4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.evoinference;
31 import java.io.FileInputStream;
32 import java.io.StringWriter;
33 import java.util.Date;
34 import java.util.List;
36 import org.forester.evoinference.distance.NeighborJoining;
37 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
38 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
39 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
40 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
41 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
42 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
43 import org.forester.evoinference.matrix.distance.DistanceMatrix;
44 import org.forester.evoinference.parsimony.DolloParsimony;
45 import org.forester.evoinference.parsimony.FitchParsimony;
46 import org.forester.io.parsers.GeneralMsaParser;
47 import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
48 import org.forester.io.parsers.nhx.NHXParser;
49 import org.forester.msa.Msa;
50 import org.forester.phylogeny.Phylogeny;
51 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
52 import org.forester.phylogeny.factories.PhylogenyFactory;
53 import org.forester.util.ForesterUtil;
55 public class TestPhylogenyReconstruction {
57 private final static double ZERO_DIFF = 1.0E-9;
58 private final static boolean TIME = false;
60 public static boolean isEqual( final double a, final double b ) {
61 return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
64 public static void main( final String[] args ) {
65 timeNeighborJoining();
68 public static boolean test( final File test_dir ) {
69 System.out.print( " Basic symmetrical distance matrix: " );
70 if ( !testBasicSymmetricalDistanceMatrix() ) {
71 System.out.println( "failed." );
74 System.out.println( "OK." );
75 System.out.print( " Basic character state matrix: " );
76 if ( !testBasicCharacterStateMatrix() ) {
77 System.out.println( "failed." );
80 System.out.println( "OK." );
81 System.out.print( " Symmetrical distance matrix parser: " );
82 if ( !testSymmetricalDistanceMatrixParser() ) {
83 System.out.println( "failed." );
86 System.out.println( "OK." );
87 System.out.print( " Distance Calculation: " );
88 if ( !testDistanceCalculationMethods( test_dir ) ) {
89 System.out.println( "failed." );
92 System.out.println( "OK." );
93 System.out.print( " Neighbor Joining: " );
94 if ( !testNeighborJoining() ) {
95 System.out.println( "failed." );
98 System.out.println( "OK." );
99 System.out.print( " Dollo Parsimony: " );
100 if ( !testDolloParsimony() ) {
101 System.out.println( "failed." );
104 System.out.println( "OK." );
105 System.out.print( " Dollo Parsimony on non binary trees: " );
106 if ( !testDolloParsimonyOnNonBinaryTree() ) {
107 System.out.println( "failed." );
110 System.out.println( "OK." );
111 System.out.print( " Fitch Parsimony: " );
112 if ( !testFitchParsimony() ) {
113 System.out.println( "failed." );
116 System.out.println( "OK." );
120 private static boolean testDistanceCalculationMethods( final File test_dir ) {
122 final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
124 final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
125 if ( pwd0.getSize() != 120 ) {
128 for( int i = 0; i < pwd0.getSize(); ++i ) {
129 if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) {
134 catch ( final Exception e ) {
135 e.printStackTrace( System.out );
141 private static boolean testBasicCharacterStateMatrix() {
143 final CharacterStateMatrix<String> matrix_0 = new BasicCharacterStateMatrix<String>( 4, 8 );
144 final CharacterStateMatrix<String> matrix_00 = new BasicCharacterStateMatrix<String>( 4, 8 );
145 matrix_0.setIdentifier( 0, "A" );
146 matrix_0.setIdentifier( 1, "B" );
147 matrix_0.setIdentifier( 2, "C" );
148 matrix_0.setIdentifier( 3, "D" );
149 matrix_0.setCharacter( 0, "0" );
150 matrix_0.setCharacter( 1, "1" );
151 matrix_0.setCharacter( 2, "2" );
152 matrix_0.setCharacter( 3, "3" );
153 matrix_0.setCharacter( 4, "4" );
154 matrix_0.setCharacter( 5, "5" );
155 matrix_0.setCharacter( 6, "6" );
156 matrix_0.setCharacter( 7, "7" );
157 matrix_00.setIdentifier( 0, "A" );
158 matrix_00.setIdentifier( 1, "B" );
159 matrix_00.setIdentifier( 2, "C" );
160 matrix_00.setIdentifier( 3, "D" );
161 matrix_00.setCharacter( 3, "3" );
162 matrix_00.setCharacter( 4, "4" );
163 if ( !matrix_0.getCharacter( 1 ).equals( "1" ) ) {
166 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
169 matrix_0.setState( 0, 0, "00" );
170 matrix_00.setState( 0, 0, "00" );
171 if ( !matrix_0.getState( 0, 0 ).equals( "00" ) ) {
174 matrix_0.setState( 0, 1, "01" );
175 matrix_00.setState( 0, 1, "01" );
176 if ( !matrix_0.getState( 0, 1 ).equals( "01" ) ) {
179 matrix_0.setState( 1, 1, "11" );
180 matrix_00.setState( 1, 1, "11" );
181 if ( !matrix_0.getState( 1, 1 ).equals( "11" ) ) {
184 matrix_0.setState( 1, 0, "10" );
185 matrix_00.setState( 1, 0, "10" );
186 if ( !matrix_0.getState( 1, 0 ).equals( "10" ) ) {
189 matrix_0.setState( 1, 2, "12" );
190 matrix_00.setState( 1, 2, "12" );
191 if ( !matrix_0.getState( 1, 2 ).equals( "12" ) ) {
194 matrix_0.setState( 3, 7, "37" );
195 matrix_00.setState( 3, 7, "37" );
196 if ( !matrix_0.getState( 3, 7 ).equals( "37" ) ) {
199 matrix_0.setState( 2, 6, "26" );
200 matrix_00.setState( 2, 6, "26" );
201 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
204 matrix_0.setState( "D", "3", "33" );
205 matrix_00.setState( "D", "3", "33" );
206 if ( !matrix_0.getState( 3, 3 ).equals( "33" ) ) {
209 if ( !matrix_0.getState( "D", "3" ).equals( "33" ) ) {
212 matrix_0.setState( "C", "4", "24" );
213 matrix_00.setState( "C", "4", "24" );
214 if ( !matrix_0.getState( 2, 4 ).equals( "24" ) ) {
217 if ( !matrix_0.getState( "C", "4" ).equals( "24" ) ) {
220 if ( matrix_0.isEmpty() ) {
223 if ( matrix_0.getNumberOfIdentifiers() != 4 ) {
226 if ( matrix_0.getNumberOfCharacters() != 8 ) {
229 if ( !matrix_0.equals( matrix_0 ) ) {
232 if ( !matrix_0.equals( matrix_00 ) ) {
235 matrix_00.setState( "C", "4", "123" );
236 if ( matrix_0.equals( matrix_00 ) ) {
239 final Integer[][] ints = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
240 final CharacterStateMatrix<Integer> matrix_000 = new BasicCharacterStateMatrix<Integer>( ints );
241 matrix_000.toString();
242 if ( matrix_000.getNumberOfCharacters() != 4 ) {
245 if ( matrix_000.getNumberOfIdentifiers() != 3 ) {
248 if ( matrix_000.getState( 0, 1 ) != 2 ) {
251 if ( matrix_000.getState( 2, 3 ) != 12 ) {
254 final Integer[][] ints0 = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
255 final CharacterStateMatrix<Integer> matrix_0000 = new BasicCharacterStateMatrix<Integer>( ints0 );
256 if ( !matrix_000.equals( matrix_0000 ) ) {
259 final Integer[][] ints00 = { { 1, 2, 3, -4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
260 final CharacterStateMatrix<Integer> matrix_00000 = new BasicCharacterStateMatrix<Integer>( ints00 );
261 if ( matrix_000.equals( matrix_00000 ) ) {
264 final CharacterStateMatrix<String> clone0 = matrix_0.copy();
265 final CharacterStateMatrix<String> clone00 = matrix_00.copy();
266 if ( !clone0.equals( matrix_0 ) ) {
269 if ( !clone00.equals( matrix_00 ) ) {
272 if ( clone00.equals( clone0 ) ) {
275 final CharacterStateMatrix<String> pivot0 = matrix_0.pivot();
276 final CharacterStateMatrix<String> pivot00 = matrix_00.pivot();
277 if ( !pivot0.getState( 1, 0 ).equals( "01" ) ) {
280 if ( !pivot0.getState( 6, 2 ).equals( "26" ) ) {
283 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
286 final CharacterStateMatrix<String> pivotpivot00 = pivot00.pivot();
287 if ( !pivotpivot00.equals( matrix_00 ) ) {
290 final CharacterStateMatrix<BinaryStates> nex = new BasicCharacterStateMatrix<BinaryStates>( 4, 3 );
291 nex.setIdentifier( 0, "amphioxus" );
292 nex.setIdentifier( 1, "sponge" );
293 nex.setIdentifier( 2, "sea_anemone" );
