // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
2228 final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
2229 final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
2230 final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
2231 final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
2232 final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
2233 final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
2234 final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
2235 final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
2236 final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
2237 final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
2238 final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
2239 final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
2240 final BasicProtein p = new BasicProtein( "p", "owl", 0 );
2241 p.addProteinDomain( B15 );
2242 p.addProteinDomain( C50 );
2243 p.addProteinDomain( A60 );
2244 p.addProteinDomain( A30 );
2245 p.addProteinDomain( C70 );
2246 p.addProteinDomain( B35 );
2247 p.addProteinDomain( B40 );
2248 p.addProteinDomain( A0 );
2249 p.addProteinDomain( A10 );
2250 p.addProteinDomain( A20 );
2251 p.addProteinDomain( B25 );
2252 p.addProteinDomain( D80 );
2253 List<String> domains_ids = new ArrayList<String>();
2254 domains_ids.add( "A" );
2255 domains_ids.add( "B" );
2256 domains_ids.add( "C" );
2257 if ( !p.contains( domains_ids, false ) ) {
2260 if ( !p.contains( domains_ids, true ) ) {
2263 domains_ids.add( "X" );
2264 if ( p.contains( domains_ids, false ) ) {
2267 if ( p.contains( domains_ids, true ) ) {
2270 domains_ids = new ArrayList<String>();
2271 domains_ids.add( "A" );
2272 domains_ids.add( "C" );
2273 domains_ids.add( "D" );
2274 if ( !p.contains( domains_ids, false ) ) {
2277 if ( !p.contains( domains_ids, true ) ) {
2280 domains_ids = new ArrayList<String>();
2281 domains_ids.add( "A" );
2282 domains_ids.add( "D" );
2283 domains_ids.add( "C" );
2284 if ( !p.contains( domains_ids, false ) ) {
2287 if ( p.contains( domains_ids, true ) ) {
2290 domains_ids = new ArrayList<String>();
2291 domains_ids.add( "A" );
2292 domains_ids.add( "A" );
2293 domains_ids.add( "B" );
2294 if ( !p.contains( domains_ids, false ) ) {
2297 if ( !p.contains( domains_ids, true ) ) {
2300 domains_ids = new ArrayList<String>();
2301 domains_ids.add( "A" );
2302 domains_ids.add( "A" );
2303 domains_ids.add( "A" );
2304 domains_ids.add( "B" );
2305 domains_ids.add( "B" );
2306 if ( !p.contains( domains_ids, false ) ) {
2309 if ( !p.contains( domains_ids, true ) ) {
2312 domains_ids = new ArrayList<String>();
2313 domains_ids.add( "A" );
2314 domains_ids.add( "A" );
2315 domains_ids.add( "B" );
2316 domains_ids.add( "A" );
2317 domains_ids.add( "B" );
2318 domains_ids.add( "B" );
2319 domains_ids.add( "A" );
2320 domains_ids.add( "B" );
2321 domains_ids.add( "C" );
2322 domains_ids.add( "A" );
2323 domains_ids.add( "C" );
2324 domains_ids.add( "D" );
2325 if ( !p.contains( domains_ids, false ) ) {
2328 if ( p.contains( domains_ids, true ) ) {
2332 catch ( final Exception e ) {
2333 e.printStackTrace( System.out );
2339 private static boolean testBasicTable() {
2341 final BasicTable<String> t0 = new BasicTable<String>();
2342 if ( t0.getNumberOfColumns() != 0 ) {
2345 if ( t0.getNumberOfRows() != 0 ) {
2348 t0.setValue( 3, 2, "23" );
2349 t0.setValue( 10, 1, "error" );
2350 t0.setValue( 10, 1, "110" );
2351 t0.setValue( 9, 1, "19" );
2352 t0.setValue( 1, 10, "101" );
2353 t0.setValue( 10, 10, "1010" );
2354 t0.setValue( 100, 10, "10100" );
2355 t0.setValue( 0, 0, "00" );
2356 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2359 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2362 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2365 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2368 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2371 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2374 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2377 if ( t0.getNumberOfColumns() != 101 ) {
2380 if ( t0.getNumberOfRows() != 11 ) {
2383 if ( t0.getValueAsString( 49, 4 ) != null ) {
2386 final String l = ForesterUtil.getLineSeparator();
2387 final StringBuffer source = new StringBuffer();
2388 source.append( "" + l );
2389 source.append( "# 1 1 1 1 1 1 1 1" + l );
2390 source.append( " 00 01 02 03" + l );
2391 source.append( " 10 11 12 13 " + l );
2392 source.append( "20 21 22 23 " + l );
2393 source.append( " 30 31 32 33" + l );
2394 source.append( "40 41 42 43" + l );
2395 source.append( " # 1 1 1 1 1 " + l );
2396 source.append( "50 51 52 53 54" + l );
2397 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
2398 if ( t1.getNumberOfColumns() != 5 ) {
2401 if ( t1.getNumberOfRows() != 6 ) {
2404 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
2407 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
2410 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
2413 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
2416 final StringBuffer source1 = new StringBuffer();
2417 source1.append( "" + l );
2418 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2419 source1.append( " 00; 01 ;02;03" + l );
2420 source1.append( " 10; 11; 12; 13 " + l );
2421 source1.append( "20; 21; 22; 23 " + l );
2422 source1.append( " 30; 31; 32; 33" + l );
2423 source1.append( "40;41;42;43" + l );
2424 source1.append( " # 1 1 1 1 1 " + l );
2425 source1.append( ";;;50 ; ;52; 53;;54 " + l );
2426 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
2427 if ( t2.getNumberOfColumns() != 5 ) {
2430 if ( t2.getNumberOfRows() != 6 ) {
2433 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
2436 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
2439 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
2442 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
2445 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
2448 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
2451 final StringBuffer source2 = new StringBuffer();
2452 source2.append( "" + l );
2453 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
2454 source2.append( " 00; 01 ;02;03" + l );
2455 source2.append( " 10; 11; 12; 13 " + l );
2456 source2.append( "20; 21; 22; 23 " + l );
2457 source2.append( " " + l );
2458 source2.append( " 30; 31; 32; 33" + l );
2459 source2.append( "40;41;42;43" + l );
2460 source2.append( " comment: 1 1 1 1 1 " + l );
2461 source2.append( ";;;50 ; 52; 53;;54 " + l );
2462 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
2468 if ( tl.size() != 2 ) {
2471 final BasicTable<String> t3 = tl.get( 0 );
2472 final BasicTable<String> t4 = tl.get( 1 );
2473 if ( t3.getNumberOfColumns() != 4 ) {
2476 if ( t3.getNumberOfRows() != 3 ) {
2479 if ( t4.getNumberOfColumns() != 4 ) {
2482 if ( t4.getNumberOfRows() != 3 ) {
2485 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
2488 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
2492 catch ( final Exception e ) {
2493 e.printStackTrace( System.out );
2499 private static boolean testBasicTolXMLparsing() {
2501 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2502 final TolParser parser = new TolParser();
2503 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
2504 if ( parser.getErrorCount() > 0 ) {
2505 System.out.println( parser.getErrorMessages().toString() );
2508 if ( phylogenies_0.length != 1 ) {
2511 final Phylogeny t1 = phylogenies_0[ 0 ];
2512 if ( t1.getNumberOfExternalNodes() != 5 ) {
2515 if ( !t1.isRooted() ) {
2518 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
2521 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
2524 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
2527 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
2530 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
2531 if ( parser.getErrorCount() > 0 ) {
2532 System.out.println( parser.getErrorMessages().toString() );
2535 if ( phylogenies_1.length != 1 ) {
2538 final Phylogeny t2 = phylogenies_1[ 0 ];
2539 if ( t2.getNumberOfExternalNodes() != 664 ) {
2542 if ( !t2.isRooted() ) {
2545 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
2548 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
2551 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2554 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
2557 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
2560 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
2561 .equals( "Aquifex" ) ) {
2564 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
2565 if ( parser.getErrorCount() > 0 ) {
2566 System.out.println( parser.getErrorMessages().toString() );
2569 if ( phylogenies_2.length != 1 ) {
2572 final Phylogeny t3 = phylogenies_2[ 0 ];
2573 if ( t3.getNumberOfExternalNodes() != 184 ) {
2576 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
2579 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
2582 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
2585 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
2586 if ( parser.getErrorCount() > 0 ) {
2587 System.out.println( parser.getErrorMessages().toString() );
2590 if ( phylogenies_3.length != 1 ) {
2593 final Phylogeny t4 = phylogenies_3[ 0 ];
2594 if ( t4.getNumberOfExternalNodes() != 1 ) {
2597 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
2600 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
2603 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
2606 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
2607 if ( parser.getErrorCount() > 0 ) {
2608 System.out.println( parser.getErrorMessages().toString() );
2611 if ( phylogenies_4.length != 1 ) {
2614 final Phylogeny t5 = phylogenies_4[ 0 ];
2615 if ( t5.getNumberOfExternalNodes() != 13 ) {
2618 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
2621 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
2624 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
2628 catch ( final Exception e ) {
2629 e.printStackTrace( System.out );
2635 private static boolean testBasicTreeMethods() {
2637 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2638 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
2639 if ( t2.getNumberOfExternalNodes() != 4 ) {
2642 if ( t2.getHeight() != 8.5 ) {
2645 if ( !t2.isCompletelyBinary() ) {
2648 if ( t2.isEmpty() ) {
2651 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
2652 if ( t3.getNumberOfExternalNodes() != 5 ) {
2655 if ( t3.getHeight() != 11 ) {
2658 if ( t3.isCompletelyBinary() ) {
2661 final PhylogenyNode n = t3.getNode( "ABC" );
2662 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 ];
2663 if ( t4.getNumberOfExternalNodes() != 9 ) {
2666 if ( t4.getHeight() != 11 ) {
2669 if ( t4.isCompletelyBinary() ) {
2672 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)" );
2673 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
2674 if ( t5.getNumberOfExternalNodes() != 8 ) {
2677 if ( t5.getHeight() != 15 ) {
2680 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)" );
2681 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
2682 if ( t6.getHeight() != 15 ) {
2685 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)" );
2686 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
2687 if ( t7.getHeight() != 15 ) {
2690 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)" );
2691 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
2692 if ( t8.getNumberOfExternalNodes() != 10 ) {
2695 if ( t8.getHeight() != 15 ) {
2698 final char[] a9 = new char[] { 'a' };
2699 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
2700 if ( t9.getHeight() != 0 ) {
2703 final char[] a10 = new char[] { 'a', ':', '6' };
2704 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
2705 if ( t10.getHeight() != 6 ) {
2709 catch ( final Exception e ) {
2710 e.printStackTrace( System.out );
2716 private static boolean testConfidenceAssessor() {
2718 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2719 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2720 final Phylogeny[] ev0 = factory
2721 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
2723 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
2724 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2727 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2730 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2731 final Phylogeny[] ev1 = factory
2732 .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)));",
2734 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2735 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2738 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2741 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2742 final Phylogeny[] ev_b = factory
2743 .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",
2745 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2746 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2749 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2753 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2754 final Phylogeny[] ev1x = factory
2755 .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)));",
2757 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2758 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2761 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2764 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2765 final Phylogeny[] ev_bx = factory
2766 .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",
2768 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2769 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2772 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2776 final Phylogeny[] t2 = factory
2777 .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);",
2779 final Phylogeny[] ev2 = factory
2780 .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);",
2782 for( final Phylogeny target : t2 ) {
2783 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2786 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2787 new NHXParser() )[ 0 ];
2788 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2789 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2790 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2793 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2796 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2800 catch ( final Exception e ) {
2801 e.printStackTrace();
2807 private static boolean testCopyOfNodeData() {
2809 final PhylogenyNode n1 = PhylogenyNode
2810 .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]" );
2811 final PhylogenyNode n2 = n1.copyNodeData();
2812 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2816 catch ( final Exception e ) {
2817 e.printStackTrace();
2823 private static boolean testTreeCopy() {
2825 final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
2826 final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
2827 final Phylogeny t1 = t0.copy();
2828 if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
2831 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2834 t0.deleteSubtree( t0.getNode( "c" ), true );
2835 t0.deleteSubtree( t0.getNode( "a" ), true );
2836 t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
2837 t0.getNode( "b" ).setName( "Bee" );
2838 if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
2841 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2844 t0.deleteSubtree( t0.getNode( "e" ), true );
2845 t0.deleteSubtree( t0.getNode( "Bee" ), true );
2846 t0.deleteSubtree( t0.getNode( "d" ), true );
2847 if ( !t1.toNewHampshireX().equals( str_0 ) ) {
2851 catch ( final Exception e ) {
2852 e.printStackTrace();
2858 private static boolean testCreateBalancedPhylogeny() {
2860 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
2861 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
2864 if ( p0.getNumberOfExternalNodes() != 15625 ) {
2867 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
2868 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
2871 if ( p1.getNumberOfExternalNodes() != 100 ) {
2875 catch ( final Exception e ) {
2876 e.printStackTrace();
2882 private static boolean testCreateUriForSeqWeb() {
2884 final PhylogenyNode n = new PhylogenyNode();
2885 n.setName( "tr|B3RJ64" );
2886 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
2889 n.setName( "B0LM41_HUMAN" );
2890 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
2893 n.setName( "NP_001025424" );
2894 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
2897 n.setName( "_NM_001030253-" );
2898 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
2901 n.setName( "XM_002122186" );
2902 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
2905 n.setName( "dgh_AAA34956_gdg" );
2906 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2909 n.setName( "AAA34956" );
2910 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
2913 n.setName( "GI:394892" );
2914 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2915 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2918 n.setName( "gi_394892" );
2919 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2920 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2923 n.setName( "gi6335_gi_394892_56635_Gi_43" );
2924 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
2925 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2928 n.setName( "P12345" );
2929 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2930 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2933 n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
2934 if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
2935 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
2939 catch ( final Exception e ) {
2940 e.printStackTrace( System.out );
2946 private static boolean testDataObjects() {
2948 final Confidence s0 = new Confidence();
2949 final Confidence s1 = new Confidence();
2950 if ( !s0.isEqual( s1 ) ) {
2953 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2954 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2955 if ( s2.isEqual( s1 ) ) {
2958 if ( !s2.isEqual( s3 ) ) {
2961 final Confidence s4 = ( Confidence ) s3.copy();
2962 if ( !s4.isEqual( s3 ) ) {
2969 final Taxonomy t1 = new Taxonomy();
2970 final Taxonomy t2 = new Taxonomy();
2971 final Taxonomy t3 = new Taxonomy();
2972 final Taxonomy t4 = new Taxonomy();
2973 final Taxonomy t5 = new Taxonomy();
2974 t1.setIdentifier( new Identifier( "ecoli" ) );
2975 t1.setTaxonomyCode( "ECOLI" );
2976 t1.setScientificName( "E. coli" );
2977 t1.setCommonName( "coli" );
2978 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2979 if ( !t1.isEqual( t0 ) ) {
2982 t2.setIdentifier( new Identifier( "ecoli" ) );
2983 t2.setTaxonomyCode( "OTHER" );
2984 t2.setScientificName( "what" );
2985 t2.setCommonName( "something" );
2986 if ( !t1.isEqual( t2 ) ) {
2989 t2.setIdentifier( new Identifier( "nemve" ) );
2990 if ( t1.isEqual( t2 ) ) {
2993 t1.setIdentifier( null );
2994 t3.setTaxonomyCode( "ECOLI" );
2995 t3.setScientificName( "what" );
2996 t3.setCommonName( "something" );
2997 if ( !t1.isEqual( t3 ) ) {
3000 t1.setIdentifier( null );
3001 t1.setTaxonomyCode( "" );
3002 t4.setScientificName( "E. ColI" );
3003 t4.setCommonName( "something" );
3004 if ( !t1.isEqual( t4 ) ) {
3007 t4.setScientificName( "B. subtilis" );
3008 t4.setCommonName( "something" );
3009 if ( t1.isEqual( t4 ) ) {
3012 t1.setIdentifier( null );
3013 t1.setTaxonomyCode( "" );
3014 t1.setScientificName( "" );
3015 t5.setCommonName( "COLI" );
3016 if ( !t1.isEqual( t5 ) ) {
3019 t5.setCommonName( "vibrio" );
3020 if ( t1.isEqual( t5 ) ) {
3025 final Identifier id0 = new Identifier( "123", "pfam" );
3026 final Identifier id1 = ( Identifier ) id0.copy();
3027 if ( !id1.isEqual( id1 ) ) {
3030 if ( !id1.isEqual( id0 ) ) {
3033 if ( !id0.isEqual( id1 ) ) {
3040 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
3041 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
3042 if ( !pd1.isEqual( pd1 ) ) {
3045 if ( !pd1.isEqual( pd0 ) ) {
3050 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
3051 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
3052 if ( !pd3.isEqual( pd3 ) ) {
3055 if ( !pd2.isEqual( pd3 ) ) {
3058 if ( !pd0.isEqual( pd3 ) ) {
3063 // DomainArchitecture
3064 // ------------------
3065 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
3066 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
3067 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
3068 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
3069 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
3070 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
3075 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
3076 if ( ds0.getNumberOfDomains() != 4 ) {
3079 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
3080 if ( !ds0.isEqual( ds0 ) ) {
3083 if ( !ds0.isEqual( ds1 ) ) {
3086 if ( ds1.getNumberOfDomains() != 4 ) {
3089 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
3094 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
3095 if ( ds0.isEqual( ds2 ) ) {
3101 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
3102 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
3103 System.out.println( ds3.toNHX() );
3106 if ( ds3.getNumberOfDomains() != 3 ) {
3111 final Event e1 = new Event( Event.EventType.fusion );
3112 if ( e1.isDuplication() ) {
3115 if ( !e1.isFusion() ) {
3118 if ( !e1.asText().toString().equals( "fusion" ) ) {
3121 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
3124 final Event e11 = new Event( Event.EventType.fusion );
3125 if ( !e11.isEqual( e1 ) ) {
3128 if ( !e11.toNHX().toString().equals( "" ) ) {
3131 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
3132 if ( e2.isDuplication() ) {
3135 if ( !e2.isSpeciationOrDuplication() ) {
3138 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
3141 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
3144 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
3147 if ( e11.isEqual( e2 ) ) {
3150 final Event e2c = ( Event ) e2.copy();
3151 if ( !e2c.isEqual( e2 ) ) {
3154 Event e3 = new Event( 1, 2, 3 );
3155 if ( e3.isDuplication() ) {
3158 if ( e3.isSpeciation() ) {
3161 if ( e3.isGeneLoss() ) {
3164 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3167 final Event e3c = ( Event ) e3.copy();
3168 final Event e3cc = ( Event ) e3c.copy();
3169 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
3173 if ( !e3c.isEqual( e3cc ) ) {
3176 Event e4 = new Event( 1, 2, 3 );
3177 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3180 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
3183 final Event e4c = ( Event ) e4.copy();
3185 final Event e4cc = ( Event ) e4c.copy();
3186 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
3189 if ( !e4c.isEqual( e4cc ) ) {
3192 final Event e5 = new Event();
3193 if ( !e5.isUnassigned() ) {
3196 if ( !e5.asText().toString().equals( "unassigned" ) ) {
3199 if ( !e5.asSimpleText().toString().equals( "" ) ) {
3202 final Event e6 = new Event( 1, 0, 0 );
3203 if ( !e6.asText().toString().equals( "duplication" ) ) {
3206 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
3209 final Event e7 = new Event( 0, 1, 0 );
3210 if ( !e7.asText().toString().equals( "speciation" ) ) {
3213 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
3216 final Event e8 = new Event( 0, 0, 1 );
3217 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
3220 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
3224 catch ( final Exception e ) {
3225 e.printStackTrace( System.out );
3231 private static boolean testDeletionOfExternalNodes() {
3233 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3234 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
3235 final PhylogenyWriter w = new PhylogenyWriter();
3236 if ( t0.isEmpty() ) {
3239 if ( t0.getNumberOfExternalNodes() != 1 ) {
3242 t0.deleteSubtree( t0.getNode( "A" ), false );
3243 if ( t0.getNumberOfExternalNodes() != 0 ) {
3246 if ( !t0.isEmpty() ) {
3249 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
3250 if ( t1.getNumberOfExternalNodes() != 2 ) {
3253 t1.deleteSubtree( t1.getNode( "A" ), false );
3254 if ( t1.getNumberOfExternalNodes() != 1 ) {
3257 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
3260 t1.deleteSubtree( t1.getNode( "B" ), false );
3261 if ( t1.getNumberOfExternalNodes() != 1 ) {
3264 t1.deleteSubtree( t1.getNode( "r" ), false );
3265 if ( !t1.isEmpty() ) {
3268 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
3269 if ( t2.getNumberOfExternalNodes() != 3 ) {
3272 t2.deleteSubtree( t2.getNode( "B" ), false );
3273 if ( t2.getNumberOfExternalNodes() != 2 ) {
3276 t2.toNewHampshireX();
3277 PhylogenyNode n = t2.getNode( "A" );
3278 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3281 t2.deleteSubtree( t2.getNode( "A" ), false );
3282 if ( t2.getNumberOfExternalNodes() != 2 ) {
3285 t2.deleteSubtree( t2.getNode( "C" ), true );
3286 if ( t2.getNumberOfExternalNodes() != 1 ) {
3289 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3290 if ( t3.getNumberOfExternalNodes() != 4 ) {
3293 t3.deleteSubtree( t3.getNode( "B" ), true );
3294 if ( t3.getNumberOfExternalNodes() != 3 ) {
3297 n = t3.getNode( "A" );
3298 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
3301 n = n.getNextExternalNode();
3302 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3305 t3.deleteSubtree( t3.getNode( "A" ), true );
3306 if ( t3.getNumberOfExternalNodes() != 2 ) {
3309 n = t3.getNode( "C" );
3310 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
3313 t3.deleteSubtree( t3.getNode( "C" ), true );
3314 if ( t3.getNumberOfExternalNodes() != 1 ) {
3317 t3.deleteSubtree( t3.getNode( "D" ), true );
3318 if ( t3.getNumberOfExternalNodes() != 0 ) {
3321 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3322 if ( t4.getNumberOfExternalNodes() != 6 ) {
3325 t4.deleteSubtree( t4.getNode( "B2" ), true );
3326 if ( t4.getNumberOfExternalNodes() != 5 ) {
3329 String s = w.toNewHampshire( t4, false, true ).toString();
3330 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3333 t4.deleteSubtree( t4.getNode( "B11" ), true );
3334 if ( t4.getNumberOfExternalNodes() != 4 ) {
3337 t4.deleteSubtree( t4.getNode( "C" ), true );
3338 if ( t4.getNumberOfExternalNodes() != 3 ) {
3341 n = t4.getNode( "A" );
3342 n = n.getNextExternalNode();
3343 if ( !n.getName().equals( "B12" ) ) {
3346 n = n.getNextExternalNode();
3347 if ( !n.getName().equals( "D" ) ) {
3350 s = w.toNewHampshire( t4, false, true ).toString();
3351 if ( !s.equals( "((A,B12),D);" ) ) {
3354 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3355 t5.deleteSubtree( t5.getNode( "A" ), true );
3356 if ( t5.getNumberOfExternalNodes() != 5 ) {
3359 s = w.toNewHampshire( t5, false, true ).toString();
3360 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
3363 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3364 t6.deleteSubtree( t6.getNode( "B11" ), true );
3365 if ( t6.getNumberOfExternalNodes() != 5 ) {
3368 s = w.toNewHampshire( t6, false, false ).toString();
3369 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
3372 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3373 t7.deleteSubtree( t7.getNode( "B12" ), true );
3374 if ( t7.getNumberOfExternalNodes() != 5 ) {
3377 s = w.toNewHampshire( t7, false, true ).toString();
3378 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
3381 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3382 t8.deleteSubtree( t8.getNode( "B2" ), true );
3383 if ( t8.getNumberOfExternalNodes() != 5 ) {
3386 s = w.toNewHampshire( t8, false, false ).toString();
3387 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
3390 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3391 t9.deleteSubtree( t9.getNode( "C" ), true );
3392 if ( t9.getNumberOfExternalNodes() != 5 ) {
3395 s = w.toNewHampshire( t9, false, true ).toString();
3396 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
3399 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
3400 t10.deleteSubtree( t10.getNode( "D" ), true );
3401 if ( t10.getNumberOfExternalNodes() != 5 ) {
3404 s = w.toNewHampshire( t10, false, true ).toString();
3405 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
3408 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
3409 t11.deleteSubtree( t11.getNode( "A" ), true );
3410 if ( t11.getNumberOfExternalNodes() != 2 ) {
3413 s = w.toNewHampshire( t11, false, true ).toString();
