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: https://sites.google.com/site/cmzmasek/home/software/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;
59 public static boolean isEqual( final double a, final double b ) {
60 return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
63 public static boolean isUnequal( final double a, final double b ) {
64 return !isEqual( a, b );
67 public static void main( final String[] args ) {
68 if ( testNeighborJoining() ) {
69 System.out.println( "OK." );
72 System.out.println( "failed." );
74 //timeNeighborJoining();
77 public static boolean test( final File test_dir ) {
78 System.out.print( " Basic symmetrical distance matrix: " );
79 if ( !testBasicSymmetricalDistanceMatrix() ) {
80 System.out.println( "failed." );
83 System.out.println( "OK." );
84 System.out.print( " Basic character state matrix: " );
85 if ( !testBasicCharacterStateMatrix() ) {
86 System.out.println( "failed." );
89 System.out.println( "OK." );
90 System.out.print( " Symmetrical distance matrix parser: " );
91 if ( !testSymmetricalDistanceMatrixParser() ) {
92 System.out.println( "failed." );
95 System.out.println( "OK." );
96 System.out.print( " Distance Calculation: " );
97 if ( !testDistanceCalculationMethods( test_dir ) ) {
98 System.out.println( "failed." );
101 System.out.println( "OK." );
102 System.out.print( " Neighbor Joining: " );
103 if ( !testNeighborJoining() ) {
104 System.out.println( "failed." );
107 System.out.println( "OK." );
108 System.out.print( " Dollo Parsimony: " );
109 if ( !testDolloParsimony() ) {
110 System.out.println( "failed." );
113 System.out.println( "OK." );
114 System.out.print( " Dollo Parsimony on non binary trees: " );
115 if ( !testDolloParsimonyOnNonBinaryTree() ) {
116 System.out.println( "failed." );
119 System.out.println( "OK." );
120 System.out.print( " Fitch Parsimony: " );
121 if ( !testFitchParsimony() ) {
122 System.out.println( "failed." );
125 System.out.println( "OK." );
129 private static boolean testDistanceCalculationMethods( final File test_dir ) {
131 final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
133 final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
134 if ( pwd0.getSize() != 120 ) {
137 for( int i = 0; i < pwd0.getSize(); ++i ) {
138 if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) {
143 catch ( final Exception e ) {
144 e.printStackTrace( System.out );
150 private static boolean testBasicCharacterStateMatrix() {
152 final CharacterStateMatrix<String> matrix_0 = new BasicCharacterStateMatrix<String>( 4, 8 );
153 final CharacterStateMatrix<String> matrix_00 = new BasicCharacterStateMatrix<String>( 4, 8 );
154 matrix_0.setIdentifier( 0, "A" );
155 matrix_0.setIdentifier( 1, "B" );
156 matrix_0.setIdentifier( 2, "C" );
157 matrix_0.setIdentifier( 3, "D" );
158 matrix_0.setCharacter( 0, "0" );
159 matrix_0.setCharacter( 1, "1" );
160 matrix_0.setCharacter( 2, "2" );
161 matrix_0.setCharacter( 3, "3" );
162 matrix_0.setCharacter( 4, "4" );
163 matrix_0.setCharacter( 5, "5" );
164 matrix_0.setCharacter( 6, "6" );
165 matrix_0.setCharacter( 7, "7" );
166 matrix_00.setIdentifier( 0, "A" );
167 matrix_00.setIdentifier( 1, "B" );
168 matrix_00.setIdentifier( 2, "C" );
169 matrix_00.setIdentifier( 3, "D" );
170 matrix_00.setCharacter( 3, "3" );
171 matrix_00.setCharacter( 4, "4" );
172 if ( !matrix_0.getCharacter( 1 ).equals( "1" ) ) {
175 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
178 matrix_0.setState( 0, 0, "00" );
179 matrix_00.setState( 0, 0, "00" );
180 if ( !matrix_0.getState( 0, 0 ).equals( "00" ) ) {
183 matrix_0.setState( 0, 1, "01" );
184 matrix_00.setState( 0, 1, "01" );
185 if ( !matrix_0.getState( 0, 1 ).equals( "01" ) ) {
188 matrix_0.setState( 1, 1, "11" );
189 matrix_00.setState( 1, 1, "11" );
190 if ( !matrix_0.getState( 1, 1 ).equals( "11" ) ) {
193 matrix_0.setState( 1, 0, "10" );
194 matrix_00.setState( 1, 0, "10" );
195 if ( !matrix_0.getState( 1, 0 ).equals( "10" ) ) {
198 matrix_0.setState( 1, 2, "12" );
199 matrix_00.setState( 1, 2, "12" );
200 if ( !matrix_0.getState( 1, 2 ).equals( "12" ) ) {
203 matrix_0.setState( 3, 7, "37" );
204 matrix_00.setState( 3, 7, "37" );
205 if ( !matrix_0.getState( 3, 7 ).equals( "37" ) ) {
208 matrix_0.setState( 2, 6, "26" );
209 matrix_00.setState( 2, 6, "26" );
210 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
213 matrix_0.setState( "D", "3", "33" );
214 matrix_00.setState( "D", "3", "33" );
215 if ( !matrix_0.getState( 3, 3 ).equals( "33" ) ) {
218 if ( !matrix_0.getState( "D", "3" ).equals( "33" ) ) {
221 matrix_0.setState( "C", "4", "24" );
222 matrix_00.setState( "C", "4", "24" );
223 if ( !matrix_0.getState( 2, 4 ).equals( "24" ) ) {
226 if ( !matrix_0.getState( "C", "4" ).equals( "24" ) ) {
229 if ( matrix_0.isEmpty() ) {
232 if ( matrix_0.getNumberOfIdentifiers() != 4 ) {
235 if ( matrix_0.getNumberOfCharacters() != 8 ) {
238 if ( !matrix_0.equals( matrix_0 ) ) {
241 if ( !matrix_0.equals( matrix_00 ) ) {
244 matrix_00.setState( "C", "4", "123" );
245 if ( matrix_0.equals( matrix_00 ) ) {
248 final Integer[][] ints = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
249 final CharacterStateMatrix<Integer> matrix_000 = new BasicCharacterStateMatrix<Integer>( ints );
250 matrix_000.toString();
251 if ( matrix_000.getNumberOfCharacters() != 4 ) {
254 if ( matrix_000.getNumberOfIdentifiers() != 3 ) {
257 if ( matrix_000.getState( 0, 1 ) != 2 ) {
260 if ( matrix_000.getState( 2, 3 ) != 12 ) {
263 final Integer[][] ints0 = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
264 final CharacterStateMatrix<Integer> matrix_0000 = new BasicCharacterStateMatrix<Integer>( ints0 );
265 if ( !matrix_000.equals( matrix_0000 ) ) {
268 final Integer[][] ints00 = { { 1, 2, 3, -4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
269 final CharacterStateMatrix<Integer> matrix_00000 = new BasicCharacterStateMatrix<Integer>( ints00 );
270 if ( matrix_000.equals( matrix_00000 ) ) {
273 final CharacterStateMatrix<String> clone0 = matrix_0.copy();
274 final CharacterStateMatrix<String> clone00 = matrix_00.copy();
275 if ( !clone0.equals( matrix_0 ) ) {
278 if ( !clone00.equals( matrix_00 ) ) {
281 if ( clone00.equals( clone0 ) ) {
284 final CharacterStateMatrix<String> pivot0 = matrix_0.pivot();
285 final CharacterStateMatrix<String> pivot00 = matrix_00.pivot();
286 if ( !pivot0.getState( 1, 0 ).equals( "01" ) ) {
289 if ( !pivot0.getState( 6, 2 ).equals( "26" ) ) {
292 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
295 final CharacterStateMatrix<String> pivotpivot00 = pivot00.pivot();
296 if ( !pivotpivot00.equals( matrix_00 ) ) {
299 final CharacterStateMatrix<BinaryStates> nex = new BasicCharacterStateMatrix<BinaryStates>( 4, 3 );
300 nex.setIdentifier( 0, "amphioxus" );
301 nex.setIdentifier( 1, "sponge" );
302 nex.setIdentifier( 2, "sea_anemone" );
303 nex.setIdentifier( 3, "cobra" );
304 nex.setCharacter( 0, "notch" );
305 nex.setCharacter( 1, "homeobox" );
306 nex.setCharacter( 2, "wnt" );
307 nex.setState( 0, 0, BinaryStates.ABSENT );
308 nex.setState( 0, 1, BinaryStates.ABSENT );
309 nex.setState( 0, 2, BinaryStates.ABSENT );
310 nex.setState( 1, 0, BinaryStates.PRESENT );
311 nex.setState( 1, 1, BinaryStates.PRESENT );
312 nex.setState( 1, 2, BinaryStates.ABSENT );
313 nex.setState( 2, 0, BinaryStates.PRESENT );
314 nex.setState( 2, 1, BinaryStates.PRESENT );
315 nex.setState( 2, 2, BinaryStates.PRESENT );
316 nex.setState( 3, 0, BinaryStates.PRESENT );
317 nex.setState( 3, 1, BinaryStates.ABSENT );
318 nex.setState( 3, 2, BinaryStates.ABSENT );
319 StringWriter w = new StringWriter();
320 nex.toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
321 //System.out.println( w.getBuffer().toString() );
322 w = new StringWriter();
323 nex.pivot().toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
324 //System.out.println( w.getBuffer().toString() );
326 catch ( final Exception e ) {
327 e.printStackTrace( System.out );
333 private static boolean testBasicSymmetricalDistanceMatrix() {
335 final DistanceMatrix matrix_0 = new BasicSymmetricalDistanceMatrix( 4 );
336 matrix_0.setIdentifier( 0, "A" );