294 nex.setIdentifier( 3, "cobra" );
295 nex.setCharacter( 0, "notch" );
296 nex.setCharacter( 1, "homeobox" );
297 nex.setCharacter( 2, "wnt" );
298 nex.setState( 0, 0, BinaryStates.ABSENT );
299 nex.setState( 0, 1, BinaryStates.ABSENT );
300 nex.setState( 0, 2, BinaryStates.ABSENT );
301 nex.setState( 1, 0, BinaryStates.PRESENT );
302 nex.setState( 1, 1, BinaryStates.PRESENT );
303 nex.setState( 1, 2, BinaryStates.ABSENT );
304 nex.setState( 2, 0, BinaryStates.PRESENT );
305 nex.setState( 2, 1, BinaryStates.PRESENT );
306 nex.setState( 2, 2, BinaryStates.PRESENT );
307 nex.setState( 3, 0, BinaryStates.PRESENT );
308 nex.setState( 3, 1, BinaryStates.ABSENT );
309 nex.setState( 3, 2, BinaryStates.ABSENT );
310 StringWriter w = new StringWriter();
311 nex.toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
312 //System.out.println( w.getBuffer().toString() );
313 w = new StringWriter();
314 nex.pivot().toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
315 //System.out.println( w.getBuffer().toString() );
317 catch ( final Exception e ) {
318 e.printStackTrace( System.out );
324 private static boolean testBasicSymmetricalDistanceMatrix() {
326 final DistanceMatrix matrix_0 = new BasicSymmetricalDistanceMatrix( 4 );
327 matrix_0.setIdentifier( 0, "A" );
328 matrix_0.setIdentifier( 1, "B" );
329 matrix_0.setIdentifier( 2, "C" );
330 matrix_0.setIdentifier( 3, "0123456789012" );
331 matrix_0.setValue( 1, 0, 0.00001 );
332 matrix_0.setValue( 0, 2, 0.0000009 );
333 matrix_0.setValue( 3, 0, 3.0 );
334 matrix_0.setValue( 1, 2, 4.0 );
335 matrix_0.setValue( 3, 1, 5.0 );
336 matrix_0.setValue( 2, 3, 6.0 );
337 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
340 if ( !matrix_0.getIdentifier( 1 ).equals( "B" ) ) {
343 if ( !matrix_0.getIdentifier( 2 ).equals( "C" ) ) {
346 if ( !matrix_0.getIdentifier( 3 ).equals( "0123456789012" ) ) {
349 if ( matrix_0.getSize() != 4 ) {
352 if ( !isEqual( matrix_0.getValue( 0, 0 ), 0.0 ) ) {
355 if ( !isEqual( matrix_0.getValue( 3, 3 ), 0.0 ) ) {
358 if ( !isEqual( matrix_0.getValue( 0, 1 ), 0.00001 ) ) {
361 if ( !isEqual( matrix_0.getValue( 0, 2 ), 0.0000009 ) ) {
364 if ( !isEqual( matrix_0.getValue( 0, 3 ), 3 ) ) {
367 if ( !isEqual( matrix_0.getValue( 1, 0 ), 0.00001 ) ) {
370 if ( !isEqual( matrix_0.getValue( 1, 2 ), 4 ) ) {
373 if ( !isEqual( matrix_0.getValue( 1, 3 ), 5 ) ) {
376 if ( !isEqual( matrix_0.getValue( 2, 0 ), 0.0000009 ) ) {
379 if ( !isEqual( matrix_0.getValue( 2, 1 ), 4 ) ) {
382 if ( !isEqual( matrix_0.getValue( 2, 3 ), 6 ) ) {
385 if ( !isEqual( matrix_0.getValue( 3, 0 ), 3 ) ) {
388 if ( !isEqual( matrix_0.getValue( 3, 1 ), 5 ) ) {
391 if ( !isEqual( matrix_0.getValue( 3, 2 ), 6 ) ) {
394 final StringBuffer matrix_0_phylip = new StringBuffer();
395 matrix_0_phylip.append( " 4" );
396 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
397 matrix_0_phylip.append( "A 0.000000 0.000010 0.000001 3.000000" );
398 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
399 matrix_0_phylip.append( "B 0.000010 0.000000 4.000000 5.000000" );
400 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
401 matrix_0_phylip.append( "C 0.000001 4.000000 0.000000 6.000000" );
402 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
403 matrix_0_phylip.append( "0123456789 3.000000 5.000000 6.000000 0.000000" );
404 if ( !matrix_0_phylip.toString()
405 .equals( matrix_0.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() ) ) {
409 catch ( final Exception e ) {
410 e.printStackTrace( System.out );
416 private static boolean testDolloParsimony() {
418 final BinaryStates PRESENT = BinaryStates.PRESENT;
419 final BinaryStates ABSENT = BinaryStates.ABSENT;
420 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
421 final DolloParsimony dollo1 = DolloParsimony.createInstance();
422 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
423 final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
424 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
425 CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
427 m1.setIdentifier( 0, "a" );
428 m1.setIdentifier( 1, "b" );
429 m1.setIdentifier( 2, "c" );
430 m1.setIdentifier( 3, "d" );
431 m1.setIdentifier( 4, "e" );
432 m1.setIdentifier( 5, "f" );
433 m1.setIdentifier( 6, "g" );
434 m1.setIdentifier( 7, "h" );
435 m1.setIdentifier( 8, "i" );
436 m1.setCharacter( 0, "0" );
437 m1.setState( "a", "0", PRESENT );
438 m1.setState( "b", "0", ABSENT );
439 m1.setState( "c", "0", PRESENT );
440 m1.setState( "d", "0", ABSENT );
441 m1.setState( "e", "0", ABSENT );
442 m1.setState( "f", "0", ABSENT );
443 m1.setState( "g", "0", ABSENT );
444 m1.setState( "h", "0", ABSENT );
445 m1.setState( "i", "0", ABSENT );
446 dollo1.execute( p1, m1 );
447 if ( dollo1.getTotalGains() != 1 ) {
450 if ( dollo1.getTotalLosses() != 1 ) {
453 if ( dollo1.getTotalUnchanged() != 15 ) {
456 m1.setState( "b", "0", PRESENT );
457 dollo1.execute( p1, m1 );
458 if ( dollo1.getTotalGains() != 1 ) {
461 if ( dollo1.getTotalLosses() != 0 ) {
464 if ( dollo1.getTotalUnchanged() != 16 ) {
467 m1.setState( "b", "0", ABSENT );
468 m1.setState( "e", "0", PRESENT );
469 dollo1.execute( p1, m1 );
470 if ( dollo1.getTotalGains() != 1 ) {
473 if ( dollo1.getTotalLosses() != 3 ) {
476 if ( dollo1.getTotalUnchanged() != 13 ) {
479 m1.setState( "a", "0", ABSENT );
480 m1.setState( "c", "0", ABSENT );
481 m1.setState( "g", "0", PRESENT );
482 dollo1.setReturnInternalStates( true );
483 dollo1.setReturnGainLossMatrix( true );
484 dollo1.execute( p1, m1 );
485 if ( dollo1.getTotalGains() != 1 ) {
488 if ( dollo1.getTotalLosses() != 3 ) {
491 if ( dollo1.getTotalUnchanged() != 13 ) {
494 final DolloParsimony dollo2 = DolloParsimony.createInstance();
495 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
496 final String p2_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root";
497 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
498 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 18,
500 m2.setIdentifier( 0, "a" );
501 m2.setIdentifier( 1, "b" );
502 m2.setIdentifier( 2, "c" );
503 m2.setIdentifier( 3, "d" );
504 m2.setIdentifier( 4, "e" );
505 m2.setIdentifier( 5, "f" );
506 m2.setIdentifier( 6, "g" );
507 m2.setIdentifier( 7, "h" );
508 m2.setIdentifier( 8, "i" );
509 m2.setIdentifier( 9, "j" );
510 m2.setIdentifier( 10, "k" );
511 m2.setIdentifier( 11, "l" );
512 m2.setIdentifier( 12, "m" );
513 m2.setIdentifier( 13, "n" );
514 m2.setIdentifier( 14, "o" );
515 m2.setIdentifier( 15, "p" );
516 m2.setIdentifier( 16, "q" );
517 m2.setIdentifier( 17, "r" );
518 m2.setCharacter( 0, "0" );
519 m2.setCharacter( 1, "1" );
520 m2.setCharacter( 2, "2" );
521 m2.setCharacter( 3, "3" );
522 m2.setState( "a", "0", PRESENT );
523 m2.setState( "b", "0", ABSENT );
524 m2.setState( "c", "0", PRESENT );
525 m2.setState( "d", "0", ABSENT );
526 m2.setState( "e", "0", ABSENT );
527 m2.setState( "f", "0", ABSENT );
528 m2.setState( "g", "0", ABSENT );
529 m2.setState( "h", "0", ABSENT );
530 m2.setState( "i", "0", ABSENT );
531 m2.setState( "j", "0", ABSENT );
532 m2.setState( "k", "0", ABSENT );
533 m2.setState( "l", "0", ABSENT );
534 m2.setState( "m", "0", ABSENT );
535 m2.setState( "n", "0", ABSENT );
536 m2.setState( "o", "0", ABSENT );
537 m2.setState( "p", "0", ABSENT );
538 m2.setState( "q", "0", ABSENT );
539 m2.setState( "r", "0", ABSENT );
540 m2.setState( "a", "1", PRESENT );
541 m2.setState( "b", "1", ABSENT );
542 m2.setState( "c", "1", PRESENT );
543 m2.setState( "d", "1", ABSENT );
544 m2.setState( "e", "1", ABSENT );
545 m2.setState( "f", "1", ABSENT );
546 m2.setState( "g", "1", PRESENT );
547 m2.setState( "h", "1", ABSENT );
548 m2.setState( "i", "1", ABSENT );
549 m2.setState( "j", "1", PRESENT );
550 m2.setState( "k", "1", ABSENT );
551 m2.setState( "l", "1", ABSENT );
552 m2.setState( "m", "1", PRESENT );