3414 if ( !s.equals( "(B,C);" ) ) {
3417 t11.deleteSubtree( t11.getNode( "C" ), true );
3418 if ( t11.getNumberOfExternalNodes() != 1 ) {
3421 s = w.toNewHampshire( t11, false, false ).toString();
3422 if ( !s.equals( "B;" ) ) {
3425 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
3426 t12.deleteSubtree( t12.getNode( "B2" ), true );
3427 if ( t12.getNumberOfExternalNodes() != 8 ) {
3430 s = w.toNewHampshire( t12, false, true ).toString();
3431 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
3434 t12.deleteSubtree( t12.getNode( "B3" ), true );
3435 if ( t12.getNumberOfExternalNodes() != 7 ) {
3438 s = w.toNewHampshire( t12, false, true ).toString();
3439 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
3442 t12.deleteSubtree( t12.getNode( "C3" ), true );
3443 if ( t12.getNumberOfExternalNodes() != 6 ) {
3446 s = w.toNewHampshire( t12, false, true ).toString();
3447 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
3450 t12.deleteSubtree( t12.getNode( "A1" ), true );
3451 if ( t12.getNumberOfExternalNodes() != 5 ) {
3454 s = w.toNewHampshire( t12, false, true ).toString();
3455 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
3458 t12.deleteSubtree( t12.getNode( "B1" ), true );
3459 if ( t12.getNumberOfExternalNodes() != 4 ) {
3462 s = w.toNewHampshire( t12, false, true ).toString();
3463 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
3466 t12.deleteSubtree( t12.getNode( "A3" ), true );
3467 if ( t12.getNumberOfExternalNodes() != 3 ) {
3470 s = w.toNewHampshire( t12, false, true ).toString();
3471 if ( !s.equals( "(A2,(C1,C2));" ) ) {
3474 t12.deleteSubtree( t12.getNode( "A2" ), true );
3475 if ( t12.getNumberOfExternalNodes() != 2 ) {
3478 s = w.toNewHampshire( t12, false, true ).toString();
3479 if ( !s.equals( "(C1,C2);" ) ) {
3482 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
3483 t13.deleteSubtree( t13.getNode( "D" ), true );
3484 if ( t13.getNumberOfExternalNodes() != 4 ) {
3487 s = w.toNewHampshire( t13, false, true ).toString();
3488 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
3491 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
3492 t14.deleteSubtree( t14.getNode( "E" ), true );
3493 if ( t14.getNumberOfExternalNodes() != 5 ) {
3496 s = w.toNewHampshire( t14, false, true ).toString();
3497 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
3500 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
3501 t15.deleteSubtree( t15.getNode( "B2" ), true );
3502 if ( t15.getNumberOfExternalNodes() != 11 ) {
3505 t15.deleteSubtree( t15.getNode( "B1" ), true );
3506 if ( t15.getNumberOfExternalNodes() != 10 ) {
3509 t15.deleteSubtree( t15.getNode( "B3" ), true );
3510 if ( t15.getNumberOfExternalNodes() != 9 ) {
3513 t15.deleteSubtree( t15.getNode( "B4" ), true );
3514 if ( t15.getNumberOfExternalNodes() != 8 ) {
3517 t15.deleteSubtree( t15.getNode( "A1" ), true );
3518 if ( t15.getNumberOfExternalNodes() != 7 ) {
3521 t15.deleteSubtree( t15.getNode( "C4" ), true );
3522 if ( t15.getNumberOfExternalNodes() != 6 ) {
3526 catch ( final Exception e ) {
3527 e.printStackTrace( System.out );
3533 private static boolean testDescriptiveStatistics() {
3535 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
3536 dss1.addValue( 82 );
3537 dss1.addValue( 78 );
3538 dss1.addValue( 70 );
3539 dss1.addValue( 58 );
3540 dss1.addValue( 42 );
3541 if ( dss1.getN() != 5 ) {
3544 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
3547 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
3550 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
3553 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
3556 if ( !Test.isEqual( dss1.median(), 70 ) ) {
3559 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
3562 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
3565 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
3568 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
3571 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
3574 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
3577 dss1.addValue( 123 );
3578 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
3581 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
3584 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
3587 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
3588 dss2.addValue( -1.85 );
3589 dss2.addValue( 57.5 );
3590 dss2.addValue( 92.78 );
3591 dss2.addValue( 57.78 );
3592 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
3595 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
3598 final double[] a = dss2.getDataAsDoubleArray();
3599 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
3602 dss2.addValue( -100 );
3603 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
3606 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
3609 final double[] ds = new double[ 14 ];
3624 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
3625 if ( bins.length != 4 ) {
3628 if ( bins[ 0 ] != 2 ) {
3631 if ( bins[ 1 ] != 3 ) {
3634 if ( bins[ 2 ] != 4 ) {
3637 if ( bins[ 3 ] != 5 ) {
3640 final double[] ds1 = new double[ 9 ];
3650 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
3651 if ( bins1.length != 4 ) {
3654 if ( bins1[ 0 ] != 2 ) {
3657 if ( bins1[ 1 ] != 3 ) {
3660 if ( bins1[ 2 ] != 0 ) {
3663 if ( bins1[ 3 ] != 4 ) {
3666 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
3667 if ( bins1_1.length != 3 ) {
3670 if ( bins1_1[ 0 ] != 3 ) {
3673 if ( bins1_1[ 1 ] != 2 ) {
3676 if ( bins1_1[ 2 ] != 4 ) {
3679 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
3680 if ( bins1_2.length != 3 ) {
3683 if ( bins1_2[ 0 ] != 2 ) {
3686 if ( bins1_2[ 1 ] != 2 ) {
3689 if ( bins1_2[ 2 ] != 2 ) {
3692 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
3706 dss3.addValue( 10 );
3707 dss3.addValue( 10 );
3708 dss3.addValue( 10 );
3709 final AsciiHistogram histo = new AsciiHistogram( dss3 );
3710 histo.toStringBuffer( 10, '=', 40, 5 );
3711 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
3713 catch ( final Exception e ) {
3714 e.printStackTrace( System.out );
3720 private static boolean testDir( final String file ) {
3722 final File f = new File( file );
3723 if ( !f.exists() ) {
3726 if ( !f.isDirectory() ) {
3729 if ( !f.canRead() ) {
3733 catch ( final Exception e ) {
3739 private static boolean testGenbankAccessorParsing() {
3740 //The format for GenBank Accession numbers are:
3741 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
3742 //Protein: 3 letters + 5 numerals
3743 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
3744 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
3747 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
3750 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
3753 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
3756 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
3759 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
3762 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
3765 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
3768 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
3771 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
3774 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
3777 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
3780 if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
3783 if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
3789 private static boolean testExternalNodeRelatedMethods() {
3791 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3792 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3793 PhylogenyNode n = t1.getNode( "A" );
3794 n = n.getNextExternalNode();
3795 if ( !n.getName().equals( "B" ) ) {
3798 n = n.getNextExternalNode();
3799 if ( !n.getName().equals( "C" ) ) {
3802 n = n.getNextExternalNode();
3803 if ( !n.getName().equals( "D" ) ) {
3806 n = t1.getNode( "B" );
3807 while ( !n.isLastExternalNode() ) {
3808 n = n.getNextExternalNode();
3810 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
3811 n = t2.getNode( "A" );
3812 n = n.getNextExternalNode();
3813 if ( !n.getName().equals( "B" ) ) {
3816 n = n.getNextExternalNode();
3817 if ( !n.getName().equals( "C" ) ) {
3820 n = n.getNextExternalNode();
3821 if ( !n.getName().equals( "D" ) ) {
3824 n = t2.getNode( "B" );
3825 while ( !n.isLastExternalNode() ) {
3826 n = n.getNextExternalNode();
3828 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
3829 n = t3.getNode( "A" );
3830 n = n.getNextExternalNode();
3831 if ( !n.getName().equals( "B" ) ) {
3834 n = n.getNextExternalNode();
3835 if ( !n.getName().equals( "C" ) ) {
3838 n = n.getNextExternalNode();
3839 if ( !n.getName().equals( "D" ) ) {
3842 n = n.getNextExternalNode();
3843 if ( !n.getName().equals( "E" ) ) {
3846 n = n.getNextExternalNode();
3847 if ( !n.getName().equals( "F" ) ) {
3850 n = n.getNextExternalNode();
3851 if ( !n.getName().equals( "G" ) ) {
3854 n = n.getNextExternalNode();
3855 if ( !n.getName().equals( "H" ) ) {
3858 n = t3.getNode( "B" );
3859 while ( !n.isLastExternalNode() ) {
3860 n = n.getNextExternalNode();
3862 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
3863 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
3864 final PhylogenyNode node = iter.next();
3866 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
3867 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
3868 final PhylogenyNode node = iter.next();
3870 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
3871 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
3872 if ( !iter.next().getName().equals( "A" ) ) {
3875 if ( !iter.next().getName().equals( "B" ) ) {
3878 if ( !iter.next().getName().equals( "C" ) ) {
3881 if ( !iter.next().getName().equals( "D" ) ) {
3884 if ( !iter.next().getName().equals( "E" ) ) {
3887 if ( !iter.next().getName().equals( "F" ) ) {
3890 if ( iter.hasNext() ) {
3894 catch ( final Exception e ) {
3895 e.printStackTrace( System.out );
3901 private static boolean testExtractSNFromNodeName() {
3903 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
3906 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
3907 .equals( "Mus musculus musculus" ) ) {
3910 if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
3911 .equals( "Mus musculus musculus" ) ) {
3914 if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
3917 if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
3918 .equals( "Mus musculus" ) ) {
3922 catch ( final Exception e ) {
3923 e.printStackTrace( System.out );
3929 private static boolean testExtractTaxonomyCodeFromNodeName() {
3931 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3934 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3935 .equals( "SOYBN" ) ) {
3938 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
3939 .equals( "ARATH" ) ) {
3942 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
3943 .equals( "ARATH" ) ) {
3946 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
3949 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
3952 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
3955 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3956 .equals( "SOYBN" ) ) {
3959 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3960 .equals( "SOYBN" ) ) {
3963 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3964 .equals( "SOYBN" ) ) {
3967 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3968 .equals( "SOYBN" ) ) {
3971 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
3972 .equals( "SOYBN" ) ) {
3975 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
3976 .equals( "SOYBN" ) ) {
3979 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
3980 .equals( "SOYBN" ) ) {
3983 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
3984 .equals( "SOYBN" ) ) {
3987 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
3990 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
3991 .equals( "SOYBN" ) ) {
3994 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
3995 TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
3998 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
3999 .equals( "9YX45" ) ) {
4002 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
4003 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4004 .equals( "MOUSE" ) ) {
4007 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
4008 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4009 .equals( "MOUSE" ) ) {
4012 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
4013 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4014 .equals( "MOUSE" ) ) {
4017 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
4018 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4021 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
4022 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4025 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4026 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4029 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
4030 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4033 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
4034 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
4037 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
4038 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4041 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
4042 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4045 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4046 .equals( "RAT" ) ) {
4049 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4050 .equals( "PIG" ) ) {
4054 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
4055 .equals( "MOUSE" ) ) {
4058 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
4059 .equals( "MOUSE" ) ) {
4062 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
4066 catch ( final Exception e ) {
4067 e.printStackTrace( System.out );
4073 private static boolean testExtractUniProtKbProteinSeqIdentifier() {
4075 PhylogenyNode n = new PhylogenyNode();
4076 n.setName( "tr|B3RJ64" );
4077 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4080 n.setName( "tr.B3RJ64" );
4081 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4084 n.setName( "tr=B3RJ64" );
4085 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4088 n.setName( "tr-B3RJ64" );
4089 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4092 n.setName( "tr/B3RJ64" );
4093 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4096 n.setName( "tr\\B3RJ64" );
4097 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4100 n.setName( "tr_B3RJ64" );
4101 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4104 n.setName( " tr|B3RJ64 " );
4105 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4108 n.setName( "-tr|B3RJ64-" );
4109 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4112 n.setName( "-tr=B3RJ64-" );
4113 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4116 n.setName( "_tr=B3RJ64_" );
4117 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4120 n.setName( " tr_tr|B3RJ64_sp|123 " );
4121 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4124 n.setName( "B3RJ64" );
4125 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4128 n.setName( "sp|B3RJ64" );
4129 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4132 n.setName( "sp|B3RJ64C" );
4133 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4136 n.setName( "sp B3RJ64" );
4137 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4140 n.setName( "sp|B3RJ6X" );
4141 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4144 n.setName( "sp|B3RJ6" );
4145 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4148 n.setName( "K1PYK7_CRAGI" );
4149 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4152 n.setName( "K1PYK7_PEA" );
4153 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
4156 n.setName( "K1PYK7_RAT" );
4157 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
4160 n.setName( "K1PYK7_PIG" );
4161 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4164 n.setName( "~K1PYK7_PIG~" );
4165 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
4168 n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
4169 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4172 n.setName( "K1PYKX_CRAGI" );
4173 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4176 n.setName( "XXXXX_CRAGI" );
4177 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
4180 n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
4181 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
4184 n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
4185 if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
4188 n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
4189 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
4192 n = new PhylogenyNode();
4193 org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
4194 seq.setSymbol( "K1PYK7_CRAGI" );
4195 n.getNodeData().addSequence( seq );
4196 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4199 seq.setSymbol( "tr|B3RJ64" );
4200 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4203 n = new PhylogenyNode();
4204 seq = new org.forester.phylogeny.data.Sequence();
4205 seq.setName( "K1PYK7_CRAGI" );
4206 n.getNodeData().addSequence( seq );
4207 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
4210 seq.setName( "tr|B3RJ64" );
4211 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4214 n = new PhylogenyNode();
4215 seq = new org.forester.phylogeny.data.Sequence();
4216 seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
4217 n.getNodeData().addSequence( seq );
4218 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
4221 n = new PhylogenyNode();
4222 seq = new org.forester.phylogeny.data.Sequence();
4223 seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
4224 n.getNodeData().addSequence( seq );
4225 if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
4229 n = new PhylogenyNode();
4230 n.setName( "ACP19736" );
4231 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4234 n = new PhylogenyNode();
4235 n.setName( "|ACP19736|" );
4236 if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
4240 catch ( final Exception e ) {
4241 e.printStackTrace( System.out );
4247 private static boolean testFastaParser() {
4249 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
4252 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
4255 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
4256 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
4259 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
4262 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
4265 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
4268 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
4271 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
4275 catch ( final Exception e ) {
4276 e.printStackTrace();
4282 private static boolean testGeneralMsaParser() {
4284 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
4285 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
4286 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
4287 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
4288 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
4289 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
4290 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
4291 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
4292 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4295 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4298 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4301 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4304 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4307 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4310 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4313 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4316 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
4319 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
4322 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
4325 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
4328 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
4329 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4332 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4335 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4338 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
4339 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
4342 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
4345 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
4348 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
4349 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
4352 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
4355 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
4359 catch ( final Exception e ) {
4360 e.printStackTrace();
4366 private static boolean testGeneralTable() {
4368 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
4369 t0.setValue( 3, 2, "23" );
4370 t0.setValue( 10, 1, "error" );
4371 t0.setValue( 10, 1, "110" );
4372 t0.setValue( 9, 1, "19" );
4373 t0.setValue( 1, 10, "101" );
4374 t0.setValue( 10, 10, "1010" );
4375 t0.setValue( 100, 10, "10100" );
4376 t0.setValue( 0, 0, "00" );
4377 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
4380 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
4383 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
4386 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
4389 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
4392 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
4395 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
4398 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
4401 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
4404 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
4405 t1.setValue( "3", "2", "23" );
4406 t1.setValue( "10", "1", "error" );
4407 t1.setValue( "10", "1", "110" );
4408 t1.setValue( "9", "1", "19" );
4409 t1.setValue( "1", "10", "101" );
4410 t1.setValue( "10", "10", "1010" );
4411 t1.setValue( "100", "10", "10100" );
4412 t1.setValue( "0", "0", "00" );
4413 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
4414 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
4417 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
4420 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
4423 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
4426 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
4429 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
4432 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
4435 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
4438 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
4441 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
4445 catch ( final Exception e ) {
4446 e.printStackTrace( System.out );
4452 private static boolean testGetDistance() {
4454 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4455 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",
4456 new NHXParser() )[ 0 ];
4457 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
4460 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
4463 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
4466 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
4469 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
4472 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
4475 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
4478 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
4481 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
4484 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
4487 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
4490 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
4493 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
4496 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
4499 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
4502 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
4505 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
4508 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
4511 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
4514 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
4517 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
4520 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
4523 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
4526 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
4529 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
4532 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
4535 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
4538 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
4541 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
4544 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
4547 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
4550 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",
4551 new NHXParser() )[ 0 ];
4552 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
4555 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
4558 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
4561 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
4564 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
4567 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
4570 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
4573 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
4576 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
4579 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
4582 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
4586 catch ( final Exception e ) {
4587 e.printStackTrace( System.out );
4593 private static boolean testGetLCA() {
4595 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4596 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
4597 new NHXParser() )[ 0 ];
4598 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
4599 if ( !A.getName().equals( "A" ) ) {
4602 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
4603 if ( !gh.getName().equals( "gh" ) ) {
4606 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
4607 if ( !ab.getName().equals( "ab" ) ) {
4610 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
4611 if ( !ab2.getName().equals( "ab" ) ) {
4614 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
4615 if ( !gh2.getName().equals( "gh" ) ) {
4618 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
4619 if ( !gh3.getName().equals( "gh" ) ) {
4622 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
4623 if ( !abc.getName().equals( "abc" ) ) {
4626 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
4627 if ( !abc2.getName().equals( "abc" ) ) {
4630 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
4631 if ( !abcd.getName().equals( "abcd" ) ) {
4634 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
4635 if ( !abcd2.getName().equals( "abcd" ) ) {
4638 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
4639 if ( !abcdef.getName().equals( "abcdef" ) ) {
4642 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
4643 if ( !abcdef2.getName().equals( "abcdef" ) ) {
4646 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
4647 if ( !abcdef3.getName().equals( "abcdef" ) ) {
4650 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
4651 if ( !abcdef4.getName().equals( "abcdef" ) ) {
4654 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
4655 if ( !abcde.getName().equals( "abcde" ) ) {
4658 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
4659 if ( !abcde2.getName().equals( "abcde" ) ) {
4662 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
4663 if ( !r.getName().equals( "abcdefgh" ) ) {
4666 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
4667 if ( !r2.getName().equals( "abcdefgh" ) ) {
4670 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
4671 if ( !r3.getName().equals( "abcdefgh" ) ) {
4674 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
4675 if ( !abcde3.getName().equals( "abcde" ) ) {
4678 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
4679 if ( !abcde4.getName().equals( "abcde" ) ) {
4682 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
4683 if ( !ab3.getName().equals( "ab" ) ) {
4686 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
4687 if ( !ab4.getName().equals( "ab" ) ) {
4690 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
4691 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