337 matrix_0.setIdentifier( 1, "B" );
338 matrix_0.setIdentifier( 2, "C" );
339 matrix_0.setIdentifier( 3, "0123456789012" );
340 matrix_0.setValue( 1, 0, 0.00001 );
341 matrix_0.setValue( 0, 2, 0.0000009 );
342 matrix_0.setValue( 3, 0, 3.0 );
343 matrix_0.setValue( 1, 2, 4.0 );
344 matrix_0.setValue( 3, 1, 5.0 );
345 matrix_0.setValue( 2, 3, 6.0 );
346 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
349 if ( !matrix_0.getIdentifier( 1 ).equals( "B" ) ) {
352 if ( !matrix_0.getIdentifier( 2 ).equals( "C" ) ) {
355 if ( !matrix_0.getIdentifier( 3 ).equals( "0123456789012" ) ) {
358 if ( matrix_0.getSize() != 4 ) {
361 if ( !isEqual( matrix_0.getValue( 0, 0 ), 0.0 ) ) {
364 if ( !isEqual( matrix_0.getValue( 3, 3 ), 0.0 ) ) {
367 if ( !isEqual( matrix_0.getValue( 0, 1 ), 0.00001 ) ) {
370 if ( !isEqual( matrix_0.getValue( 0, 2 ), 0.0000009 ) ) {
373 if ( !isEqual( matrix_0.getValue( 0, 3 ), 3 ) ) {
376 if ( !isEqual( matrix_0.getValue( 1, 0 ), 0.00001 ) ) {
379 if ( !isEqual( matrix_0.getValue( 1, 2 ), 4 ) ) {
382 if ( !isEqual( matrix_0.getValue( 1, 3 ), 5 ) ) {
385 if ( !isEqual( matrix_0.getValue( 2, 0 ), 0.0000009 ) ) {
388 if ( !isEqual( matrix_0.getValue( 2, 1 ), 4 ) ) {
391 if ( !isEqual( matrix_0.getValue( 2, 3 ), 6 ) ) {
394 if ( !isEqual( matrix_0.getValue( 3, 0 ), 3 ) ) {
397 if ( !isEqual( matrix_0.getValue( 3, 1 ), 5 ) ) {
400 if ( !isEqual( matrix_0.getValue( 3, 2 ), 6 ) ) {
403 final StringBuffer matrix_0_phylip = new StringBuffer();
404 matrix_0_phylip.append( " 4" );
405 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
406 matrix_0_phylip.append( "A 0.000000 0.000010 0.000001 3.000000" );
407 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
408 matrix_0_phylip.append( "B 0.000010 0.000000 4.000000 5.000000" );
409 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
410 matrix_0_phylip.append( "C 0.000001 4.000000 0.000000 6.000000" );
411 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
412 matrix_0_phylip.append( "0123456789 3.000000 5.000000 6.000000 0.000000" );
413 if ( !matrix_0_phylip.toString()
414 .equals( matrix_0.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() ) ) {
418 catch ( final Exception e ) {
419 e.printStackTrace( System.out );
425 private static boolean testDolloParsimony() {
427 final BinaryStates PRESENT = BinaryStates.PRESENT;
428 final BinaryStates ABSENT = BinaryStates.ABSENT;
429 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
430 final DolloParsimony dollo1 = DolloParsimony.createInstance();
431 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
432 final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
433 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
434 CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
436 m1.setIdentifier( 0, "a" );
437 m1.setIdentifier( 1, "b" );
438 m1.setIdentifier( 2, "c" );
439 m1.setIdentifier( 3, "d" );
440 m1.setIdentifier( 4, "e" );
441 m1.setIdentifier( 5, "f" );
442 m1.setIdentifier( 6, "g" );
443 m1.setIdentifier( 7, "h" );
444 m1.setIdentifier( 8, "i" );
445 m1.setCharacter( 0, "0" );
446 m1.setState( "a", "0", PRESENT );
447 m1.setState( "b", "0", ABSENT );
448 m1.setState( "c", "0", PRESENT );
449 m1.setState( "d", "0", ABSENT );
450 m1.setState( "e", "0", ABSENT );
451 m1.setState( "f", "0", ABSENT );
452 m1.setState( "g", "0", ABSENT );
453 m1.setState( "h", "0", ABSENT );
454 m1.setState( "i", "0", ABSENT );
455 dollo1.execute( p1, m1 );
456 if ( dollo1.getTotalGains() != 1 ) {
459 if ( dollo1.getTotalLosses() != 1 ) {
462 if ( dollo1.getTotalUnchanged() != 15 ) {
465 m1.setState( "b", "0", PRESENT );
466 dollo1.execute( p1, m1 );
467 if ( dollo1.getTotalGains() != 1 ) {
470 if ( dollo1.getTotalLosses() != 0 ) {
473 if ( dollo1.getTotalUnchanged() != 16 ) {
476 m1.setState( "b", "0", ABSENT );
477 m1.setState( "e", "0", PRESENT );
478 dollo1.execute( p1, m1 );
479 if ( dollo1.getTotalGains() != 1 ) {
482 if ( dollo1.getTotalLosses() != 3 ) {
485 if ( dollo1.getTotalUnchanged() != 13 ) {
488 m1.setState( "a", "0", ABSENT );
489 m1.setState( "c", "0", ABSENT );
490 m1.setState( "g", "0", PRESENT );
491 dollo1.setReturnInternalStates( true );
492 dollo1.setReturnGainLossMatrix( true );
493 dollo1.execute( p1, m1 );
494 if ( dollo1.getTotalGains() != 1 ) {
497 if ( dollo1.getTotalLosses() != 3 ) {
500 if ( dollo1.getTotalUnchanged() != 13 ) {
503 final DolloParsimony dollo2 = DolloParsimony.createInstance();
504 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
505 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";
506 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
507 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 18,
509 m2.setIdentifier( 0, "a" );
510 m2.setIdentifier( 1, "b" );
511 m2.setIdentifier( 2, "c" );
512 m2.setIdentifier( 3, "d" );
513 m2.setIdentifier( 4, "e" );
514 m2.setIdentifier( 5, "f" );
515 m2.setIdentifier( 6, "g" );
516 m2.setIdentifier( 7, "h" );
517 m2.setIdentifier( 8, "i" );
518 m2.setIdentifier( 9, "j" );
519 m2.setIdentifier( 10, "k" );
520 m2.setIdentifier( 11, "l" );
521 m2.setIdentifier( 12, "m" );
522 m2.setIdentifier( 13, "n" );
523 m2.setIdentifier( 14, "o" );
524 m2.setIdentifier( 15, "p" );
525 m2.setIdentifier( 16, "q" );
526 m2.setIdentifier( 17, "r" );
527 m2.setCharacter( 0, "0" );
528 m2.setCharacter( 1, "1" );
529 m2.setCharacter( 2, "2" );
530 m2.setCharacter( 3, "3" );
531 m2.setState( "a", "0", PRESENT );
532 m2.setState( "b", "0", ABSENT );
533 m2.setState( "c", "0", PRESENT );
534 m2.setState( "d", "0", ABSENT );
535 m2.setState( "e", "0", ABSENT );
536 m2.setState( "f", "0", ABSENT );
537 m2.setState( "g", "0", ABSENT );
538 m2.setState( "h", "0", ABSENT );
539 m2.setState( "i", "0", ABSENT );
540 m2.setState( "j", "0", ABSENT );
541 m2.setState( "k", "0", ABSENT );
542 m2.setState( "l", "0", ABSENT );
543 m2.setState( "m", "0", ABSENT );
544 m2.setState( "n", "0", ABSENT );
545 m2.setState( "o", "0", ABSENT );
546 m2.setState( "p", "0", ABSENT );
547 m2.setState( "q", "0", ABSENT );
548 m2.setState( "r", "0", ABSENT );
549 m2.setState( "a", "1", PRESENT );
550 m2.setState( "b", "1", ABSENT );
551 m2.setState( "c", "1", PRESENT );
552 m2.setState( "d", "1", ABSENT );
553 m2.setState( "e", "1", ABSENT );
554 m2.setState( "f", "1", ABSENT );
555 m2.setState( "g", "1", PRESENT );
556 m2.setState( "h", "1", ABSENT );
557 m2.setState( "i", "1", ABSENT );
558 m2.setState( "j", "1", PRESENT );
559 m2.setState( "k", "1", ABSENT );
560 m2.setState( "l", "1", ABSENT );
561 m2.setState( "m", "1", PRESENT );
562 m2.setState( "n", "1", ABSENT );
563 m2.setState( "o", "1", ABSENT );
564 m2.setState( "p", "1", ABSENT );
565 m2.setState( "q", "1", ABSENT );
566 m2.setState( "r", "1", ABSENT );
567 m2.setState( "a", "2", ABSENT );
568 m2.setState( "b", "2", ABSENT );
569 m2.setState( "c", "2", ABSENT );
570 m2.setState( "d", "2", ABSENT );
571 m2.setState( "e", "2", ABSENT );
572 m2.setState( "f", "2", ABSENT );
573 m2.setState( "g", "2", ABSENT );
574 m2.setState( "h", "2", ABSENT );
575 m2.setState( "i", "2", ABSENT );
576 m2.setState( "j", "2", PRESENT );
577 m2.setState( "k", "2", ABSENT );
578 m2.setState( "l", "2", ABSENT );
579 m2.setState( "m", "2", PRESENT );
580 m2.setState( "n", "2", ABSENT );
581 m2.setState( "o", "2", ABSENT );
582 m2.setState( "p", "2", PRESENT );
583 m2.setState( "q", "2", ABSENT );
584 m2.setState( "r", "2", ABSENT );
585 m2.setState( "a", "3", ABSENT );
586 m2.setState( "b", "3", ABSENT );
587 m2.setState( "c", "3", PRESENT );
588 m2.setState( "d", "3", ABSENT );
589 m2.setState( "e", "3", ABSENT );
590 m2.setState( "f", "3", ABSENT );
591 m2.setState( "g", "3", PRESENT );
592 m2.setState( "h", "3", ABSENT );
593 m2.setState( "i", "3", ABSENT );
594 m2.setState( "j", "3", ABSENT );
595 m2.setState( "k", "3", ABSENT );
596 m2.setState( "l", "3", ABSENT );
597 m2.setState( "m", "3", ABSENT );
598 m2.setState( "n", "3", ABSENT );
599 m2.setState( "o", "3", ABSENT );
600 m2.setState( "p", "3", ABSENT );
601 m2.setState( "q", "3", ABSENT );
602 m2.setState( "r", "3", ABSENT );
603 dollo2.setReturnInternalStates( true );
604 dollo2.setReturnGainLossMatrix( true );
605 dollo2.execute( p2, m2 );