553 m2.setState( "n", "1", ABSENT );
554 m2.setState( "o", "1", ABSENT );
555 m2.setState( "p", "1", ABSENT );
556 m2.setState( "q", "1", ABSENT );
557 m2.setState( "r", "1", ABSENT );
558 m2.setState( "a", "2", ABSENT );
559 m2.setState( "b", "2", ABSENT );
560 m2.setState( "c", "2", ABSENT );
561 m2.setState( "d", "2", ABSENT );
562 m2.setState( "e", "2", ABSENT );
563 m2.setState( "f", "2", ABSENT );
564 m2.setState( "g", "2", ABSENT );
565 m2.setState( "h", "2", ABSENT );
566 m2.setState( "i", "2", ABSENT );
567 m2.setState( "j", "2", PRESENT );
568 m2.setState( "k", "2", ABSENT );
569 m2.setState( "l", "2", ABSENT );
570 m2.setState( "m", "2", PRESENT );
571 m2.setState( "n", "2", ABSENT );
572 m2.setState( "o", "2", ABSENT );
573 m2.setState( "p", "2", PRESENT );
574 m2.setState( "q", "2", ABSENT );
575 m2.setState( "r", "2", ABSENT );
576 m2.setState( "a", "3", ABSENT );
577 m2.setState( "b", "3", ABSENT );
578 m2.setState( "c", "3", PRESENT );
579 m2.setState( "d", "3", ABSENT );
580 m2.setState( "e", "3", ABSENT );
581 m2.setState( "f", "3", ABSENT );
582 m2.setState( "g", "3", PRESENT );
583 m2.setState( "h", "3", ABSENT );
584 m2.setState( "i", "3", ABSENT );
585 m2.setState( "j", "3", ABSENT );
586 m2.setState( "k", "3", ABSENT );
587 m2.setState( "l", "3", ABSENT );
588 m2.setState( "m", "3", ABSENT );
589 m2.setState( "n", "3", ABSENT );
590 m2.setState( "o", "3", ABSENT );
591 m2.setState( "p", "3", ABSENT );
592 m2.setState( "q", "3", ABSENT );
593 m2.setState( "r", "3", ABSENT );
594 dollo2.setReturnInternalStates( true );
595 dollo2.setReturnGainLossMatrix( true );
596 dollo2.execute( p2, m2 );
597 final CharacterStateMatrix<BinaryStates> i_m = dollo2.getInternalStatesMatrix();
598 final CharacterStateMatrix<GainLossStates> gl_m = dollo2.getGainLossMatrix();
599 if ( dollo2.getTotalGains() != 3 ) {
602 if ( dollo2.getTotalLosses() != 22 ) {
605 if ( dollo2.getTotalUnchanged() != 95 ) {
608 if ( i_m.getState( "ab", "0" ) != PRESENT ) {
611 if ( i_m.getState( "ac", "0" ) != PRESENT ) {
614 if ( i_m.getState( "ad", "0" ) != ABSENT ) {
617 if ( i_m.getState( "af", "0" ) != ABSENT ) {
620 if ( i_m.getState( "ef", "0" ) != ABSENT ) {
623 if ( i_m.getState( "ai", "0" ) != ABSENT ) {
626 if ( i_m.getState( "gi", "0" ) != ABSENT ) {
629 if ( i_m.getState( "jl", "0" ) != ABSENT ) {
632 if ( i_m.getState( "mo", "0" ) != ABSENT ) {
635 if ( i_m.getState( "pr", "0" ) != ABSENT ) {
638 if ( i_m.getState( "jr", "0" ) != ABSENT ) {
641 if ( i_m.getState( "root", "0" ) != ABSENT ) {
644 if ( i_m.getState( "ab", "1" ) != PRESENT ) {
647 if ( i_m.getState( "ac", "1" ) != PRESENT ) {
650 if ( i_m.getState( "ad", "1" ) != PRESENT ) {
653 if ( i_m.getState( "af", "1" ) != PRESENT ) {
656 if ( i_m.getState( "ef", "1" ) != ABSENT ) {
659 if ( i_m.getState( "ai", "1" ) != PRESENT ) {
662 if ( i_m.getState( "gi", "1" ) != PRESENT ) {
665 if ( i_m.getState( "jl", "1" ) != PRESENT ) {
668 if ( i_m.getState( "mo", "1" ) != PRESENT ) {
671 if ( i_m.getState( "pr", "1" ) != ABSENT ) {
674 if ( i_m.getState( "jr", "1" ) != PRESENT ) {
677 if ( i_m.getState( "root", "1" ) != PRESENT ) {
680 if ( i_m.getState( "ab", "2" ) != ABSENT ) {
683 if ( i_m.getState( "ac", "2" ) != ABSENT ) {
686 if ( i_m.getState( "ad", "2" ) != ABSENT ) {
689 if ( i_m.getState( "af", "2" ) != ABSENT ) {
692 if ( i_m.getState( "ef", "2" ) != ABSENT ) {
695 if ( i_m.getState( "ai", "2" ) != ABSENT ) {
698 if ( i_m.getState( "gi", "2" ) != ABSENT ) {
701 if ( i_m.getState( "jl", "2" ) != PRESENT ) {
704 if ( i_m.getState( "mo", "2" ) != PRESENT ) {
707 if ( i_m.getState( "pr", "2" ) != PRESENT ) {
710 if ( i_m.getState( "jr", "2" ) != PRESENT ) {
713 if ( i_m.getState( "root", "2" ) != ABSENT ) {
716 if ( i_m.getState( "ab", "3" ) != ABSENT ) {
719 if ( i_m.getState( "ac", "3" ) != PRESENT ) {
722 if ( i_m.getState( "ad", "3" ) != PRESENT ) {
725 if ( i_m.getState( "af", "3" ) != PRESENT ) {
728 if ( i_m.getState( "ef", "3" ) != ABSENT ) {
731 if ( i_m.getState( "ai", "3" ) != PRESENT ) {
734 if ( i_m.getState( "gi", "3" ) != PRESENT ) {
737 if ( i_m.getState( "jl", "3" ) != ABSENT ) {
740 if ( i_m.getState( "mo", "3" ) != ABSENT ) {
743 if ( i_m.getState( "pr", "3" ) != ABSENT ) {
746 if ( i_m.getState( "jr", "3" ) != ABSENT ) {
749 if ( i_m.getState( "root", "3" ) != ABSENT ) {
752 if ( gl_m.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
755 final DolloParsimony dollo9 = DolloParsimony.createInstance();
756 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
757 final String p9_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
758 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
759 m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9, 3 );
760 m1.setIdentifier( 0, "a" );
761 m1.setIdentifier( 1, "b" );
762 m1.setIdentifier( 2, "c" );
763 m1.setIdentifier( 3, "d" );
764 m1.setIdentifier( 4, "e" );
765 m1.setIdentifier( 5, "f" );
766 m1.setIdentifier( 6, "g" );
767 m1.setIdentifier( 7, "h" );
768 m1.setIdentifier( 8, "i" );
769 m1.setState( 0, 0, PRESENT );
770 m1.setState( 1, 0, ABSENT );
771 m1.setState( 2, 0, PRESENT );
772 m1.setState( 3, 0, ABSENT );
773 m1.setState( 4, 0, ABSENT );
774 m1.setState( 5, 0, ABSENT );
775 m1.setState( 6, 0, ABSENT );
776 m1.setState( 7, 0, ABSENT );
777 m1.setState( 8, 0, ABSENT );
778 m1.setState( 0, 1, PRESENT );
779 m1.setState( 1, 1, PRESENT );
780 m1.setState( 2, 1, PRESENT );
781 m1.setState( 3, 1, PRESENT );
782 m1.setState( 4, 1, ABSENT );
783 m1.setState( 5, 1, ABSENT );
784 m1.setState( 6, 1, ABSENT );
785 m1.setState( 7, 1, ABSENT );
786 m1.setState( 8, 1, ABSENT );
787 m1.setState( 0, 2, PRESENT );
788 m1.setState( 1, 2, ABSENT );
789 m1.setState( 2, 2, ABSENT );
790 m1.setState( 3, 2, ABSENT );
791 m1.setState( 4, 2, ABSENT );
792 m1.setState( 5, 2, ABSENT );
793 m1.setState( 6, 2, ABSENT );
794 m1.setState( 7, 2, PRESENT );
795 m1.setState( 8, 2, ABSENT );
796 dollo9.execute( p9, m1 );
797 if ( dollo9.getTotalGains() != 3 ) {
800 if ( dollo9.getTotalLosses() != 6 ) {
803 final DolloParsimony dollo10 = DolloParsimony.createInstance();
804 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
805 final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
806 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
807 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m10 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
809 m10.setIdentifier( 0, "a" );
810 m10.setIdentifier( 1, "b" );
811 m10.setIdentifier( 2, "c" );
812 m10.setIdentifier( 3, "d" );
813 m10.setIdentifier( 4, "e" );
814 m10.setIdentifier( 5, "f" );
815 m10.setIdentifier( 6, "g" );
816 m10.setIdentifier( 7, "h" );
817 m10.setIdentifier( 8, "i" );
818 m10.setState( 0, 0, PRESENT );
819 m10.setState( 1, 0, ABSENT );
820 m10.setState( 2, 0, PRESENT );
821 m10.setState( 3, 0, ABSENT );
822 m10.setState( 4, 0, ABSENT );
823 m10.setState( 5, 0, ABSENT );
824 m10.setState( 6, 0, ABSENT );
825 m10.setState( 7, 0, ABSENT );
826 m10.setState( 8, 0, ABSENT );
827 dollo10.execute( p10, m10 );
828 if ( dollo10.getTotalGains() != 1 ) {
831 if ( dollo10.getTotalLosses() != 1 ) {
835 catch ( final Exception e ) {
836 e.printStackTrace( System.out );
842 private static boolean testDolloParsimonyOnNonBinaryTree() {
844 final BinaryStates PRESENT = BinaryStates.PRESENT;
845 final BinaryStates ABSENT = BinaryStates.ABSENT;
846 final DolloParsimony dollo1 = DolloParsimony.createInstance();
847 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
848 final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
849 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
850 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
852 m1.setIdentifier( 0, "a" );
853 m1.setIdentifier( 1, "b" );
854 m1.setIdentifier( 2, "y" );
855 m1.setIdentifier( 3, "c" );
856 m1.setIdentifier( 4, "d" );