4692 if ( !cd.getName().equals( "cd" ) ) {
4695 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
4696 if ( !cd2.getName().equals( "cd" ) ) {
4699 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
4700 if ( !cde.getName().equals( "cde" ) ) {
4703 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
4704 if ( !cde2.getName().equals( "cde" ) ) {
4707 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
4708 if ( !cdef.getName().equals( "cdef" ) ) {
4711 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
4712 if ( !cdef2.getName().equals( "cdef" ) ) {
4715 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
4716 if ( !cdef3.getName().equals( "cdef" ) ) {
4719 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
4720 if ( !rt.getName().equals( "r" ) ) {
4723 final Phylogeny p3 = factory
4724 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
4725 new NHXParser() )[ 0 ];
4726 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
4727 if ( !bc_3.getName().equals( "bc" ) ) {
4730 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
4731 if ( !ac_3.getName().equals( "abc" ) ) {
4734 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
4735 if ( !ad_3.getName().equals( "abcde" ) ) {
4738 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
4739 if ( !af_3.getName().equals( "abcdef" ) ) {
4742 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
4743 if ( !ag_3.getName().equals( "" ) ) {
4746 if ( !ag_3.isRoot() ) {
4749 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
4750 if ( !al_3.getName().equals( "" ) ) {
4753 if ( !al_3.isRoot() ) {
4756 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
4757 if ( !kl_3.getName().equals( "" ) ) {
4760 if ( !kl_3.isRoot() ) {
4763 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
4764 if ( !fl_3.getName().equals( "" ) ) {
4767 if ( !fl_3.isRoot() ) {
4770 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
4771 if ( !gk_3.getName().equals( "ghijk" ) ) {
4774 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
4775 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
4776 if ( !r_4.getName().equals( "r" ) ) {
4779 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
4780 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
4781 if ( !r_5.getName().equals( "root" ) ) {
4784 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
4785 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
4786 if ( !r_6.getName().equals( "rot" ) ) {
4789 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
4790 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
4791 if ( !r_7.getName().equals( "rott" ) ) {
4795 catch ( final Exception e ) {
4796 e.printStackTrace( System.out );
4802 private static boolean testGetLCA2() {
4804 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4805 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
4806 PhylogenyMethods.preOrderReId( p_a );
4807 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
4808 p_a.getNode( "a" ) );
4809 if ( !p_a_1.getName().equals( "a" ) ) {
4812 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
4813 PhylogenyMethods.preOrderReId( p_b );
4814 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
4815 p_b.getNode( "a" ) );
4816 if ( !p_b_1.getName().equals( "b" ) ) {
4819 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
4820 p_b.getNode( "b" ) );
4821 if ( !p_b_2.getName().equals( "b" ) ) {
4824 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
4825 PhylogenyMethods.preOrderReId( p_c );
4826 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
4827 p_c.getNode( "a" ) );
4828 if ( !p_c_1.getName().equals( "b" ) ) {
4831 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
4832 p_c.getNode( "c" ) );
4833 if ( !p_c_2.getName().equals( "c" ) ) {
4834 System.out.println( p_c_2.getName() );
4838 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
4839 p_c.getNode( "b" ) );
4840 if ( !p_c_3.getName().equals( "b" ) ) {
4843 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
4844 p_c.getNode( "a" ) );
4845 if ( !p_c_4.getName().equals( "c" ) ) {
4848 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
4849 new NHXParser() )[ 0 ];
4850 PhylogenyMethods.preOrderReId( p1 );
4851 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4852 p1.getNode( "A" ) );
4853 if ( !A.getName().equals( "A" ) ) {
4856 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
4857 p1.getNode( "gh" ) );
4858 if ( !gh.getName().equals( "gh" ) ) {
4861 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4862 p1.getNode( "B" ) );
4863 if ( !ab.getName().equals( "ab" ) ) {
4866 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
4867 p1.getNode( "A" ) );
4868 if ( !ab2.getName().equals( "ab" ) ) {
4871 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
4872 p1.getNode( "G" ) );
4873 if ( !gh2.getName().equals( "gh" ) ) {
4876 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
4877 p1.getNode( "H" ) );
4878 if ( !gh3.getName().equals( "gh" ) ) {
4881 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
4882 p1.getNode( "A" ) );
4883 if ( !abc.getName().equals( "abc" ) ) {
4886 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4887 p1.getNode( "C" ) );
4888 if ( !abc2.getName().equals( "abc" ) ) {
4891 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4892 p1.getNode( "D" ) );
4893 if ( !abcd.getName().equals( "abcd" ) ) {
4896 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
4897 p1.getNode( "A" ) );
4898 if ( !abcd2.getName().equals( "abcd" ) ) {
4901 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4902 p1.getNode( "F" ) );
4903 if ( !abcdef.getName().equals( "abcdef" ) ) {
4906 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
4907 p1.getNode( "A" ) );
4908 if ( !abcdef2.getName().equals( "abcdef" ) ) {
4911 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
4912 p1.getNode( "F" ) );
4913 if ( !abcdef3.getName().equals( "abcdef" ) ) {
4916 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
4917 p1.getNode( "ab" ) );
4918 if ( !abcdef4.getName().equals( "abcdef" ) ) {
4921 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4922 p1.getNode( "E" ) );
4923 if ( !abcde.getName().equals( "abcde" ) ) {
4926 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
4927 p1.getNode( "A" ) );
4928 if ( !abcde2.getName().equals( "abcde" ) ) {
4931 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
4932 p1.getNode( "abcdefgh" ) );
4933 if ( !r.getName().equals( "abcdefgh" ) ) {
4936 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
4937 p1.getNode( "H" ) );
4938 if ( !r2.getName().equals( "abcdefgh" ) ) {
4941 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
4942 p1.getNode( "A" ) );
4943 if ( !r3.getName().equals( "abcdefgh" ) ) {
4946 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
4947 p1.getNode( "abcde" ) );
4948 if ( !abcde3.getName().equals( "abcde" ) ) {
4951 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
4952 p1.getNode( "E" ) );
4953 if ( !abcde4.getName().equals( "abcde" ) ) {
4956 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
4957 p1.getNode( "B" ) );
4958 if ( !ab3.getName().equals( "ab" ) ) {
4961 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
4962 p1.getNode( "ab" ) );
4963 if ( !ab4.getName().equals( "ab" ) ) {
4966 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
4967 PhylogenyMethods.preOrderReId( p2 );
4968 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4969 p2.getNode( "d" ) );
4970 if ( !cd.getName().equals( "cd" ) ) {
4973 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
4974 p2.getNode( "c" ) );
4975 if ( !cd2.getName().equals( "cd" ) ) {
4978 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4979 p2.getNode( "e" ) );
4980 if ( !cde.getName().equals( "cde" ) ) {
4983 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
4984 p2.getNode( "c" ) );
4985 if ( !cde2.getName().equals( "cde" ) ) {
4988 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
4989 p2.getNode( "f" ) );
4990 if ( !cdef.getName().equals( "cdef" ) ) {
4993 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
4994 p2.getNode( "f" ) );
4995 if ( !cdef2.getName().equals( "cdef" ) ) {
4998 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
4999 p2.getNode( "d" ) );
5000 if ( !cdef3.getName().equals( "cdef" ) ) {
5003 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
5004 p2.getNode( "a" ) );
5005 if ( !rt.getName().equals( "r" ) ) {
5008 final Phylogeny p3 = factory
5009 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
5010 new NHXParser() )[ 0 ];
5011 PhylogenyMethods.preOrderReId( p3 );
5012 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
5013 p3.getNode( "c" ) );
5014 if ( !bc_3.getName().equals( "bc" ) ) {
5017 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5018 p3.getNode( "c" ) );
5019 if ( !ac_3.getName().equals( "abc" ) ) {
5022 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5023 p3.getNode( "d" ) );
5024 if ( !ad_3.getName().equals( "abcde" ) ) {
5027 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5028 p3.getNode( "f" ) );
5029 if ( !af_3.getName().equals( "abcdef" ) ) {
5032 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5033 p3.getNode( "g" ) );
5034 if ( !ag_3.getName().equals( "" ) ) {
5037 if ( !ag_3.isRoot() ) {
5040 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
5041 p3.getNode( "l" ) );
5042 if ( !al_3.getName().equals( "" ) ) {
5045 if ( !al_3.isRoot() ) {
5048 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
5049 p3.getNode( "l" ) );
5050 if ( !kl_3.getName().equals( "" ) ) {
5053 if ( !kl_3.isRoot() ) {
5056 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
5057 p3.getNode( "l" ) );
5058 if ( !fl_3.getName().equals( "" ) ) {
5061 if ( !fl_3.isRoot() ) {
5064 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
5065 p3.getNode( "k" ) );
5066 if ( !gk_3.getName().equals( "ghijk" ) ) {
5069 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
5070 PhylogenyMethods.preOrderReId( p4 );
5071 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
5072 p4.getNode( "c" ) );
5073 if ( !r_4.getName().equals( "r" ) ) {
5076 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
5077 PhylogenyMethods.preOrderReId( p5 );
5078 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
5079 p5.getNode( "c" ) );
5080 if ( !r_5.getName().equals( "root" ) ) {
5083 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
5084 PhylogenyMethods.preOrderReId( p6 );
5085 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
5086 p6.getNode( "a" ) );
5087 if ( !r_6.getName().equals( "rot" ) ) {
5090 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
5091 PhylogenyMethods.preOrderReId( p7 );
5092 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
5093 p7.getNode( "e" ) );
5094 if ( !r_7.getName().equals( "rott" ) ) {
5097 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5098 p7.getNode( "a" ) );
5099 if ( !r_71.getName().equals( "rott" ) ) {
5102 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5103 p7.getNode( "rott" ) );
5104 if ( !r_72.getName().equals( "rott" ) ) {
5107 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5108 p7.getNode( "a" ) );
5109 if ( !r_73.getName().equals( "rott" ) ) {
5112 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
5113 p7.getNode( "rott" ) );
5114 if ( !r_74.getName().equals( "rott" ) ) {
5117 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
5118 p7.getNode( "e" ) );
5119 if ( !r_75.getName().equals( "e" ) ) {
5123 catch ( final Exception e ) {
5124 e.printStackTrace( System.out );
5130 private static boolean testHmmscanOutputParser() {
5131 final String test_dir = Test.PATH_TO_TEST_DATA;
5133 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
5134 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5136 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
5137 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
5138 final List<Protein> proteins = parser2.parse();
5139 if ( parser2.getProteinsEncountered() != 4 ) {
5142 if ( proteins.size() != 4 ) {
5145 if ( parser2.getDomainsEncountered() != 69 ) {
5148 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
5151 if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
5154 if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
5157 final Protein p1 = proteins.get( 0 );
5158 if ( p1.getNumberOfProteinDomains() != 15 ) {
5161 if ( p1.getLength() != 850 ) {
5164 final Protein p2 = proteins.get( 1 );
5165 if ( p2.getNumberOfProteinDomains() != 51 ) {
5168 if ( p2.getLength() != 1291 ) {
5171 final Protein p3 = proteins.get( 2 );
5172 if ( p3.getNumberOfProteinDomains() != 2 ) {
5175 final Protein p4 = proteins.get( 3 );
5176 if ( p4.getNumberOfProteinDomains() != 1 ) {
5179 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
5182 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
5185 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
5188 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
5191 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
5194 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
5197 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
5201 catch ( final Exception e ) {
5202 e.printStackTrace( System.out );
5208 private static boolean testLastExternalNodeMethods() {
5210 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5211 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
5212 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
5213 final PhylogenyNode n1 = t0.getNode( "A" );
5214 if ( n1.isLastExternalNode() ) {
5217 final PhylogenyNode n2 = t0.getNode( "B" );
5218 if ( n2.isLastExternalNode() ) {
5221 final PhylogenyNode n3 = t0.getNode( "C" );
5222 if ( n3.isLastExternalNode() ) {
5225 final PhylogenyNode n4 = t0.getNode( "D" );
5226 if ( !n4.isLastExternalNode() ) {
5230 catch ( final Exception e ) {
5231 e.printStackTrace( System.out );
5237 private static boolean testLevelOrderIterator() {
5239 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5240 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5241 PhylogenyNodeIterator it0;
5242 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
5245 for( it0.reset(); it0.hasNext(); ) {
5248 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
5249 if ( !it.next().getName().equals( "r" ) ) {
5252 if ( !it.next().getName().equals( "ab" ) ) {
5255 if ( !it.next().getName().equals( "cd" ) ) {
5258 if ( !it.next().getName().equals( "A" ) ) {
5261 if ( !it.next().getName().equals( "B" ) ) {
5264 if ( !it.next().getName().equals( "C" ) ) {
5267 if ( !it.next().getName().equals( "D" ) ) {
5270 if ( it.hasNext() ) {
5273 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",
5274 new NHXParser() )[ 0 ];
5275 PhylogenyNodeIterator it2;
5276 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
5279 for( it2.reset(); it2.hasNext(); ) {
5282 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
5283 if ( !it3.next().getName().equals( "r" ) ) {
5286 if ( !it3.next().getName().equals( "abc" ) ) {
5289 if ( !it3.next().getName().equals( "defg" ) ) {
5292 if ( !it3.next().getName().equals( "A" ) ) {
5295 if ( !it3.next().getName().equals( "B" ) ) {
5298 if ( !it3.next().getName().equals( "C" ) ) {
5301 if ( !it3.next().getName().equals( "D" ) ) {
5304 if ( !it3.next().getName().equals( "E" ) ) {
5307 if ( !it3.next().getName().equals( "F" ) ) {
5310 if ( !it3.next().getName().equals( "G" ) ) {
5313 if ( !it3.next().getName().equals( "1" ) ) {
5316 if ( !it3.next().getName().equals( "2" ) ) {
5319 if ( !it3.next().getName().equals( "3" ) ) {
5322 if ( !it3.next().getName().equals( "4" ) ) {
5325 if ( !it3.next().getName().equals( "5" ) ) {
5328 if ( !it3.next().getName().equals( "6" ) ) {
5331 if ( !it3.next().getName().equals( "f1" ) ) {
5334 if ( !it3.next().getName().equals( "f2" ) ) {
5337 if ( !it3.next().getName().equals( "f3" ) ) {
5340 if ( !it3.next().getName().equals( "a" ) ) {
5343 if ( !it3.next().getName().equals( "b" ) ) {
5346 if ( !it3.next().getName().equals( "f21" ) ) {
5349 if ( !it3.next().getName().equals( "X" ) ) {
5352 if ( !it3.next().getName().equals( "Y" ) ) {
5355 if ( !it3.next().getName().equals( "Z" ) ) {
5358 if ( it3.hasNext() ) {
5361 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
5362 PhylogenyNodeIterator it4;
5363 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
5366 for( it4.reset(); it4.hasNext(); ) {
5369 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
5370 if ( !it5.next().getName().equals( "r" ) ) {
5373 if ( !it5.next().getName().equals( "A" ) ) {
5376 if ( !it5.next().getName().equals( "B" ) ) {
5379 if ( !it5.next().getName().equals( "C" ) ) {
5382 if ( !it5.next().getName().equals( "D" ) ) {
5385 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
5386 PhylogenyNodeIterator it6;
5387 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
5390 for( it6.reset(); it6.hasNext(); ) {
5393 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
5394 if ( !it7.next().getName().equals( "A" ) ) {
5397 if ( it.hasNext() ) {
5401 catch ( final Exception e ) {
5402 e.printStackTrace( System.out );
5408 private static boolean testMafft( final String path ) {
5410 final List<String> opts = new ArrayList<String>();
5411 opts.add( "--maxiterate" );
5413 opts.add( "--localpair" );
5414 opts.add( "--quiet" );
5416 final MsaInferrer mafft = Mafft.createInstance( path );
5417 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
5418 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
5421 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
5425 catch ( final Exception e ) {
5426 e.printStackTrace( System.out );
5432 private static boolean testMidpointrooting() {
5434 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5435 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
5436 PhylogenyMethods.midpointRoot( t0 );
5437 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
5440 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
5443 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
5447 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",
5448 new NHXParser() )[ 0 ];
5449 if ( !t1.isRooted() ) {
5452 PhylogenyMethods.midpointRoot( t1 );
5453 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5456 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5459 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5462 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5465 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5468 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5471 t1.reRoot( t1.getNode( "A" ) );
5472 PhylogenyMethods.midpointRoot( t1 );
5473 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5476 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5479 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5482 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
5485 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
5489 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
5493 catch ( final Exception e ) {
5494 e.printStackTrace( System.out );
5500 private static boolean testMsaQualityMethod() {
5502 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
5503 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
5504 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
5505 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
5506 final List<Sequence> l = new ArrayList<Sequence>();
5511 final Msa msa = BasicMsa.createInstance( l );
5512 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
5515 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
5518 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
5521 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
5525 catch ( final Exception e ) {
5526 e.printStackTrace( System.out );
5532 private static boolean testNextNodeWithCollapsing() {
5534 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5536 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
5537 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5538 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
5539 t0.getNode( "cd" ).setCollapse( true );
5540 t0.getNode( "cde" ).setCollapse( true );
5541 n = t0.getFirstExternalNode();
5542 while ( n != null ) {
5544 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5546 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5549 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5552 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
5555 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
5558 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
5561 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
5565 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5566 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
5567 t1.getNode( "ab" ).setCollapse( true );
5568 t1.getNode( "cd" ).setCollapse( true );
5569 t1.getNode( "cde" ).setCollapse( true );
5570 n = t1.getNode( "ab" );
5571 ext = new ArrayList<PhylogenyNode>();
5572 while ( n != null ) {
5574 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5576 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5579 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5582 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5585 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
5588 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
5594 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5595 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
5596 t2.getNode( "ab" ).setCollapse( true );
5597 t2.getNode( "cd" ).setCollapse( true );
5598 t2.getNode( "cde" ).setCollapse( true );
5599 t2.getNode( "c" ).setCollapse( true );
5600 t2.getNode( "d" ).setCollapse( true );
5601 t2.getNode( "e" ).setCollapse( true );
5602 t2.getNode( "gh" ).setCollapse( true );
5603 n = t2.getNode( "ab" );
5604 ext = new ArrayList<PhylogenyNode>();
5605 while ( n != null ) {
5607 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5609 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5612 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5615 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
5618 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
5624 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5625 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
5626 t3.getNode( "ab" ).setCollapse( true );
5627 t3.getNode( "cd" ).setCollapse( true );
5628 t3.getNode( "cde" ).setCollapse( true );
5629 t3.getNode( "c" ).setCollapse( true );
5630 t3.getNode( "d" ).setCollapse( true );
5631 t3.getNode( "e" ).setCollapse( true );
5632 t3.getNode( "gh" ).setCollapse( true );
5633 t3.getNode( "fgh" ).setCollapse( true );
5634 n = t3.getNode( "ab" );
5635 ext = new ArrayList<PhylogenyNode>();
5636 while ( n != null ) {
5638 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5640 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5643 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
5646 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
5652 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5653 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
5654 t4.getNode( "ab" ).setCollapse( true );
5655 t4.getNode( "cd" ).setCollapse( true );
5656 t4.getNode( "cde" ).setCollapse( true );
5657 t4.getNode( "c" ).setCollapse( true );
5658 t4.getNode( "d" ).setCollapse( true );
5659 t4.getNode( "e" ).setCollapse( true );
5660 t4.getNode( "gh" ).setCollapse( true );
5661 t4.getNode( "fgh" ).setCollapse( true );
5662 t4.getNode( "abcdefgh" ).setCollapse( true );
5663 n = t4.getNode( "abcdefgh" );
5664 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
5669 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5670 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
5672 n = t5.getFirstExternalNode();
5673 while ( n != null ) {
5675 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5677 if ( ext.size() != 8 ) {
5680 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5683 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5686 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5689 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5692 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5695 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5698 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
5701 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
5706 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5707 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
5709 t6.getNode( "ab" ).setCollapse( true );
5710 n = t6.getNode( "ab" );
5711 while ( n != null ) {
5713 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5715 if ( ext.size() != 7 ) {
5718 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5721 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5724 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5727 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5730 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5733 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5736 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5741 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5742 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
5744 t7.getNode( "cd" ).setCollapse( true );
5745 n = t7.getNode( "a" );
5746 while ( n != null ) {
5748 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5750 if ( ext.size() != 7 ) {
5753 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5756 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5759 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
5762 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5765 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5768 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5771 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5776 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
5777 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
5779 t8.getNode( "cd" ).setCollapse( true );
5780 t8.getNode( "c" ).setCollapse( true );
5781 t8.getNode( "d" ).setCollapse( true );
5782 n = t8.getNode( "a" );
5783 while ( n != null ) {
5785 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5787 if ( ext.size() != 7 ) {
5790 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5793 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5796 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
5797 System.out.println( "2 fail" );
5800 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5803 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
5806 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
5809 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
5814 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5815 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
5817 t9.getNode( "gh" ).setCollapse( true );
5818 n = t9.getNode( "a" );
5819 while ( n != null ) {
5821 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5823 if ( ext.size() != 7 ) {
5826 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5829 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5832 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5835 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5838 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5841 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5844 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
5849 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5850 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
5852 t10.getNode( "gh" ).setCollapse( true );
5853 t10.getNode( "g" ).setCollapse( true );
5854 t10.getNode( "h" ).setCollapse( true );
5855 n = t10.getNode( "a" );
5856 while ( n != null ) {
5858 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5860 if ( ext.size() != 7 ) {
5863 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5866 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5869 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5872 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5875 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5878 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
5881 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
5886 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5887 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
5889 t11.getNode( "gh" ).setCollapse( true );
5890 t11.getNode( "fgh" ).setCollapse( true );
5891 n = t11.getNode( "a" );
5892 while ( n != null ) {
5894 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5896 if ( ext.size() != 6 ) {