606 final CharacterStateMatrix<BinaryStates> i_m = dollo2.getInternalStatesMatrix();
607 final CharacterStateMatrix<GainLossStates> gl_m = dollo2.getGainLossMatrix();
608 if ( dollo2.getTotalGains() != 3 ) {
611 if ( dollo2.getTotalLosses() != 22 ) {
614 if ( dollo2.getTotalUnchanged() != 95 ) {
617 if ( i_m.getState( "ab", "0" ) != PRESENT ) {
620 if ( i_m.getState( "ac", "0" ) != PRESENT ) {
623 if ( i_m.getState( "ad", "0" ) != ABSENT ) {
626 if ( i_m.getState( "af", "0" ) != ABSENT ) {
629 if ( i_m.getState( "ef", "0" ) != ABSENT ) {
632 if ( i_m.getState( "ai", "0" ) != ABSENT ) {
635 if ( i_m.getState( "gi", "0" ) != ABSENT ) {
638 if ( i_m.getState( "jl", "0" ) != ABSENT ) {
641 if ( i_m.getState( "mo", "0" ) != ABSENT ) {
644 if ( i_m.getState( "pr", "0" ) != ABSENT ) {
647 if ( i_m.getState( "jr", "0" ) != ABSENT ) {
650 if ( i_m.getState( "root", "0" ) != ABSENT ) {
653 if ( i_m.getState( "ab", "1" ) != PRESENT ) {
656 if ( i_m.getState( "ac", "1" ) != PRESENT ) {
659 if ( i_m.getState( "ad", "1" ) != PRESENT ) {
662 if ( i_m.getState( "af", "1" ) != PRESENT ) {
665 if ( i_m.getState( "ef", "1" ) != ABSENT ) {
668 if ( i_m.getState( "ai", "1" ) != PRESENT ) {
671 if ( i_m.getState( "gi", "1" ) != PRESENT ) {
674 if ( i_m.getState( "jl", "1" ) != PRESENT ) {
677 if ( i_m.getState( "mo", "1" ) != PRESENT ) {
680 if ( i_m.getState( "pr", "1" ) != ABSENT ) {
683 if ( i_m.getState( "jr", "1" ) != PRESENT ) {
686 if ( i_m.getState( "root", "1" ) != PRESENT ) {
689 if ( i_m.getState( "ab", "2" ) != ABSENT ) {
692 if ( i_m.getState( "ac", "2" ) != ABSENT ) {
695 if ( i_m.getState( "ad", "2" ) != ABSENT ) {
698 if ( i_m.getState( "af", "2" ) != ABSENT ) {
701 if ( i_m.getState( "ef", "2" ) != ABSENT ) {
704 if ( i_m.getState( "ai", "2" ) != ABSENT ) {
707 if ( i_m.getState( "gi", "2" ) != ABSENT ) {
710 if ( i_m.getState( "jl", "2" ) != PRESENT ) {
713 if ( i_m.getState( "mo", "2" ) != PRESENT ) {
716 if ( i_m.getState( "pr", "2" ) != PRESENT ) {
719 if ( i_m.getState( "jr", "2" ) != PRESENT ) {
722 if ( i_m.getState( "root", "2" ) != ABSENT ) {
725 if ( i_m.getState( "ab", "3" ) != ABSENT ) {
728 if ( i_m.getState( "ac", "3" ) != PRESENT ) {
731 if ( i_m.getState( "ad", "3" ) != PRESENT ) {
734 if ( i_m.getState( "af", "3" ) != PRESENT ) {
737 if ( i_m.getState( "ef", "3" ) != ABSENT ) {
740 if ( i_m.getState( "ai", "3" ) != PRESENT ) {
743 if ( i_m.getState( "gi", "3" ) != PRESENT ) {
746 if ( i_m.getState( "jl", "3" ) != ABSENT ) {
749 if ( i_m.getState( "mo", "3" ) != ABSENT ) {
752 if ( i_m.getState( "pr", "3" ) != ABSENT ) {
755 if ( i_m.getState( "jr", "3" ) != ABSENT ) {
758 if ( i_m.getState( "root", "3" ) != ABSENT ) {
761 if ( gl_m.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
764 final DolloParsimony dollo9 = DolloParsimony.createInstance();
765 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
766 final String p9_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
767 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
768 m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9, 3 );
769 m1.setIdentifier( 0, "a" );
770 m1.setIdentifier( 1, "b" );
771 m1.setIdentifier( 2, "c" );
772 m1.setIdentifier( 3, "d" );
773 m1.setIdentifier( 4, "e" );
774 m1.setIdentifier( 5, "f" );
775 m1.setIdentifier( 6, "g" );
776 m1.setIdentifier( 7, "h" );
777 m1.setIdentifier( 8, "i" );
778 m1.setState( 0, 0, PRESENT );
779 m1.setState( 1, 0, ABSENT );
780 m1.setState( 2, 0, PRESENT );
781 m1.setState( 3, 0, ABSENT );
782 m1.setState( 4, 0, ABSENT );
783 m1.setState( 5, 0, ABSENT );
784 m1.setState( 6, 0, ABSENT );
785 m1.setState( 7, 0, ABSENT );
786 m1.setState( 8, 0, ABSENT );
787 m1.setState( 0, 1, PRESENT );
788 m1.setState( 1, 1, PRESENT );
789 m1.setState( 2, 1, PRESENT );
790 m1.setState( 3, 1, PRESENT );
791 m1.setState( 4, 1, ABSENT );
792 m1.setState( 5, 1, ABSENT );
793 m1.setState( 6, 1, ABSENT );
794 m1.setState( 7, 1, ABSENT );
795 m1.setState( 8, 1, ABSENT );
796 m1.setState( 0, 2, PRESENT );
797 m1.setState( 1, 2, ABSENT );
798 m1.setState( 2, 2, ABSENT );
799 m1.setState( 3, 2, ABSENT );
800 m1.setState( 4, 2, ABSENT );
801 m1.setState( 5, 2, ABSENT );
802 m1.setState( 6, 2, ABSENT );
803 m1.setState( 7, 2, PRESENT );
804 m1.setState( 8, 2, ABSENT );
805 dollo9.execute( p9, m1 );
806 if ( dollo9.getTotalGains() != 3 ) {
809 if ( dollo9.getTotalLosses() != 6 ) {
812 final DolloParsimony dollo10 = DolloParsimony.createInstance();
813 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
814 final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
815 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
816 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m10 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
818 m10.setIdentifier( 0, "a" );
819 m10.setIdentifier( 1, "b" );
820 m10.setIdentifier( 2, "c" );
821 m10.setIdentifier( 3, "d" );
822 m10.setIdentifier( 4, "e" );
823 m10.setIdentifier( 5, "f" );
824 m10.setIdentifier( 6, "g" );
825 m10.setIdentifier( 7, "h" );
826 m10.setIdentifier( 8, "i" );
827 m10.setState( 0, 0, PRESENT );
828 m10.setState( 1, 0, ABSENT );
829 m10.setState( 2, 0, PRESENT );
830 m10.setState( 3, 0, ABSENT );
831 m10.setState( 4, 0, ABSENT );
832 m10.setState( 5, 0, ABSENT );
833 m10.setState( 6, 0, ABSENT );
834 m10.setState( 7, 0, ABSENT );
835 m10.setState( 8, 0, ABSENT );
836 dollo10.execute( p10, m10 );
837 if ( dollo10.getTotalGains() != 1 ) {
840 if ( dollo10.getTotalLosses() != 1 ) {
844 catch ( final Exception e ) {
845 e.printStackTrace( System.out );
851 private static boolean testDolloParsimonyOnNonBinaryTree() {
853 final BinaryStates PRESENT = BinaryStates.PRESENT;
854 final BinaryStates ABSENT = BinaryStates.ABSENT;
855 final DolloParsimony dollo1 = DolloParsimony.createInstance();
856 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
857 final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
858 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
859 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
861 m1.setIdentifier( 0, "a" );
862 m1.setIdentifier( 1, "b" );
863 m1.setIdentifier( 2, "y" );
864 m1.setIdentifier( 3, "c" );
865 m1.setIdentifier( 4, "d" );
866 m1.setIdentifier( 5, "e" );
867 m1.setIdentifier( 6, "f" );
868 m1.setIdentifier( 7, "g" );
869 m1.setIdentifier( 8, "h" );
870 m1.setIdentifier( 9, "i" );
871 m1.setCharacter( 0, "0" );
872 m1.setState( "a", "0", PRESENT );
873 m1.setState( "b", "0", ABSENT );
874 m1.setState( "y", "0", PRESENT );
875 m1.setState( "c", "0", PRESENT );
876 m1.setState( "d", "0", ABSENT );
877 m1.setState( "e", "0", ABSENT );
878 m1.setState( "f", "0", ABSENT );
879 m1.setState( "g", "0", ABSENT );
880 m1.setState( "h", "0", ABSENT );
881 m1.setState( "i", "0", ABSENT );
882 dollo1.execute( p1, m1 );
883 if ( dollo1.getTotalGains() != 1 ) {
886 if ( dollo1.getTotalLosses() != 1 ) {
889 if ( dollo1.getTotalUnchanged() != 16 ) {
892 m1.setState( "b", "0", PRESENT );
893 dollo1.execute( p1, m1 );
894 if ( dollo1.getTotalGains() != 1 ) {
897 if ( dollo1.getTotalLosses() != 0 ) {
900 if ( dollo1.getTotalUnchanged() != 17 ) {
903 m1.setState( "a", "0", ABSENT );
904 m1.setState( "b", "0", ABSENT );
905 dollo1.execute( p1, m1 );
906 if ( dollo1.getTotalGains() != 1 ) {
909 if ( dollo1.getTotalLosses() != 2 ) {
912 if ( dollo1.getTotalUnchanged() != 15 ) {
915 m1.setState( "y", "0", ABSENT );
916 dollo1.execute( p1, m1 );
917 if ( dollo1.getTotalGains() != 1 ) {
920 if ( dollo1.getTotalLosses() != 0 ) {
923 if ( dollo1.getTotalUnchanged() != 17 ) {
926 final DolloParsimony dollo2 = DolloParsimony.createInstance();
927 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
928 final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r";
929 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
930 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
932 m2.setIdentifier( 0, "a" );
933 m2.setIdentifier( 1, "b" );
934 m2.setIdentifier( 2, "y" );
935 m2.setIdentifier( 3, "c" );
936 m2.setIdentifier( 4, "d" );
937 m2.setIdentifier( 5, "e" );
938 m2.setIdentifier( 6, "f" );
939 m2.setIdentifier( 7, "g" );
940 m2.setIdentifier( 8, "h" );
941 m2.setIdentifier( 9, "i" );
942 m2.setCharacter( 0, "0" );