857 m1.setIdentifier( 5, "e" );
858 m1.setIdentifier( 6, "f" );
859 m1.setIdentifier( 7, "g" );
860 m1.setIdentifier( 8, "h" );
861 m1.setIdentifier( 9, "i" );
862 m1.setCharacter( 0, "0" );
863 m1.setState( "a", "0", PRESENT );
864 m1.setState( "b", "0", ABSENT );
865 m1.setState( "y", "0", PRESENT );
866 m1.setState( "c", "0", PRESENT );
867 m1.setState( "d", "0", ABSENT );
868 m1.setState( "e", "0", ABSENT );
869 m1.setState( "f", "0", ABSENT );
870 m1.setState( "g", "0", ABSENT );
871 m1.setState( "h", "0", ABSENT );
872 m1.setState( "i", "0", ABSENT );
873 dollo1.execute( p1, m1 );
874 if ( dollo1.getTotalGains() != 1 ) {
877 if ( dollo1.getTotalLosses() != 1 ) {
880 if ( dollo1.getTotalUnchanged() != 16 ) {
883 m1.setState( "b", "0", PRESENT );
884 dollo1.execute( p1, m1 );
885 if ( dollo1.getTotalGains() != 1 ) {
888 if ( dollo1.getTotalLosses() != 0 ) {
891 if ( dollo1.getTotalUnchanged() != 17 ) {
894 m1.setState( "a", "0", ABSENT );
895 m1.setState( "b", "0", ABSENT );
896 dollo1.execute( p1, m1 );
897 if ( dollo1.getTotalGains() != 1 ) {
900 if ( dollo1.getTotalLosses() != 2 ) {
903 if ( dollo1.getTotalUnchanged() != 15 ) {
906 m1.setState( "y", "0", ABSENT );
907 dollo1.execute( p1, m1 );
908 if ( dollo1.getTotalGains() != 1 ) {
911 if ( dollo1.getTotalLosses() != 0 ) {
914 if ( dollo1.getTotalUnchanged() != 17 ) {
917 final DolloParsimony dollo2 = DolloParsimony.createInstance();
918 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
919 final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r";
920 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
921 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
923 m2.setIdentifier( 0, "a" );
924 m2.setIdentifier( 1, "b" );
925 m2.setIdentifier( 2, "y" );
926 m2.setIdentifier( 3, "c" );
927 m2.setIdentifier( 4, "d" );
928 m2.setIdentifier( 5, "e" );
929 m2.setIdentifier( 6, "f" );
930 m2.setIdentifier( 7, "g" );
931 m2.setIdentifier( 8, "h" );
932 m2.setIdentifier( 9, "i" );
933 m2.setCharacter( 0, "0" );
934 m2.setState( "a", "0", PRESENT );
935 m2.setState( "b", "0", ABSENT );
936 m2.setState( "y", "0", PRESENT );
937 m2.setState( "c", "0", PRESENT );
938 m2.setState( "d", "0", ABSENT );
939 m2.setState( "e", "0", ABSENT );
940 m2.setState( "f", "0", ABSENT );
941 m2.setState( "g", "0", ABSENT );
942 m2.setState( "h", "0", ABSENT );
943 m2.setState( "i", "0", ABSENT );
944 dollo2.setReturnInternalStates( true );
945 dollo2.execute( p2, m2 );
946 CharacterStateMatrix<BinaryStates> i_m2 = dollo2.getInternalStatesMatrix();
947 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
950 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
953 if ( i_m2.getState( "af", "0" ) != ABSENT ) {
956 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
959 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
962 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
965 if ( dollo2.getTotalGains() != 1 ) {
968 if ( dollo2.getTotalLosses() != 2 ) {
971 if ( dollo2.getTotalUnchanged() != 14 ) {
974 m2.setState( "b", "0", PRESENT );
975 dollo2.execute( p2, m2 );
976 if ( dollo2.getTotalGains() != 1 ) {
979 if ( dollo2.getTotalLosses() != 1 ) {
982 if ( dollo2.getTotalUnchanged() != 15 ) {
985 m2.setState( "a", "0", ABSENT );
986 m2.setState( "b", "0", ABSENT );
987 dollo2.execute( p2, m2 );
988 if ( dollo2.getTotalGains() != 1 ) {
991 if ( dollo2.getTotalLosses() != 3 ) {
994 if ( dollo2.getTotalUnchanged() != 13 ) {
997 m2.setState( "y", "0", ABSENT );
998 dollo2.execute( p2, m2 );
999 if ( dollo2.getTotalGains() != 1 ) {
1002 if ( dollo2.getTotalLosses() != 0 ) {
1005 if ( dollo2.getTotalUnchanged() != 16 ) {
1008 m2.setState( "c", "0", ABSENT );
1009 dollo2.execute( p2, m2 );
1010 if ( dollo2.getTotalGains() != 0 ) {
1013 if ( dollo2.getTotalLosses() != 0 ) {
1016 if ( dollo2.getTotalUnchanged() != 17 ) {
1019 m2.setState( "y", "0", PRESENT );
1020 m2.setState( "e", "0", PRESENT );
1021 dollo2.execute( p2, m2 );
1022 if ( dollo2.getTotalGains() != 1 ) {
1025 if ( dollo2.getTotalLosses() != 5 ) {
1028 if ( dollo2.getTotalUnchanged() != 11 ) {
1031 i_m2 = dollo2.getInternalStatesMatrix();
1032 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
1035 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
1038 if ( i_m2.getState( "af", "0" ) != PRESENT ) {
1041 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
1044 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
1047 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
1051 catch ( final Exception e ) {
1052 e.printStackTrace( System.out );
1058 private static boolean testFitchParsimony() {
1060 final BinaryStates PRESENT = BinaryStates.PRESENT;
1061 final BinaryStates ABSENT = BinaryStates.ABSENT;
1062 final GainLossStates GAIN = GainLossStates.GAIN;
1063 final GainLossStates LOSS = GainLossStates.LOSS;
1064 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
1065 final GainLossStates UNCHANGED_ABSENT = GainLossStates.UNCHANGED_ABSENT;
1066 final FitchParsimony<String> fitch1 = new FitchParsimony<String>();
1067 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
1068 final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root";
1069 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
1070 final CharacterStateMatrix<String> m1 = new BasicCharacterStateMatrix<String>( 18, 1 );
1071 m1.setIdentifier( 0, "a" );
1072 m1.setIdentifier( 1, "b" );
1073 m1.setIdentifier( 2, "c" );
1074 m1.setIdentifier( 3, "d" );
1075 m1.setIdentifier( 4, "e" );
1076 m1.setIdentifier( 5, "f" );
1077 m1.setIdentifier( 6, "g" );
1078 m1.setIdentifier( 7, "h" );
1079 m1.setIdentifier( 8, "i" );
1080 m1.setIdentifier( 9, "j" );
1081 m1.setIdentifier( 10, "k" );
1082 m1.setIdentifier( 11, "l" );
1083 m1.setIdentifier( 12, "m" );
1084 m1.setIdentifier( 13, "n" );
1085 m1.setIdentifier( 14, "o" );
1086 m1.setIdentifier( 15, "p" );
1087 m1.setIdentifier( 16, "q" );
1088 m1.setIdentifier( 17, "r" );
1089 m1.setCharacter( 0, "0" );
1090 m1.setState( "a", "0", "A" );
1091 m1.setState( "b", "0", "A" );
1092 m1.setState( "c", "0", "B" );
1093 m1.setState( "d", "0", "C" );
1094 m1.setState( "e", "0", "D" );
1095 m1.setState( "f", "0", "A" );
1096 m1.setState( "g", "0", "A" );
1097 m1.setState( "h", "0", "B" );
1098 m1.setState( "i", "0", "C" );
1099 m1.setState( "j", "0", "A" );
1100 m1.setState( "k", "0", "B" );
1101 m1.setState( "l", "0", "C" );
1102 m1.setState( "m", "0", "B" );
1103 m1.setState( "n", "0", "B" );
1104 m1.setState( "o", "0", "B" );
1105 m1.setState( "p", "0", "A" );
1106 m1.setState( "q", "0", "C" );
1107 m1.setState( "r", "0", "D" );
1108 fitch1.setReturnInternalStates( true );
1109 fitch1.setReturnGainLossMatrix( false );
1110 fitch1.setRandomize( false );
1111 fitch1.execute( p1, m1 );
1112 final CharacterStateMatrix<String> i_m = fitch1.getInternalStatesMatrix();
1113 final CharacterStateMatrix<List<String>> i_m_all = fitch1.getInternalStatesMatrixPriorToTraceback();
1114 if ( fitch1.getCost() != 10 ) {
1117 if ( !i_m.getState( "ab", "0" ).equals( "A" ) ) {
1120 if ( !i_m.getState( "ac", "0" ).equals( "A" ) ) {
1123 if ( !i_m.getState( "ad", "0" ).equals( "A" ) ) {
1126 if ( !i_m.getState( "ef", "0" ).equals( "A" ) ) {
1129 if ( !i_m.getState( "ai", "0" ).equals( "A" ) ) {
1132 if ( !i_m.getState( "gi", "0" ).equals( "A" ) ) {
1135 if ( !i_m.getState( "jl", "0" ).equals( "A" ) ) {
1138 if ( !i_m.getState( "mo", "0" ).equals( "B" ) ) {
1141 if ( !i_m.getState( "pr", "0" ).equals( "A" ) ) {
1144 if ( i_m_all.getState( "ab", "0" ).size() != 1 ) {
1147 if ( !i_m_all.getState( "ab", "0" ).contains( "A" ) ) {
1150 if ( i_m_all.getState( "ac", "0" ).size() != 2 ) {
1153 if ( !i_m_all.getState( "ac", "0" ).contains( "A" ) ) {
1156 if ( !i_m_all.getState( "ac", "0" ).contains( "B" ) ) {
1159 if ( i_m_all.getState( "ad", "0" ).size() != 3 ) {