5899 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5902 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5905 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5908 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5911 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5914 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
5919 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5920 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
5922 t12.getNode( "gh" ).setCollapse( true );
5923 t12.getNode( "fgh" ).setCollapse( true );
5924 t12.getNode( "g" ).setCollapse( true );
5925 t12.getNode( "h" ).setCollapse( true );
5926 t12.getNode( "f" ).setCollapse( true );
5927 n = t12.getNode( "a" );
5928 while ( n != null ) {
5930 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5932 if ( ext.size() != 6 ) {
5935 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
5938 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
5941 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
5944 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
5947 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
5950 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
5955 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
5956 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
5958 t13.getNode( "ab" ).setCollapse( true );
5959 t13.getNode( "b" ).setCollapse( true );
5960 t13.getNode( "fgh" ).setCollapse( true );
5961 t13.getNode( "gh" ).setCollapse( true );
5962 n = t13.getNode( "ab" );
5963 while ( n != null ) {
5965 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5967 if ( ext.size() != 5 ) {
5970 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
5973 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
5976 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
5979 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
5982 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
5987 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
5988 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
5990 t14.getNode( "ab" ).setCollapse( true );
5991 t14.getNode( "a" ).setCollapse( true );
5992 t14.getNode( "fgh" ).setCollapse( true );
5993 t14.getNode( "gh" ).setCollapse( true );
5994 n = t14.getNode( "ab" );
5995 while ( n != null ) {
5997 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
5999 if ( ext.size() != 5 ) {
6002 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6005 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6008 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6011 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6014 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
6019 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" );
6020 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
6022 t15.getNode( "ab" ).setCollapse( true );
6023 t15.getNode( "a" ).setCollapse( true );
6024 t15.getNode( "fgh" ).setCollapse( true );
6025 t15.getNode( "gh" ).setCollapse( true );
6026 n = t15.getNode( "ab" );
6027 while ( n != null ) {
6029 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6031 if ( ext.size() != 6 ) {
6034 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6037 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
6040 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
6043 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
6046 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
6049 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
6054 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" );
6055 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
6057 t16.getNode( "ab" ).setCollapse( true );
6058 t16.getNode( "a" ).setCollapse( true );
6059 t16.getNode( "fgh" ).setCollapse( true );
6060 t16.getNode( "gh" ).setCollapse( true );
6061 t16.getNode( "cd" ).setCollapse( true );
6062 t16.getNode( "cde" ).setCollapse( true );
6063 t16.getNode( "d" ).setCollapse( true );
6064 t16.getNode( "x" ).setCollapse( true );
6065 n = t16.getNode( "ab" );
6066 while ( n != null ) {
6068 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
6070 if ( ext.size() != 4 ) {
6073 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
6076 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
6079 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
6082 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
6086 catch ( final Exception e ) {
6087 e.printStackTrace( System.out );
6093 private static boolean testNexusCharactersParsing() {
6095 final NexusCharactersParser parser = new NexusCharactersParser();
6096 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
6098 String[] labels = parser.getCharStateLabels();
6099 if ( labels.length != 7 ) {
6102 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6105 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6108 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6111 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6114 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6117 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6120 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6123 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6125 labels = parser.getCharStateLabels();
6126 if ( labels.length != 7 ) {
6129 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6132 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6135 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6138 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6141 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6144 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6147 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6151 catch ( final Exception e ) {
6152 e.printStackTrace( System.out );
6158 private static boolean testNexusMatrixParsing() {
6160 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
6161 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
6163 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
6164 if ( m.getNumberOfCharacters() != 9 ) {
6167 if ( m.getNumberOfIdentifiers() != 5 ) {
6170 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
6173 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
6176 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
6179 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
6182 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
6185 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
6188 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
6191 // if ( labels.length != 7 ) {
6194 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6197 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6200 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6203 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6206 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6209 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6212 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6215 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
6217 // labels = parser.getCharStateLabels();
6218 // if ( labels.length != 7 ) {
6221 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
6224 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
6227 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
6230 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
6233 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
6236 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
6239 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
6243 catch ( final Exception e ) {
6244 e.printStackTrace( System.out );
6250 private static boolean testNexusTreeParsing() {
6252 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6253 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6254 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
6255 if ( phylogenies.length != 1 ) {
6258 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
6261 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6265 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
6266 if ( phylogenies.length != 1 ) {
6269 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6272 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
6276 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
6277 if ( phylogenies.length != 1 ) {
6280 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6283 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
6286 if ( phylogenies[ 0 ].isRooted() ) {
6290 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
6291 if ( phylogenies.length != 18 ) {
6294 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
6297 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
6300 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
6303 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
6306 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
6309 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
6312 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
6315 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
6318 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
6321 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
6324 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
6327 if ( phylogenies[ 8 ].isRooted() ) {
6330 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
6333 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
6336 if ( !phylogenies[ 9 ].isRooted() ) {
6339 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
6342 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
6345 if ( !phylogenies[ 10 ].isRooted() ) {
6348 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
6351 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
6354 if ( phylogenies[ 11 ].isRooted() ) {
6357 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
6360 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
6363 if ( !phylogenies[ 12 ].isRooted() ) {
6366 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
6369 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
6372 if ( !phylogenies[ 13 ].isRooted() ) {
6375 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
6378 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
6381 if ( !phylogenies[ 14 ].isRooted() ) {
6384 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
6387 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
6390 if ( phylogenies[ 15 ].isRooted() ) {
6393 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
6396 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
6399 if ( !phylogenies[ 16 ].isRooted() ) {
6402 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
6405 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
6408 if ( phylogenies[ 17 ].isRooted() ) {
6411 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
6415 catch ( final Exception e ) {
6416 e.printStackTrace( System.out );
6422 private static boolean testNexusTreeParsingIterating() {
6424 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
6425 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
6426 if ( !p.hasNext() ) {
6429 Phylogeny phy = p.next();
6430 if ( phy == null ) {
6433 if ( phy.getNumberOfExternalNodes() != 25 ) {
6436 if ( !phy.getName().equals( "" ) ) {
6439 if ( p.hasNext() ) {
6443 if ( phy != null ) {
6448 if ( !p.hasNext() ) {
6452 if ( phy == null ) {
6455 if ( phy.getNumberOfExternalNodes() != 25 ) {
6458 if ( !phy.getName().equals( "" ) ) {
6461 if ( p.hasNext() ) {
6465 if ( phy != null ) {
6469 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
6470 if ( !p.hasNext() ) {
6474 if ( phy == null ) {
6477 if ( phy.getNumberOfExternalNodes() != 10 ) {
6480 if ( !phy.getName().equals( "name" ) ) {
6483 if ( p.hasNext() ) {
6487 if ( phy != null ) {
6492 if ( !p.hasNext() ) {
6496 if ( phy == null ) {
6499 if ( phy.getNumberOfExternalNodes() != 10 ) {
6502 if ( !phy.getName().equals( "name" ) ) {
6505 if ( p.hasNext() ) {
6509 if ( phy != null ) {
6513 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
6514 if ( !p.hasNext() ) {
6518 if ( phy == null ) {
6521 if ( phy.getNumberOfExternalNodes() != 3 ) {
6524 if ( !phy.getName().equals( "" ) ) {
6527 if ( phy.isRooted() ) {
6530 if ( p.hasNext() ) {
6534 if ( phy != null ) {
6539 if ( !p.hasNext() ) {
6543 if ( phy == null ) {
6546 if ( phy.getNumberOfExternalNodes() != 3 ) {
6549 if ( !phy.getName().equals( "" ) ) {
6552 if ( p.hasNext() ) {
6556 if ( phy != null ) {
6560 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
6561 // if ( phylogenies.length != 18 ) {
6565 if ( !p.hasNext() ) {
6569 if ( phy == null ) {
6572 if ( phy.getNumberOfExternalNodes() != 10 ) {
6575 if ( !phy.getName().equals( "tree 0" ) ) {
6579 if ( !p.hasNext() ) {
6583 if ( phy == null ) {
6586 if ( phy.getNumberOfExternalNodes() != 10 ) {
6589 if ( !phy.getName().equals( "tree 1" ) ) {
6593 if ( !p.hasNext() ) {
6597 if ( phy == null ) {
6600 if ( phy.getNumberOfExternalNodes() != 3 ) {
6603 if ( !phy.getName().equals( "" ) ) {
6606 if ( phy.isRooted() ) {
6610 if ( !p.hasNext() ) {
6614 if ( phy == null ) {
6617 if ( phy.getNumberOfExternalNodes() != 4 ) {
6620 if ( !phy.getName().equals( "" ) ) {
6623 if ( !phy.isRooted() ) {
6627 if ( !p.hasNext() ) {
6631 if ( phy == null ) {
6634 if ( phy.getNumberOfExternalNodes() != 5 ) {
6635 System.out.println( phy.getNumberOfExternalNodes() );
6638 if ( !phy.getName().equals( "" ) ) {
6641 if ( !phy.isRooted() ) {
6645 if ( !p.hasNext() ) {
6649 if ( phy == null ) {
6652 if ( phy.getNumberOfExternalNodes() != 3 ) {
6655 if ( !phy.getName().equals( "" ) ) {
6658 if ( phy.isRooted() ) {
6662 if ( !p.hasNext() ) {
6666 if ( phy == null ) {
6669 if ( phy.getNumberOfExternalNodes() != 2 ) {
6672 if ( !phy.getName().equals( "" ) ) {
6675 if ( !phy.isRooted() ) {
6679 if ( !p.hasNext() ) {
6683 if ( phy.getNumberOfExternalNodes() != 3 ) {
6686 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6689 if ( !phy.isRooted() ) {
6693 if ( !p.hasNext() ) {
6697 if ( phy.getNumberOfExternalNodes() != 3 ) {
6700 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
6703 if ( !phy.getName().equals( "tree 8" ) ) {
6707 if ( !p.hasNext() ) {
6711 if ( phy.getNumberOfExternalNodes() != 3 ) {
6714 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
6717 if ( !phy.getName().equals( "tree 9" ) ) {
6721 if ( !p.hasNext() ) {
6725 if ( phy.getNumberOfExternalNodes() != 3 ) {
6728 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6731 if ( !phy.getName().equals( "tree 10" ) ) {
6734 if ( !phy.isRooted() ) {
6738 if ( !p.hasNext() ) {
6742 if ( phy.getNumberOfExternalNodes() != 3 ) {
6745 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
6748 if ( !phy.getName().equals( "tree 11" ) ) {
6751 if ( phy.isRooted() ) {
6755 if ( !p.hasNext() ) {
6759 if ( phy.getNumberOfExternalNodes() != 3 ) {
6762 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
6765 if ( !phy.getName().equals( "tree 12" ) ) {
6768 if ( !phy.isRooted() ) {
6772 if ( !p.hasNext() ) {
6776 if ( phy.getNumberOfExternalNodes() != 3 ) {
6779 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
6782 if ( !phy.getName().equals( "tree 13" ) ) {
6785 if ( !phy.isRooted() ) {
6789 if ( !p.hasNext() ) {
6793 if ( phy.getNumberOfExternalNodes() != 10 ) {
6794 System.out.println( phy.getNumberOfExternalNodes() );
6799 .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;" ) ) {
6800 System.out.println( phy.toNewHampshire() );
6803 if ( !phy.getName().equals( "tree 14" ) ) {
6806 if ( !phy.isRooted() ) {
6810 if ( !p.hasNext() ) {
6814 if ( phy.getNumberOfExternalNodes() != 10 ) {
6815 System.out.println( phy.getNumberOfExternalNodes() );
6820 .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;" ) ) {
6821 System.out.println( phy.toNewHampshire() );
6824 if ( !phy.getName().equals( "tree 15" ) ) {
6827 if ( phy.isRooted() ) {
6831 if ( !p.hasNext() ) {
6835 if ( phy.getNumberOfExternalNodes() != 10 ) {
6836 System.out.println( phy.getNumberOfExternalNodes() );
6841 .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;" ) ) {
6842 System.out.println( phy.toNewHampshire() );
6845 if ( !phy.getName().equals( "tree 16" ) ) {
6848 if ( !phy.isRooted() ) {
6852 if ( !p.hasNext() ) {
6856 if ( phy.getNumberOfExternalNodes() != 10 ) {
6857 System.out.println( phy.getNumberOfExternalNodes() );
6862 .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;" ) ) {
6863 System.out.println( phy.toNewHampshire() );
6866 if ( !phy.getName().equals( "tree 17" ) ) {
6869 if ( phy.isRooted() ) {
6873 if ( p.hasNext() ) {
6877 if ( phy != null ) {
6882 if ( !p.hasNext() ) {
6886 if ( phy == null ) {
6889 if ( phy.getNumberOfExternalNodes() != 10 ) {
6892 if ( !phy.getName().equals( "tree 0" ) ) {
6896 if ( !p.hasNext() ) {
6900 if ( phy == null ) {
6903 if ( phy.getNumberOfExternalNodes() != 10 ) {
6906 if ( !phy.getName().equals( "tree 1" ) ) {
6910 if ( !p.hasNext() ) {
6914 if ( phy == null ) {
6917 if ( phy.getNumberOfExternalNodes() != 3 ) {
6920 if ( !phy.getName().equals( "" ) ) {
6923 if ( phy.isRooted() ) {
6927 if ( !p.hasNext() ) {
6931 if ( phy == null ) {
6934 if ( phy.getNumberOfExternalNodes() != 4 ) {
6937 if ( !phy.getName().equals( "" ) ) {
6940 if ( !phy.isRooted() ) {
6944 if ( !p.hasNext() ) {
6948 if ( phy == null ) {
6951 if ( phy.getNumberOfExternalNodes() != 5 ) {
6952 System.out.println( phy.getNumberOfExternalNodes() );
6955 if ( !phy.getName().equals( "" ) ) {
6958 if ( !phy.isRooted() ) {
6962 if ( !p.hasNext() ) {
6966 if ( phy == null ) {
6969 if ( phy.getNumberOfExternalNodes() != 3 ) {
6972 if ( !phy.getName().equals( "" ) ) {
6975 if ( phy.isRooted() ) {
6979 catch ( final Exception e ) {
6980 e.printStackTrace( System.out );
6986 private static boolean testNexusTreeParsingTranslating() {
6988 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6989 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
6990 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
6991 if ( phylogenies.length != 1 ) {
6994 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
6997 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7000 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7003 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7006 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7007 .equals( "Aranaeus" ) ) {
7011 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
7012 if ( phylogenies.length != 3 ) {
7015 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7018 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7021 if ( phylogenies[ 0 ].isRooted() ) {
7024 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7027 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7030 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7031 .equals( "Aranaeus" ) ) {
7034 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7037 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7040 if ( phylogenies[ 1 ].isRooted() ) {
7043 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7046 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7049 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7050 .equals( "Aranaeus" ) ) {
7053 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7056 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7059 if ( !phylogenies[ 2 ].isRooted() ) {
7062 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7065 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7068 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7069 .equals( "Aranaeus" ) ) {
7073 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
7074 if ( phylogenies.length != 3 ) {
7077 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
7080 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
7083 if ( phylogenies[ 0 ].isRooted() ) {
7086 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7089 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7092 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7093 .equals( "Aranaeus" ) ) {
7096 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
7099 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
7102 if ( phylogenies[ 1 ].isRooted() ) {
7105 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7108 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7111 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7112 .equals( "Aranaeus" ) ) {
7115 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
7118 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
7121 if ( !phylogenies[ 2 ].isRooted() ) {
7124 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
7127 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
7130 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
7131 .equals( "Aranaeus" ) ) {
7135 catch ( final Exception e ) {
7136 e.printStackTrace( System.out );
7142 private static boolean testNHParsing() {
7144 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7145 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
7146 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
7149 final NHXParser nhxp = new NHXParser();
7150 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
7151 nhxp.setReplaceUnderscores( true );
7152 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
7153 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
7156 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
7159 final Phylogeny p1b = factory
7160 .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 ",
7161 new NHXParser() )[ 0 ];
7162 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
7165 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
7168 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
7169 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
7170 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
7171 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
7172 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
7173 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
7174 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
7175 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
7176 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
7177 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
7178 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
7179 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
7180 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
7182 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
7185 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
7188 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
7191 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
7194 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
7195 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
7196 final String p16_S = "((A,B),C)";
7197 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
7198 if ( p16.length != 1 ) {
7201 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
7204 final String p17_S = "(C,(A,B))";
7205 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
7206 if ( p17.length != 1 ) {
7209 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
7212 final String p18_S = "((A,B),(C,D))";
7213 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
7214 if ( p18.length != 1 ) {
7217 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
7220 final String p19_S = "(((A,B),C),D)";
7221 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
7222 if ( p19.length != 1 ) {
7225 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
7228 final String p20_S = "(A,(B,(C,D)))";
7229 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
7230 if ( p20.length != 1 ) {
7233 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
7236 final String p21_S = "(A,(B,(C,(D,E))))";
7237 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
7238 if ( p21.length != 1 ) {
7241 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
7244 final String p22_S = "((((A,B),C),D),E)";
7245 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
7246 if ( p22.length != 1 ) {
7249 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
7252 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7253 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
7254 if ( p23.length != 1 ) {
7255 System.out.println( "xl=" + p23.length );
7259 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
7262 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7263 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
7264 if ( p24.length != 1 ) {
7267 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
7270 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7271 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7272 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
7273 if ( p241.length != 2 ) {
7276 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
7279 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
7282 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
7283 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
7284 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
7285 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
7286 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
7287 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
7288 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
7289 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
7290 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
7291 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
7294 final String p26_S = "(A,B)ab";
7295 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
7296 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
7299 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7300 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
7301 if ( p27s.length != 1 ) {
7302 System.out.println( "xxl=" + p27s.length );
7306 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7307 System.out.println( p27s[ 0 ].toNewHampshireX() );
7311 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
7313 if ( p27.length != 1 ) {
7314 System.out.println( "yl=" + p27.length );
7318 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
7319 System.out.println( p27[ 0 ].toNewHampshireX() );
7323 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7324 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7325 final String p28_S3 = "(A,B)ab";
7326 final String p28_S4 = "((((A,B),C),D),;E;)";
7327 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
7329 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
7332 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
7335 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
7338 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
7341 if ( p28.length != 4 ) {
7344 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";
7345 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
7346 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
7349 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";
7350 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
7351 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
7354 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
7355 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
7356 if ( ( p32.length != 0 ) ) {
7359 final String p33_S = "A";
7360 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
7361 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
7364 final String p34_S = "B;";
7365 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
7366 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
7369 final String p35_S = "B:0.2";
7370 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
7371 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
7374 final String p36_S = "(A)";
7375 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
7376 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
7379 final String p37_S = "((A))";
7380 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
7381 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
7384 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7385 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
7386 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
7389 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
7390 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
7391 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
7394 final String p40_S = "(A,B,C)";
7395 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
7396 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