943 m2.setState( "a", "0", PRESENT );
944 m2.setState( "b", "0", ABSENT );
945 m2.setState( "y", "0", PRESENT );
946 m2.setState( "c", "0", PRESENT );
947 m2.setState( "d", "0", ABSENT );
948 m2.setState( "e", "0", ABSENT );
949 m2.setState( "f", "0", ABSENT );
950 m2.setState( "g", "0", ABSENT );
951 m2.setState( "h", "0", ABSENT );
952 m2.setState( "i", "0", ABSENT );
953 dollo2.setReturnInternalStates( true );
954 dollo2.execute( p2, m2 );
955 CharacterStateMatrix<BinaryStates> i_m2 = dollo2.getInternalStatesMatrix();
956 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
959 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
962 if ( i_m2.getState( "af", "0" ) != ABSENT ) {
965 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
968 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
971 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
974 if ( dollo2.getTotalGains() != 1 ) {
977 if ( dollo2.getTotalLosses() != 2 ) {
980 if ( dollo2.getTotalUnchanged() != 14 ) {
983 m2.setState( "b", "0", PRESENT );
984 dollo2.execute( p2, m2 );
985 if ( dollo2.getTotalGains() != 1 ) {
988 if ( dollo2.getTotalLosses() != 1 ) {
991 if ( dollo2.getTotalUnchanged() != 15 ) {
994 m2.setState( "a", "0", ABSENT );
995 m2.setState( "b", "0", ABSENT );
996 dollo2.execute( p2, m2 );
997 if ( dollo2.getTotalGains() != 1 ) {
1000 if ( dollo2.getTotalLosses() != 3 ) {
1003 if ( dollo2.getTotalUnchanged() != 13 ) {
1006 m2.setState( "y", "0", ABSENT );
1007 dollo2.execute( p2, m2 );
1008 if ( dollo2.getTotalGains() != 1 ) {
1011 if ( dollo2.getTotalLosses() != 0 ) {
1014 if ( dollo2.getTotalUnchanged() != 16 ) {
1017 m2.setState( "c", "0", ABSENT );
1018 dollo2.execute( p2, m2 );
1019 if ( dollo2.getTotalGains() != 0 ) {
1022 if ( dollo2.getTotalLosses() != 0 ) {
1025 if ( dollo2.getTotalUnchanged() != 17 ) {
1028 m2.setState( "y", "0", PRESENT );
1029 m2.setState( "e", "0", PRESENT );
1030 dollo2.execute( p2, m2 );
1031 if ( dollo2.getTotalGains() != 1 ) {
1034 if ( dollo2.getTotalLosses() != 5 ) {
1037 if ( dollo2.getTotalUnchanged() != 11 ) {
1040 i_m2 = dollo2.getInternalStatesMatrix();
1041 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
1044 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
1047 if ( i_m2.getState( "af", "0" ) != PRESENT ) {
1050 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
1053 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
1056 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
1060 catch ( final Exception e ) {
1061 e.printStackTrace( System.out );
1067 private static boolean testFitchParsimony() {
1069 final BinaryStates PRESENT = BinaryStates.PRESENT;
1070 final BinaryStates ABSENT = BinaryStates.ABSENT;
1071 final GainLossStates GAIN = GainLossStates.GAIN;
1072 final GainLossStates LOSS = GainLossStates.LOSS;
1073 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
1074 final GainLossStates UNCHANGED_ABSENT = GainLossStates.UNCHANGED_ABSENT;
1075 final FitchParsimony<String> fitch1 = new FitchParsimony<String>();
1076 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
1077 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";
1078 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
1079 final CharacterStateMatrix<String> m1 = new BasicCharacterStateMatrix<String>( 18, 1 );
1080 m1.setIdentifier( 0, "a" );
1081 m1.setIdentifier( 1, "b" );
1082 m1.setIdentifier( 2, "c" );
1083 m1.setIdentifier( 3, "d" );
1084 m1.setIdentifier( 4, "e" );
1085 m1.setIdentifier( 5, "f" );
1086 m1.setIdentifier( 6, "g" );
1087 m1.setIdentifier( 7, "h" );
1088 m1.setIdentifier( 8, "i" );
1089 m1.setIdentifier( 9, "j" );
1090 m1.setIdentifier( 10, "k" );
1091 m1.setIdentifier( 11, "l" );
1092 m1.setIdentifier( 12, "m" );
1093 m1.setIdentifier( 13, "n" );
1094 m1.setIdentifier( 14, "o" );
1095 m1.setIdentifier( 15, "p" );
1096 m1.setIdentifier( 16, "q" );
1097 m1.setIdentifier( 17, "r" );
1098 m1.setCharacter( 0, "0" );
1099 m1.setState( "a", "0", "A" );
1100 m1.setState( "b", "0", "A" );
1101 m1.setState( "c", "0", "B" );
1102 m1.setState( "d", "0", "C" );
1103 m1.setState( "e", "0", "D" );
1104 m1.setState( "f", "0", "A" );
1105 m1.setState( "g", "0", "A" );
1106 m1.setState( "h", "0", "B" );
1107 m1.setState( "i", "0", "C" );
1108 m1.setState( "j", "0", "A" );
1109 m1.setState( "k", "0", "B" );
1110 m1.setState( "l", "0", "C" );
1111 m1.setState( "m", "0", "B" );
1112 m1.setState( "n", "0", "B" );
1113 m1.setState( "o", "0", "B" );
1114 m1.setState( "p", "0", "A" );
1115 m1.setState( "q", "0", "C" );
1116 m1.setState( "r", "0", "D" );
1117 fitch1.setReturnInternalStates( true );
1118 fitch1.setReturnGainLossMatrix( false );
1119 fitch1.setRandomize( false );
1120 fitch1.execute( p1, m1 );
1121 final CharacterStateMatrix<String> i_m = fitch1.getInternalStatesMatrix();
1122 final CharacterStateMatrix<List<String>> i_m_all = fitch1.getInternalStatesMatrixPriorToTraceback();
1123 if ( fitch1.getCost() != 10 ) {
1126 if ( !i_m.getState( "ab", "0" ).equals( "A" ) ) {
1129 if ( !i_m.getState( "ac", "0" ).equals( "A" ) ) {
1132 if ( !i_m.getState( "ad", "0" ).equals( "A" ) ) {
1135 if ( !i_m.getState( "ef", "0" ).equals( "A" ) ) {
1138 if ( !i_m.getState( "ai", "0" ).equals( "A" ) ) {
1141 if ( !i_m.getState( "gi", "0" ).equals( "A" ) ) {
1144 if ( !i_m.getState( "jl", "0" ).equals( "A" ) ) {
1147 if ( !i_m.getState( "mo", "0" ).equals( "B" ) ) {
1150 if ( !i_m.getState( "pr", "0" ).equals( "A" ) ) {
1153 if ( i_m_all.getState( "ab", "0" ).size() != 1 ) {
1156 if ( !i_m_all.getState( "ab", "0" ).contains( "A" ) ) {
1159 if ( i_m_all.getState( "ac", "0" ).size() != 2 ) {
1162 if ( !i_m_all.getState( "ac", "0" ).contains( "A" ) ) {
1165 if ( !i_m_all.getState( "ac", "0" ).contains( "B" ) ) {
1168 if ( i_m_all.getState( "ad", "0" ).size() != 3 ) {
1171 if ( !i_m_all.getState( "ad", "0" ).contains( "A" ) ) {
1174 if ( !i_m_all.getState( "ad", "0" ).contains( "B" ) ) {
1177 if ( !i_m_all.getState( "ad", "0" ).contains( "C" ) ) {
1180 if ( i_m_all.getState( "af", "0" ).size() != 1 ) {
1183 if ( !i_m_all.getState( "af", "0" ).contains( "A" ) ) {
1186 if ( i_m_all.getState( "ef", "0" ).size() != 2 ) {
1189 if ( !i_m_all.getState( "ef", "0" ).contains( "A" ) ) {
1192 if ( !i_m_all.getState( "ef", "0" ).contains( "D" ) ) {
1195 if ( i_m_all.getState( "gi", "0" ).size() != 3 ) {
1198 if ( !i_m_all.getState( "gi", "0" ).contains( "A" ) ) {
1201 if ( !i_m_all.getState( "gi", "0" ).contains( "B" ) ) {
1204 if ( !i_m_all.getState( "gi", "0" ).contains( "C" ) ) {
1207 if ( i_m_all.getState( "ai", "0" ).size() != 1 ) {
1210 if ( !i_m_all.getState( "ai", "0" ).contains( "A" ) ) {
1213 if ( i_m_all.getState( "jl", "0" ).size() != 3 ) {
1216 if ( !i_m_all.getState( "jl", "0" ).contains( "A" ) ) {
1219 if ( !i_m_all.getState( "jl", "0" ).contains( "B" ) ) {
1222 if ( !i_m_all.getState( "jl", "0" ).contains( "C" ) ) {
1225 if ( i_m_all.getState( "mo", "0" ).size() != 1 ) {
1228 if ( !i_m_all.getState( "mo", "0" ).contains( "B" ) ) {
1231 if ( i_m_all.getState( "pr", "0" ).size() != 3 ) {
1234 if ( !i_m_all.getState( "pr", "0" ).contains( "A" ) ) {
1237 if ( !i_m_all.getState( "pr", "0" ).contains( "C" ) ) {
1240 if ( !i_m_all.getState( "pr", "0" ).contains( "D" ) ) {
1243 if ( i_m_all.getState( "jr", "0" ).size() != 4 ) {
1246 if ( !i_m_all.getState( "jr", "0" ).contains( "A" ) ) {
1249 if ( !i_m_all.getState( "jr", "0" ).contains( "B" ) ) {
1252 if ( !i_m_all.getState( "jr", "0" ).contains( "C" ) ) {
1255 if ( !i_m_all.getState( "jr", "0" ).contains( "D" ) ) {
1258 final FitchParsimony<String> fitch2 = new FitchParsimony<String>();
1259 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1260 final String p2_str = "((a,b)ab,(c,(d,e)de)cde)r";
1261 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
1262 final CharacterStateMatrix<String> m2 = new BasicCharacterStateMatrix<String>( 5, 1 );
1263 m2.setIdentifier( 0, "a" );
1264 m2.setIdentifier( 1, "b" );
1265 m2.setIdentifier( 2, "c" );
1266 m2.setIdentifier( 3, "d" );
1267 m2.setIdentifier( 4, "e" );
1268 m2.setCharacter( 0, "0" );
1269 m2.setState( "a", "0", "C" );
1270 m2.setState( "b", "0", "A" );
1271 m2.setState( "c", "0", "C" );