1162 if ( !i_m_all.getState( "ad", "0" ).contains( "A" ) ) {
1165 if ( !i_m_all.getState( "ad", "0" ).contains( "B" ) ) {
1168 if ( !i_m_all.getState( "ad", "0" ).contains( "C" ) ) {
1171 if ( i_m_all.getState( "af", "0" ).size() != 1 ) {
1174 if ( !i_m_all.getState( "af", "0" ).contains( "A" ) ) {
1177 if ( i_m_all.getState( "ef", "0" ).size() != 2 ) {
1180 if ( !i_m_all.getState( "ef", "0" ).contains( "A" ) ) {
1183 if ( !i_m_all.getState( "ef", "0" ).contains( "D" ) ) {
1186 if ( i_m_all.getState( "gi", "0" ).size() != 3 ) {
1189 if ( !i_m_all.getState( "gi", "0" ).contains( "A" ) ) {
1192 if ( !i_m_all.getState( "gi", "0" ).contains( "B" ) ) {
1195 if ( !i_m_all.getState( "gi", "0" ).contains( "C" ) ) {
1198 if ( i_m_all.getState( "ai", "0" ).size() != 1 ) {
1201 if ( !i_m_all.getState( "ai", "0" ).contains( "A" ) ) {
1204 if ( i_m_all.getState( "jl", "0" ).size() != 3 ) {
1207 if ( !i_m_all.getState( "jl", "0" ).contains( "A" ) ) {
1210 if ( !i_m_all.getState( "jl", "0" ).contains( "B" ) ) {
1213 if ( !i_m_all.getState( "jl", "0" ).contains( "C" ) ) {
1216 if ( i_m_all.getState( "mo", "0" ).size() != 1 ) {
1219 if ( !i_m_all.getState( "mo", "0" ).contains( "B" ) ) {
1222 if ( i_m_all.getState( "pr", "0" ).size() != 3 ) {
1225 if ( !i_m_all.getState( "pr", "0" ).contains( "A" ) ) {
1228 if ( !i_m_all.getState( "pr", "0" ).contains( "C" ) ) {
1231 if ( !i_m_all.getState( "pr", "0" ).contains( "D" ) ) {
1234 if ( i_m_all.getState( "jr", "0" ).size() != 4 ) {
1237 if ( !i_m_all.getState( "jr", "0" ).contains( "A" ) ) {
1240 if ( !i_m_all.getState( "jr", "0" ).contains( "B" ) ) {
1243 if ( !i_m_all.getState( "jr", "0" ).contains( "C" ) ) {
1246 if ( !i_m_all.getState( "jr", "0" ).contains( "D" ) ) {
1249 final FitchParsimony<String> fitch2 = new FitchParsimony<String>();
1250 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1251 final String p2_str = "((a,b)ab,(c,(d,e)de)cde)r";
1252 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
1253 final CharacterStateMatrix<String> m2 = new BasicCharacterStateMatrix<String>( 5, 1 );
1254 m2.setIdentifier( 0, "a" );
1255 m2.setIdentifier( 1, "b" );
1256 m2.setIdentifier( 2, "c" );
1257 m2.setIdentifier( 3, "d" );
1258 m2.setIdentifier( 4, "e" );
1259 m2.setCharacter( 0, "0" );
1260 m2.setState( "a", "0", "C" );
1261 m2.setState( "b", "0", "A" );
1262 m2.setState( "c", "0", "C" );
1263 m2.setState( "d", "0", "A" );
1264 m2.setState( "e", "0", "G" );
1265 fitch2.setReturnInternalStates( true );
1266 fitch2.setReturnGainLossMatrix( false );
1267 fitch2.execute( p2, m2 );
1268 final CharacterStateMatrix<String> i_m2 = fitch2.getInternalStatesMatrix();
1269 final CharacterStateMatrix<List<String>> i_m_all2 = fitch2.getInternalStatesMatrixPriorToTraceback();
1270 if ( fitch2.getCost() != 3 ) {
1273 if ( !i_m2.getState( "ab", "0" ).equals( "A" ) ) {
1276 if ( !i_m2.getState( "de", "0" ).equals( "A" ) ) {
1279 if ( !i_m2.getState( "cde", "0" ).equals( "A" ) ) {
1282 if ( !i_m2.getState( "r", "0" ).equals( "A" ) ) {
1285 if ( i_m_all2.getState( "cde", "0" ).size() != 3 ) {
1288 if ( !i_m_all2.getState( "cde", "0" ).contains( "A" ) ) {
1291 if ( !i_m_all2.getState( "cde", "0" ).contains( "C" ) ) {
1294 if ( !i_m_all2.getState( "cde", "0" ).contains( "G" ) ) {
1297 if ( i_m_all2.getState( "ab", "0" ).size() != 2 ) {
1300 if ( !i_m_all2.getState( "ab", "0" ).contains( "A" ) ) {
1303 if ( !i_m_all2.getState( "ab", "0" ).contains( "C" ) ) {
1306 fitch2.setReturnInternalStates( true );
1307 fitch2.setReturnGainLossMatrix( false );
1308 fitch2.setUseLast( true );
1309 fitch2.execute( p2, m2 );
1310 final CharacterStateMatrix<String> i_m21 = fitch2.getInternalStatesMatrix();
1311 final CharacterStateMatrix<List<String>> i_m_all21 = fitch2.getInternalStatesMatrixPriorToTraceback();
1312 if ( fitch2.getCost() != 3 ) {
1315 if ( !i_m21.getState( "ab", "0" ).equals( "C" ) ) {
1318 if ( !i_m21.getState( "de", "0" ).equals( "G" ) ) {
1321 if ( !i_m21.getState( "cde", "0" ).equals( "C" ) ) {
1324 if ( !i_m21.getState( "r", "0" ).equals( "C" ) ) {
1327 if ( i_m_all21.getState( "cde", "0" ).size() != 3 ) {
1330 if ( !i_m_all21.getState( "cde", "0" ).contains( "A" ) ) {
1333 if ( !i_m_all21.getState( "cde", "0" ).contains( "C" ) ) {
1336 if ( !i_m_all21.getState( "cde", "0" ).contains( "G" ) ) {
1339 final FitchParsimony<String> fitch3 = new FitchParsimony<String>();
1340 final PhylogenyFactory factory3 = ParserBasedPhylogenyFactory.getInstance();
1341 final String p3_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1342 final Phylogeny p3 = factory3.create( p3_str, new NHXParser() )[ 0 ];
1343 final CharacterStateMatrix<String> m3 = new BasicCharacterStateMatrix<String>( 6, 1 );
1344 m3.setIdentifier( 0, "a" );
1345 m3.setIdentifier( 1, "b" );
1346 m3.setIdentifier( 2, "c" );
1347 m3.setIdentifier( 3, "d" );
1348 m3.setIdentifier( 4, "e" );
1349 m3.setIdentifier( 5, "f" );
1350 m3.setCharacter( 0, "0" );
1351 m3.setState( "a", "0", "C" );
1352 m3.setState( "b", "0", "U" );
1353 m3.setState( "c", "0", "G" );
1354 m3.setState( "d", "0", "U" );
1355 m3.setState( "e", "0", "A" );
1356 m3.setState( "f", "0", "A" );
1357 fitch3.setReturnInternalStates( true );
1358 fitch3.setReturnGainLossMatrix( false );
1359 fitch3.execute( p3, m3 );
1360 final CharacterStateMatrix<String> i_m3 = fitch3.getInternalStatesMatrix();
1361 final CharacterStateMatrix<List<String>> i_m_all3 = fitch3.getInternalStatesMatrixPriorToTraceback();
1362 if ( fitch3.getCost() != 4 ) {
1365 if ( !i_m3.getState( "ab", "0" ).equals( "U" ) ) {
1368 if ( !i_m3.getState( "cd", "0" ).equals( "U" ) ) {
1371 if ( !i_m3.getState( "cde", "0" ).equals( "U" ) ) {
1374 if ( !i_m3.getState( "abcde", "0" ).equals( "U" ) ) {
1377 if ( !i_m3.getState( "r", "0" ).equals( "A" ) ) {
1380 if ( i_m_all3.getState( "cde", "0" ).size() != 3 ) {
1383 if ( !i_m_all3.getState( "cde", "0" ).contains( "A" ) ) {
1386 if ( !i_m_all3.getState( "cde", "0" ).contains( "G" ) ) {
1389 if ( !i_m_all3.getState( "cde", "0" ).contains( "U" ) ) {
1392 if ( i_m_all3.getState( "ab", "0" ).size() != 2 ) {
1395 if ( !i_m_all3.getState( "ab", "0" ).contains( "C" ) ) {
1398 if ( !i_m_all3.getState( "ab", "0" ).contains( "U" ) ) {
1401 if ( i_m_all3.getState( "cd", "0" ).size() != 2 ) {
1404 if ( !i_m_all3.getState( "cd", "0" ).contains( "G" ) ) {
1407 if ( !i_m_all3.getState( "cd", "0" ).contains( "U" ) ) {
1410 if ( i_m_all3.getState( "abcde", "0" ).size() != 1 ) {
1413 if ( !i_m_all3.getState( "abcde", "0" ).contains( "U" ) ) {
1416 if ( i_m_all3.getState( "r", "0" ).size() != 2 ) {
1419 if ( !i_m_all3.getState( "r", "0" ).contains( "A" ) ) {
1422 if ( !i_m_all3.getState( "r", "0" ).contains( "U" ) ) {
1425 final FitchParsimony<BinaryStates> fitch4 = new FitchParsimony<BinaryStates>();
1426 final PhylogenyFactory factory4 = ParserBasedPhylogenyFactory.getInstance();
1427 final String p4_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1428 final Phylogeny p4 = factory4.create( p4_str, new NHXParser() )[ 0 ];
1429 final CharacterStateMatrix<BinaryStates> m4 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1430 m4.setIdentifier( 0, "a" );
1431 m4.setIdentifier( 1, "b" );
1432 m4.setIdentifier( 2, "c" );
1433 m4.setIdentifier( 3, "d" );
1434 m4.setIdentifier( 4, "e" );
1435 m4.setIdentifier( 5, "f" );
1436 m4.setCharacter( 0, "0" );
1437 m4.setState( "a", "0", PRESENT );
1438 m4.setState( "b", "0", ABSENT );
1439 m4.setState( "c", "0", PRESENT );
1440 m4.setState( "d", "0", PRESENT );
1441 m4.setState( "e", "0", ABSENT );
1442 m4.setState( "f", "0", ABSENT );
1443 fitch4.setReturnInternalStates( true );
1444 fitch4.setReturnGainLossMatrix( true );
1445 fitch4.execute( p4, m4 );
1446 final CharacterStateMatrix<GainLossStates> gl_m_4 = fitch4.getGainLossMatrix();
1447 if ( fitch4.getCost() != 2 ) {
1450 if ( fitch4.getTotalLosses() != 0 ) {