7399 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
7400 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
7401 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
7404 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
7405 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
7406 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
7409 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)";
7410 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
7411 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
7414 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)))";
7415 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
7416 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
7419 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
7420 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
7421 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
7424 final String p46_S = "";
7425 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
7426 if ( p46.length != 0 ) {
7429 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
7430 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7433 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7434 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7437 final Phylogeny p49 = factory
7438 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
7439 new NHXParser() )[ 0 ];
7440 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
7443 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7444 if ( p50.getNode( "A" ) == null ) {
7447 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7448 .equals( "((A,B)ab:2.0[88],C);" ) ) {
7451 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
7454 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
7455 .equals( "((A,B)88:2.0,C);" ) ) {
7458 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7459 if ( p51.getNode( "A(A" ) == null ) {
7462 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
7463 if ( p52.getNode( "A(A" ) == null ) {
7466 final Phylogeny p53 = factory
7467 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
7468 new NHXParser() )[ 0 ];
7469 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
7473 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
7474 if ( p54.getNode( "A" ) == null ) {
7477 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
7478 .equals( "((A,B)[88],C);" ) ) {
7482 catch ( final Exception e ) {
7483 e.printStackTrace( System.out );
7489 private static boolean testNHParsingIter() {
7491 final String p0_str = "(A,B);";
7492 final NHXParser p = new NHXParser();
7493 p.setSource( p0_str );
7494 if ( !p.hasNext() ) {
7497 final Phylogeny p0 = p.next();
7498 if ( !p0.toNewHampshire().equals( p0_str ) ) {
7499 System.out.println( p0.toNewHampshire() );
7502 if ( p.hasNext() ) {
7505 if ( p.next() != null ) {
7509 final String p00_str = "(A,B)root;";
7510 p.setSource( p00_str );
7511 final Phylogeny p00 = p.next();
7512 if ( !p00.toNewHampshire().equals( p00_str ) ) {
7513 System.out.println( p00.toNewHampshire() );
7517 final String p000_str = "A;";
7518 p.setSource( p000_str );
7519 final Phylogeny p000 = p.next();
7520 if ( !p000.toNewHampshire().equals( p000_str ) ) {
7521 System.out.println( p000.toNewHampshire() );
7525 final String p0000_str = "A";
7526 p.setSource( p0000_str );
7527 final Phylogeny p0000 = p.next();
7528 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
7529 System.out.println( p0000.toNewHampshire() );
7533 p.setSource( "(A)" );
7534 final Phylogeny p00000 = p.next();
7535 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
7536 System.out.println( p00000.toNewHampshire() );
7540 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
7541 p.setSource( p1_str );
7542 if ( !p.hasNext() ) {
7545 final Phylogeny p1_0 = p.next();
7546 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
7547 System.out.println( p1_0.toNewHampshire() );
7550 if ( !p.hasNext() ) {
7553 final Phylogeny p1_1 = p.next();
7554 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
7555 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
7558 if ( !p.hasNext() ) {
7561 final Phylogeny p1_2 = p.next();
7562 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
7563 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
7566 if ( !p.hasNext() ) {
7569 final Phylogeny p1_3 = p.next();
7570 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
7571 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
7574 if ( p.hasNext() ) {
7577 if ( p.next() != null ) {
7581 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
7582 p.setSource( p2_str );
7583 if ( !p.hasNext() ) {
7586 Phylogeny p2_0 = p.next();
7587 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7588 System.out.println( p2_0.toNewHampshire() );
7591 if ( !p.hasNext() ) {
7594 Phylogeny p2_1 = p.next();
7595 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7596 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7599 if ( !p.hasNext() ) {
7602 Phylogeny p2_2 = p.next();
7603 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
7604 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
7607 if ( !p.hasNext() ) {
7610 Phylogeny p2_3 = p.next();
7611 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
7612 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
7615 if ( !p.hasNext() ) {
7618 Phylogeny p2_4 = p.next();
7619 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
7620 System.out.println( "(X) != " + p2_4.toNewHampshire() );
7623 if ( p.hasNext() ) {
7626 if ( p.next() != null ) {
7631 if ( !p.hasNext() ) {
7635 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
7636 System.out.println( p2_0.toNewHampshire() );
7639 if ( !p.hasNext() ) {
7643 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
7644 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
7647 if ( !p.hasNext() ) {
7651 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
7652 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
7655 if ( !p.hasNext() ) {
7659 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
7660 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
7663 if ( !p.hasNext() ) {
7667 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
7668 System.out.println( "(X) != " + p2_4.toNewHampshire() );
7671 if ( p.hasNext() ) {
7674 if ( p.next() != null ) {
7678 final String p3_str = "((A,B),C)abc";
7679 p.setSource( p3_str );
7680 if ( !p.hasNext() ) {
7683 final Phylogeny p3_0 = p.next();
7684 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
7687 if ( p.hasNext() ) {
7690 if ( p.next() != null ) {
7694 final String p4_str = "((A,B)ab,C)abc";
7695 p.setSource( p4_str );
7696 if ( !p.hasNext() ) {
7699 final Phylogeny p4_0 = p.next();
7700 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
7703 if ( p.hasNext() ) {
7706 if ( p.next() != null ) {
7710 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
7711 p.setSource( p5_str );
7712 if ( !p.hasNext() ) {
7715 final Phylogeny p5_0 = p.next();
7716 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
7719 if ( p.hasNext() ) {
7722 if ( p.next() != null ) {
7726 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
7727 p.setSource( p6_str );
7728 if ( !p.hasNext() ) {
7731 Phylogeny p6_0 = p.next();
7732 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
7735 if ( p.hasNext() ) {
7738 if ( p.next() != null ) {
7742 if ( !p.hasNext() ) {
7746 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
7749 if ( p.hasNext() ) {
7752 if ( p.next() != null ) {
7756 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
7757 p.setSource( p7_str );
7758 if ( !p.hasNext() ) {
7761 Phylogeny p7_0 = p.next();
7762 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7765 if ( p.hasNext() ) {
7768 if ( p.next() != null ) {
7772 if ( !p.hasNext() ) {
7776 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7779 if ( p.hasNext() ) {
7782 if ( p.next() != null ) {
7786 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
7787 p.setSource( p8_str );
7788 if ( !p.hasNext() ) {
7791 Phylogeny p8_0 = p.next();
7792 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7795 if ( !p.hasNext() ) {
7798 if ( !p.hasNext() ) {
7801 Phylogeny p8_1 = p.next();
7802 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
7805 if ( p.hasNext() ) {
7808 if ( p.next() != null ) {
7812 if ( !p.hasNext() ) {
7816 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
7819 if ( !p.hasNext() ) {
7823 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
7826 if ( p.hasNext() ) {
7829 if ( p.next() != null ) {
7835 if ( p.hasNext() ) {
7839 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
7840 if ( !p.hasNext() ) {
7843 Phylogeny p_27 = p.next();
7844 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
7845 System.out.println( p_27.toNewHampshireX() );
7849 if ( p.hasNext() ) {
7852 if ( p.next() != null ) {
7856 if ( !p.hasNext() ) {
7860 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
7861 System.out.println( p_27.toNewHampshireX() );
7865 if ( p.hasNext() ) {
7868 if ( p.next() != null ) {
7872 catch ( final Exception e ) {
7873 e.printStackTrace( System.out );
7879 private static boolean testNHXconversion() {
7881 final PhylogenyNode n1 = new PhylogenyNode();
7882 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
7883 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
7884 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
7885 final PhylogenyNode n5 = PhylogenyNode
7886 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
7887 final PhylogenyNode n6 = PhylogenyNode
7888 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
7889 if ( !n1.toNewHampshireX().equals( "" ) ) {
7892 if ( !n2.toNewHampshireX().equals( "" ) ) {
7895 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
7898 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
7901 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
7904 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
7905 System.out.println( n6.toNewHampshireX() );
7909 catch ( final Exception e ) {
7910 e.printStackTrace( System.out );
7916 private static boolean testNHXNodeParsing() {
7918 final PhylogenyNode n1 = new PhylogenyNode();
7919 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
7920 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
7921 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
7922 final PhylogenyNode n5 = PhylogenyNode
7923 .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]" );
7924 if ( !n3.getName().equals( "n3" ) ) {
7927 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
7930 if ( n3.isDuplication() ) {
7933 if ( n3.isHasAssignedEvent() ) {
7936 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
7939 if ( !n4.getName().equals( "n4" ) ) {
7942 if ( n4.getDistanceToParent() != 0.01 ) {
7945 if ( !n5.getName().equals( "n5" ) ) {
7948 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
7951 if ( n5.getDistanceToParent() != 0.1 ) {
7954 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
7957 if ( !n5.isDuplication() ) {
7960 if ( !n5.isHasAssignedEvent() ) {
7963 final PhylogenyNode n8 = PhylogenyNode
7964 .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
7965 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7966 if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
7969 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
7972 final PhylogenyNode n9 = PhylogenyNode
7973 .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
7974 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7975 if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
7978 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
7981 final PhylogenyNode n10 = PhylogenyNode
7982 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7983 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
7986 final PhylogenyNode n20 = PhylogenyNode
7987 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
7988 if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
7991 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
7994 final PhylogenyNode n20x = PhylogenyNode
7995 .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
7996 if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
7999 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
8002 final PhylogenyNode n20xx = PhylogenyNode
8003 .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8004 if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
8007 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
8010 final PhylogenyNode n20xxx = PhylogenyNode
8011 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8012 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
8015 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
8018 final PhylogenyNode n20xxxx = PhylogenyNode
8019 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8020 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
8023 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
8026 final PhylogenyNode n21 = PhylogenyNode
8027 .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8028 if ( !n21.getName().equals( "N21_PIG" ) ) {
8031 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
8034 final PhylogenyNode n21x = PhylogenyNode
8035 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8036 if ( !n21x.getName().equals( "n21_PIG" ) ) {
8039 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
8042 final PhylogenyNode n22 = PhylogenyNode
8043 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8044 if ( !n22.getName().equals( "n22/PIG" ) ) {
8047 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
8050 final PhylogenyNode n23 = PhylogenyNode
8051 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8052 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
8055 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
8058 final PhylogenyNode a = PhylogenyNode
8059 .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8060 if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
8063 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
8066 final PhylogenyNode c1 = PhylogenyNode
8067 .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
8068 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8069 if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
8072 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
8075 final PhylogenyNode c2 = PhylogenyNode
8076 .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
8077 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8078 if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
8081 if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
8084 final PhylogenyNode e3 = PhylogenyNode
8085 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8086 if ( !e3.getName().equals( "n10_RAT~" ) ) {
8089 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
8092 final PhylogenyNode n11 = PhylogenyNode
8093 .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
8094 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8095 if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
8098 if ( n11.getDistanceToParent() != 0.4 ) {
8101 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
8104 final PhylogenyNode n12 = PhylogenyNode
8105 .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
8106 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8107 if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
8110 if ( n12.getDistanceToParent() != 0.4 ) {
8113 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
8116 final PhylogenyNode o = PhylogenyNode
8117 .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8118 if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
8121 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
8124 if ( n1.getName().compareTo( "" ) != 0 ) {
8127 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8130 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8133 if ( n2.getName().compareTo( "" ) != 0 ) {
8136 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
8139 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
8142 final PhylogenyNode n00 = PhylogenyNode
8143 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
8144 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
8147 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
8150 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
8151 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
8154 final PhylogenyNode n13 = PhylogenyNode
8155 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8156 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
8159 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
8162 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8165 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8168 final PhylogenyNode n14 = PhylogenyNode
8169 .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8170 if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
8173 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
8176 final PhylogenyNode n15 = PhylogenyNode
8177 .createInstanceFromNhxString( "something_wicked[123]",
8178 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8179 if ( !n15.getName().equals( "something_wicked" ) ) {
8182 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
8185 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
8188 final PhylogenyNode n16 = PhylogenyNode
8189 .createInstanceFromNhxString( "something_wicked2[9]",
8190 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8191 if ( !n16.getName().equals( "something_wicked2" ) ) {
8194 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
8197 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
8200 final PhylogenyNode n17 = PhylogenyNode
8201 .createInstanceFromNhxString( "something_wicked3[a]",
8202 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8203 if ( !n17.getName().equals( "something_wicked3" ) ) {
8206 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
8209 final PhylogenyNode n18 = PhylogenyNode
8210 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8211 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
8214 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
8217 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
8220 final PhylogenyNode n19 = PhylogenyNode
8221 .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8222 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
8225 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8228 final PhylogenyNode n30 = PhylogenyNode
8229 .createInstanceFromNhxString( "blah_1234567-roejojoej",
8230 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8231 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
8234 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
8237 final PhylogenyNode n31 = PhylogenyNode
8238 .createInstanceFromNhxString( "blah_12345678-roejojoej",
8239 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8240 if ( n31.getNodeData().isHasTaxonomy() ) {
8243 final PhylogenyNode n32 = PhylogenyNode
8244 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8245 if ( n32.getNodeData().isHasTaxonomy() ) {
8248 final PhylogenyNode n40 = PhylogenyNode
8249 .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8250 if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
8253 final PhylogenyNode n41 = PhylogenyNode
8254 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8255 if ( n41.getNodeData().isHasTaxonomy() ) {
8258 final PhylogenyNode n42 = PhylogenyNode
8259 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
8260 if ( n42.getNodeData().isHasTaxonomy() ) {
8263 final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
8264 NHXParser.TAXONOMY_EXTRACTION.NO );
8265 if ( n43.getNodeData().isHasTaxonomy() ) {
8268 final PhylogenyNode n44 = PhylogenyNode
8269 .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
8270 if ( n44.getNodeData().isHasTaxonomy() ) {
8274 catch ( final Exception e ) {
8275 e.printStackTrace( System.out );
8281 private static boolean testNHXParsing() {
8283 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8284 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
8285 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
8288 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]";
8289 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
8290 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8293 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]";
8294 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
8295 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
8298 final Phylogeny[] p3 = factory
8299 .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]",
8301 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8304 final Phylogeny[] p4 = factory
8305 .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(]",
8307 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8310 final Phylogeny[] p5 = factory
8311 .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(((]",
8313 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
8316 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)";
8317 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)";
8318 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
8319 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
8322 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)))";
8323 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)))";
8324 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
8325 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
8328 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]) ))[,,, ])))))))";
8329 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
8330 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
8331 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
8334 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
8335 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8338 final Phylogeny p10 = factory
8339 .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]",
8340 new NHXParser() )[ 0 ];
8341 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
8345 catch ( final Exception e ) {
8346 e.printStackTrace( System.out );
8352 private static boolean testNHXParsingMB() {
8354 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8355 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
8356 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8357 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8358 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8359 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8360 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8361 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8362 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8363 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
8364 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
8367 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
8370 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
8371 0.1100000000000000e+00 ) ) {
8374 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
8377 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
8380 final Phylogeny p2 = factory
8381 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
8382 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8383 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
8384 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
8385 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
8386 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
8387 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
8388 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
8389 + "7.369400000000000e-02}])",
8390 new NHXParser() )[ 0 ];
8391 if ( p2.getNode( "1" ) == null ) {
8394 if ( p2.getNode( "2" ) == null ) {
8398 catch ( final Exception e ) {
8399 e.printStackTrace( System.out );
8406 private static boolean testNHXParsingQuotes() {
8408 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8409 final NHXParser p = new NHXParser();
8410 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
8411 if ( phylogenies_0.length != 5 ) {
8414 final Phylogeny phy = phylogenies_0[ 4 ];
8415 if ( phy.getNumberOfExternalNodes() != 7 ) {
8418 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
8421 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
8424 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
8425 .getScientificName().equals( "hsapiens" ) ) {
8428 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
8431 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
8434 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
8437 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
8440 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
8443 final NHXParser p1p = new NHXParser();
8444 p1p.setIgnoreQuotes( true );
8445 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
8446 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
8449 final NHXParser p2p = new NHXParser();
8450 p1p.setIgnoreQuotes( false );
8451 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
8452 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
8455 final NHXParser p3p = new NHXParser();
8456 p3p.setIgnoreQuotes( false );
8457 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
8458 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
8461 final NHXParser p4p = new NHXParser();
8462 p4p.setIgnoreQuotes( false );
8463 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
8464 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
8467 final Phylogeny p10 = factory
8468 .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]",
8469 new NHXParser() )[ 0 ];
8470 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]";
8471 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
8474 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
8475 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
8479 final Phylogeny p12 = factory
8480 .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]",
8481 new NHXParser() )[ 0 ];
8482 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]";
8483 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
8486 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
8487 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
8490 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;";
8491 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
8494 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
8495 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
8499 catch ( final Exception e ) {
8500 e.printStackTrace( System.out );
8506 private static boolean testNodeRemoval() {
8508 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8509 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
8510 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
8511 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
8514 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
8515 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
8516 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
8519 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
8520 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
8521 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
8525 catch ( final Exception e ) {
8526 e.printStackTrace( System.out );
8532 private static boolean testPhylogenyBranch() {
8534 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
8535 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
8536 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
8537 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
8538 if ( !a1b1.equals( a1b1 ) ) {
8541 if ( !a1b1.equals( b1a1 ) ) {
8544 if ( !b1a1.equals( a1b1 ) ) {
8547 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
8548 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
8549 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
8550 if ( a1_b1.equals( b1_a1 ) ) {
8553 if ( a1_b1.equals( a1_b1_ ) ) {
8556 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
8557 if ( !a1_b1.equals( b1_a1_ ) ) {
8560 if ( a1_b1_.equals( b1_a1_ ) ) {
8563 if ( !a1_b1_.equals( b1_a1 ) ) {
8567 catch ( final Exception e ) {
8568 e.printStackTrace( System.out );
8574 private static boolean testPhyloXMLparsingOfDistributionElement() {
8576 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8577 PhyloXmlParser xml_parser = null;
8579 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
8581 catch ( final Exception e ) {
8582 // Do nothing -- means were not running from jar.