1272 m2.setState( "d", "0", "A" );
1273 m2.setState( "e", "0", "G" );
1274 fitch2.setReturnInternalStates( true );
1275 fitch2.setReturnGainLossMatrix( false );
1276 fitch2.execute( p2, m2 );
1277 final CharacterStateMatrix<String> i_m2 = fitch2.getInternalStatesMatrix();
1278 final CharacterStateMatrix<List<String>> i_m_all2 = fitch2.getInternalStatesMatrixPriorToTraceback();
1279 if ( fitch2.getCost() != 3 ) {
1282 if ( !i_m2.getState( "ab", "0" ).equals( "A" ) ) {
1285 if ( !i_m2.getState( "de", "0" ).equals( "A" ) ) {
1288 if ( !i_m2.getState( "cde", "0" ).equals( "A" ) ) {
1291 if ( !i_m2.getState( "r", "0" ).equals( "A" ) ) {
1294 if ( i_m_all2.getState( "cde", "0" ).size() != 3 ) {
1297 if ( !i_m_all2.getState( "cde", "0" ).contains( "A" ) ) {
1300 if ( !i_m_all2.getState( "cde", "0" ).contains( "C" ) ) {
1303 if ( !i_m_all2.getState( "cde", "0" ).contains( "G" ) ) {
1306 if ( i_m_all2.getState( "ab", "0" ).size() != 2 ) {
1309 if ( !i_m_all2.getState( "ab", "0" ).contains( "A" ) ) {
1312 if ( !i_m_all2.getState( "ab", "0" ).contains( "C" ) ) {
1315 fitch2.setReturnInternalStates( true );
1316 fitch2.setReturnGainLossMatrix( false );
1317 fitch2.setUseLast( true );
1318 fitch2.execute( p2, m2 );
1319 final CharacterStateMatrix<String> i_m21 = fitch2.getInternalStatesMatrix();
1320 final CharacterStateMatrix<List<String>> i_m_all21 = fitch2.getInternalStatesMatrixPriorToTraceback();
1321 if ( fitch2.getCost() != 3 ) {
1324 if ( !i_m21.getState( "ab", "0" ).equals( "C" ) ) {
1327 if ( !i_m21.getState( "de", "0" ).equals( "G" ) ) {
1330 if ( !i_m21.getState( "cde", "0" ).equals( "C" ) ) {
1333 if ( !i_m21.getState( "r", "0" ).equals( "C" ) ) {
1336 if ( i_m_all21.getState( "cde", "0" ).size() != 3 ) {
1339 if ( !i_m_all21.getState( "cde", "0" ).contains( "A" ) ) {
1342 if ( !i_m_all21.getState( "cde", "0" ).contains( "C" ) ) {
1345 if ( !i_m_all21.getState( "cde", "0" ).contains( "G" ) ) {
1348 final FitchParsimony<String> fitch3 = new FitchParsimony<String>();
1349 final PhylogenyFactory factory3 = ParserBasedPhylogenyFactory.getInstance();
1350 final String p3_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1351 final Phylogeny p3 = factory3.create( p3_str, new NHXParser() )[ 0 ];
1352 final CharacterStateMatrix<String> m3 = new BasicCharacterStateMatrix<String>( 6, 1 );
1353 m3.setIdentifier( 0, "a" );
1354 m3.setIdentifier( 1, "b" );
1355 m3.setIdentifier( 2, "c" );
1356 m3.setIdentifier( 3, "d" );
1357 m3.setIdentifier( 4, "e" );
1358 m3.setIdentifier( 5, "f" );
1359 m3.setCharacter( 0, "0" );
1360 m3.setState( "a", "0", "C" );
1361 m3.setState( "b", "0", "U" );
1362 m3.setState( "c", "0", "G" );
1363 m3.setState( "d", "0", "U" );
1364 m3.setState( "e", "0", "A" );
1365 m3.setState( "f", "0", "A" );
1366 fitch3.setReturnInternalStates( true );
1367 fitch3.setReturnGainLossMatrix( false );
1368 fitch3.execute( p3, m3 );
1369 final CharacterStateMatrix<String> i_m3 = fitch3.getInternalStatesMatrix();
1370 final CharacterStateMatrix<List<String>> i_m_all3 = fitch3.getInternalStatesMatrixPriorToTraceback();
1371 if ( fitch3.getCost() != 4 ) {
1374 if ( !i_m3.getState( "ab", "0" ).equals( "U" ) ) {
1377 if ( !i_m3.getState( "cd", "0" ).equals( "U" ) ) {
1380 if ( !i_m3.getState( "cde", "0" ).equals( "U" ) ) {
1383 if ( !i_m3.getState( "abcde", "0" ).equals( "U" ) ) {
1386 if ( !i_m3.getState( "r", "0" ).equals( "A" ) ) {
1389 if ( i_m_all3.getState( "cde", "0" ).size() != 3 ) {
1392 if ( !i_m_all3.getState( "cde", "0" ).contains( "A" ) ) {
1395 if ( !i_m_all3.getState( "cde", "0" ).contains( "G" ) ) {
1398 if ( !i_m_all3.getState( "cde", "0" ).contains( "U" ) ) {
1401 if ( i_m_all3.getState( "ab", "0" ).size() != 2 ) {
1404 if ( !i_m_all3.getState( "ab", "0" ).contains( "C" ) ) {
1407 if ( !i_m_all3.getState( "ab", "0" ).contains( "U" ) ) {
1410 if ( i_m_all3.getState( "cd", "0" ).size() != 2 ) {
1413 if ( !i_m_all3.getState( "cd", "0" ).contains( "G" ) ) {
1416 if ( !i_m_all3.getState( "cd", "0" ).contains( "U" ) ) {
1419 if ( i_m_all3.getState( "abcde", "0" ).size() != 1 ) {
1422 if ( !i_m_all3.getState( "abcde", "0" ).contains( "U" ) ) {
1425 if ( i_m_all3.getState( "r", "0" ).size() != 2 ) {
1428 if ( !i_m_all3.getState( "r", "0" ).contains( "A" ) ) {
1431 if ( !i_m_all3.getState( "r", "0" ).contains( "U" ) ) {
1434 final FitchParsimony<BinaryStates> fitch4 = new FitchParsimony<BinaryStates>();
1435 final PhylogenyFactory factory4 = ParserBasedPhylogenyFactory.getInstance();
1436 final String p4_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1437 final Phylogeny p4 = factory4.create( p4_str, new NHXParser() )[ 0 ];
1438 final CharacterStateMatrix<BinaryStates> m4 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1439 m4.setIdentifier( 0, "a" );
1440 m4.setIdentifier( 1, "b" );
1441 m4.setIdentifier( 2, "c" );
1442 m4.setIdentifier( 3, "d" );
1443 m4.setIdentifier( 4, "e" );
1444 m4.setIdentifier( 5, "f" );
1445 m4.setCharacter( 0, "0" );
1446 m4.setState( "a", "0", PRESENT );
1447 m4.setState( "b", "0", ABSENT );
1448 m4.setState( "c", "0", PRESENT );
1449 m4.setState( "d", "0", PRESENT );
1450 m4.setState( "e", "0", ABSENT );
1451 m4.setState( "f", "0", ABSENT );
1452 fitch4.setReturnInternalStates( true );
1453 fitch4.setReturnGainLossMatrix( true );
1454 fitch4.execute( p4, m4 );
1455 final CharacterStateMatrix<GainLossStates> gl_m_4 = fitch4.getGainLossMatrix();
1456 if ( fitch4.getCost() != 2 ) {
1459 if ( fitch4.getTotalLosses() != 0 ) {
1462 if ( fitch4.getTotalGains() != 2 ) {
1465 if ( fitch4.getTotalUnchanged() != 9 ) {
1468 if ( gl_m_4.getState( "a", "0" ) != GAIN ) {
1471 if ( gl_m_4.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1474 if ( gl_m_4.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1477 if ( gl_m_4.getState( "cd", "0" ) != GAIN ) {
1480 if ( gl_m_4.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1483 final FitchParsimony<BinaryStates> fitch5 = new FitchParsimony<BinaryStates>();
1484 final PhylogenyFactory factory5 = ParserBasedPhylogenyFactory.getInstance();
1485 final String p5_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1486 final Phylogeny p5 = factory5.create( p5_str, new NHXParser() )[ 0 ];
1487 final CharacterStateMatrix<BinaryStates> m5 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1488 m5.setIdentifier( 0, "a" );
1489 m5.setIdentifier( 1, "b" );
1490 m5.setIdentifier( 2, "c" );
1491 m5.setIdentifier( 3, "d" );
1492 m5.setIdentifier( 4, "e" );
1493 m5.setIdentifier( 5, "f" );
1494 m5.setCharacter( 0, "0" );
1495 m5.setState( "a", "0", PRESENT );
1496 m5.setState( "b", "0", ABSENT );
1497 m5.setState( "c", "0", PRESENT );
1498 m5.setState( "d", "0", ABSENT );
1499 m5.setState( "e", "0", PRESENT );
1500 m5.setState( "f", "0", ABSENT );
1501 fitch5.setReturnInternalStates( true );
1502 fitch5.setReturnGainLossMatrix( true );
1503 fitch5.execute( p5, m5 );
1504 final CharacterStateMatrix<GainLossStates> gl_m_5 = fitch5.getGainLossMatrix();
1505 if ( fitch5.getCost() != 3 ) {
1508 if ( fitch5.getTotalLosses() != 2 ) {
1511 if ( fitch5.getTotalGains() != 1 ) {
1514 if ( fitch5.getTotalUnchanged() != 8 ) {
1517 if ( gl_m_5.getState( "abcde", "0" ) != GAIN ) {
1520 if ( gl_m_5.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1523 if ( gl_m_5.getState( "b", "0" ) != LOSS ) {
1526 if ( gl_m_5.getState( "d", "0" ) != LOSS ) {
1529 if ( gl_m_5.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1532 final FitchParsimony<BinaryStates> fitch6 = new FitchParsimony<BinaryStates>();
1533 final PhylogenyFactory factory6 = ParserBasedPhylogenyFactory.getInstance();
1534 final String p6_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1535 final Phylogeny p6 = factory6.create( p6_str, new NHXParser() )[ 0 ];
1536 final CharacterStateMatrix<BinaryStates> m6 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1537 m6.setIdentifier( 0, "a" );
1538 m6.setIdentifier( 1, "b" );
1539 m6.setIdentifier( 2, "c" );
1540 m6.setIdentifier( 3, "d" );
1541 m6.setIdentifier( 4, "e" );
1542 m6.setIdentifier( 5, "f" );
1543 m6.setCharacter( 0, "0" );
1544 m6.setState( "a", "0", PRESENT );
1545 m6.setState( "b", "0", ABSENT );
1546 m6.setState( "c", "0", PRESENT );