1453 if ( fitch4.getTotalGains() != 2 ) {
1456 if ( fitch4.getTotalUnchanged() != 9 ) {
1459 if ( gl_m_4.getState( "a", "0" ) != GAIN ) {
1462 if ( gl_m_4.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1465 if ( gl_m_4.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1468 if ( gl_m_4.getState( "cd", "0" ) != GAIN ) {
1471 if ( gl_m_4.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1474 final FitchParsimony<BinaryStates> fitch5 = new FitchParsimony<BinaryStates>();
1475 final PhylogenyFactory factory5 = ParserBasedPhylogenyFactory.getInstance();
1476 final String p5_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1477 final Phylogeny p5 = factory5.create( p5_str, new NHXParser() )[ 0 ];
1478 final CharacterStateMatrix<BinaryStates> m5 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1479 m5.setIdentifier( 0, "a" );
1480 m5.setIdentifier( 1, "b" );
1481 m5.setIdentifier( 2, "c" );
1482 m5.setIdentifier( 3, "d" );
1483 m5.setIdentifier( 4, "e" );
1484 m5.setIdentifier( 5, "f" );
1485 m5.setCharacter( 0, "0" );
1486 m5.setState( "a", "0", PRESENT );
1487 m5.setState( "b", "0", ABSENT );
1488 m5.setState( "c", "0", PRESENT );
1489 m5.setState( "d", "0", ABSENT );
1490 m5.setState( "e", "0", PRESENT );
1491 m5.setState( "f", "0", ABSENT );
1492 fitch5.setReturnInternalStates( true );
1493 fitch5.setReturnGainLossMatrix( true );
1494 fitch5.execute( p5, m5 );
1495 final CharacterStateMatrix<GainLossStates> gl_m_5 = fitch5.getGainLossMatrix();
1496 if ( fitch5.getCost() != 3 ) {
1499 if ( fitch5.getTotalLosses() != 2 ) {
1502 if ( fitch5.getTotalGains() != 1 ) {
1505 if ( fitch5.getTotalUnchanged() != 8 ) {
1508 if ( gl_m_5.getState( "abcde", "0" ) != GAIN ) {
1511 if ( gl_m_5.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1514 if ( gl_m_5.getState( "b", "0" ) != LOSS ) {
1517 if ( gl_m_5.getState( "d", "0" ) != LOSS ) {
1520 if ( gl_m_5.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1523 final FitchParsimony<BinaryStates> fitch6 = new FitchParsimony<BinaryStates>();
1524 final PhylogenyFactory factory6 = ParserBasedPhylogenyFactory.getInstance();
1525 final String p6_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1526 final Phylogeny p6 = factory6.create( p6_str, new NHXParser() )[ 0 ];
1527 final CharacterStateMatrix<BinaryStates> m6 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1528 m6.setIdentifier( 0, "a" );
1529 m6.setIdentifier( 1, "b" );
1530 m6.setIdentifier( 2, "c" );
1531 m6.setIdentifier( 3, "d" );
1532 m6.setIdentifier( 4, "e" );
1533 m6.setIdentifier( 5, "f" );
1534 m6.setCharacter( 0, "0" );
1535 m6.setState( "a", "0", PRESENT );
1536 m6.setState( "b", "0", ABSENT );
1537 m6.setState( "c", "0", PRESENT );
1538 m6.setState( "d", "0", PRESENT );
1539 m6.setState( "e", "0", ABSENT );
1540 m6.setState( "f", "0", PRESENT );
1541 fitch6.setReturnInternalStates( true );
1542 fitch6.setReturnGainLossMatrix( true );
1543 fitch6.execute( p6, m6 );
1544 final CharacterStateMatrix<GainLossStates> gl_m_6 = fitch6.getGainLossMatrix();
1545 if ( fitch6.getCost() != 2 ) {
1548 if ( fitch6.getTotalLosses() != 2 ) {
1551 if ( fitch6.getTotalGains() != 0 ) {
1554 if ( fitch6.getTotalUnchanged() != 9 ) {
1557 if ( gl_m_6.getState( "abcde", "0" ) != UNCHANGED_PRESENT ) {
1560 if ( gl_m_6.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1563 if ( gl_m_6.getState( "b", "0" ) != LOSS ) {
1566 if ( gl_m_6.getState( "e", "0" ) != LOSS ) {
1569 final FitchParsimony<BinaryStates> fitch7 = new FitchParsimony<BinaryStates>();
1570 final PhylogenyFactory factory7 = ParserBasedPhylogenyFactory.getInstance();
1571 final String p7_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1572 final Phylogeny p7 = factory7.create( p7_str, new NHXParser() )[ 0 ];
1573 final CharacterStateMatrix<BinaryStates> m7 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1574 m7.setIdentifier( 0, "a" );
1575 m7.setIdentifier( 1, "b" );
1576 m7.setIdentifier( 2, "c" );
1577 m7.setIdentifier( 3, "d" );
1578 m7.setIdentifier( 4, "e" );
1579 m7.setIdentifier( 5, "f" );
1580 m7.setIdentifier( 6, "g" );
1581 m7.setIdentifier( 7, "h" );
1582 m7.setCharacter( 0, "0" );
1583 m7.setState( "a", "0", PRESENT );
1584 m7.setState( "b", "0", ABSENT );
1585 m7.setState( "c", "0", PRESENT );
1586 m7.setState( "d", "0", ABSENT );
1587 m7.setState( "e", "0", PRESENT );
1588 m7.setState( "f", "0", ABSENT );
1589 m7.setState( "g", "0", PRESENT );
1590 m7.setState( "h", "0", ABSENT );
1591 fitch7.setReturnInternalStates( true );
1592 fitch7.setReturnGainLossMatrix( true );
1593 fitch7.execute( p7, m7 );
1594 final CharacterStateMatrix<GainLossStates> gl_m_7 = fitch7.getGainLossMatrix();
1595 if ( fitch7.getCost() != 4 ) {
1598 if ( fitch7.getTotalLosses() != 0 ) {
1601 if ( fitch7.getTotalGains() != 4 ) {
1604 if ( fitch7.getTotalUnchanged() != 11 ) {
1607 if ( gl_m_7.getState( "a", "0" ) != GAIN ) {
1610 if ( gl_m_7.getState( "c", "0" ) != GAIN ) {
1613 if ( gl_m_7.getState( "e", "0" ) != GAIN ) {
1616 if ( gl_m_7.getState( "g", "0" ) != GAIN ) {
1619 if ( gl_m_7.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1622 fitch7.setReturnInternalStates( true );
1623 fitch7.setReturnGainLossMatrix( true );
1624 fitch7.setUseLast( true );
1625 fitch7.execute( p7, m7 );
1626 final CharacterStateMatrix<GainLossStates> gl_m_71 = fitch7.getGainLossMatrix();
1627 if ( fitch7.getCost() != 4 ) {
1630 if ( fitch7.getTotalLosses() != 4 ) {
1633 if ( fitch7.getTotalGains() != 0 ) {
1636 if ( fitch7.getTotalUnchanged() != 11 ) {
1639 if ( gl_m_71.getState( "b", "0" ) != LOSS ) {
1642 if ( gl_m_71.getState( "d", "0" ) != LOSS ) {
1645 if ( gl_m_71.getState( "f", "0" ) != LOSS ) {
1648 if ( gl_m_71.getState( "h", "0" ) != LOSS ) {
1651 if ( gl_m_71.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1654 final FitchParsimony<BinaryStates> fitch8 = new FitchParsimony<BinaryStates>();
1655 final PhylogenyFactory factory8 = ParserBasedPhylogenyFactory.getInstance();
1656 final String p8_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1657 final Phylogeny p8 = factory8.create( p8_str, new NHXParser() )[ 0 ];
1658 final CharacterStateMatrix<BinaryStates> m8 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1659 m8.setIdentifier( 0, "a" );
1660 m8.setIdentifier( 1, "b" );
1661 m8.setIdentifier( 2, "c" );
1662 m8.setIdentifier( 3, "d" );
1663 m8.setIdentifier( 4, "e" );
1664 m8.setIdentifier( 5, "f" );
1665 m8.setIdentifier( 6, "g" );
1666 m8.setIdentifier( 7, "h" );
1667 m8.setCharacter( 0, "0" );
1668 m8.setState( "a", "0", PRESENT );
1669 m8.setState( "b", "0", PRESENT );
1670 m8.setState( "c", "0", PRESENT );
1671 m8.setState( "d", "0", ABSENT );
1672 m8.setState( "e", "0", ABSENT );
1673 m8.setState( "f", "0", ABSENT );
1674 m8.setState( "g", "0", ABSENT );
1675 m8.setState( "h", "0", ABSENT );
1676 fitch8.setReturnInternalStates( true );
1677 fitch8.setReturnGainLossMatrix( true );
1678 fitch8.execute( p8, m8 );
1679 final CharacterStateMatrix<GainLossStates> gl_m_8 = fitch8.getGainLossMatrix();
1680 if ( fitch8.getCost() != 2 ) {
1683 if ( fitch8.getTotalLosses() != 1 ) {
1686 if ( fitch8.getTotalGains() != 1 ) {
1689 if ( fitch8.getTotalUnchanged() != 13 ) {
1692 if ( gl_m_8.getState( "d", "0" ) != LOSS ) {
1695 if ( gl_m_8.getState( "abcd", "0" ) != GAIN ) {
1698 final FitchParsimony<BinaryStates> fitch9 = new FitchParsimony<BinaryStates>();
1699 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
1700 final String p9_str = "(((a,b)ab,c)abc,d)abcd";
1701 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
1702 final CharacterStateMatrix<BinaryStates> m9 = new BasicCharacterStateMatrix<BinaryStates>( 4, 1 );
1703 m9.setIdentifier( 0, "a" );
1704 m9.setIdentifier( 1, "b" );
1705 m9.setIdentifier( 2, "c" );
1706 m9.setIdentifier( 3, "d" );
1707 m9.setCharacter( 0, "0" );