8584 if ( xml_parser == null ) {
8585 xml_parser = PhyloXmlParser.createPhyloXmlParser();
8586 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
8587 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
8590 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
8593 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
8595 if ( xml_parser.getErrorCount() > 0 ) {
8596 System.out.println( xml_parser.getErrorMessages().toString() );
8599 if ( phylogenies_0.length != 1 ) {
8602 final Phylogeny t1 = phylogenies_0[ 0 ];
8603 PhylogenyNode n = null;
8604 Distribution d = null;
8605 n = t1.getNode( "root node" );
8606 if ( !n.getNodeData().isHasDistribution() ) {
8609 if ( n.getNodeData().getDistributions().size() != 1 ) {
8612 d = n.getNodeData().getDistribution();
8613 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
8616 if ( d.getPoints().size() != 1 ) {
8619 if ( d.getPolygons() != null ) {
8622 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
8625 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8628 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8631 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
8634 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
8637 n = t1.getNode( "node a" );
8638 if ( !n.getNodeData().isHasDistribution() ) {
8641 if ( n.getNodeData().getDistributions().size() != 2 ) {
8644 d = n.getNodeData().getDistribution( 1 );
8645 if ( !d.getDesc().equals( "San Diego" ) ) {
8648 if ( d.getPoints().size() != 1 ) {
8651 if ( d.getPolygons() != null ) {
8654 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
8657 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8660 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8663 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
8666 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
8669 n = t1.getNode( "node bb" );
8670 if ( !n.getNodeData().isHasDistribution() ) {
8673 if ( n.getNodeData().getDistributions().size() != 1 ) {
8676 d = n.getNodeData().getDistribution( 0 );
8677 if ( d.getPoints().size() != 3 ) {
8680 if ( d.getPolygons().size() != 2 ) {
8683 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
8686 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
8689 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
8692 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
8695 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
8698 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
8701 Polygon p = d.getPolygons().get( 0 );
8702 if ( p.getPoints().size() != 3 ) {
8705 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
8708 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
8711 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8714 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
8717 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
8720 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
8723 p = d.getPolygons().get( 1 );
8724 if ( p.getPoints().size() != 3 ) {
8727 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
8730 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
8733 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8737 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
8738 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
8739 if ( rt.length != 1 ) {
8742 final Phylogeny t1_rt = rt[ 0 ];
8743 n = t1_rt.getNode( "root node" );
8744 if ( !n.getNodeData().isHasDistribution() ) {
8747 if ( n.getNodeData().getDistributions().size() != 1 ) {
8750 d = n.getNodeData().getDistribution();
8751 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
8754 if ( d.getPoints().size() != 1 ) {
8757 if ( d.getPolygons() != null ) {
8760 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
8763 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8766 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8769 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
8772 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
8775 n = t1_rt.getNode( "node a" );
8776 if ( !n.getNodeData().isHasDistribution() ) {
8779 if ( n.getNodeData().getDistributions().size() != 2 ) {
8782 d = n.getNodeData().getDistribution( 1 );
8783 if ( !d.getDesc().equals( "San Diego" ) ) {
8786 if ( d.getPoints().size() != 1 ) {
8789 if ( d.getPolygons() != null ) {
8792 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
8795 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
8798 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
8801 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
8804 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
8807 n = t1_rt.getNode( "node bb" );
8808 if ( !n.getNodeData().isHasDistribution() ) {
8811 if ( n.getNodeData().getDistributions().size() != 1 ) {
8814 d = n.getNodeData().getDistribution( 0 );
8815 if ( d.getPoints().size() != 3 ) {
8818 if ( d.getPolygons().size() != 2 ) {
8821 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
8824 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
8827 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
8830 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
8833 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
8836 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
8839 p = d.getPolygons().get( 0 );
8840 if ( p.getPoints().size() != 3 ) {
8843 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
8846 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
8849 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8852 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
8855 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
8858 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
8861 p = d.getPolygons().get( 1 );
8862 if ( p.getPoints().size() != 3 ) {
8865 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
8868 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
8871 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
8875 catch ( final Exception e ) {
8876 e.printStackTrace( System.out );
8882 private static boolean testPostOrderIterator() {
8884 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8885 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
8886 PhylogenyNodeIterator it0;
8887 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
8890 for( it0.reset(); it0.hasNext(); ) {
8893 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
8894 final PhylogenyNodeIterator it = t1.iteratorPostorder();
8895 if ( !it.next().getName().equals( "A" ) ) {
8898 if ( !it.next().getName().equals( "B" ) ) {
8901 if ( !it.next().getName().equals( "ab" ) ) {
8904 if ( !it.next().getName().equals( "C" ) ) {
8907 if ( !it.next().getName().equals( "D" ) ) {
8910 if ( !it.next().getName().equals( "cd" ) ) {
8913 if ( !it.next().getName().equals( "abcd" ) ) {
8916 if ( !it.next().getName().equals( "E" ) ) {
8919 if ( !it.next().getName().equals( "F" ) ) {
8922 if ( !it.next().getName().equals( "ef" ) ) {
8925 if ( !it.next().getName().equals( "G" ) ) {
8928 if ( !it.next().getName().equals( "H" ) ) {
8931 if ( !it.next().getName().equals( "gh" ) ) {
8934 if ( !it.next().getName().equals( "efgh" ) ) {
8937 if ( !it.next().getName().equals( "r" ) ) {
8940 if ( it.hasNext() ) {
8944 catch ( final Exception e ) {
8945 e.printStackTrace( System.out );
8951 private static boolean testPreOrderIterator() {
8953 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8954 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
8955 PhylogenyNodeIterator it0;
8956 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
8959 for( it0.reset(); it0.hasNext(); ) {
8962 PhylogenyNodeIterator it = t0.iteratorPreorder();
8963 if ( !it.next().getName().equals( "r" ) ) {
8966 if ( !it.next().getName().equals( "ab" ) ) {
8969 if ( !it.next().getName().equals( "A" ) ) {
8972 if ( !it.next().getName().equals( "B" ) ) {
8975 if ( !it.next().getName().equals( "cd" ) ) {
8978 if ( !it.next().getName().equals( "C" ) ) {
8981 if ( !it.next().getName().equals( "D" ) ) {
8984 if ( it.hasNext() ) {
8987 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
8988 it = t1.iteratorPreorder();
8989 if ( !it.next().getName().equals( "r" ) ) {
8992 if ( !it.next().getName().equals( "abcd" ) ) {
8995 if ( !it.next().getName().equals( "ab" ) ) {
8998 if ( !it.next().getName().equals( "A" ) ) {
9001 if ( !it.next().getName().equals( "B" ) ) {
9004 if ( !it.next().getName().equals( "cd" ) ) {
9007 if ( !it.next().getName().equals( "C" ) ) {
9010 if ( !it.next().getName().equals( "D" ) ) {
9013 if ( !it.next().getName().equals( "efgh" ) ) {
9016 if ( !it.next().getName().equals( "ef" ) ) {
9019 if ( !it.next().getName().equals( "E" ) ) {
9022 if ( !it.next().getName().equals( "F" ) ) {
9025 if ( !it.next().getName().equals( "gh" ) ) {
9028 if ( !it.next().getName().equals( "G" ) ) {
9031 if ( !it.next().getName().equals( "H" ) ) {
9034 if ( it.hasNext() ) {
9038 catch ( final Exception e ) {
9039 e.printStackTrace( System.out );
9045 private static boolean testPropertiesMap() {
9047 final PropertiesMap pm = new PropertiesMap();
9048 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9049 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
9050 final Property p2 = new Property( "something:else",
9052 "improbable:research",
9055 pm.addProperty( p0 );
9056 pm.addProperty( p1 );
9057 pm.addProperty( p2 );
9058 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
9061 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
9064 if ( pm.getProperties().size() != 3 ) {
9067 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
9070 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9073 if ( pm.getProperties().size() != 3 ) {
9076 pm.removeProperty( "dimensions:diameter" );
9077 if ( pm.getProperties().size() != 2 ) {
9080 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
9083 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
9087 catch ( final Exception e ) {
9088 e.printStackTrace( System.out );
9094 private static boolean testProteinId() {
9096 final ProteinId id1 = new ProteinId( "a" );
9097 final ProteinId id2 = new ProteinId( "a" );
9098 final ProteinId id3 = new ProteinId( "A" );
9099 final ProteinId id4 = new ProteinId( "b" );
9100 if ( !id1.equals( id1 ) ) {
9103 if ( id1.getId().equals( "x" ) ) {
9106 if ( id1.getId().equals( null ) ) {
9109 if ( !id1.equals( id2 ) ) {
9112 if ( id1.equals( id3 ) ) {
9115 if ( id1.hashCode() != id1.hashCode() ) {
9118 if ( id1.hashCode() != id2.hashCode() ) {
9121 if ( id1.hashCode() == id3.hashCode() ) {
9124 if ( id1.compareTo( id1 ) != 0 ) {
9127 if ( id1.compareTo( id2 ) != 0 ) {
9130 if ( id1.compareTo( id3 ) != 0 ) {
9133 if ( id1.compareTo( id4 ) >= 0 ) {
9136 if ( id4.compareTo( id1 ) <= 0 ) {
9139 if ( !id4.getId().equals( "b" ) ) {
9142 final ProteinId id5 = new ProteinId( " C " );
9143 if ( !id5.getId().equals( "C" ) ) {
9146 if ( id5.equals( id1 ) ) {
9150 catch ( final Exception e ) {
9151 e.printStackTrace( System.out );
9157 private static boolean testReIdMethods() {
9159 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9160 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
9161 final long count = PhylogenyNode.getNodeCount();
9163 if ( p.getNode( "r" ).getId() != count ) {
9166 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
9169 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
9172 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
9175 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
9178 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
9181 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
9184 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
9187 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
9190 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
9193 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
9196 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
9199 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
9202 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
9205 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
9209 catch ( final Exception e ) {
9210 e.printStackTrace( System.out );
9216 private static boolean testRerooting() {
9218 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9219 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",
9220 new NHXParser() )[ 0 ];
9221 if ( !t1.isRooted() ) {
9224 t1.reRoot( t1.getNode( "D" ) );
9225 t1.reRoot( t1.getNode( "CD" ) );
9226 t1.reRoot( t1.getNode( "A" ) );
9227 t1.reRoot( t1.getNode( "B" ) );
9228 t1.reRoot( t1.getNode( "AB" ) );
9229 t1.reRoot( t1.getNode( "D" ) );
9230 t1.reRoot( t1.getNode( "C" ) );
9231 t1.reRoot( t1.getNode( "CD" ) );
9232 t1.reRoot( t1.getNode( "A" ) );
9233 t1.reRoot( t1.getNode( "B" ) );
9234 t1.reRoot( t1.getNode( "AB" ) );
9235 t1.reRoot( t1.getNode( "D" ) );
9236 t1.reRoot( t1.getNode( "D" ) );
9237 t1.reRoot( t1.getNode( "C" ) );
9238 t1.reRoot( t1.getNode( "A" ) );
9239 t1.reRoot( t1.getNode( "B" ) );
9240 t1.reRoot( t1.getNode( "AB" ) );
9241 t1.reRoot( t1.getNode( "C" ) );
9242 t1.reRoot( t1.getNode( "D" ) );
9243 t1.reRoot( t1.getNode( "CD" ) );
9244 t1.reRoot( t1.getNode( "D" ) );
9245 t1.reRoot( t1.getNode( "A" ) );
9246 t1.reRoot( t1.getNode( "B" ) );
9247 t1.reRoot( t1.getNode( "AB" ) );
9248 t1.reRoot( t1.getNode( "C" ) );
9249 t1.reRoot( t1.getNode( "D" ) );
9250 t1.reRoot( t1.getNode( "CD" ) );
9251 t1.reRoot( t1.getNode( "D" ) );
9252 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
9255 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
9258 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
9261 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
9264 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
9267 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
9270 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",
9271 new NHXParser() )[ 0 ];
9272 t2.reRoot( t2.getNode( "A" ) );
9273 t2.reRoot( t2.getNode( "D" ) );
9274 t2.reRoot( t2.getNode( "ABC" ) );
9275 t2.reRoot( t2.getNode( "A" ) );
9276 t2.reRoot( t2.getNode( "B" ) );
9277 t2.reRoot( t2.getNode( "D" ) );
9278 t2.reRoot( t2.getNode( "C" ) );
9279 t2.reRoot( t2.getNode( "ABC" ) );
9280 t2.reRoot( t2.getNode( "A" ) );
9281 t2.reRoot( t2.getNode( "B" ) );
9282 t2.reRoot( t2.getNode( "AB" ) );
9283 t2.reRoot( t2.getNode( "AB" ) );
9284 t2.reRoot( t2.getNode( "D" ) );
9285 t2.reRoot( t2.getNode( "C" ) );
9286 t2.reRoot( t2.getNode( "B" ) );
9287 t2.reRoot( t2.getNode( "AB" ) );
9288 t2.reRoot( t2.getNode( "D" ) );
9289 t2.reRoot( t2.getNode( "D" ) );
9290 t2.reRoot( t2.getNode( "ABC" ) );
9291 t2.reRoot( t2.getNode( "A" ) );
9292 t2.reRoot( t2.getNode( "B" ) );
9293 t2.reRoot( t2.getNode( "AB" ) );
9294 t2.reRoot( t2.getNode( "D" ) );
9295 t2.reRoot( t2.getNode( "C" ) );
9296 t2.reRoot( t2.getNode( "ABC" ) );
9297 t2.reRoot( t2.getNode( "A" ) );
9298 t2.reRoot( t2.getNode( "B" ) );
9299 t2.reRoot( t2.getNode( "AB" ) );
9300 t2.reRoot( t2.getNode( "D" ) );
9301 t2.reRoot( t2.getNode( "D" ) );
9302 t2.reRoot( t2.getNode( "C" ) );
9303 t2.reRoot( t2.getNode( "A" ) );
9304 t2.reRoot( t2.getNode( "B" ) );
9305 t2.reRoot( t2.getNode( "AB" ) );
9306 t2.reRoot( t2.getNode( "C" ) );
9307 t2.reRoot( t2.getNode( "D" ) );
9308 t2.reRoot( t2.getNode( "ABC" ) );
9309 t2.reRoot( t2.getNode( "D" ) );
9310 t2.reRoot( t2.getNode( "A" ) );
9311 t2.reRoot( t2.getNode( "B" ) );
9312 t2.reRoot( t2.getNode( "AB" ) );
9313 t2.reRoot( t2.getNode( "C" ) );
9314 t2.reRoot( t2.getNode( "D" ) );
9315 t2.reRoot( t2.getNode( "ABC" ) );
9316 t2.reRoot( t2.getNode( "D" ) );
9317 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9320 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9323 t2.reRoot( t2.getNode( "ABC" ) );
9324 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9327 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9330 t2.reRoot( t2.getNode( "AB" ) );
9331 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9334 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9337 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9340 t2.reRoot( t2.getNode( "AB" ) );
9341 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9344 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9347 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9350 t2.reRoot( t2.getNode( "D" ) );
9351 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9354 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9357 t2.reRoot( t2.getNode( "ABC" ) );
9358 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
9361 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
9364 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
9365 new NHXParser() )[ 0 ];
9366 t3.reRoot( t3.getNode( "B" ) );
9367 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9370 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9373 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9376 t3.reRoot( t3.getNode( "B" ) );
9377 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9380 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9383 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9386 t3.reRoot( t3.getRoot() );
9387 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9390 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
9393 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
9397 catch ( final Exception e ) {
9398 e.printStackTrace( System.out );
9404 private static boolean testSDIse() {
9406 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9407 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
9408 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
9409 gene1.setRooted( true );
9410 species1.setRooted( true );
9411 final SDI sdi = new SDI( gene1, species1 );
9412 if ( !gene1.getRoot().isDuplication() ) {
9415 final Phylogeny species2 = factory
9416 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9417 new NHXParser() )[ 0 ];
9418 final Phylogeny gene2 = factory
9419 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9420 new NHXParser() )[ 0 ];
9421 species2.setRooted( true );
9422 gene2.setRooted( true );
9423 final SDI sdi2 = new SDI( gene2, species2 );
9424 if ( sdi2.getDuplicationsSum() != 0 ) {
9427 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
9430 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
9433 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
9436 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
9439 if ( !gene2.getNode( "r" ).isSpeciation() ) {
9442 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
9445 final Phylogeny species3 = factory
9446 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9447 new NHXParser() )[ 0 ];
9448 final Phylogeny gene3 = factory
9449 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9450 new NHXParser() )[ 0 ];
9451 species3.setRooted( true );
9452 gene3.setRooted( true );
9453 final SDI sdi3 = new SDI( gene3, species3 );
9454 if ( sdi3.getDuplicationsSum() != 1 ) {
9457 if ( !gene3.getNode( "aa" ).isDuplication() ) {
9460 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
9463 final Phylogeny species4 = factory
9464 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9465 new NHXParser() )[ 0 ];
9466 final Phylogeny gene4 = factory
9467 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9468 new NHXParser() )[ 0 ];
9469 species4.setRooted( true );
9470 gene4.setRooted( true );
9471 final SDI sdi4 = new SDI( gene4, species4 );
9472 if ( sdi4.getDuplicationsSum() != 1 ) {
9475 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
9478 if ( !gene4.getNode( "abc" ).isDuplication() ) {
9481 if ( gene4.getNode( "abcd" ).isDuplication() ) {
9484 if ( species4.getNumberOfExternalNodes() != 6 ) {
9487 if ( gene4.getNumberOfExternalNodes() != 6 ) {
9490 final Phylogeny species5 = factory
9491 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9492 new NHXParser() )[ 0 ];
9493 final Phylogeny gene5 = factory
9494 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
9495 new NHXParser() )[ 0 ];
9496 species5.setRooted( true );
9497 gene5.setRooted( true );
9498 final SDI sdi5 = new SDI( gene5, species5 );
9499 if ( sdi5.getDuplicationsSum() != 2 ) {
9502 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
9505 if ( !gene5.getNode( "adc" ).isDuplication() ) {
9508 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
9511 if ( species5.getNumberOfExternalNodes() != 6 ) {
9514 if ( gene5.getNumberOfExternalNodes() != 6 ) {
9517 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
9518 // Conjecture for Comparing Molecular Phylogenies"
9519 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
9520 final Phylogeny species6 = factory
9521 .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,"
9522 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9523 new NHXParser() )[ 0 ];
9524 final Phylogeny gene6 = factory
9525 .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,"
9526 + "((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,"
9527 + "(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;",
9528 new NHXParser() )[ 0 ];
9529 species6.setRooted( true );
9530 gene6.setRooted( true );
9531 final SDI sdi6 = new SDI( gene6, species6 );
9532 if ( sdi6.getDuplicationsSum() != 3 ) {
9535 if ( !gene6.getNode( "r" ).isDuplication() ) {
9538 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
9541 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
9544 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
9547 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
9550 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
9553 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
9556 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
9559 sdi6.computeMappingCostL();
9560 if ( sdi6.computeMappingCostL() != 17 ) {
9563 if ( species6.getNumberOfExternalNodes() != 9 ) {
9566 if ( gene6.getNumberOfExternalNodes() != 9 ) {
9569 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
9570 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
9571 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
9572 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
9573 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
9574 species7.setRooted( true );
9575 final Phylogeny gene7_1 = Test
9576 .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])" );
9577 gene7_1.setRooted( true );
9578 final SDI sdi7 = new SDI( gene7_1, species7 );
9579 if ( sdi7.getDuplicationsSum() != 0 ) {
9582 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
9585 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
9588 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
9591 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
9594 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
9597 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
9600 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
9603 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
9606 final Phylogeny gene7_2 = Test
9607 .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])" );
9608 gene7_2.setRooted( true );
9609 final SDI sdi7_2 = new SDI( gene7_2, species7 );
9610 if ( sdi7_2.getDuplicationsSum() != 1 ) {
9613 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
9616 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
9619 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
9622 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
9625 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
9628 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
9631 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
9634 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
9637 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
9641 catch ( final Exception e ) {
9647 private static boolean testSDIunrooted() {
9649 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9650 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
9651 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
9652 final Iterator<PhylogenyBranch> iter = l.iterator();
9653 PhylogenyBranch br = iter.next();
9654 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
9657 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
9661 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
9664 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
9668 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
9671 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
9675 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9678 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9682 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9685 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9689 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
9692 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
9696 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9699 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9703 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9706 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9710 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9713 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9717 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
9720 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
9724 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
9727 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
9731 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
9734 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
9738 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
9741 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
9745 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
9748 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
9752 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
9755 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
9758 if ( iter.hasNext() ) {
9761 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
9762 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
9763 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
9765 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
9768 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
9772 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9775 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9779 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9782 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9785 if ( iter1.hasNext() ) {
9788 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
9789 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
9790 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
9792 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
9795 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
9799 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
9802 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
9806 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
9809 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
9812 if ( iter2.hasNext() ) {
9815 final Phylogeny species0 = factory
9816 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
9817 new NHXParser() )[ 0 ];
9818 final Phylogeny gene1 = factory
9819 .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])",
9820 new NHXParser() )[ 0 ];
9821 species0.setRooted( true );
9822 gene1.setRooted( true );
9823 final SDIR sdi_unrooted = new SDIR();