1547 m6.setState( "d", "0", PRESENT );
1548 m6.setState( "e", "0", ABSENT );
1549 m6.setState( "f", "0", PRESENT );
1550 fitch6.setReturnInternalStates( true );
1551 fitch6.setReturnGainLossMatrix( true );
1552 fitch6.execute( p6, m6 );
1553 final CharacterStateMatrix<GainLossStates> gl_m_6 = fitch6.getGainLossMatrix();
1554 if ( fitch6.getCost() != 2 ) {
1557 if ( fitch6.getTotalLosses() != 2 ) {
1560 if ( fitch6.getTotalGains() != 0 ) {
1563 if ( fitch6.getTotalUnchanged() != 9 ) {
1566 if ( gl_m_6.getState( "abcde", "0" ) != UNCHANGED_PRESENT ) {
1569 if ( gl_m_6.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1572 if ( gl_m_6.getState( "b", "0" ) != LOSS ) {
1575 if ( gl_m_6.getState( "e", "0" ) != LOSS ) {
1578 final FitchParsimony<BinaryStates> fitch7 = new FitchParsimony<BinaryStates>();
1579 final PhylogenyFactory factory7 = ParserBasedPhylogenyFactory.getInstance();
1580 final String p7_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1581 final Phylogeny p7 = factory7.create( p7_str, new NHXParser() )[ 0 ];
1582 final CharacterStateMatrix<BinaryStates> m7 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1583 m7.setIdentifier( 0, "a" );
1584 m7.setIdentifier( 1, "b" );
1585 m7.setIdentifier( 2, "c" );
1586 m7.setIdentifier( 3, "d" );
1587 m7.setIdentifier( 4, "e" );
1588 m7.setIdentifier( 5, "f" );
1589 m7.setIdentifier( 6, "g" );
1590 m7.setIdentifier( 7, "h" );
1591 m7.setCharacter( 0, "0" );
1592 m7.setState( "a", "0", PRESENT );
1593 m7.setState( "b", "0", ABSENT );
1594 m7.setState( "c", "0", PRESENT );
1595 m7.setState( "d", "0", ABSENT );
1596 m7.setState( "e", "0", PRESENT );
1597 m7.setState( "f", "0", ABSENT );
1598 m7.setState( "g", "0", PRESENT );
1599 m7.setState( "h", "0", ABSENT );
1600 fitch7.setReturnInternalStates( true );
1601 fitch7.setReturnGainLossMatrix( true );
1602 fitch7.execute( p7, m7 );
1603 final CharacterStateMatrix<GainLossStates> gl_m_7 = fitch7.getGainLossMatrix();
1604 if ( fitch7.getCost() != 4 ) {
1607 if ( fitch7.getTotalLosses() != 0 ) {
1610 if ( fitch7.getTotalGains() != 4 ) {
1613 if ( fitch7.getTotalUnchanged() != 11 ) {
1616 if ( gl_m_7.getState( "a", "0" ) != GAIN ) {
1619 if ( gl_m_7.getState( "c", "0" ) != GAIN ) {
1622 if ( gl_m_7.getState( "e", "0" ) != GAIN ) {
1625 if ( gl_m_7.getState( "g", "0" ) != GAIN ) {
1628 if ( gl_m_7.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1631 fitch7.setReturnInternalStates( true );
1632 fitch7.setReturnGainLossMatrix( true );
1633 fitch7.setUseLast( true );
1634 fitch7.execute( p7, m7 );
1635 final CharacterStateMatrix<GainLossStates> gl_m_71 = fitch7.getGainLossMatrix();
1636 if ( fitch7.getCost() != 4 ) {
1639 if ( fitch7.getTotalLosses() != 4 ) {
1642 if ( fitch7.getTotalGains() != 0 ) {
1645 if ( fitch7.getTotalUnchanged() != 11 ) {
1648 if ( gl_m_71.getState( "b", "0" ) != LOSS ) {
1651 if ( gl_m_71.getState( "d", "0" ) != LOSS ) {
1654 if ( gl_m_71.getState( "f", "0" ) != LOSS ) {
1657 if ( gl_m_71.getState( "h", "0" ) != LOSS ) {
1660 if ( gl_m_71.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1663 final FitchParsimony<BinaryStates> fitch8 = new FitchParsimony<BinaryStates>();
1664 final PhylogenyFactory factory8 = ParserBasedPhylogenyFactory.getInstance();
1665 final String p8_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1666 final Phylogeny p8 = factory8.create( p8_str, new NHXParser() )[ 0 ];
1667 final CharacterStateMatrix<BinaryStates> m8 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1668 m8.setIdentifier( 0, "a" );
1669 m8.setIdentifier( 1, "b" );
1670 m8.setIdentifier( 2, "c" );
1671 m8.setIdentifier( 3, "d" );
1672 m8.setIdentifier( 4, "e" );
1673 m8.setIdentifier( 5, "f" );
1674 m8.setIdentifier( 6, "g" );
1675 m8.setIdentifier( 7, "h" );
1676 m8.setCharacter( 0, "0" );
1677 m8.setState( "a", "0", PRESENT );
1678 m8.setState( "b", "0", PRESENT );
1679 m8.setState( "c", "0", PRESENT );
1680 m8.setState( "d", "0", ABSENT );
1681 m8.setState( "e", "0", ABSENT );
1682 m8.setState( "f", "0", ABSENT );
1683 m8.setState( "g", "0", ABSENT );
1684 m8.setState( "h", "0", ABSENT );
1685 fitch8.setReturnInternalStates( true );
1686 fitch8.setReturnGainLossMatrix( true );
1687 fitch8.execute( p8, m8 );
1688 final CharacterStateMatrix<GainLossStates> gl_m_8 = fitch8.getGainLossMatrix();
1689 if ( fitch8.getCost() != 2 ) {
1692 if ( fitch8.getTotalLosses() != 1 ) {
1695 if ( fitch8.getTotalGains() != 1 ) {
1698 if ( fitch8.getTotalUnchanged() != 13 ) {
1701 if ( gl_m_8.getState( "d", "0" ) != LOSS ) {
1704 if ( gl_m_8.getState( "abcd", "0" ) != GAIN ) {
1707 final FitchParsimony<BinaryStates> fitch9 = new FitchParsimony<BinaryStates>();
1708 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
1709 final String p9_str = "(((a,b)ab,c)abc,d)abcd";
1710 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
1711 final CharacterStateMatrix<BinaryStates> m9 = new BasicCharacterStateMatrix<BinaryStates>( 4, 1 );
1712 m9.setIdentifier( 0, "a" );
1713 m9.setIdentifier( 1, "b" );
1714 m9.setIdentifier( 2, "c" );
1715 m9.setIdentifier( 3, "d" );
1716 m9.setCharacter( 0, "0" );
1717 m9.setState( "a", "0", PRESENT );
1718 m9.setState( "b", "0", ABSENT );
1719 m9.setState( "c", "0", PRESENT );
1720 m9.setState( "d", "0", ABSENT );
1721 fitch9.setReturnInternalStates( true );
1722 fitch9.setReturnGainLossMatrix( true );
1723 fitch9.setUseLast( false );
1724 fitch9.execute( p9, m9 );
1725 final CharacterStateMatrix<GainLossStates> gl_m_9a = fitch9.getGainLossMatrix();
1726 if ( fitch9.getCost() != 2 ) {
1729 if ( fitch9.getTotalLosses() != 1 ) {
1732 if ( fitch9.getTotalGains() != 1 ) {
1735 if ( fitch9.getTotalUnchanged() != 5 ) {
1738 if ( gl_m_9a.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1741 if ( gl_m_9a.getState( "b", "0" ) != LOSS ) {
1744 if ( gl_m_9a.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1747 if ( gl_m_9a.getState( "d", "0" ) != UNCHANGED_ABSENT ) {
1750 if ( gl_m_9a.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1753 if ( gl_m_9a.getState( "abc", "0" ) != GAIN ) {
1756 if ( gl_m_9a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1759 fitch9.setUseLast( true );
1760 fitch9.execute( p9, m9 );
1761 final CharacterStateMatrix<GainLossStates> gl_m_9b = fitch9.getGainLossMatrix();
1762 if ( fitch9.getCost() != 2 ) {
1765 if ( fitch9.getTotalLosses() != 2 ) {
1768 if ( fitch9.getTotalGains() != 0 ) {
1771 if ( fitch9.getTotalUnchanged() != 5 ) {
1774 if ( gl_m_9b.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1777 if ( gl_m_9b.getState( "b", "0" ) != LOSS ) {
1780 if ( gl_m_9b.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1783 if ( gl_m_9b.getState( "d", "0" ) != LOSS ) {
1786 if ( gl_m_9b.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1789 if ( gl_m_9b.getState( "abc", "0" ) != UNCHANGED_PRESENT ) {
1792 if ( gl_m_9b.getState( "abcd", "0" ) != UNCHANGED_PRESENT ) {
1795 fitch9.setUseLast( false );
1796 fitch9.setRandomize( true );
1797 fitch9.setRandomNumberSeed( 8722445 );
1798 fitch9.execute( p9, m9 );
1799 fitch9.getGainLossMatrix();
1800 if ( fitch9.getCost() != 2 ) {
1803 if ( fitch9.getTotalLosses() != 1 ) {
1806 if ( fitch9.getTotalGains() != 1 ) {
1809 if ( fitch9.getTotalUnchanged() != 5 ) {
1812 final FitchParsimony<BinaryStates> fitch10 = new FitchParsimony<BinaryStates>();
1813 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
1814 final String p10_str = "((((a,b)ab,c)abc,d)abcd,e)abcde";
1815 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
1816 final CharacterStateMatrix<BinaryStates> m10 = new BasicCharacterStateMatrix<BinaryStates>( 5, 1 );
1817 m10.setIdentifier( 0, "a" );
1818 m10.setIdentifier( 1, "b" );
1819 m10.setIdentifier( 2, "c" );
1820 m10.setIdentifier( 3, "d" );
1821 m10.setIdentifier( 4, "e" );
1822 m10.setCharacter( 0, "0" );
1823 m10.setState( "a", "0", PRESENT );
1824 m10.setState( "b", "0", ABSENT );
1825 m10.setState( "c", "0", ABSENT );
1826 m10.setState( "d", "0", PRESENT );
1827 m10.setState( "e", "0", ABSENT );
1828 fitch10.setReturnInternalStates( true );
1829 fitch10.setReturnGainLossMatrix( true );
1830 fitch10.setUseLast( false );
1831 fitch10.execute( p10, m10 );