1708 m9.setState( "a", "0", PRESENT );
1709 m9.setState( "b", "0", ABSENT );
1710 m9.setState( "c", "0", PRESENT );
1711 m9.setState( "d", "0", ABSENT );
1712 fitch9.setReturnInternalStates( true );
1713 fitch9.setReturnGainLossMatrix( true );
1714 fitch9.setUseLast( false );
1715 fitch9.execute( p9, m9 );
1716 final CharacterStateMatrix<GainLossStates> gl_m_9a = fitch9.getGainLossMatrix();
1717 if ( fitch9.getCost() != 2 ) {
1720 if ( fitch9.getTotalLosses() != 1 ) {
1723 if ( fitch9.getTotalGains() != 1 ) {
1726 if ( fitch9.getTotalUnchanged() != 5 ) {
1729 if ( gl_m_9a.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1732 if ( gl_m_9a.getState( "b", "0" ) != LOSS ) {
1735 if ( gl_m_9a.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1738 if ( gl_m_9a.getState( "d", "0" ) != UNCHANGED_ABSENT ) {
1741 if ( gl_m_9a.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1744 if ( gl_m_9a.getState( "abc", "0" ) != GAIN ) {
1747 if ( gl_m_9a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1750 fitch9.setUseLast( true );
1751 fitch9.execute( p9, m9 );
1752 final CharacterStateMatrix<GainLossStates> gl_m_9b = fitch9.getGainLossMatrix();
1753 if ( fitch9.getCost() != 2 ) {
1756 if ( fitch9.getTotalLosses() != 2 ) {
1759 if ( fitch9.getTotalGains() != 0 ) {
1762 if ( fitch9.getTotalUnchanged() != 5 ) {
1765 if ( gl_m_9b.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1768 if ( gl_m_9b.getState( "b", "0" ) != LOSS ) {
1771 if ( gl_m_9b.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1774 if ( gl_m_9b.getState( "d", "0" ) != LOSS ) {
1777 if ( gl_m_9b.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1780 if ( gl_m_9b.getState( "abc", "0" ) != UNCHANGED_PRESENT ) {
1783 if ( gl_m_9b.getState( "abcd", "0" ) != UNCHANGED_PRESENT ) {
1786 fitch9.setUseLast( false );
1787 fitch9.setRandomize( true );
1788 fitch9.setRandomNumberSeed( 8722445 );
1789 fitch9.execute( p9, m9 );
1790 fitch9.getGainLossMatrix();
1791 if ( fitch9.getCost() != 2 ) {
1794 if ( fitch9.getTotalLosses() != 1 ) {
1797 if ( fitch9.getTotalGains() != 1 ) {
1800 if ( fitch9.getTotalUnchanged() != 5 ) {
1803 final FitchParsimony<BinaryStates> fitch10 = new FitchParsimony<BinaryStates>();
1804 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
1805 final String p10_str = "((((a,b)ab,c)abc,d)abcd,e)abcde";
1806 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
1807 final CharacterStateMatrix<BinaryStates> m10 = new BasicCharacterStateMatrix<BinaryStates>( 5, 1 );
1808 m10.setIdentifier( 0, "a" );
1809 m10.setIdentifier( 1, "b" );
1810 m10.setIdentifier( 2, "c" );
1811 m10.setIdentifier( 3, "d" );
1812 m10.setIdentifier( 4, "e" );
1813 m10.setCharacter( 0, "0" );
1814 m10.setState( "a", "0", PRESENT );
1815 m10.setState( "b", "0", ABSENT );
1816 m10.setState( "c", "0", ABSENT );
1817 m10.setState( "d", "0", PRESENT );
1818 m10.setState( "e", "0", ABSENT );
1819 fitch10.setReturnInternalStates( true );
1820 fitch10.setReturnGainLossMatrix( true );
1821 fitch10.setUseLast( false );
1822 fitch10.execute( p10, m10 );
1823 final CharacterStateMatrix<GainLossStates> gl_m_10a = fitch10.getGainLossMatrix();
1824 if ( fitch10.getCost() != 2 ) {
1827 if ( fitch10.getTotalLosses() != 0 ) {
1830 if ( fitch10.getTotalGains() != 2 ) {
1833 if ( fitch10.getTotalUnchanged() != 7 ) {
1836 if ( gl_m_10a.getState( "a", "0" ) != GAIN ) {
1839 if ( gl_m_10a.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1842 if ( gl_m_10a.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1845 if ( gl_m_10a.getState( "d", "0" ) != GAIN ) {
1848 if ( gl_m_10a.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1851 if ( gl_m_10a.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1854 if ( gl_m_10a.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1857 if ( gl_m_10a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1860 if ( gl_m_10a.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1863 fitch10.setUseLast( true );
1864 fitch10.execute( p10, m10 );
1865 final CharacterStateMatrix<GainLossStates> gl_m_10b = fitch10.getGainLossMatrix();
1866 if ( fitch10.getCost() != 2 ) {
1869 if ( fitch10.getTotalLosses() != 0 ) {
1872 if ( fitch10.getTotalGains() != 2 ) {
1875 if ( fitch10.getTotalUnchanged() != 7 ) {
1878 if ( gl_m_10b.getState( "a", "0" ) != GAIN ) {
1881 if ( gl_m_10b.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1884 if ( gl_m_10b.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1887 if ( gl_m_10b.getState( "d", "0" ) != GAIN ) {
1890 if ( gl_m_10b.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1893 if ( gl_m_10b.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1896 if ( gl_m_10b.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1899 if ( gl_m_10b.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1902 if ( gl_m_10b.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1906 catch ( final Exception e ) {
1907 e.printStackTrace( System.out );
1913 private static boolean testNeighborJoining() {
1915 BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
1917 m.setRow( "4 7", 2 );
1918 m.setRow( "7 10 7", 3 );
1919 m.setRow( "6 9 6 5", 4 );
1920 m.setRow( "8 11 8 9 8", 5 );
1921 m.setIdentifier( 0, "A" );
1922 m.setIdentifier( 1, "B" );
1923 m.setIdentifier( 2, "C" );
1924 m.setIdentifier( 3, "D" );
1925 m.setIdentifier( 4, "E" );
1926 m.setIdentifier( 5, "F" );
1927 final NeighborJoining nj = NeighborJoining.createInstance();
1928 nj.setVerbose( false );
1930 m = new BasicSymmetricalDistanceMatrix( 7 );
1931 m.setIdentifier( 0, "Bovine" );
1932 m.setIdentifier( 1, "Mouse" );
1933 m.setIdentifier( 2, "Gibbon" );
1934 m.setIdentifier( 3, "Orang" );
1935 m.setIdentifier( 4, "Gorilla" );
1936 m.setIdentifier( 5, "Chimp" );
1937 m.setIdentifier( 6, "Human" );
1938 m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
1939 m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
1940 m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
1941 m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
1942 m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
1943 m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
1944 m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
1946 m = new BasicSymmetricalDistanceMatrix( 4 );
1947 m.setIdentifier( 0, "A" );
1948 m.setIdentifier( 1, "B" );
1949 m.setIdentifier( 2, "C" );
1950 m.setIdentifier( 3, "D" );
1951 m.setRow( "0.00 0.95 0.17 0.98", 0 );
1952 m.setRow( "0.95 0.00 1.02 1.83", 1 );
1953 m.setRow( "0.17 1.02 0.00 1.01", 2 );
1954 m.setRow( "0.98 1.83 1.01 0.00", 3 );
1955 final Phylogeny p3 = nj.execute( m );
1959 // ----------------------- B 0.90
1963 // ------------------------- D 0.91
1964 p3.reRoot( p3.getNode( "C" ).getParent() );
1965 if ( !isEqual( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) {
1968 if ( !isEqual( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) {
1971 if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.10 ) ) {
1974 if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) {
1978 timeNeighborJoining();
1981 catch ( final Exception e ) {
1982 e.printStackTrace( System.out );
1988 private static boolean testSymmetricalDistanceMatrixParser() {
1990 final String l = ForesterUtil.getLineSeparator();
1991 StringBuffer source = new StringBuffer();
1992 source.append( " 4" + l );
1993 source.append( "A 0 0 0 0" + l );
1994 source.append( "B 1 0 0 0" + l );
1995 source.append( "C 2 4 0 0" + l );
1996 source.append( "D 3 5 6 0" + l );
1998 source.append( " 4" + l );
1999 source.append( "A 0 11 12 13" + l );
2000 source.append( "B 11 0 14 15" + l );
2001 source.append( "C 12 14 0 16" + l );
2002 source.append( "D 13 15 16 0" + l );
2005 source.append( " " + l );
2006 source.append( " 4" + l );
2007 source.append( " A 0 " + l );
2008 source.append( " B 21 0" + l );
2009 source.append( " C 22 24 0 " + l );
2010 source.append( " # 2 222 2 2 " + l );
2011 source.append( " D 23 25 26 0" + l );
2014 source.append( " " + l );
2015 final SymmetricalDistanceMatrixParser p0 = SymmetricalDistanceMatrixParser.createInstance();
2016 final DistanceMatrix[] ma0 = p0.parse( source.toString() );
2017 if ( ma0.length != 3 ) {
2020 if ( !isEqual( ma0[ 0 ].getValue( 0, 0 ), 0 ) ) {
2023 if ( !isEqual( ma0[ 0 ].getValue( 1, 0 ), 1 ) ) {
2026 if ( !isEqual( ma0[ 0 ].getValue( 2, 0 ), 2 ) ) {
2029 if ( !isEqual( ma0[ 0 ].getValue( 3, 0 ), 3 ) ) {
2032 if ( !isEqual( ma0[ 0 ].getValue( 0, 1 ), 1 ) ) {
2035 if ( !isEqual( ma0[ 0 ].getValue( 1, 1 ), 0 ) ) {
2038 if ( !isEqual( ma0[ 0 ].getValue( 2, 1 ), 4 ) ) {
2041 if ( !isEqual( ma0[ 0 ].getValue( 3, 1 ), 5 ) ) {
2044 if ( !isEqual( ma0[ 1 ].getValue( 0, 0 ), 0 ) ) {
2047 if ( !isEqual( ma0[ 1 ].getValue( 1, 0 ), 11 ) ) {
2050 if ( !isEqual( ma0[ 1 ].getValue( 2, 0 ), 12 ) ) {
2053 if ( !isEqual( ma0[ 1 ].getValue( 3, 0 ), 13 ) ) {
2056 if ( !isEqual( ma0[ 1 ].getValue( 0, 1 ), 11 ) ) {
2059 if ( !isEqual( ma0[ 1 ].getValue( 1, 1 ), 0 ) ) {
2062 if ( !isEqual( ma0[ 1 ].getValue( 2, 1 ), 14 ) ) {
2065 if ( !isEqual( ma0[ 1 ].getValue( 3, 1 ), 15 ) ) {
2068 if ( !isEqual( ma0[ 2 ].getValue( 0, 0 ), 0 ) ) {
2071 if ( !isEqual( ma0[ 2 ].getValue( 1, 0 ), 21 ) ) {
2074 if ( !isEqual( ma0[ 2 ].getValue( 2, 0 ), 22 ) ) {
2077 if ( !isEqual( ma0[ 2 ].getValue( 3, 0 ), 23 ) ) {
2080 if ( !isEqual( ma0[ 2 ].getValue( 0, 1 ), 21 ) ) {
2083 if ( !isEqual( ma0[ 2 ].getValue( 1, 1 ), 0 ) ) {
2086 if ( !isEqual( ma0[ 2 ].getValue( 2, 1 ), 24 ) ) {
2089 if ( !isEqual( ma0[ 2 ].getValue( 3, 1 ), 25 ) ) {
2092 source = new StringBuffer();
2093 source.append( "A 0 0 0 0" + l );
2094 source.append( "B 1 0 0 0" + l );
2095 source.append( "C 2 4 0 0" + l );
2096 source.append( "D 3 5 6 0" + l );
2097 source.append( " " + l );
2098 source.append( "A 0 11 12 13" + l );
2099 source.append( "B 11 0 14 15" + l );
2100 source.append( "C 12 14 0 16" + l );
2101 source.append( "D 13 15 16 0" + l );
2103 source.append( " A 0 " + l );
2104 source.append( " B 21 0" + l );
2105 source.append( " C 22 24 0 " + l );
2106 source.append( " # 2 222 2 2 " + l );
2107 source.append( " D 23 25 26 0" + l );
2108 final DistanceMatrix[] ma1 = p0.parse( source.toString() );
2109 if ( ma1.length != 3 ) {
2112 if ( !isEqual( ma1[ 0 ].getValue( 0, 0 ), 0 ) ) {
2115 if ( !isEqual( ma1[ 0 ].getValue( 1, 0 ), 1 ) ) {
2118 if ( !isEqual( ma1[ 0 ].getValue( 2, 0 ), 2 ) ) {
2121 if ( !isEqual( ma1[ 0 ].getValue( 3, 0 ), 3 ) ) {
2124 if ( !isEqual( ma1[ 0 ].getValue( 0, 1 ), 1 ) ) {
2127 if ( !isEqual( ma1[ 0 ].getValue( 1, 1 ), 0 ) ) {
2130 if ( !isEqual( ma1[ 0 ].getValue( 2, 1 ), 4 ) ) {
2133 if ( !isEqual( ma1[ 0 ].getValue( 3, 1 ), 5 ) ) {
2136 if ( !isEqual( ma1[ 1 ].getValue( 0, 0 ), 0 ) ) {
2139 if ( !isEqual( ma1[ 1 ].getValue( 1, 0 ), 11 ) ) {
2142 if ( !isEqual( ma1[ 1 ].getValue( 2, 0 ), 12 ) ) {
2145 if ( !isEqual( ma1[ 1 ].getValue( 3, 0 ), 13 ) ) {
2148 if ( !isEqual( ma1[ 1 ].getValue( 0, 1 ), 11 ) ) {
2151 if ( !isEqual( ma1[ 1 ].getValue( 1, 1 ), 0 ) ) {
2154 if ( !isEqual( ma1[ 1 ].getValue( 2, 1 ), 14 ) ) {
2157 if ( !isEqual( ma1[ 1 ].getValue( 3, 1 ), 15 ) ) {
2160 if ( !isEqual( ma1[ 2 ].getValue( 0, 0 ), 0 ) ) {
2163 if ( !isEqual( ma1[ 2 ].getValue( 1, 0 ), 21 ) ) {
2166 if ( !isEqual( ma1[ 2 ].getValue( 2, 0 ), 22 ) ) {
2169 if ( !isEqual( ma1[ 2 ].getValue( 3, 0 ), 23 ) ) {
2172 if ( !isEqual( ma1[ 2 ].getValue( 0, 1 ), 21 ) ) {
2175 if ( !isEqual( ma1[ 2 ].getValue( 1, 1 ), 0 ) ) {
2178 if ( !isEqual( ma1[ 2 ].getValue( 2, 1 ), 24 ) ) {
2181 if ( !isEqual( ma1[ 2 ].getValue( 3, 1 ), 25 ) ) {
2184 source = new StringBuffer();
2185 source.append( "A 0" + l );
2186 source.append( "B 10 0" + l );
2187 final DistanceMatrix[] ma2 = p0.parse( source.toString() );
2188 if ( ma2.length != 1 ) {
2191 if ( !isEqual( ma2[ 0 ].getValue( 0, 1 ), 10 ) ) {
2194 source = new StringBuffer();
2195 source.append( " " + l );
2196 source.append( "#" + l );
2197 final DistanceMatrix[] ma3 = p0.parse( source.toString() );
2198 if ( ma3.length != 0 ) {
2201 source = new StringBuffer();
2202 source.append( " " + l );
2203 source.append( "A 0 11 12 13" + l );
2204 source.append( "B 0 14 15" + l );
2205 source.append( "C 0 16" + l );
2206 source.append( "D 0" + l );
2208 source.append( "A 0 21 22 23" + l );
2209 source.append( "B 0 24 25" + l );
2210 source.append( "C 0 26" + l );
2211 source.append( "D 0" + l );
2212 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2213 final DistanceMatrix[] ma4 = p0.parse( source );
2214 if ( ma4.length != 2 ) {
2217 if ( !isEqual( ma4[ 0 ].getValue( 0, 0 ), 0 ) ) {
2220 if ( !isEqual( ma4[ 0 ].getValue( 1, 0 ), 11 ) ) {
2223 if ( !isEqual( ma4[ 0 ].getValue( 2, 0 ), 12 ) ) {
2226 if ( !isEqual( ma4[ 0 ].getValue( 3, 0 ), 13 ) ) {
2229 if ( !isEqual( ma4[ 0 ].getValue( 0, 1 ), 11 ) ) {
2232 if ( !isEqual( ma4[ 0 ].getValue( 1, 1 ), 0 ) ) {
2235 if ( !isEqual( ma4[ 0 ].getValue( 2, 1 ), 14 ) ) {
2238 if ( !isEqual( ma4[ 0 ].getValue( 3, 1 ), 15 ) ) {
2241 if ( !isEqual( ma4[ 0 ].getValue( 0, 2 ), 12 ) ) {
2244 if ( !isEqual( ma4[ 0 ].getValue( 1, 2 ), 14 ) ) {
2247 if ( !isEqual( ma4[ 0 ].getValue( 2, 2 ), 0 ) ) {
2250 if ( !isEqual( ma4[ 0 ].getValue( 3, 2 ), 16 ) ) {
2253 if ( !isEqual( ma4[ 0 ].getValue( 0, 3 ), 13 ) ) {
2256 if ( !isEqual( ma4[ 0 ].getValue( 1, 3 ), 15 ) ) {
2259 if ( !isEqual( ma4[ 0 ].getValue( 2, 3 ), 16 ) ) {
2262 if ( !isEqual( ma4[ 0 ].getValue( 3, 3 ), 0 ) ) {
2265 source = new StringBuffer();
2266 source.append( " 4 " + l );
2267 source.append( "A 0 11 12 13" + l );
2268 source.append( "B 0 14 15" + l );
2269 source.append( "C 0 16" + l );
2270 source.append( "D 0" + l );
2271 source.append( " 4" + l );
2272 source.append( "A 0 21 22 23" + l );
2273 source.append( "B 0 24 25" + l );
2274 source.append( "C 0 26" + l );
2275 source.append( "D 0" + l );
2276 source.append( " " + l );
2277 source.append( " 4" + l );
2278 source.append( "A 0 21 22 23" + l );
2279 source.append( "B 0 24 25" + l );
2280 source.append( "C 0 26" + l );
2281 source.append( "D 0" + l );
2283 source.append( "A 0 21 22 23" + l );
2284 source.append( "B 0 24 25" + l );
2285 source.append( "C 0 26" + l );
2286 source.append( "D 0" + l );
2287 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2288 final DistanceMatrix[] ma5 = p0.parse( source );
2289 if ( ma5.length != 4 ) {
2292 if ( !isEqual( ma5[ 0 ].getValue( 0, 0 ), 0 ) ) {
2295 if ( !isEqual( ma5[ 0 ].getValue( 1, 0 ), 11 ) ) {
2298 if ( !isEqual( ma5[ 0 ].getValue( 2, 0 ), 12 ) ) {
2301 if ( !isEqual( ma5[ 0 ].getValue( 3, 0 ), 13 ) ) {
2304 if ( !isEqual( ma5[ 0 ].getValue( 0, 1 ), 11 ) ) {
2307 if ( !isEqual( ma5[ 0 ].getValue( 1, 1 ), 0 ) ) {
2310 if ( !isEqual( ma5[ 0 ].getValue( 2, 1 ), 14 ) ) {
2313 if ( !isEqual( ma5[ 0 ].getValue( 3, 1 ), 15 ) ) {
2316 if ( !isEqual( ma5[ 0 ].getValue( 0, 2 ), 12 ) ) {
2319 if ( !isEqual( ma5[ 0 ].getValue( 1, 2 ), 14 ) ) {
2322 if ( !isEqual( ma5[ 0 ].getValue( 2, 2 ), 0 ) ) {
2325 if ( !isEqual( ma5[ 0 ].getValue( 3, 2 ), 16 ) ) {
2328 if ( !isEqual( ma5[ 0 ].getValue( 0, 3 ), 13 ) ) {
2331 if ( !isEqual( ma5[ 0 ].getValue( 1, 3 ), 15 ) ) {
2334 if ( !isEqual( ma5[ 0 ].getValue( 2, 3 ), 16 ) ) {
2337 if ( !isEqual( ma5[ 0 ].getValue( 3, 3 ), 0 ) ) {
2341 catch ( final Exception e ) {
2342 e.printStackTrace( System.out );
2348 private static void timeNeighborJoining() {
2349 final NeighborJoining nj = NeighborJoining.createInstance();
2350 for( int n = 3; n <= 12; ++n ) {
2351 final int x = ( int ) Math.pow( 2, n );
2352 final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
2353 mt.randomize( new Date().getTime() );
2354 final long start_time = new Date().getTime();
2356 System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms." );