9824 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
9825 if ( sdi_unrooted.getCount() != 1 ) {
9828 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
9831 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
9834 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
9837 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9840 final Phylogeny gene2 = factory
9841 .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])",
9842 new NHXParser() )[ 0 ];
9843 gene2.setRooted( true );
9844 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
9845 if ( sdi_unrooted.getCount() != 1 ) {
9848 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9851 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9854 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
9857 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9860 final Phylogeny species6 = factory
9861 .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,"
9862 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9863 new NHXParser() )[ 0 ];
9864 final Phylogeny gene6 = factory
9865 .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],"
9866 + "(((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],"
9867 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9868 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9869 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9870 new NHXParser() )[ 0 ];
9871 species6.setRooted( true );
9872 gene6.setRooted( true );
9873 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
9874 if ( sdi_unrooted.getCount() != 1 ) {
9877 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9880 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9883 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9886 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9889 if ( !p6[ 0 ].getRoot().isDuplication() ) {
9892 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
9895 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
9898 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
9901 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
9904 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
9907 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
9910 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
9914 final Phylogeny species7 = factory
9915 .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,"
9916 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9917 new NHXParser() )[ 0 ];
9918 final Phylogeny gene7 = factory
9919 .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],"
9920 + "(((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],"
9921 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9922 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9923 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9924 new NHXParser() )[ 0 ];
9925 species7.setRooted( true );
9926 gene7.setRooted( true );
9927 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
9928 if ( sdi_unrooted.getCount() != 1 ) {
9931 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9934 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9937 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9940 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
9943 if ( !p7[ 0 ].getRoot().isDuplication() ) {
9946 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
9949 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
9952 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
9955 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
9958 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
9961 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
9964 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
9968 final Phylogeny species8 = factory
9969 .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,"
9970 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
9971 new NHXParser() )[ 0 ];
9972 final Phylogeny gene8 = factory
9973 .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],"
9974 + "(((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],"
9975 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
9976 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
9977 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
9978 new NHXParser() )[ 0 ];
9979 species8.setRooted( true );
9980 gene8.setRooted( true );
9981 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
9982 if ( sdi_unrooted.getCount() != 1 ) {
9985 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
9988 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
9991 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
9994 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
9997 if ( !p8[ 0 ].getRoot().isDuplication() ) {
10000 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
10003 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
10006 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
10009 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
10012 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
10015 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
10018 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
10023 catch ( final Exception e ) {
10024 e.printStackTrace( System.out );
10030 private static boolean testSequenceIdParsing() {
10032 Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
10033 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10034 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10035 if ( id != null ) {
10036 System.out.println( "value =" + id.getValue() );
10037 System.out.println( "provider=" + id.getSource() );
10042 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
10043 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10044 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10045 if ( id != null ) {
10046 System.out.println( "value =" + id.getValue() );
10047 System.out.println( "provider=" + id.getSource() );
10052 id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
10053 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10054 || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
10055 if ( id != null ) {
10056 System.out.println( "value =" + id.getValue() );
10057 System.out.println( "provider=" + id.getSource() );
10062 id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
10063 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10064 || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
10065 if ( id != null ) {
10066 System.out.println( "value =" + id.getValue() );
10067 System.out.println( "provider=" + id.getSource() );
10072 id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
10073 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10074 || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
10075 if ( id != null ) {
10076 System.out.println( "value =" + id.getValue() );
10077 System.out.println( "provider=" + id.getSource() );
10082 id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
10083 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10084 || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
10085 if ( id != null ) {
10086 System.out.println( "value =" + id.getValue() );
10087 System.out.println( "provider=" + id.getSource() );
10092 id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
10093 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10094 || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
10095 if ( id != null ) {
10096 System.out.println( "value =" + id.getValue() );
10097 System.out.println( "provider=" + id.getSource() );
10102 id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
10103 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10104 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10105 if ( id != null ) {
10106 System.out.println( "value =" + id.getValue() );
10107 System.out.println( "provider=" + id.getSource() );
10112 id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
10113 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10114 || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
10115 if ( id != null ) {
10116 System.out.println( "value =" + id.getValue() );
10117 System.out.println( "provider=" + id.getSource() );
10122 id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
10123 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
10124 || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
10125 if ( id != null ) {
10126 System.out.println( "value =" + id.getValue() );
10127 System.out.println( "provider=" + id.getSource() );
10131 id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
10132 if ( id != null ) {
10133 System.out.println( "value =" + id.getValue() );
10134 System.out.println( "provider=" + id.getSource() );
10138 catch ( final Exception e ) {
10139 e.printStackTrace( System.out );
10145 private static boolean testSequenceWriter() {
10147 final String n = ForesterUtil.LINE_SEPARATOR;
10148 if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
10151 if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
10154 if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
10157 if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
10160 if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
10161 .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
10164 if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
10165 .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
10169 catch ( final Exception e ) {
10170 e.printStackTrace();
10176 private static boolean testSpecies() {
10178 final Species s1 = new BasicSpecies( "a" );
10179 final Species s2 = new BasicSpecies( "a" );
10180 final Species s3 = new BasicSpecies( "A" );
10181 final Species s4 = new BasicSpecies( "b" );
10182 if ( !s1.equals( s1 ) ) {
10185 if ( s1.getSpeciesId().equals( "x" ) ) {
10188 if ( s1.getSpeciesId().equals( null ) ) {
10191 if ( !s1.equals( s2 ) ) {
10194 if ( s1.equals( s3 ) ) {
10197 if ( s1.hashCode() != s1.hashCode() ) {
10200 if ( s1.hashCode() != s2.hashCode() ) {
10203 if ( s1.hashCode() == s3.hashCode() ) {
10206 if ( s1.compareTo( s1 ) != 0 ) {
10209 if ( s1.compareTo( s2 ) != 0 ) {
10212 if ( s1.compareTo( s3 ) != 0 ) {
10215 if ( s1.compareTo( s4 ) >= 0 ) {
10218 if ( s4.compareTo( s1 ) <= 0 ) {
10221 if ( !s4.getSpeciesId().equals( "b" ) ) {
10224 final Species s5 = new BasicSpecies( " C " );
10225 if ( !s5.getSpeciesId().equals( "C" ) ) {
10228 if ( s5.equals( s1 ) ) {
10232 catch ( final Exception e ) {
10233 e.printStackTrace( System.out );
10239 private static boolean testSplit() {
10241 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10242 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
10243 //Archaeopteryx.createApplication( p0 );
10244 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
10245 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10246 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10247 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10248 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10249 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10250 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10251 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10252 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10253 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10254 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
10255 // System.out.println( s0.toString() );
10257 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
10258 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10259 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10260 if ( s0.match( query_nodes ) ) {
10263 query_nodes = new HashSet<PhylogenyNode>();
10264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10265 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10266 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10267 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10268 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10269 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10271 if ( !s0.match( query_nodes ) ) {
10275 query_nodes = new HashSet<PhylogenyNode>();
10276 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10277 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10279 if ( !s0.match( query_nodes ) ) {
10283 query_nodes = new HashSet<PhylogenyNode>();
10284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10288 if ( !s0.match( query_nodes ) ) {
10292 query_nodes = new HashSet<PhylogenyNode>();
10293 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10294 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10297 if ( !s0.match( query_nodes ) ) {
10301 query_nodes = new HashSet<PhylogenyNode>();
10302 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10303 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10305 if ( !s0.match( query_nodes ) ) {
10309 query_nodes = new HashSet<PhylogenyNode>();
10310 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10311 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10312 if ( !s0.match( query_nodes ) ) {
10316 query_nodes = new HashSet<PhylogenyNode>();
10317 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10318 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10319 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10322 if ( !s0.match( query_nodes ) ) {
10326 query_nodes = new HashSet<PhylogenyNode>();
10327 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10328 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10329 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10330 if ( !s0.match( query_nodes ) ) {
10334 query_nodes = new HashSet<PhylogenyNode>();
10335 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10336 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10337 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10338 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10339 if ( !s0.match( query_nodes ) ) {
10343 query_nodes = new HashSet<PhylogenyNode>();
10344 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10345 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10346 if ( s0.match( query_nodes ) ) {
10350 query_nodes = new HashSet<PhylogenyNode>();
10351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10352 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10353 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10354 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10355 if ( s0.match( query_nodes ) ) {
10359 query_nodes = new HashSet<PhylogenyNode>();
10360 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10361 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10362 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
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( "B" ) );
10372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10373 if ( s0.match( query_nodes ) ) {
10377 query_nodes = new HashSet<PhylogenyNode>();
10378 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
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 if ( s0.match( query_nodes ) ) {
10391 query_nodes = new HashSet<PhylogenyNode>();
10392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10394 if ( s0.match( query_nodes ) ) {
10398 query_nodes = new HashSet<PhylogenyNode>();
10399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10401 if ( s0.match( query_nodes ) ) {
10405 query_nodes = new HashSet<PhylogenyNode>();
10406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10407 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10408 if ( s0.match( query_nodes ) ) {
10412 query_nodes = new HashSet<PhylogenyNode>();
10413 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10415 if ( s0.match( query_nodes ) ) {
10419 query_nodes = new HashSet<PhylogenyNode>();
10420 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10421 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10422 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10423 if ( s0.match( query_nodes ) ) {
10427 query_nodes = new HashSet<PhylogenyNode>();
10428 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10429 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10430 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10431 if ( s0.match( query_nodes ) ) {
10435 query_nodes = new HashSet<PhylogenyNode>();
10436 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10437 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10438 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10439 if ( s0.match( query_nodes ) ) {
10443 query_nodes = new HashSet<PhylogenyNode>();
10444 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10445 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10448 if ( s0.match( query_nodes ) ) {
10452 // query_nodes = new HashSet<PhylogenyNode>();
10453 // query_nodes.add( new PhylogenyNode( "X" ) );
10454 // query_nodes.add( new PhylogenyNode( "Y" ) );
10455 // query_nodes.add( new PhylogenyNode( "A" ) );
10456 // query_nodes.add( new PhylogenyNode( "B" ) );
10457 // query_nodes.add( new PhylogenyNode( "C" ) );
10458 // query_nodes.add( new PhylogenyNode( "D" ) );
10459 // query_nodes.add( new PhylogenyNode( "E" ) );
10460 // query_nodes.add( new PhylogenyNode( "F" ) );
10461 // query_nodes.add( new PhylogenyNode( "G" ) );
10462 // if ( !s0.match( query_nodes ) ) {
10465 // query_nodes = new HashSet<PhylogenyNode>();
10466 // query_nodes.add( new PhylogenyNode( "X" ) );
10467 // query_nodes.add( new PhylogenyNode( "Y" ) );
10468 // query_nodes.add( new PhylogenyNode( "A" ) );
10469 // query_nodes.add( new PhylogenyNode( "B" ) );
10470 // query_nodes.add( new PhylogenyNode( "C" ) );
10471 // if ( !s0.match( query_nodes ) ) {
10475 // query_nodes = new HashSet<PhylogenyNode>();
10476 // query_nodes.add( new PhylogenyNode( "X" ) );
10477 // query_nodes.add( new PhylogenyNode( "Y" ) );
10478 // query_nodes.add( new PhylogenyNode( "D" ) );
10479 // query_nodes.add( new PhylogenyNode( "E" ) );
10480 // query_nodes.add( new PhylogenyNode( "F" ) );
10481 // query_nodes.add( new PhylogenyNode( "G" ) );
10482 // if ( !s0.match( query_nodes ) ) {
10486 // query_nodes = new HashSet<PhylogenyNode>();
10487 // query_nodes.add( new PhylogenyNode( "X" ) );
10488 // query_nodes.add( new PhylogenyNode( "Y" ) );
10489 // query_nodes.add( new PhylogenyNode( "A" ) );
10490 // query_nodes.add( new PhylogenyNode( "B" ) );
10491 // query_nodes.add( new PhylogenyNode( "C" ) );
10492 // query_nodes.add( new PhylogenyNode( "D" ) );
10493 // if ( !s0.match( query_nodes ) ) {
10497 // query_nodes = new HashSet<PhylogenyNode>();
10498 // query_nodes.add( new PhylogenyNode( "X" ) );
10499 // query_nodes.add( new PhylogenyNode( "Y" ) );
10500 // query_nodes.add( new PhylogenyNode( "E" ) );
10501 // query_nodes.add( new PhylogenyNode( "F" ) );
10502 // query_nodes.add( new PhylogenyNode( "G" ) );
10503 // if ( !s0.match( query_nodes ) ) {
10507 // query_nodes = new HashSet<PhylogenyNode>();
10508 // query_nodes.add( new PhylogenyNode( "X" ) );
10509 // query_nodes.add( new PhylogenyNode( "Y" ) );
10510 // query_nodes.add( new PhylogenyNode( "F" ) );
10511 // query_nodes.add( new PhylogenyNode( "G" ) );
10512 // if ( !s0.match( query_nodes ) ) {
10516 query_nodes = new HashSet<PhylogenyNode>();
10517 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10518 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10519 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10521 if ( s0.match( query_nodes ) ) {
10525 query_nodes = new HashSet<PhylogenyNode>();
10526 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10527 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10528 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10529 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10530 if ( s0.match( query_nodes ) ) {
10533 ///////////////////////////
10535 query_nodes = new HashSet<PhylogenyNode>();
10536 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10537 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10540 if ( s0.match( query_nodes ) ) {
10544 query_nodes = new HashSet<PhylogenyNode>();
10545 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10549 if ( s0.match( query_nodes ) ) {
10553 query_nodes = new HashSet<PhylogenyNode>();
10554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10558 if ( s0.match( query_nodes ) ) {
10562 query_nodes = new HashSet<PhylogenyNode>();
10563 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10564 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10567 if ( s0.match( query_nodes ) ) {
10571 query_nodes = new HashSet<PhylogenyNode>();
10572 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10576 if ( s0.match( query_nodes ) ) {
10580 query_nodes = new HashSet<PhylogenyNode>();
10581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10584 if ( s0.match( query_nodes ) ) {
10588 query_nodes = new HashSet<PhylogenyNode>();
10589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10594 if ( s0.match( query_nodes ) ) {
10598 query_nodes = new HashSet<PhylogenyNode>();
10599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10604 if ( s0.match( query_nodes ) ) {
10608 query_nodes = new HashSet<PhylogenyNode>();
10609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10614 if ( s0.match( query_nodes ) ) {
10618 query_nodes = new HashSet<PhylogenyNode>();
10619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
10620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
10621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10625 if ( s0.match( query_nodes ) ) {
10629 catch ( final Exception e ) {
10630 e.printStackTrace();
10636 private static boolean testSplitStrict() {
10638 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10639 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
10640 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
10641 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10642 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10643 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10644 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10645 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10646 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10647 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10648 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
10649 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
10650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10652 if ( s0.match( query_nodes ) ) {
10655 query_nodes = new HashSet<PhylogenyNode>();
10656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10663 if ( !s0.match( query_nodes ) ) {
10667 query_nodes = new HashSet<PhylogenyNode>();
10668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10671 if ( !s0.match( query_nodes ) ) {
10675 query_nodes = new HashSet<PhylogenyNode>();
10676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10680 if ( !s0.match( query_nodes ) ) {
10684 query_nodes = new HashSet<PhylogenyNode>();
10685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10689 if ( !s0.match( query_nodes ) ) {
10693 query_nodes = new HashSet<PhylogenyNode>();
10694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10697 if ( !s0.match( query_nodes ) ) {
10701 query_nodes = new HashSet<PhylogenyNode>();
10702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10704 if ( !s0.match( query_nodes ) ) {
10708 query_nodes = new HashSet<PhylogenyNode>();
10709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10714 if ( !s0.match( query_nodes ) ) {
10718 query_nodes = new HashSet<PhylogenyNode>();
10719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10721 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10722 if ( !s0.match( query_nodes ) ) {
10726 query_nodes = new HashSet<PhylogenyNode>();
10727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10731 if ( !s0.match( query_nodes ) ) {
10735 query_nodes = new HashSet<PhylogenyNode>();
10736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10738 if ( s0.match( query_nodes ) ) {
10742 query_nodes = new HashSet<PhylogenyNode>();
10743 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10745 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10747 if ( s0.match( query_nodes ) ) {
10751 query_nodes = new HashSet<PhylogenyNode>();
10752 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
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( "B" ) );
10764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10765 if ( s0.match( query_nodes ) ) {
10769 query_nodes = new HashSet<PhylogenyNode>();
10770 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
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 if ( s0.match( query_nodes ) ) {
10783 query_nodes = new HashSet<PhylogenyNode>();
10784 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
10786 if ( s0.match( query_nodes ) ) {
10790 query_nodes = new HashSet<PhylogenyNode>();
10791 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10792 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10793 if ( s0.match( query_nodes ) ) {
10797 query_nodes = new HashSet<PhylogenyNode>();
10798 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10799 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10800 if ( s0.match( query_nodes ) ) {
10804 query_nodes = new HashSet<PhylogenyNode>();
10805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10807 if ( s0.match( query_nodes ) ) {
10811 query_nodes = new HashSet<PhylogenyNode>();
10812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
10814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10815 if ( s0.match( query_nodes ) ) {
10819 query_nodes = new HashSet<PhylogenyNode>();
10820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10821 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
10822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10823 if ( s0.match( query_nodes ) ) {
10827 query_nodes = new HashSet<PhylogenyNode>();
10828 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10829 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10831 if ( s0.match( query_nodes ) ) {
10835 query_nodes = new HashSet<PhylogenyNode>();
10836 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
10837 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
10838 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
10839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
10840 if ( s0.match( query_nodes ) ) {
10844 catch ( final Exception e ) {
10845 e.printStackTrace();
10851 private static boolean testSubtreeDeletion() {
10853 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10854 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
10855 t1.deleteSubtree( t1.getNode( "A" ), false );
10856 if ( t1.getNumberOfExternalNodes() != 5 ) {
10859 t1.toNewHampshireX();
10860 t1.deleteSubtree( t1.getNode( "E" ), false );
10861 if ( t1.getNumberOfExternalNodes() != 4 ) {
10864 t1.toNewHampshireX();
10865 t1.deleteSubtree( t1.getNode( "F" ), false );
10866 if ( t1.getNumberOfExternalNodes() != 3 ) {
10869 t1.toNewHampshireX();
10870 t1.deleteSubtree( t1.getNode( "D" ), false );
10871 t1.toNewHampshireX();
10872 if ( t1.getNumberOfExternalNodes() != 3 ) {
10875 t1.deleteSubtree( t1.getNode( "def" ), false );
10876 t1.toNewHampshireX();
10877 if ( t1.getNumberOfExternalNodes() != 2 ) {
10880 t1.deleteSubtree( t1.getNode( "B" ), false );
10881 t1.toNewHampshireX();
10882 if ( t1.getNumberOfExternalNodes() != 1 ) {
10885 t1.deleteSubtree( t1.getNode( "C" ), false );
10886 t1.toNewHampshireX();
10887 if ( t1.getNumberOfExternalNodes() != 1 ) {
10890 t1.deleteSubtree( t1.getNode( "abc" ), false );
10891 t1.toNewHampshireX();
10892 if ( t1.getNumberOfExternalNodes() != 1 ) {
10895 t1.deleteSubtree( t1.getNode( "r" ), false );
10896 if ( t1.getNumberOfExternalNodes() != 0 ) {
10899 if ( !t1.isEmpty() ) {
10902 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
10903 t2.deleteSubtree( t2.getNode( "A" ), false );
10904 t2.toNewHampshireX();
10905 if ( t2.getNumberOfExternalNodes() != 5 ) {
10908 t2.deleteSubtree( t2.getNode( "abc" ), false );
10909 t2.toNewHampshireX();
10910 if ( t2.getNumberOfExternalNodes() != 3 ) {
10913 t2.deleteSubtree( t2.getNode( "def" ), false );
10914 t2.toNewHampshireX();
10915 if ( t2.getNumberOfExternalNodes() != 1 ) {
10919 catch ( final Exception e ) {
10920 e.printStackTrace( System.out );
10926 private static boolean testSupportCount() {
10928 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
10929 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
10930 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
10931 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
10932 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
10933 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
10934 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
10936 SupportCount.count( t0_1, phylogenies_1, true, false );
10937 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
10938 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
10939 + "(((((A,B),C),D),E),((F,G),X))"
10940 + "(((((A,Y),B),C),D),((F,G),E))"
10941 + "(((((A,B),C),D),E),(F,G))"
10942 + "(((((A,B),C),D),E),(F,G))"
10943 + "(((((A,B),C),D),E),(F,G))"
10944 + "(((((A,B),C),D),E),(F,G),Z)"
10945 + "(((((A,B),C),D),E),(F,G))"
10946 + "((((((A,B),C),D),E),F),G)"
10947 + "(((((X,Y),F,G),E),((A,B),C)),D)",
10949 SupportCount.count( t0_2, phylogenies_2, true, false );
10950 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
10951 while ( it.hasNext() ) {
10952 final PhylogenyNode n = it.next();
10953 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
10957 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
10958 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
10959 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
10960 SupportCount.count( t0_3, phylogenies_3, true, false );
10961 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
10962 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
10965 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
10968 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
10971 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
10974 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
10977 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
10980 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
10983 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
10986 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
10989 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
10992 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
10993 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
10994 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
10995 SupportCount.count( t0_4, phylogenies_4, true, false );
10996 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
10997 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
11000 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
11003 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
11006 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
11009 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
11012 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
11015 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
11018 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
11021 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
11024 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
11027 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11028 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11029 double d = SupportCount.compare( b1, a, true, true, true );
11030 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
11033 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11034 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11035 d = SupportCount.compare( b2, a, true, true, true );
11036 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
11039 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
11040 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
11041 d = SupportCount.compare( b3, a, true, true, true );
11042 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
11045 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
11046 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
11047 d = SupportCount.compare( b4, a, true, true, false );
11048 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
11052 catch ( final Exception e ) {
11053 e.printStackTrace( System.out );
11059 private static boolean testSupportTransfer() {
11061 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11062 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)",
11063 new NHXParser() )[ 0 ];
11064 final Phylogeny p2 = factory
11065 .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 ];
11066 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
11069 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
11072 support_transfer.moveBranchLengthsToBootstrap( p1 );
11073 support_transfer.transferSupportValues( p1, p2 );
11074 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
11077 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
11080 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
11083 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
11086 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
11089 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
11092 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
11095 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
11099 catch ( final Exception e ) {
11100 e.printStackTrace( System.out );
11106 private static boolean testTaxonomyExtraction() {
11108 final PhylogenyNode n0 = PhylogenyNode
11109 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11110 if ( n0.getNodeData().isHasTaxonomy() ) {
11113 final PhylogenyNode n1 = PhylogenyNode
11114 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11115 if ( n1.getNodeData().isHasTaxonomy() ) {
11116 System.out.println( n1.toString() );
11119 final PhylogenyNode n2x = PhylogenyNode
11120 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11121 if ( n2x.getNodeData().isHasTaxonomy() ) {
11124 final PhylogenyNode n3 = PhylogenyNode
11125 .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11126 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11127 System.out.println( n3.toString() );
11130 final PhylogenyNode n4 = PhylogenyNode
11131 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11132 if ( n4.getNodeData().isHasTaxonomy() ) {
11133 System.out.println( n4.toString() );
11136 final PhylogenyNode n5 = PhylogenyNode
11137 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11138 if ( n5.getNodeData().isHasTaxonomy() ) {
11139 System.out.println( n5.toString() );
11142 final PhylogenyNode n6 = PhylogenyNode
11143 .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11144 if ( n6.getNodeData().isHasTaxonomy() ) {
11145 System.out.println( n6.toString() );
11148 final PhylogenyNode n7 = PhylogenyNode
11149 .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11150 if ( n7.getNodeData().isHasTaxonomy() ) {
11151 System.out.println( n7.toString() );
11154 final PhylogenyNode n8 = PhylogenyNode
11155 .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11156 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11157 System.out.println( n8.toString() );
11160 final PhylogenyNode n9 = PhylogenyNode
11161 .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11162 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
11163 System.out.println( n9.toString() );
11166 final PhylogenyNode n10x = PhylogenyNode
11167 .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11168 if ( n10x.getNodeData().isHasTaxonomy() ) {
11169 System.out.println( n10x.toString() );
11172 final PhylogenyNode n10xx = PhylogenyNode
11173 .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11174 if ( n10xx.getNodeData().isHasTaxonomy() ) {
11175 System.out.println( n10xx.toString() );
11178 final PhylogenyNode n10 = PhylogenyNode
11179 .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
11180 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
11181 System.out.println( n10.toString() );
11184 final PhylogenyNode n11 = PhylogenyNode
11185 .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11186 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
11187 System.out.println( n11.toString() );
11190 final PhylogenyNode n12 = PhylogenyNode
11191 .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
11192 NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11193 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
11194 System.out.println( n12.toString() );
11197 final PhylogenyNode n13 = PhylogenyNode
11198 .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
11199 if ( n13.getNodeData().isHasTaxonomy() ) {
11200 System.out.println( n13.toString() );
11204 catch ( final Exception e ) {
11205 e.printStackTrace( System.out );
11211 private static boolean testTreeMethods() {
11213 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
11214 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
11215 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
11216 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
11217 System.out.println( t0.toNewHampshireX() );
11220 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
11221 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
11222 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
11225 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
11228 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
11232 catch ( final Exception e ) {
11233 e.printStackTrace( System.out );
11239 private static boolean testSequenceDbWsTools1() {
11241 final PhylogenyNode n = new PhylogenyNode();
11242 n.setName( "NP_001025424" );
11243 Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
11244 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11245 || !acc.getValue().equals( "NP_001025424" ) ) {
11248 n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
11249 acc = SequenceDbWsTools.obtainSeqAccession( n );
11250 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11251 || !acc.getValue().equals( "NP_001025424" ) ) {
11254 n.setName( "NP_001025424.1" );
11255 acc = SequenceDbWsTools.obtainSeqAccession( n );
11256 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11257 || !acc.getValue().equals( "NP_001025424" ) ) {
11260 n.setName( "NM_001030253" );
11261 acc = SequenceDbWsTools.obtainSeqAccession( n );
11262 if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
11263 || !acc.getValue().equals( "NM_001030253" ) ) {
11266 n.setName( "BCL2_HUMAN" );
11267 acc = SequenceDbWsTools.obtainSeqAccession( n );
11268 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11269 || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
11270 System.out.println( acc.toString() );
11273 n.setName( "P10415" );
11274 acc = SequenceDbWsTools.obtainSeqAccession( n );
11275 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11276 || !acc.getValue().equals( "P10415" ) ) {
11277 System.out.println( acc.toString() );
11280 n.setName( " P10415 " );
11281 acc = SequenceDbWsTools.obtainSeqAccession( n );
11282 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11283 || !acc.getValue().equals( "P10415" ) ) {
11284 System.out.println( acc.toString() );
11287 n.setName( "_P10415|" );
11288 acc = SequenceDbWsTools.obtainSeqAccession( n );
11289 if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
11290 || !acc.getValue().equals( "P10415" ) ) {
11291 System.out.println( acc.toString() );
11294 n.setName( "AY695820" );
11295 acc = SequenceDbWsTools.obtainSeqAccession( n );
11296 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11297 || !acc.getValue().equals( "AY695820" ) ) {
11298 System.out.println( acc.toString() );
11301 n.setName( "_AY695820_" );
11302 acc = SequenceDbWsTools.obtainSeqAccession( n );
11303 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11304 || !acc.getValue().equals( "AY695820" ) ) {
11305 System.out.println( acc.toString() );
11308 n.setName( "AAA59452" );
11309 acc = SequenceDbWsTools.obtainSeqAccession( n );
11310 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11311 || !acc.getValue().equals( "AAA59452" ) ) {
11312 System.out.println( acc.toString() );
11315 n.setName( "_AAA59452_" );
11316 acc = SequenceDbWsTools.obtainSeqAccession( n );
11317 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11318 || !acc.getValue().equals( "AAA59452" ) ) {
11319 System.out.println( acc.toString() );
11322 n.setName( "AAA59452.1" );
11323 acc = SequenceDbWsTools.obtainSeqAccession( n );
11324 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11325 || !acc.getValue().equals( "AAA59452.1" ) ) {
11326 System.out.println( acc.toString() );
11329 n.setName( "_AAA59452.1_" );
11330 acc = SequenceDbWsTools.obtainSeqAccession( n );
11331 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11332 || !acc.getValue().equals( "AAA59452.1" ) ) {
11333 System.out.println( acc.toString() );
11336 n.setName( "GI:94894583" );
11337 acc = SequenceDbWsTools.obtainSeqAccession( n );
11338 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11339 || !acc.getValue().equals( "94894583" ) ) {
11340 System.out.println( acc.toString() );
11343 n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11344 acc = SequenceDbWsTools.obtainSeqAccession( n );
11345 if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
11346 || !acc.getValue().equals( "71845847" ) ) {
11347 System.out.println( acc.toString() );
11350 n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
11351 acc = SequenceDbWsTools.obtainSeqAccession( n );
11352 if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
11353 || !acc.getValue().equals( "AAZ45343.1" ) ) {
11354 System.out.println( acc.toString() );
11358 catch ( final Exception e ) {
11364 private static boolean testSequenceDbWsTools2() {
11366 final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
11367 SequenceDbWsTools.obtainSeqInformation( n1 );
11368 if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
11371 if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11374 if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11377 if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
11380 final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
11381 SequenceDbWsTools.obtainSeqInformation( n2 );
11382 if ( !n2.getNodeData().getSequence().getName()
11383 .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
11386 if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
11389 if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11392 if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
11395 final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
11396 SequenceDbWsTools.obtainSeqInformation( n3 );
11397 if ( !n3.getNodeData().getSequence().getName()
11398 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11401 if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
11404 if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
11407 if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
11411 catch ( final IOException e ) {
11412 System.out.println();
11413 System.out.println( "the following might be due to absence internet connection:" );
11414 e.printStackTrace( System.out );
11417 catch ( final Exception e ) {
11418 e.printStackTrace();
11424 private static boolean testEbiEntryRetrieval() {
11426 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
11427 if ( !entry.getAccession().equals( "AAK41263" ) ) {
11428 System.out.println( entry.getAccession() );
11431 if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
11432 System.out.println( entry.getTaxonomyScientificName() );
11435 if ( !entry.getSequenceName()
11436 .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
11437 System.out.println( entry.getSequenceName() );
11440 // if ( !entry.getSequenceSymbol().equals( "" ) ) {
11441 // System.out.println( entry.getSequenceSymbol() );
11444 if ( !entry.getGeneName().equals( "treX-like" ) ) {
11445 System.out.println( entry.getGeneName() );
11448 if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
11449 System.out.println( entry.getTaxonomyIdentifier() );
11452 if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
11453 System.out.println( entry.getAnnotations().first().getRefValue() );
11456 if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
11457 System.out.println( entry.getAnnotations().first().getRefSource() );
11460 if ( entry.getCrossReferences().size() != 5 ) {
11464 final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
11465 if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
11468 if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
11469 System.out.println( entry1.getTaxonomyScientificName() );
11472 if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
11473 System.out.println( entry1.getSequenceName() );
11476 if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
11477 System.out.println( entry1.getTaxonomyIdentifier() );
11480 if ( !entry1.getGeneName().equals( "BCL2" ) ) {
11481 System.out.println( entry1.getGeneName() );
11484 if ( entry1.getCrossReferences().size() != 6 ) {
11488 final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
11489 if ( !entry2.getAccession().equals( "NM_184234" ) ) {
11492 if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
11493 System.out.println( entry2.getTaxonomyScientificName() );
11496 if ( !entry2.getSequenceName()
11497 .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
11498 System.out.println( entry2.getSequenceName() );
11501 if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
11502 System.out.println( entry2.getTaxonomyIdentifier() );
11505 if ( !entry2.getGeneName().equals( "RBM39" ) ) {
11506 System.out.println( entry2.getGeneName() );
11509 if ( entry2.getCrossReferences().size() != 3 ) {
11513 final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
11514 if ( !entry3.getAccession().equals( "HM043801" ) ) {
11517 if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
11518 System.out.println( entry3.getTaxonomyScientificName() );
11521 if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
11522 System.out.println( entry3.getSequenceName() );
11525 if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
11526 System.out.println( entry3.getTaxonomyIdentifier() );
11529 if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
11530 System.out.println( entry3.getSequenceSymbol() );
11533 if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
11536 if ( entry3.getCrossReferences().size() != 8 ) {
11541 final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
11542 if ( !entry4.getAccession().equals( "AAA36557" ) ) {
11545 if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
11546 System.out.println( entry4.getTaxonomyScientificName() );
11549 if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
11550 System.out.println( entry4.getSequenceName() );
11553 if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
11554 System.out.println( entry4.getTaxonomyIdentifier() );
11557 if ( !entry4.getGeneName().equals( "ras" ) ) {
11558 System.out.println( entry4.getGeneName() );
11561 // if ( !entry4.getChromosome().equals( "ras" ) ) {
11562 // System.out.println( entry4.getChromosome() );
11565 // if ( !entry4.getMap().equals( "ras" ) ) {
11566 // System.out.println( entry4.getMap() );
11572 // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
11573 // if ( !entry5.getAccession().equals( "HM043801" ) ) {
11576 final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
11577 if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
11580 if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
11581 System.out.println( entry5.getTaxonomyScientificName() );
11584 if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
11585 System.out.println( entry5.getSequenceName() );
11588 if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
11589 System.out.println( entry5.getTaxonomyIdentifier() );
11593 catch ( final IOException e ) {
11594 System.out.println();
11595 System.out.println( "the following might be due to absence internet connection:" );
11596 e.printStackTrace( System.out );
11599 catch ( final Exception e ) {
11600 e.printStackTrace();
11606 private static boolean testUniprotEntryRetrieval() {
11608 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
11609 if ( !entry.getAccession().equals( "P12345" ) ) {
11612 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
11615 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
11618 if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
11621 if ( !entry.getGeneName().equals( "GOT2" ) ) {
11624 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
11628 catch ( final IOException e ) {
11629 System.out.println();
11630 System.out.println( "the following might be due to absence internet connection:" );
11631 e.printStackTrace( System.out );
11634 catch ( final Exception e ) {
11640 private static boolean testUniprotTaxonomySearch() {
11642 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
11644 if ( results.size() != 1 ) {
11647 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11650 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11653 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11656 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11659 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11663 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
11664 if ( results.size() != 1 ) {
11667 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11670 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11673 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11676 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11679 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11683 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
11684 if ( results.size() != 1 ) {
11687 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11690 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11693 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11696 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11699 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11703 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
11704 if ( results.size() != 1 ) {
11707 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
11710 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
11713 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
11716 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11719 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
11722 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
11725 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
11728 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11729 .equals( "Nematostella vectensis" ) ) {
11730 System.out.println( results.get( 0 ).getLineage() );
11735 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
11736 if ( results.size() != 1 ) {
11739 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11742 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11745 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11748 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11751 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11754 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11755 .equals( "Xenopus tropicalis" ) ) {
11756 System.out.println( results.get( 0 ).getLineage() );
11761 results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
11762 if ( results.size() != 1 ) {
11765 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11768 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11771 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11774 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11777 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11780 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11781 .equals( "Xenopus tropicalis" ) ) {
11782 System.out.println( results.get( 0 ).getLineage() );
11787 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
11788 if ( results.size() != 1 ) {
11791 if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
11794 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
11797 if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
11800 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
11803 if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
11806 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
11807 .equals( "Xenopus tropicalis" ) ) {
11808 System.out.println( results.get( 0 ).getLineage() );
11812 catch ( final IOException e ) {
11813 System.out.println();
11814 System.out.println( "the following might be due to absence internet connection:" );
11815 e.printStackTrace( System.out );
11818 catch ( final Exception e ) {
11824 private static boolean testWabiTxSearch() {
11826 String result = "";
11827 result = TxSearch.searchSimple( "nematostella" );
11828 result = TxSearch.getTxId( "nematostella" );
11829 if ( !result.equals( "45350" ) ) {
11832 result = TxSearch.getTxName( "45350" );
11833 if ( !result.equals( "Nematostella" ) ) {
11836 result = TxSearch.getTxId( "nematostella vectensis" );
11837 if ( !result.equals( "45351" ) ) {
11840 result = TxSearch.getTxName( "45351" );
11841 if ( !result.equals( "Nematostella vectensis" ) ) {
11844 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
11845 if ( !result.equals( "536089" ) ) {
11848 result = TxSearch.getTxName( "536089" );
11849 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
11852 final List<String> queries = new ArrayList<String>();
11853 queries.add( "Campylobacter coli" );
11854 queries.add( "Escherichia coli" );
11855 queries.add( "Arabidopsis" );
11856 queries.add( "Trichoplax" );
11857 queries.add( "Samanea saman" );
11858 queries.add( "Kluyveromyces marxianus" );
11859 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
11860 queries.add( "Bornavirus parrot/PDD/2008" );
11861 final List<RANKS> ranks = new ArrayList<RANKS>();
11862 ranks.add( RANKS.SUPERKINGDOM );
11863 ranks.add( RANKS.KINGDOM );
11864 ranks.add( RANKS.FAMILY );
11865 ranks.add( RANKS.GENUS );
11866 ranks.add( RANKS.TRIBE );
11867 result = TxSearch.searchLineage( queries, ranks );
11868 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
11869 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
11871 catch ( final Exception e ) {
11872 System.out.println();
11873 System.out.println( "the following might be due to absence internet connection:" );
11874 e.printStackTrace( System.out );