1832 final CharacterStateMatrix<GainLossStates> gl_m_10a = fitch10.getGainLossMatrix();
1833 if ( fitch10.getCost() != 2 ) {
1836 if ( fitch10.getTotalLosses() != 0 ) {
1839 if ( fitch10.getTotalGains() != 2 ) {
1842 if ( fitch10.getTotalUnchanged() != 7 ) {
1845 if ( gl_m_10a.getState( "a", "0" ) != GAIN ) {
1848 if ( gl_m_10a.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1851 if ( gl_m_10a.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1854 if ( gl_m_10a.getState( "d", "0" ) != GAIN ) {
1857 if ( gl_m_10a.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1860 if ( gl_m_10a.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1863 if ( gl_m_10a.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1866 if ( gl_m_10a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1869 if ( gl_m_10a.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1872 fitch10.setUseLast( true );
1873 fitch10.execute( p10, m10 );
1874 final CharacterStateMatrix<GainLossStates> gl_m_10b = fitch10.getGainLossMatrix();
1875 if ( fitch10.getCost() != 2 ) {
1878 if ( fitch10.getTotalLosses() != 0 ) {
1881 if ( fitch10.getTotalGains() != 2 ) {
1884 if ( fitch10.getTotalUnchanged() != 7 ) {
1887 if ( gl_m_10b.getState( "a", "0" ) != GAIN ) {
1890 if ( gl_m_10b.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1893 if ( gl_m_10b.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1896 if ( gl_m_10b.getState( "d", "0" ) != GAIN ) {
1899 if ( gl_m_10b.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1902 if ( gl_m_10b.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1905 if ( gl_m_10b.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1908 if ( gl_m_10b.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1911 if ( gl_m_10b.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1915 catch ( final Exception e ) {
1916 e.printStackTrace( System.out );
1922 private static boolean testNeighborJoining() {
1924 NeighborJoining nj = NeighborJoining.createInstance();
1925 final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
1926 m0.setIdentifier( 0, "A" );
1927 m0.setIdentifier( 1, "B" );
1928 m0.setIdentifier( 2, "C" );
1929 m0.setIdentifier( 3, "D" );
1930 m0.setRow( "5 ", 1 );
1931 m0.setRow( "3 6 ", 2 );
1932 m0.setRow( "7.5 10.5 5.5", 3 );
1933 final Phylogeny p0 = nj.execute( m0 );
1934 p0.reRoot( p0.getNode( "D" ) );
1935 if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) {
1938 if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
1941 if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
1944 if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
1947 if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
1950 if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
1953 nj = NeighborJoining.createInstance();
1954 final BasicSymmetricalDistanceMatrix m00 = new BasicSymmetricalDistanceMatrix( 4 );
1955 m00.setIdentifier( 0, "A" );
1956 m00.setIdentifier( 1, "B" );
1957 m00.setIdentifier( 2, "C" );
1958 m00.setIdentifier( 3, "D" );
1959 m00.setRow( "2.01 ", 1 );
1960 m00.setRow( "3 3.01 ", 2 );
1961 m00.setRow( "3.01 3.02 1.01", 3 );
1962 final Phylogeny p00 = nj.execute( m00 );
1963 p00.reRoot( p00.getNode( "D" ) );
1964 if ( isUnequal( p00.getNode( "A" ).getDistanceToParent(), 1 ) ) {
1967 if ( isUnequal( p00.getNode( "B" ).getDistanceToParent(), 1.01 ) ) {
1970 if ( isUnequal( p00.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
1973 if ( isUnequal( p00.getNode( "D" ).getDistanceToParent(), 0.255 ) ) {
1976 if ( isUnequal( p00.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
1979 if ( isUnequal( p00.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.255 ) ) {
1982 BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
1984 m.setRow( "4 7", 2 );
1985 m.setRow( "7 10 7", 3 );
1986 m.setRow( "6 9 6 5", 4 );
1987 m.setRow( "8 11 8 9 8", 5 );
1988 m.setIdentifier( 0, "A" );
1989 m.setIdentifier( 1, "B" );
1990 m.setIdentifier( 2, "C" );
1991 m.setIdentifier( 3, "D" );
1992 m.setIdentifier( 4, "E" );
1993 m.setIdentifier( 5, "F" );
1994 nj = NeighborJoining.createInstance();
1995 final Phylogeny p1 = nj.execute( m );
1996 p1.reRoot( p1.getNode( "F" ) );
1997 if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
2000 if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) {
2003 if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) {
2006 if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) {
2009 if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) {
2012 if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) {
2015 if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) {
2018 if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) {
2021 if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) {
2024 if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) {
2027 if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) {
2030 if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) {
2033 m = new BasicSymmetricalDistanceMatrix( 7 );
2034 m.setIdentifier( 0, "Bovine" );
2035 m.setIdentifier( 1, "Mouse" );
2036 m.setIdentifier( 2, "Gibbon" );
2037 m.setIdentifier( 3, "Orang" );
2038 m.setIdentifier( 4, "Gorilla" );
2039 m.setIdentifier( 5, "Chimp" );
2040 m.setIdentifier( 6, "Human" );
2041 m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
2042 m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
2043 m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
2044 m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
2045 m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
2046 m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
2047 m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
2048 nj = NeighborJoining.createInstance( false, 6 );
2049 final Phylogeny p2 = nj.execute( m );
2050 p2.reRoot( p2.getNode( "Bovine" ) );
2051 if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
2054 if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) {
2057 if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) {
2060 if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) {
2063 if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) {
2066 if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) {
2069 if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) {
2072 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) {
2075 if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) {
2078 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) {
2081 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) {
2084 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(),
2088 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
2089 .getDistanceToParent(), 0.458845 ) ) {
2092 m = new BasicSymmetricalDistanceMatrix( 4 );
2093 m.setIdentifier( 0, "A" );
2094 m.setIdentifier( 1, "B" );
2095 m.setIdentifier( 2, "C" );
2096 m.setIdentifier( 3, "D" );
2097 m.setRow( "0.00 0.95 0.17 0.98", 0 );
2098 m.setRow( "0.95 0.00 1.02 1.83", 1 );
2099 m.setRow( "0.17 1.02 0.00 1.01", 2 );
2100 m.setRow( "0.98 1.83 1.01 0.00", 3 );
2101 final Phylogeny p3 = nj.execute( m );
2102 p3.reRoot( p3.getNode( "C" ) );
2103 if ( isUnequal( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) {
2106 if ( isUnequal( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) {
2109 if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.05 ) ) {
2112 if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) {
2115 if ( isUnequal( p3.getNode( "A" ).getParent().getDistanceToParent(), 0.02 ) ) {
2118 if ( isUnequal( p3.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.05 ) ) {
2122 // timeNeighborJoining();
2125 catch ( final Exception e ) {
2126 e.printStackTrace( System.out );
2132 private static boolean testSymmetricalDistanceMatrixParser() {
2134 final String l = ForesterUtil.getLineSeparator();
2135 StringBuffer source = new StringBuffer();
2136 source.append( " 4" + l );
2137 source.append( "A 0 0 0 0" + l );
2138 source.append( "B 1 0 0 0" + l );
2139 source.append( "C 2 4 0 0" + l );
2140 source.append( "D 3 5 6 0" + l );
2142 source.append( " 4" + l );
2143 source.append( "A 0 11 12 13" + l );
2144 source.append( "B 11 0 14 15" + l );
2145 source.append( "C 12 14 0 16" + l );
2146 source.append( "D 13 15 16 0" + l );
2149 source.append( " " + l );
2150 source.append( " 4" + l );
2151 source.append( " A 0 " + l );
2152 source.append( " B 21 0" + l );
2153 source.append( " C 22 24 0 " + l );
2154 source.append( " # 2 222 2 2 " + l );
2155 source.append( " D 23 25 26 0" + l );
2158 source.append( " " + l );
2159 final SymmetricalDistanceMatrixParser p0 = SymmetricalDistanceMatrixParser.createInstance();
2160 final DistanceMatrix[] ma0 = p0.parse( source.toString() );
2161 if ( ma0.length != 3 ) {
2164 if ( !isEqual( ma0[ 0 ].getValue( 0, 0 ), 0 ) ) {
2167 if ( !isEqual( ma0[ 0 ].getValue( 1, 0 ), 1 ) ) {
2170 if ( !isEqual( ma0[ 0 ].getValue( 2, 0 ), 2 ) ) {
2173 if ( !isEqual( ma0[ 0 ].getValue( 3, 0 ), 3 ) ) {
2176 if ( !isEqual( ma0[ 0 ].getValue( 0, 1 ), 1 ) ) {
2179 if ( !isEqual( ma0[ 0 ].getValue( 1, 1 ), 0 ) ) {
2182 if ( !isEqual( ma0[ 0 ].getValue( 2, 1 ), 4 ) ) {
2185 if ( !isEqual( ma0[ 0 ].getValue( 3, 1 ), 5 ) ) {
2188 if ( !isEqual( ma0[ 1 ].getValue( 0, 0 ), 0 ) ) {
2191 if ( !isEqual( ma0[ 1 ].getValue( 1, 0 ), 11 ) ) {
2194 if ( !isEqual( ma0[ 1 ].getValue( 2, 0 ), 12 ) ) {
2197 if ( !isEqual( ma0[ 1 ].getValue( 3, 0 ), 13 ) ) {
2200 if ( !isEqual( ma0[ 1 ].getValue( 0, 1 ), 11 ) ) {
2203 if ( !isEqual( ma0[ 1 ].getValue( 1, 1 ), 0 ) ) {
2206 if ( !isEqual( ma0[ 1 ].getValue( 2, 1 ), 14 ) ) {
2209 if ( !isEqual( ma0[ 1 ].getValue( 3, 1 ), 15 ) ) {
2212 if ( !isEqual( ma0[ 2 ].getValue( 0, 0 ), 0 ) ) {
2215 if ( !isEqual( ma0[ 2 ].getValue( 1, 0 ), 21 ) ) {
2218 if ( !isEqual( ma0[ 2 ].getValue( 2, 0 ), 22 ) ) {
2221 if ( !isEqual( ma0[ 2 ].getValue( 3, 0 ), 23 ) ) {
2224 if ( !isEqual( ma0[ 2 ].getValue( 0, 1 ), 21 ) ) {
2227 if ( !isEqual( ma0[ 2 ].getValue( 1, 1 ), 0 ) ) {
2230 if ( !isEqual( ma0[ 2 ].getValue( 2, 1 ), 24 ) ) {
2233 if ( !isEqual( ma0[ 2 ].getValue( 3, 1 ), 25 ) ) {
2236 source = new StringBuffer();
2237 source.append( "A 0 0 0 0" + l );
2238 source.append( "B 1 0 0 0" + l );
2239 source.append( "C 2 4 0 0" + l );
2240 source.append( "D 3 5 6 0" + l );
2241 source.append( " " + l );
2242 source.append( "A 0 11 12 13" + l );
2243 source.append( "B 11 0 14 15" + l );
2244 source.append( "C 12 14 0 16" + l );
2245 source.append( "D 13 15 16 0" + l );
2247 source.append( " A 0 " + l );
2248 source.append( " B 21 0" + l );
2249 source.append( " C 22 24 0 " + l );
2250 source.append( " # 2 222 2 2 " + l );
2251 source.append( " D 23 25 26 0" + l );
2252 final DistanceMatrix[] ma1 = p0.parse( source.toString() );
2253 if ( ma1.length != 3 ) {
2256 if ( !isEqual( ma1[ 0 ].getValue( 0, 0 ), 0 ) ) {
2259 if ( !isEqual( ma1[ 0 ].getValue( 1, 0 ), 1 ) ) {
2262 if ( !isEqual( ma1[ 0 ].getValue( 2, 0 ), 2 ) ) {
2265 if ( !isEqual( ma1[ 0 ].getValue( 3, 0 ), 3 ) ) {
2268 if ( !isEqual( ma1[ 0 ].getValue( 0, 1 ), 1 ) ) {
2271 if ( !isEqual( ma1[ 0 ].getValue( 1, 1 ), 0 ) ) {
2274 if ( !isEqual( ma1[ 0 ].getValue( 2, 1 ), 4 ) ) {
2277 if ( !isEqual( ma1[ 0 ].getValue( 3, 1 ), 5 ) ) {
2280 if ( !isEqual( ma1[ 1 ].getValue( 0, 0 ), 0 ) ) {
2283 if ( !isEqual( ma1[ 1 ].getValue( 1, 0 ), 11 ) ) {
2286 if ( !isEqual( ma1[ 1 ].getValue( 2, 0 ), 12 ) ) {
2289 if ( !isEqual( ma1[ 1 ].getValue( 3, 0 ), 13 ) ) {
2292 if ( !isEqual( ma1[ 1 ].getValue( 0, 1 ), 11 ) ) {
2295 if ( !isEqual( ma1[ 1 ].getValue( 1, 1 ), 0 ) ) {
2298 if ( !isEqual( ma1[ 1 ].getValue( 2, 1 ), 14 ) ) {
2301 if ( !isEqual( ma1[ 1 ].getValue( 3, 1 ), 15 ) ) {
2304 if ( !isEqual( ma1[ 2 ].getValue( 0, 0 ), 0 ) ) {
2307 if ( !isEqual( ma1[ 2 ].getValue( 1, 0 ), 21 ) ) {
2310 if ( !isEqual( ma1[ 2 ].getValue( 2, 0 ), 22 ) ) {
2313 if ( !isEqual( ma1[ 2 ].getValue( 3, 0 ), 23 ) ) {
2316 if ( !isEqual( ma1[ 2 ].getValue( 0, 1 ), 21 ) ) {
2319 if ( !isEqual( ma1[ 2 ].getValue( 1, 1 ), 0 ) ) {
2322 if ( !isEqual( ma1[ 2 ].getValue( 2, 1 ), 24 ) ) {
2325 if ( !isEqual( ma1[ 2 ].getValue( 3, 1 ), 25 ) ) {
2328 source = new StringBuffer();
2329 source.append( "A 0" + l );
2330 source.append( "B 10 0" + l );
2331 final DistanceMatrix[] ma2 = p0.parse( source.toString() );
2332 if ( ma2.length != 1 ) {
2335 if ( !isEqual( ma2[ 0 ].getValue( 0, 1 ), 10 ) ) {
2338 source = new StringBuffer();
2339 source.append( " " + l );
2340 source.append( "#" + l );
2341 final DistanceMatrix[] ma3 = p0.parse( source.toString() );
2342 if ( ma3.length != 0 ) {
2345 source = new StringBuffer();
2346 source.append( " " + l );
2347 source.append( "A 0 11 12 13" + l );
2348 source.append( "B 0 14 15" + l );
2349 source.append( "C 0 16" + l );
2350 source.append( "D 0" + l );
2352 source.append( "A 0 21 22 23" + l );
2353 source.append( "B 0 24 25" + l );
2354 source.append( "C 0 26" + l );
2355 source.append( "D 0" + l );
2356 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2357 final DistanceMatrix[] ma4 = p0.parse( source );
2358 if ( ma4.length != 2 ) {
2361 if ( !isEqual( ma4[ 0 ].getValue( 0, 0 ), 0 ) ) {
2364 if ( !isEqual( ma4[ 0 ].getValue( 1, 0 ), 11 ) ) {
2367 if ( !isEqual( ma4[ 0 ].getValue( 2, 0 ), 12 ) ) {
2370 if ( !isEqual( ma4[ 0 ].getValue( 3, 0 ), 13 ) ) {
2373 if ( !isEqual( ma4[ 0 ].getValue( 0, 1 ), 11 ) ) {
2376 if ( !isEqual( ma4[ 0 ].getValue( 1, 1 ), 0 ) ) {
2379 if ( !isEqual( ma4[ 0 ].getValue( 2, 1 ), 14 ) ) {
2382 if ( !isEqual( ma4[ 0 ].getValue( 3, 1 ), 15 ) ) {
2385 if ( !isEqual( ma4[ 0 ].getValue( 0, 2 ), 12 ) ) {
2388 if ( !isEqual( ma4[ 0 ].getValue( 1, 2 ), 14 ) ) {
2391 if ( !isEqual( ma4[ 0 ].getValue( 2, 2 ), 0 ) ) {
2394 if ( !isEqual( ma4[ 0 ].getValue( 3, 2 ), 16 ) ) {
2397 if ( !isEqual( ma4[ 0 ].getValue( 0, 3 ), 13 ) ) {
2400 if ( !isEqual( ma4[ 0 ].getValue( 1, 3 ), 15 ) ) {
2403 if ( !isEqual( ma4[ 0 ].getValue( 2, 3 ), 16 ) ) {
2406 if ( !isEqual( ma4[ 0 ].getValue( 3, 3 ), 0 ) ) {
2409 source = new StringBuffer();
2410 source.append( " 4 " + l );
2411 source.append( "A 0 11 12 13" + l );
2412 source.append( "B 0 14 15" + l );
2413 source.append( "C 0 16" + l );
2414 source.append( "D 0" + l );
2415 source.append( " 4" + l );
2416 source.append( "A 0 21 22 23" + l );
2417 source.append( "B 0 24 25" + l );
2418 source.append( "C 0 26" + l );
2419 source.append( "D 0" + l );
2420 source.append( " " + l );
2421 source.append( " 4" + l );
2422 source.append( "A 0 21 22 23" + l );
2423 source.append( "B 0 24 25" + l );
2424 source.append( "C 0 26" + l );
2425 source.append( "D 0" + l );
2427 source.append( "A 0 21 22 23" + l );
2428 source.append( "B 0 24 25" + l );
2429 source.append( "C 0 26" + l );
2430 source.append( "D 0" + l );
2431 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2432 final DistanceMatrix[] ma5 = p0.parse( source );
2433 if ( ma5.length != 4 ) {
2436 if ( !isEqual( ma5[ 0 ].getValue( 0, 0 ), 0 ) ) {
2439 if ( !isEqual( ma5[ 0 ].getValue( 1, 0 ), 11 ) ) {
2442 if ( !isEqual( ma5[ 0 ].getValue( 2, 0 ), 12 ) ) {
2445 if ( !isEqual( ma5[ 0 ].getValue( 3, 0 ), 13 ) ) {
2448 if ( !isEqual( ma5[ 0 ].getValue( 0, 1 ), 11 ) ) {
2451 if ( !isEqual( ma5[ 0 ].getValue( 1, 1 ), 0 ) ) {
2454 if ( !isEqual( ma5[ 0 ].getValue( 2, 1 ), 14 ) ) {
2457 if ( !isEqual( ma5[ 0 ].getValue( 3, 1 ), 15 ) ) {
2460 if ( !isEqual( ma5[ 0 ].getValue( 0, 2 ), 12 ) ) {
2463 if ( !isEqual( ma5[ 0 ].getValue( 1, 2 ), 14 ) ) {
2466 if ( !isEqual( ma5[ 0 ].getValue( 2, 2 ), 0 ) ) {
2469 if ( !isEqual( ma5[ 0 ].getValue( 3, 2 ), 16 ) ) {
2472 if ( !isEqual( ma5[ 0 ].getValue( 0, 3 ), 13 ) ) {
2475 if ( !isEqual( ma5[ 0 ].getValue( 1, 3 ), 15 ) ) {
2478 if ( !isEqual( ma5[ 0 ].getValue( 2, 3 ), 16 ) ) {
2481 if ( !isEqual( ma5[ 0 ].getValue( 3, 3 ), 0 ) ) {
2485 catch ( final Exception e ) {
2486 e.printStackTrace( System.out );
2492 private static void timeNeighborJoining() {
2493 final NeighborJoining nj = NeighborJoining.createInstance();
2494 for( int n = 3; n <= 10; ++n ) {
2495 final int x = ( int ) Math.pow( 2, n );
2496 final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
2497 mt.randomize( new Date().getTime() );
2498 // for( int i = 0; i < mt.getSize(); i++ ) {
2499 // mt.setIdentifier( i, i + "i" );
2501 // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
2502 final long start_time = new Date().getTime();
2504 System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );