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.NeighborJoiningX;
38 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
39 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
40 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
41 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
42 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
43 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
44 import org.forester.evoinference.matrix.distance.DistanceMatrix;
45 import org.forester.evoinference.parsimony.DolloParsimony;
46 import org.forester.evoinference.parsimony.FitchParsimony;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
49 import org.forester.io.parsers.nhx.NHXParser;
50 import org.forester.msa.Msa;
51 import org.forester.phylogeny.Phylogeny;
52 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
53 import org.forester.phylogeny.factories.PhylogenyFactory;
54 import org.forester.util.ForesterUtil;
56 public class TestPhylogenyReconstruction {
58 private final static double ZERO_DIFF = 1.0E-9;
60 public static boolean isEqual( final double a, final double b ) {
61 return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
64 public static boolean isUnequal( final double a, final double b ) {
65 return !isEqual( a, b );
68 public static void main( final String[] args ) {
69 if ( testNeighborJoining() ) {
70 System.out.println( "OK." );
73 System.out.println( "failed." );
75 timeNeighborJoining();
78 public static boolean test( final File test_dir ) {
79 System.out.print( " Basic symmetrical distance matrix: " );
80 if ( !testBasicSymmetricalDistanceMatrix() ) {
81 System.out.println( "failed." );
84 System.out.println( "OK." );
85 System.out.print( " Basic character state matrix: " );
86 if ( !testBasicCharacterStateMatrix() ) {
87 System.out.println( "failed." );
90 System.out.println( "OK." );
91 System.out.print( " Symmetrical distance matrix parser: " );
92 if ( !testSymmetricalDistanceMatrixParser() ) {
93 System.out.println( "failed." );
96 System.out.println( "OK." );
97 System.out.print( " Distance Calculation: " );
98 if ( !testDistanceCalculationMethods( test_dir ) ) {
99 System.out.println( "failed." );
102 System.out.println( "OK." );
103 System.out.print( " Neighbor Joining: " );
104 if ( !testNeighborJoining() ) {
105 System.out.println( "failed." );
108 System.out.println( "OK." );
109 System.out.print( " Dollo Parsimony: " );
110 if ( !testDolloParsimony() ) {
111 System.out.println( "failed." );
114 System.out.println( "OK." );
115 System.out.print( " Dollo Parsimony on non binary trees: " );
116 if ( !testDolloParsimonyOnNonBinaryTree() ) {
117 System.out.println( "failed." );
120 System.out.println( "OK." );
121 System.out.print( " Fitch Parsimony: " );
122 if ( !testFitchParsimony() ) {
123 System.out.println( "failed." );
126 System.out.println( "OK." );
130 private static boolean testDistanceCalculationMethods( final File test_dir ) {
132 final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
134 final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
135 if ( pwd0.getSize() != 120 ) {
138 for( int i = 0; i < pwd0.getSize(); ++i ) {
139 if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) {
144 catch ( final Exception e ) {
145 e.printStackTrace( System.out );
151 private static boolean testBasicCharacterStateMatrix() {
153 final CharacterStateMatrix<String> matrix_0 = new BasicCharacterStateMatrix<String>( 4, 8 );
154 final CharacterStateMatrix<String> matrix_00 = new BasicCharacterStateMatrix<String>( 4, 8 );
155 matrix_0.setIdentifier( 0, "A" );
156 matrix_0.setIdentifier( 1, "B" );
157 matrix_0.setIdentifier( 2, "C" );
158 matrix_0.setIdentifier( 3, "D" );
159 matrix_0.setCharacter( 0, "0" );
160 matrix_0.setCharacter( 1, "1" );
161 matrix_0.setCharacter( 2, "2" );
162 matrix_0.setCharacter( 3, "3" );
163 matrix_0.setCharacter( 4, "4" );
164 matrix_0.setCharacter( 5, "5" );
165 matrix_0.setCharacter( 6, "6" );
166 matrix_0.setCharacter( 7, "7" );
167 matrix_00.setIdentifier( 0, "A" );
168 matrix_00.setIdentifier( 1, "B" );
169 matrix_00.setIdentifier( 2, "C" );
170 matrix_00.setIdentifier( 3, "D" );
171 matrix_00.setCharacter( 3, "3" );
172 matrix_00.setCharacter( 4, "4" );
173 if ( !matrix_0.getCharacter( 1 ).equals( "1" ) ) {
176 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
179 matrix_0.setState( 0, 0, "00" );
180 matrix_00.setState( 0, 0, "00" );
181 if ( !matrix_0.getState( 0, 0 ).equals( "00" ) ) {
184 matrix_0.setState( 0, 1, "01" );
185 matrix_00.setState( 0, 1, "01" );
186 if ( !matrix_0.getState( 0, 1 ).equals( "01" ) ) {
189 matrix_0.setState( 1, 1, "11" );
190 matrix_00.setState( 1, 1, "11" );
191 if ( !matrix_0.getState( 1, 1 ).equals( "11" ) ) {
194 matrix_0.setState( 1, 0, "10" );
195 matrix_00.setState( 1, 0, "10" );
196 if ( !matrix_0.getState( 1, 0 ).equals( "10" ) ) {
199 matrix_0.setState( 1, 2, "12" );
200 matrix_00.setState( 1, 2, "12" );
201 if ( !matrix_0.getState( 1, 2 ).equals( "12" ) ) {
204 matrix_0.setState( 3, 7, "37" );
205 matrix_00.setState( 3, 7, "37" );
206 if ( !matrix_0.getState( 3, 7 ).equals( "37" ) ) {
209 matrix_0.setState( 2, 6, "26" );
210 matrix_00.setState( 2, 6, "26" );
211 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
214 matrix_0.setState( "D", "3", "33" );
215 matrix_00.setState( "D", "3", "33" );
216 if ( !matrix_0.getState( 3, 3 ).equals( "33" ) ) {
219 if ( !matrix_0.getState( "D", "3" ).equals( "33" ) ) {
222 matrix_0.setState( "C", "4", "24" );
223 matrix_00.setState( "C", "4", "24" );
224 if ( !matrix_0.getState( 2, 4 ).equals( "24" ) ) {
227 if ( !matrix_0.getState( "C", "4" ).equals( "24" ) ) {
230 if ( matrix_0.isEmpty() ) {
233 if ( matrix_0.getNumberOfIdentifiers() != 4 ) {
236 if ( matrix_0.getNumberOfCharacters() != 8 ) {
239 if ( !matrix_0.equals( matrix_0 ) ) {
242 if ( !matrix_0.equals( matrix_00 ) ) {
245 matrix_00.setState( "C", "4", "123" );
246 if ( matrix_0.equals( matrix_00 ) ) {
249 final Integer[][] ints = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
250 final CharacterStateMatrix<Integer> matrix_000 = new BasicCharacterStateMatrix<Integer>( ints );
251 matrix_000.toString();
252 if ( matrix_000.getNumberOfCharacters() != 4 ) {
255 if ( matrix_000.getNumberOfIdentifiers() != 3 ) {
258 if ( matrix_000.getState( 0, 1 ) != 2 ) {
261 if ( matrix_000.getState( 2, 3 ) != 12 ) {
264 final Integer[][] ints0 = { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
265 final CharacterStateMatrix<Integer> matrix_0000 = new BasicCharacterStateMatrix<Integer>( ints0 );
266 if ( !matrix_000.equals( matrix_0000 ) ) {
269 final Integer[][] ints00 = { { 1, 2, 3, -4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12 } };
270 final CharacterStateMatrix<Integer> matrix_00000 = new BasicCharacterStateMatrix<Integer>( ints00 );
271 if ( matrix_000.equals( matrix_00000 ) ) {
274 final CharacterStateMatrix<String> clone0 = matrix_0.copy();
275 final CharacterStateMatrix<String> clone00 = matrix_00.copy();
276 if ( !clone0.equals( matrix_0 ) ) {
279 if ( !clone00.equals( matrix_00 ) ) {
282 if ( clone00.equals( clone0 ) ) {
285 final CharacterStateMatrix<String> pivot0 = matrix_0.pivot();
286 final CharacterStateMatrix<String> pivot00 = matrix_00.pivot();
287 if ( !pivot0.getState( 1, 0 ).equals( "01" ) ) {
290 if ( !pivot0.getState( 6, 2 ).equals( "26" ) ) {
293 if ( !matrix_0.getState( 2, 6 ).equals( "26" ) ) {
296 final CharacterStateMatrix<String> pivotpivot00 = pivot00.pivot();
297 if ( !pivotpivot00.equals( matrix_00 ) ) {
300 final CharacterStateMatrix<BinaryStates> nex = new BasicCharacterStateMatrix<BinaryStates>( 4, 3 );
301 nex.setIdentifier( 0, "amphioxus" );
302 nex.setIdentifier( 1, "sponge" );
303 nex.setIdentifier( 2, "sea_anemone" );
304 nex.setIdentifier( 3, "cobra" );
305 nex.setCharacter( 0, "notch" );
306 nex.setCharacter( 1, "homeobox" );
307 nex.setCharacter( 2, "wnt" );
308 nex.setState( 0, 0, BinaryStates.ABSENT );
309 nex.setState( 0, 1, BinaryStates.ABSENT );
310 nex.setState( 0, 2, BinaryStates.ABSENT );
311 nex.setState( 1, 0, BinaryStates.PRESENT );
312 nex.setState( 1, 1, BinaryStates.PRESENT );
313 nex.setState( 1, 2, BinaryStates.ABSENT );
314 nex.setState( 2, 0, BinaryStates.PRESENT );
315 nex.setState( 2, 1, BinaryStates.PRESENT );
316 nex.setState( 2, 2, BinaryStates.PRESENT );
317 nex.setState( 3, 0, BinaryStates.PRESENT );
318 nex.setState( 3, 1, BinaryStates.ABSENT );
319 nex.setState( 3, 2, BinaryStates.ABSENT );
320 StringWriter w = new StringWriter();
321 nex.toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
322 //System.out.println( w.getBuffer().toString() );
323 w = new StringWriter();
324 nex.pivot().toWriter( w, CharacterStateMatrix.Format.NEXUS_BINARY );
325 //System.out.println( w.getBuffer().toString() );
327 catch ( final Exception e ) {
328 e.printStackTrace( System.out );
334 private static boolean testBasicSymmetricalDistanceMatrix() {
336 final DistanceMatrix matrix_0 = new BasicSymmetricalDistanceMatrix( 4 );
337 matrix_0.setIdentifier( 0, "A" );
338 matrix_0.setIdentifier( 1, "B" );
339 matrix_0.setIdentifier( 2, "C" );
340 matrix_0.setIdentifier( 3, "0123456789012" );
341 matrix_0.setValue( 1, 0, 0.00001 );
342 matrix_0.setValue( 0, 2, 0.0000009 );
343 matrix_0.setValue( 3, 0, 3.0 );
344 matrix_0.setValue( 1, 2, 4.0 );
345 matrix_0.setValue( 3, 1, 5.0 );
346 matrix_0.setValue( 2, 3, 6.0 );
347 if ( !matrix_0.getIdentifier( 0 ).equals( "A" ) ) {
350 if ( !matrix_0.getIdentifier( 1 ).equals( "B" ) ) {
353 if ( !matrix_0.getIdentifier( 2 ).equals( "C" ) ) {
356 if ( !matrix_0.getIdentifier( 3 ).equals( "0123456789012" ) ) {
359 if ( matrix_0.getSize() != 4 ) {
362 if ( !isEqual( matrix_0.getValue( 0, 0 ), 0.0 ) ) {
365 if ( !isEqual( matrix_0.getValue( 3, 3 ), 0.0 ) ) {
368 if ( !isEqual( matrix_0.getValue( 0, 1 ), 0.00001 ) ) {
371 if ( !isEqual( matrix_0.getValue( 0, 2 ), 0.0000009 ) ) {
374 if ( !isEqual( matrix_0.getValue( 0, 3 ), 3 ) ) {
377 if ( !isEqual( matrix_0.getValue( 1, 0 ), 0.00001 ) ) {
380 if ( !isEqual( matrix_0.getValue( 1, 2 ), 4 ) ) {
383 if ( !isEqual( matrix_0.getValue( 1, 3 ), 5 ) ) {
386 if ( !isEqual( matrix_0.getValue( 2, 0 ), 0.0000009 ) ) {
389 if ( !isEqual( matrix_0.getValue( 2, 1 ), 4 ) ) {
392 if ( !isEqual( matrix_0.getValue( 2, 3 ), 6 ) ) {
395 if ( !isEqual( matrix_0.getValue( 3, 0 ), 3 ) ) {
398 if ( !isEqual( matrix_0.getValue( 3, 1 ), 5 ) ) {
401 if ( !isEqual( matrix_0.getValue( 3, 2 ), 6 ) ) {
404 final StringBuffer matrix_0_phylip = new StringBuffer();
405 matrix_0_phylip.append( " 4" );
406 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
407 matrix_0_phylip.append( "A 0.000000 0.000010 0.000001 3.000000" );
408 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
409 matrix_0_phylip.append( "B 0.000010 0.000000 4.000000 5.000000" );
410 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
411 matrix_0_phylip.append( "C 0.000001 4.000000 0.000000 6.000000" );
412 matrix_0_phylip.append( ForesterUtil.LINE_SEPARATOR );
413 matrix_0_phylip.append( "0123456789 3.000000 5.000000 6.000000 0.000000" );
414 if ( !matrix_0_phylip.toString()
415 .equals( matrix_0.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() ) ) {
419 catch ( final Exception e ) {
420 e.printStackTrace( System.out );
426 private static boolean testDolloParsimony() {
428 final BinaryStates PRESENT = BinaryStates.PRESENT;
429 final BinaryStates ABSENT = BinaryStates.ABSENT;
430 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
431 final DolloParsimony dollo1 = DolloParsimony.createInstance();
432 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
433 final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
434 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
435 CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
437 m1.setIdentifier( 0, "a" );
438 m1.setIdentifier( 1, "b" );
439 m1.setIdentifier( 2, "c" );
440 m1.setIdentifier( 3, "d" );
441 m1.setIdentifier( 4, "e" );
442 m1.setIdentifier( 5, "f" );
443 m1.setIdentifier( 6, "g" );
444 m1.setIdentifier( 7, "h" );
445 m1.setIdentifier( 8, "i" );
446 m1.setCharacter( 0, "0" );
447 m1.setState( "a", "0", PRESENT );
448 m1.setState( "b", "0", ABSENT );
449 m1.setState( "c", "0", PRESENT );
450 m1.setState( "d", "0", ABSENT );
451 m1.setState( "e", "0", ABSENT );
452 m1.setState( "f", "0", ABSENT );
453 m1.setState( "g", "0", ABSENT );
454 m1.setState( "h", "0", ABSENT );
455 m1.setState( "i", "0", ABSENT );
456 dollo1.execute( p1, m1 );
457 if ( dollo1.getTotalGains() != 1 ) {
460 if ( dollo1.getTotalLosses() != 1 ) {
463 if ( dollo1.getTotalUnchanged() != 15 ) {
466 m1.setState( "b", "0", PRESENT );
467 dollo1.execute( p1, m1 );
468 if ( dollo1.getTotalGains() != 1 ) {
471 if ( dollo1.getTotalLosses() != 0 ) {
474 if ( dollo1.getTotalUnchanged() != 16 ) {
477 m1.setState( "b", "0", ABSENT );
478 m1.setState( "e", "0", PRESENT );
479 dollo1.execute( p1, m1 );
480 if ( dollo1.getTotalGains() != 1 ) {
483 if ( dollo1.getTotalLosses() != 3 ) {
486 if ( dollo1.getTotalUnchanged() != 13 ) {
489 m1.setState( "a", "0", ABSENT );
490 m1.setState( "c", "0", ABSENT );
491 m1.setState( "g", "0", PRESENT );
492 dollo1.setReturnInternalStates( true );
493 dollo1.setReturnGainLossMatrix( true );
494 dollo1.execute( p1, m1 );
495 if ( dollo1.getTotalGains() != 1 ) {
498 if ( dollo1.getTotalLosses() != 3 ) {
501 if ( dollo1.getTotalUnchanged() != 13 ) {
504 final DolloParsimony dollo2 = DolloParsimony.createInstance();
505 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
506 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";
507 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
508 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 18,
510 m2.setIdentifier( 0, "a" );
511 m2.setIdentifier( 1, "b" );
512 m2.setIdentifier( 2, "c" );
513 m2.setIdentifier( 3, "d" );
514 m2.setIdentifier( 4, "e" );
515 m2.setIdentifier( 5, "f" );
516 m2.setIdentifier( 6, "g" );
517 m2.setIdentifier( 7, "h" );
518 m2.setIdentifier( 8, "i" );
519 m2.setIdentifier( 9, "j" );
520 m2.setIdentifier( 10, "k" );
521 m2.setIdentifier( 11, "l" );
522 m2.setIdentifier( 12, "m" );
523 m2.setIdentifier( 13, "n" );
524 m2.setIdentifier( 14, "o" );
525 m2.setIdentifier( 15, "p" );
526 m2.setIdentifier( 16, "q" );
527 m2.setIdentifier( 17, "r" );
528 m2.setCharacter( 0, "0" );
529 m2.setCharacter( 1, "1" );
530 m2.setCharacter( 2, "2" );
531 m2.setCharacter( 3, "3" );
532 m2.setState( "a", "0", PRESENT );
533 m2.setState( "b", "0", ABSENT );
534 m2.setState( "c", "0", PRESENT );
535 m2.setState( "d", "0", ABSENT );
536 m2.setState( "e", "0", ABSENT );
537 m2.setState( "f", "0", ABSENT );
538 m2.setState( "g", "0", ABSENT );
539 m2.setState( "h", "0", ABSENT );
540 m2.setState( "i", "0", ABSENT );
541 m2.setState( "j", "0", ABSENT );
542 m2.setState( "k", "0", ABSENT );
543 m2.setState( "l", "0", ABSENT );
544 m2.setState( "m", "0", ABSENT );
545 m2.setState( "n", "0", ABSENT );
546 m2.setState( "o", "0", ABSENT );
547 m2.setState( "p", "0", ABSENT );
548 m2.setState( "q", "0", ABSENT );
549 m2.setState( "r", "0", ABSENT );
550 m2.setState( "a", "1", PRESENT );
551 m2.setState( "b", "1", ABSENT );
552 m2.setState( "c", "1", PRESENT );
553 m2.setState( "d", "1", ABSENT );
554 m2.setState( "e", "1", ABSENT );
555 m2.setState( "f", "1", ABSENT );
556 m2.setState( "g", "1", PRESENT );
557 m2.setState( "h", "1", ABSENT );
558 m2.setState( "i", "1", ABSENT );
559 m2.setState( "j", "1", PRESENT );
560 m2.setState( "k", "1", ABSENT );
561 m2.setState( "l", "1", ABSENT );
562 m2.setState( "m", "1", PRESENT );
563 m2.setState( "n", "1", ABSENT );
564 m2.setState( "o", "1", ABSENT );
565 m2.setState( "p", "1", ABSENT );
566 m2.setState( "q", "1", ABSENT );
567 m2.setState( "r", "1", ABSENT );
568 m2.setState( "a", "2", ABSENT );
569 m2.setState( "b", "2", ABSENT );
570 m2.setState( "c", "2", ABSENT );
571 m2.setState( "d", "2", ABSENT );
572 m2.setState( "e", "2", ABSENT );
573 m2.setState( "f", "2", ABSENT );
574 m2.setState( "g", "2", ABSENT );
575 m2.setState( "h", "2", ABSENT );
576 m2.setState( "i", "2", ABSENT );
577 m2.setState( "j", "2", PRESENT );
578 m2.setState( "k", "2", ABSENT );
579 m2.setState( "l", "2", ABSENT );
580 m2.setState( "m", "2", PRESENT );
581 m2.setState( "n", "2", ABSENT );
582 m2.setState( "o", "2", ABSENT );
583 m2.setState( "p", "2", PRESENT );
584 m2.setState( "q", "2", ABSENT );
585 m2.setState( "r", "2", ABSENT );
586 m2.setState( "a", "3", ABSENT );
587 m2.setState( "b", "3", ABSENT );
588 m2.setState( "c", "3", PRESENT );
589 m2.setState( "d", "3", ABSENT );
590 m2.setState( "e", "3", ABSENT );
591 m2.setState( "f", "3", ABSENT );
592 m2.setState( "g", "3", PRESENT );
593 m2.setState( "h", "3", ABSENT );
594 m2.setState( "i", "3", ABSENT );
595 m2.setState( "j", "3", ABSENT );
596 m2.setState( "k", "3", ABSENT );
597 m2.setState( "l", "3", ABSENT );
598 m2.setState( "m", "3", ABSENT );
599 m2.setState( "n", "3", ABSENT );
600 m2.setState( "o", "3", ABSENT );
601 m2.setState( "p", "3", ABSENT );
602 m2.setState( "q", "3", ABSENT );
603 m2.setState( "r", "3", ABSENT );
604 dollo2.setReturnInternalStates( true );
605 dollo2.setReturnGainLossMatrix( true );
606 dollo2.execute( p2, m2 );
607 final CharacterStateMatrix<BinaryStates> i_m = dollo2.getInternalStatesMatrix();
608 final CharacterStateMatrix<GainLossStates> gl_m = dollo2.getGainLossMatrix();
609 if ( dollo2.getTotalGains() != 3 ) {
612 if ( dollo2.getTotalLosses() != 22 ) {
615 if ( dollo2.getTotalUnchanged() != 95 ) {
618 if ( i_m.getState( "ab", "0" ) != PRESENT ) {
621 if ( i_m.getState( "ac", "0" ) != PRESENT ) {
624 if ( i_m.getState( "ad", "0" ) != ABSENT ) {
627 if ( i_m.getState( "af", "0" ) != ABSENT ) {
630 if ( i_m.getState( "ef", "0" ) != ABSENT ) {
633 if ( i_m.getState( "ai", "0" ) != ABSENT ) {
636 if ( i_m.getState( "gi", "0" ) != ABSENT ) {
639 if ( i_m.getState( "jl", "0" ) != ABSENT ) {
642 if ( i_m.getState( "mo", "0" ) != ABSENT ) {
645 if ( i_m.getState( "pr", "0" ) != ABSENT ) {
648 if ( i_m.getState( "jr", "0" ) != ABSENT ) {
651 if ( i_m.getState( "root", "0" ) != ABSENT ) {
654 if ( i_m.getState( "ab", "1" ) != PRESENT ) {
657 if ( i_m.getState( "ac", "1" ) != PRESENT ) {
660 if ( i_m.getState( "ad", "1" ) != PRESENT ) {
663 if ( i_m.getState( "af", "1" ) != PRESENT ) {
666 if ( i_m.getState( "ef", "1" ) != ABSENT ) {
669 if ( i_m.getState( "ai", "1" ) != PRESENT ) {
672 if ( i_m.getState( "gi", "1" ) != PRESENT ) {
675 if ( i_m.getState( "jl", "1" ) != PRESENT ) {
678 if ( i_m.getState( "mo", "1" ) != PRESENT ) {
681 if ( i_m.getState( "pr", "1" ) != ABSENT ) {
684 if ( i_m.getState( "jr", "1" ) != PRESENT ) {
687 if ( i_m.getState( "root", "1" ) != PRESENT ) {
690 if ( i_m.getState( "ab", "2" ) != ABSENT ) {
693 if ( i_m.getState( "ac", "2" ) != ABSENT ) {
696 if ( i_m.getState( "ad", "2" ) != ABSENT ) {
699 if ( i_m.getState( "af", "2" ) != ABSENT ) {
702 if ( i_m.getState( "ef", "2" ) != ABSENT ) {
705 if ( i_m.getState( "ai", "2" ) != ABSENT ) {
708 if ( i_m.getState( "gi", "2" ) != ABSENT ) {
711 if ( i_m.getState( "jl", "2" ) != PRESENT ) {
714 if ( i_m.getState( "mo", "2" ) != PRESENT ) {
717 if ( i_m.getState( "pr", "2" ) != PRESENT ) {
720 if ( i_m.getState( "jr", "2" ) != PRESENT ) {
723 if ( i_m.getState( "root", "2" ) != ABSENT ) {
726 if ( i_m.getState( "ab", "3" ) != ABSENT ) {
729 if ( i_m.getState( "ac", "3" ) != PRESENT ) {
732 if ( i_m.getState( "ad", "3" ) != PRESENT ) {
735 if ( i_m.getState( "af", "3" ) != PRESENT ) {
738 if ( i_m.getState( "ef", "3" ) != ABSENT ) {
741 if ( i_m.getState( "ai", "3" ) != PRESENT ) {
744 if ( i_m.getState( "gi", "3" ) != PRESENT ) {
747 if ( i_m.getState( "jl", "3" ) != ABSENT ) {
750 if ( i_m.getState( "mo", "3" ) != ABSENT ) {
753 if ( i_m.getState( "pr", "3" ) != ABSENT ) {
756 if ( i_m.getState( "jr", "3" ) != ABSENT ) {
759 if ( i_m.getState( "root", "3" ) != ABSENT ) {
762 if ( gl_m.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
765 final DolloParsimony dollo9 = DolloParsimony.createInstance();
766 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
767 final String p9_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
768 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
769 m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9, 3 );
770 m1.setIdentifier( 0, "a" );
771 m1.setIdentifier( 1, "b" );
772 m1.setIdentifier( 2, "c" );
773 m1.setIdentifier( 3, "d" );
774 m1.setIdentifier( 4, "e" );
775 m1.setIdentifier( 5, "f" );
776 m1.setIdentifier( 6, "g" );
777 m1.setIdentifier( 7, "h" );
778 m1.setIdentifier( 8, "i" );
779 m1.setState( 0, 0, PRESENT );
780 m1.setState( 1, 0, ABSENT );
781 m1.setState( 2, 0, PRESENT );
782 m1.setState( 3, 0, ABSENT );
783 m1.setState( 4, 0, ABSENT );
784 m1.setState( 5, 0, ABSENT );
785 m1.setState( 6, 0, ABSENT );
786 m1.setState( 7, 0, ABSENT );
787 m1.setState( 8, 0, ABSENT );
788 m1.setState( 0, 1, PRESENT );
789 m1.setState( 1, 1, PRESENT );
790 m1.setState( 2, 1, PRESENT );
791 m1.setState( 3, 1, PRESENT );
792 m1.setState( 4, 1, ABSENT );
793 m1.setState( 5, 1, ABSENT );
794 m1.setState( 6, 1, ABSENT );
795 m1.setState( 7, 1, ABSENT );
796 m1.setState( 8, 1, ABSENT );
797 m1.setState( 0, 2, PRESENT );
798 m1.setState( 1, 2, ABSENT );
799 m1.setState( 2, 2, ABSENT );
800 m1.setState( 3, 2, ABSENT );
801 m1.setState( 4, 2, ABSENT );
802 m1.setState( 5, 2, ABSENT );
803 m1.setState( 6, 2, ABSENT );
804 m1.setState( 7, 2, PRESENT );
805 m1.setState( 8, 2, ABSENT );
806 dollo9.execute( p9, m1 );
807 if ( dollo9.getTotalGains() != 3 ) {
810 if ( dollo9.getTotalLosses() != 6 ) {
813 final DolloParsimony dollo10 = DolloParsimony.createInstance();
814 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
815 final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
816 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
817 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m10 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
819 m10.setIdentifier( 0, "a" );
820 m10.setIdentifier( 1, "b" );
821 m10.setIdentifier( 2, "c" );
822 m10.setIdentifier( 3, "d" );
823 m10.setIdentifier( 4, "e" );
824 m10.setIdentifier( 5, "f" );
825 m10.setIdentifier( 6, "g" );
826 m10.setIdentifier( 7, "h" );
827 m10.setIdentifier( 8, "i" );
828 m10.setState( 0, 0, PRESENT );
829 m10.setState( 1, 0, ABSENT );
830 m10.setState( 2, 0, PRESENT );
831 m10.setState( 3, 0, ABSENT );
832 m10.setState( 4, 0, ABSENT );
833 m10.setState( 5, 0, ABSENT );
834 m10.setState( 6, 0, ABSENT );
835 m10.setState( 7, 0, ABSENT );
836 m10.setState( 8, 0, ABSENT );
837 dollo10.execute( p10, m10 );
838 if ( dollo10.getTotalGains() != 1 ) {
841 if ( dollo10.getTotalLosses() != 1 ) {
845 catch ( final Exception e ) {
846 e.printStackTrace( System.out );
852 private static boolean testDolloParsimonyOnNonBinaryTree() {
854 final BinaryStates PRESENT = BinaryStates.PRESENT;
855 final BinaryStates ABSENT = BinaryStates.ABSENT;
856 final DolloParsimony dollo1 = DolloParsimony.createInstance();
857 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
858 final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
859 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
860 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
862 m1.setIdentifier( 0, "a" );
863 m1.setIdentifier( 1, "b" );
864 m1.setIdentifier( 2, "y" );
865 m1.setIdentifier( 3, "c" );
866 m1.setIdentifier( 4, "d" );
867 m1.setIdentifier( 5, "e" );
868 m1.setIdentifier( 6, "f" );
869 m1.setIdentifier( 7, "g" );
870 m1.setIdentifier( 8, "h" );
871 m1.setIdentifier( 9, "i" );
872 m1.setCharacter( 0, "0" );
873 m1.setState( "a", "0", PRESENT );
874 m1.setState( "b", "0", ABSENT );
875 m1.setState( "y", "0", PRESENT );
876 m1.setState( "c", "0", PRESENT );
877 m1.setState( "d", "0", ABSENT );
878 m1.setState( "e", "0", ABSENT );
879 m1.setState( "f", "0", ABSENT );
880 m1.setState( "g", "0", ABSENT );
881 m1.setState( "h", "0", ABSENT );
882 m1.setState( "i", "0", ABSENT );
883 dollo1.execute( p1, m1 );
884 if ( dollo1.getTotalGains() != 1 ) {
887 if ( dollo1.getTotalLosses() != 1 ) {
890 if ( dollo1.getTotalUnchanged() != 16 ) {
893 m1.setState( "b", "0", PRESENT );
894 dollo1.execute( p1, m1 );
895 if ( dollo1.getTotalGains() != 1 ) {
898 if ( dollo1.getTotalLosses() != 0 ) {
901 if ( dollo1.getTotalUnchanged() != 17 ) {
904 m1.setState( "a", "0", ABSENT );
905 m1.setState( "b", "0", ABSENT );
906 dollo1.execute( p1, m1 );
907 if ( dollo1.getTotalGains() != 1 ) {
910 if ( dollo1.getTotalLosses() != 2 ) {
913 if ( dollo1.getTotalUnchanged() != 15 ) {
916 m1.setState( "y", "0", ABSENT );
917 dollo1.execute( p1, m1 );
918 if ( dollo1.getTotalGains() != 1 ) {
921 if ( dollo1.getTotalLosses() != 0 ) {
924 if ( dollo1.getTotalUnchanged() != 17 ) {
927 final DolloParsimony dollo2 = DolloParsimony.createInstance();
928 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
929 final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r";
930 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
931 final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
933 m2.setIdentifier( 0, "a" );
934 m2.setIdentifier( 1, "b" );
935 m2.setIdentifier( 2, "y" );
936 m2.setIdentifier( 3, "c" );
937 m2.setIdentifier( 4, "d" );
938 m2.setIdentifier( 5, "e" );
939 m2.setIdentifier( 6, "f" );
940 m2.setIdentifier( 7, "g" );
941 m2.setIdentifier( 8, "h" );
942 m2.setIdentifier( 9, "i" );
943 m2.setCharacter( 0, "0" );
944 m2.setState( "a", "0", PRESENT );
945 m2.setState( "b", "0", ABSENT );
946 m2.setState( "y", "0", PRESENT );
947 m2.setState( "c", "0", PRESENT );
948 m2.setState( "d", "0", ABSENT );
949 m2.setState( "e", "0", ABSENT );
950 m2.setState( "f", "0", ABSENT );
951 m2.setState( "g", "0", ABSENT );
952 m2.setState( "h", "0", ABSENT );
953 m2.setState( "i", "0", ABSENT );
954 dollo2.setReturnInternalStates( true );
955 dollo2.execute( p2, m2 );
956 CharacterStateMatrix<BinaryStates> i_m2 = dollo2.getInternalStatesMatrix();
957 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
960 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
963 if ( i_m2.getState( "af", "0" ) != ABSENT ) {
966 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
969 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
972 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
975 if ( dollo2.getTotalGains() != 1 ) {
978 if ( dollo2.getTotalLosses() != 2 ) {
981 if ( dollo2.getTotalUnchanged() != 14 ) {
984 m2.setState( "b", "0", PRESENT );
985 dollo2.execute( p2, m2 );
986 if ( dollo2.getTotalGains() != 1 ) {
989 if ( dollo2.getTotalLosses() != 1 ) {
992 if ( dollo2.getTotalUnchanged() != 15 ) {
995 m2.setState( "a", "0", ABSENT );
996 m2.setState( "b", "0", ABSENT );
997 dollo2.execute( p2, m2 );
998 if ( dollo2.getTotalGains() != 1 ) {
1001 if ( dollo2.getTotalLosses() != 3 ) {
1004 if ( dollo2.getTotalUnchanged() != 13 ) {
1007 m2.setState( "y", "0", ABSENT );
1008 dollo2.execute( p2, m2 );
1009 if ( dollo2.getTotalGains() != 1 ) {
1012 if ( dollo2.getTotalLosses() != 0 ) {
1015 if ( dollo2.getTotalUnchanged() != 16 ) {
1018 m2.setState( "c", "0", ABSENT );
1019 dollo2.execute( p2, m2 );
1020 if ( dollo2.getTotalGains() != 0 ) {
1023 if ( dollo2.getTotalLosses() != 0 ) {
1026 if ( dollo2.getTotalUnchanged() != 17 ) {
1029 m2.setState( "y", "0", PRESENT );
1030 m2.setState( "e", "0", PRESENT );
1031 dollo2.execute( p2, m2 );
1032 if ( dollo2.getTotalGains() != 1 ) {
1035 if ( dollo2.getTotalLosses() != 5 ) {
1038 if ( dollo2.getTotalUnchanged() != 11 ) {
1041 i_m2 = dollo2.getInternalStatesMatrix();
1042 if ( i_m2.getState( "aby", "0" ) != PRESENT ) {
1045 if ( i_m2.getState( "cad", "0" ) != PRESENT ) {
1048 if ( i_m2.getState( "af", "0" ) != PRESENT ) {
1051 if ( i_m2.getState( "gh", "0" ) != ABSENT ) {
1054 if ( i_m2.getState( "ah", "0" ) != ABSENT ) {
1057 if ( i_m2.getState( "r", "0" ) != ABSENT ) {
1061 catch ( final Exception e ) {
1062 e.printStackTrace( System.out );
1068 private static boolean testFitchParsimony() {
1070 final BinaryStates PRESENT = BinaryStates.PRESENT;
1071 final BinaryStates ABSENT = BinaryStates.ABSENT;
1072 final GainLossStates GAIN = GainLossStates.GAIN;
1073 final GainLossStates LOSS = GainLossStates.LOSS;
1074 final GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
1075 final GainLossStates UNCHANGED_ABSENT = GainLossStates.UNCHANGED_ABSENT;
1076 final FitchParsimony<String> fitch1 = new FitchParsimony<String>();
1077 final PhylogenyFactory factory1 = ParserBasedPhylogenyFactory.getInstance();
1078 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";
1079 final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
1080 final CharacterStateMatrix<String> m1 = new BasicCharacterStateMatrix<String>( 18, 1 );
1081 m1.setIdentifier( 0, "a" );
1082 m1.setIdentifier( 1, "b" );
1083 m1.setIdentifier( 2, "c" );
1084 m1.setIdentifier( 3, "d" );
1085 m1.setIdentifier( 4, "e" );
1086 m1.setIdentifier( 5, "f" );
1087 m1.setIdentifier( 6, "g" );
1088 m1.setIdentifier( 7, "h" );
1089 m1.setIdentifier( 8, "i" );
1090 m1.setIdentifier( 9, "j" );
1091 m1.setIdentifier( 10, "k" );
1092 m1.setIdentifier( 11, "l" );
1093 m1.setIdentifier( 12, "m" );
1094 m1.setIdentifier( 13, "n" );
1095 m1.setIdentifier( 14, "o" );
1096 m1.setIdentifier( 15, "p" );
1097 m1.setIdentifier( 16, "q" );
1098 m1.setIdentifier( 17, "r" );
1099 m1.setCharacter( 0, "0" );
1100 m1.setState( "a", "0", "A" );
1101 m1.setState( "b", "0", "A" );
1102 m1.setState( "c", "0", "B" );
1103 m1.setState( "d", "0", "C" );
1104 m1.setState( "e", "0", "D" );
1105 m1.setState( "f", "0", "A" );
1106 m1.setState( "g", "0", "A" );
1107 m1.setState( "h", "0", "B" );
1108 m1.setState( "i", "0", "C" );
1109 m1.setState( "j", "0", "A" );
1110 m1.setState( "k", "0", "B" );
1111 m1.setState( "l", "0", "C" );
1112 m1.setState( "m", "0", "B" );
1113 m1.setState( "n", "0", "B" );
1114 m1.setState( "o", "0", "B" );
1115 m1.setState( "p", "0", "A" );
1116 m1.setState( "q", "0", "C" );
1117 m1.setState( "r", "0", "D" );
1118 fitch1.setReturnInternalStates( true );
1119 fitch1.setReturnGainLossMatrix( false );
1120 fitch1.setRandomize( false );
1121 fitch1.execute( p1, m1 );
1122 final CharacterStateMatrix<String> i_m = fitch1.getInternalStatesMatrix();
1123 final CharacterStateMatrix<List<String>> i_m_all = fitch1.getInternalStatesMatrixPriorToTraceback();
1124 if ( fitch1.getCost() != 10 ) {
1127 if ( !i_m.getState( "ab", "0" ).equals( "A" ) ) {
1130 if ( !i_m.getState( "ac", "0" ).equals( "A" ) ) {
1133 if ( !i_m.getState( "ad", "0" ).equals( "A" ) ) {
1136 if ( !i_m.getState( "ef", "0" ).equals( "A" ) ) {
1139 if ( !i_m.getState( "ai", "0" ).equals( "A" ) ) {
1142 if ( !i_m.getState( "gi", "0" ).equals( "A" ) ) {
1145 if ( !i_m.getState( "jl", "0" ).equals( "A" ) ) {
1148 if ( !i_m.getState( "mo", "0" ).equals( "B" ) ) {
1151 if ( !i_m.getState( "pr", "0" ).equals( "A" ) ) {
1154 if ( i_m_all.getState( "ab", "0" ).size() != 1 ) {
1157 if ( !i_m_all.getState( "ab", "0" ).contains( "A" ) ) {
1160 if ( i_m_all.getState( "ac", "0" ).size() != 2 ) {
1163 if ( !i_m_all.getState( "ac", "0" ).contains( "A" ) ) {
1166 if ( !i_m_all.getState( "ac", "0" ).contains( "B" ) ) {
1169 if ( i_m_all.getState( "ad", "0" ).size() != 3 ) {
1172 if ( !i_m_all.getState( "ad", "0" ).contains( "A" ) ) {
1175 if ( !i_m_all.getState( "ad", "0" ).contains( "B" ) ) {
1178 if ( !i_m_all.getState( "ad", "0" ).contains( "C" ) ) {
1181 if ( i_m_all.getState( "af", "0" ).size() != 1 ) {
1184 if ( !i_m_all.getState( "af", "0" ).contains( "A" ) ) {
1187 if ( i_m_all.getState( "ef", "0" ).size() != 2 ) {
1190 if ( !i_m_all.getState( "ef", "0" ).contains( "A" ) ) {
1193 if ( !i_m_all.getState( "ef", "0" ).contains( "D" ) ) {
1196 if ( i_m_all.getState( "gi", "0" ).size() != 3 ) {
1199 if ( !i_m_all.getState( "gi", "0" ).contains( "A" ) ) {
1202 if ( !i_m_all.getState( "gi", "0" ).contains( "B" ) ) {
1205 if ( !i_m_all.getState( "gi", "0" ).contains( "C" ) ) {
1208 if ( i_m_all.getState( "ai", "0" ).size() != 1 ) {
1211 if ( !i_m_all.getState( "ai", "0" ).contains( "A" ) ) {
1214 if ( i_m_all.getState( "jl", "0" ).size() != 3 ) {
1217 if ( !i_m_all.getState( "jl", "0" ).contains( "A" ) ) {
1220 if ( !i_m_all.getState( "jl", "0" ).contains( "B" ) ) {
1223 if ( !i_m_all.getState( "jl", "0" ).contains( "C" ) ) {
1226 if ( i_m_all.getState( "mo", "0" ).size() != 1 ) {
1229 if ( !i_m_all.getState( "mo", "0" ).contains( "B" ) ) {
1232 if ( i_m_all.getState( "pr", "0" ).size() != 3 ) {
1235 if ( !i_m_all.getState( "pr", "0" ).contains( "A" ) ) {
1238 if ( !i_m_all.getState( "pr", "0" ).contains( "C" ) ) {
1241 if ( !i_m_all.getState( "pr", "0" ).contains( "D" ) ) {
1244 if ( i_m_all.getState( "jr", "0" ).size() != 4 ) {
1247 if ( !i_m_all.getState( "jr", "0" ).contains( "A" ) ) {
1250 if ( !i_m_all.getState( "jr", "0" ).contains( "B" ) ) {
1253 if ( !i_m_all.getState( "jr", "0" ).contains( "C" ) ) {
1256 if ( !i_m_all.getState( "jr", "0" ).contains( "D" ) ) {
1259 final FitchParsimony<String> fitch2 = new FitchParsimony<String>();
1260 final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
1261 final String p2_str = "((a,b)ab,(c,(d,e)de)cde)r";
1262 final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
1263 final CharacterStateMatrix<String> m2 = new BasicCharacterStateMatrix<String>( 5, 1 );
1264 m2.setIdentifier( 0, "a" );
1265 m2.setIdentifier( 1, "b" );
1266 m2.setIdentifier( 2, "c" );
1267 m2.setIdentifier( 3, "d" );
1268 m2.setIdentifier( 4, "e" );
1269 m2.setCharacter( 0, "0" );
1270 m2.setState( "a", "0", "C" );
1271 m2.setState( "b", "0", "A" );
1272 m2.setState( "c", "0", "C" );
1273 m2.setState( "d", "0", "A" );
1274 m2.setState( "e", "0", "G" );
1275 fitch2.setReturnInternalStates( true );
1276 fitch2.setReturnGainLossMatrix( false );
1277 fitch2.execute( p2, m2 );
1278 final CharacterStateMatrix<String> i_m2 = fitch2.getInternalStatesMatrix();
1279 final CharacterStateMatrix<List<String>> i_m_all2 = fitch2.getInternalStatesMatrixPriorToTraceback();
1280 if ( fitch2.getCost() != 3 ) {
1283 if ( !i_m2.getState( "ab", "0" ).equals( "A" ) ) {
1286 if ( !i_m2.getState( "de", "0" ).equals( "A" ) ) {
1289 if ( !i_m2.getState( "cde", "0" ).equals( "A" ) ) {
1292 if ( !i_m2.getState( "r", "0" ).equals( "A" ) ) {
1295 if ( i_m_all2.getState( "cde", "0" ).size() != 3 ) {
1298 if ( !i_m_all2.getState( "cde", "0" ).contains( "A" ) ) {
1301 if ( !i_m_all2.getState( "cde", "0" ).contains( "C" ) ) {
1304 if ( !i_m_all2.getState( "cde", "0" ).contains( "G" ) ) {
1307 if ( i_m_all2.getState( "ab", "0" ).size() != 2 ) {
1310 if ( !i_m_all2.getState( "ab", "0" ).contains( "A" ) ) {
1313 if ( !i_m_all2.getState( "ab", "0" ).contains( "C" ) ) {
1316 fitch2.setReturnInternalStates( true );
1317 fitch2.setReturnGainLossMatrix( false );
1318 fitch2.setUseLast( true );
1319 fitch2.execute( p2, m2 );
1320 final CharacterStateMatrix<String> i_m21 = fitch2.getInternalStatesMatrix();
1321 final CharacterStateMatrix<List<String>> i_m_all21 = fitch2.getInternalStatesMatrixPriorToTraceback();
1322 if ( fitch2.getCost() != 3 ) {
1325 if ( !i_m21.getState( "ab", "0" ).equals( "C" ) ) {
1328 if ( !i_m21.getState( "de", "0" ).equals( "G" ) ) {
1331 if ( !i_m21.getState( "cde", "0" ).equals( "C" ) ) {
1334 if ( !i_m21.getState( "r", "0" ).equals( "C" ) ) {
1337 if ( i_m_all21.getState( "cde", "0" ).size() != 3 ) {
1340 if ( !i_m_all21.getState( "cde", "0" ).contains( "A" ) ) {
1343 if ( !i_m_all21.getState( "cde", "0" ).contains( "C" ) ) {
1346 if ( !i_m_all21.getState( "cde", "0" ).contains( "G" ) ) {
1349 final FitchParsimony<String> fitch3 = new FitchParsimony<String>();
1350 final PhylogenyFactory factory3 = ParserBasedPhylogenyFactory.getInstance();
1351 final String p3_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1352 final Phylogeny p3 = factory3.create( p3_str, new NHXParser() )[ 0 ];
1353 final CharacterStateMatrix<String> m3 = new BasicCharacterStateMatrix<String>( 6, 1 );
1354 m3.setIdentifier( 0, "a" );
1355 m3.setIdentifier( 1, "b" );
1356 m3.setIdentifier( 2, "c" );
1357 m3.setIdentifier( 3, "d" );
1358 m3.setIdentifier( 4, "e" );
1359 m3.setIdentifier( 5, "f" );
1360 m3.setCharacter( 0, "0" );
1361 m3.setState( "a", "0", "C" );
1362 m3.setState( "b", "0", "U" );
1363 m3.setState( "c", "0", "G" );
1364 m3.setState( "d", "0", "U" );
1365 m3.setState( "e", "0", "A" );
1366 m3.setState( "f", "0", "A" );
1367 fitch3.setReturnInternalStates( true );
1368 fitch3.setReturnGainLossMatrix( false );
1369 fitch3.execute( p3, m3 );
1370 final CharacterStateMatrix<String> i_m3 = fitch3.getInternalStatesMatrix();
1371 final CharacterStateMatrix<List<String>> i_m_all3 = fitch3.getInternalStatesMatrixPriorToTraceback();
1372 if ( fitch3.getCost() != 4 ) {
1375 if ( !i_m3.getState( "ab", "0" ).equals( "U" ) ) {
1378 if ( !i_m3.getState( "cd", "0" ).equals( "U" ) ) {
1381 if ( !i_m3.getState( "cde", "0" ).equals( "U" ) ) {
1384 if ( !i_m3.getState( "abcde", "0" ).equals( "U" ) ) {
1387 if ( !i_m3.getState( "r", "0" ).equals( "A" ) ) {
1390 if ( i_m_all3.getState( "cde", "0" ).size() != 3 ) {
1393 if ( !i_m_all3.getState( "cde", "0" ).contains( "A" ) ) {
1396 if ( !i_m_all3.getState( "cde", "0" ).contains( "G" ) ) {
1399 if ( !i_m_all3.getState( "cde", "0" ).contains( "U" ) ) {
1402 if ( i_m_all3.getState( "ab", "0" ).size() != 2 ) {
1405 if ( !i_m_all3.getState( "ab", "0" ).contains( "C" ) ) {
1408 if ( !i_m_all3.getState( "ab", "0" ).contains( "U" ) ) {
1411 if ( i_m_all3.getState( "cd", "0" ).size() != 2 ) {
1414 if ( !i_m_all3.getState( "cd", "0" ).contains( "G" ) ) {
1417 if ( !i_m_all3.getState( "cd", "0" ).contains( "U" ) ) {
1420 if ( i_m_all3.getState( "abcde", "0" ).size() != 1 ) {
1423 if ( !i_m_all3.getState( "abcde", "0" ).contains( "U" ) ) {
1426 if ( i_m_all3.getState( "r", "0" ).size() != 2 ) {
1429 if ( !i_m_all3.getState( "r", "0" ).contains( "A" ) ) {
1432 if ( !i_m_all3.getState( "r", "0" ).contains( "U" ) ) {
1435 final FitchParsimony<BinaryStates> fitch4 = new FitchParsimony<BinaryStates>();
1436 final PhylogenyFactory factory4 = ParserBasedPhylogenyFactory.getInstance();
1437 final String p4_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1438 final Phylogeny p4 = factory4.create( p4_str, new NHXParser() )[ 0 ];
1439 final CharacterStateMatrix<BinaryStates> m4 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1440 m4.setIdentifier( 0, "a" );
1441 m4.setIdentifier( 1, "b" );
1442 m4.setIdentifier( 2, "c" );
1443 m4.setIdentifier( 3, "d" );
1444 m4.setIdentifier( 4, "e" );
1445 m4.setIdentifier( 5, "f" );
1446 m4.setCharacter( 0, "0" );
1447 m4.setState( "a", "0", PRESENT );
1448 m4.setState( "b", "0", ABSENT );
1449 m4.setState( "c", "0", PRESENT );
1450 m4.setState( "d", "0", PRESENT );
1451 m4.setState( "e", "0", ABSENT );
1452 m4.setState( "f", "0", ABSENT );
1453 fitch4.setReturnInternalStates( true );
1454 fitch4.setReturnGainLossMatrix( true );
1455 fitch4.execute( p4, m4 );
1456 final CharacterStateMatrix<GainLossStates> gl_m_4 = fitch4.getGainLossMatrix();
1457 if ( fitch4.getCost() != 2 ) {
1460 if ( fitch4.getTotalLosses() != 0 ) {
1463 if ( fitch4.getTotalGains() != 2 ) {
1466 if ( fitch4.getTotalUnchanged() != 9 ) {
1469 if ( gl_m_4.getState( "a", "0" ) != GAIN ) {
1472 if ( gl_m_4.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1475 if ( gl_m_4.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1478 if ( gl_m_4.getState( "cd", "0" ) != GAIN ) {
1481 if ( gl_m_4.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1484 final FitchParsimony<BinaryStates> fitch5 = new FitchParsimony<BinaryStates>();
1485 final PhylogenyFactory factory5 = ParserBasedPhylogenyFactory.getInstance();
1486 final String p5_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1487 final Phylogeny p5 = factory5.create( p5_str, new NHXParser() )[ 0 ];
1488 final CharacterStateMatrix<BinaryStates> m5 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1489 m5.setIdentifier( 0, "a" );
1490 m5.setIdentifier( 1, "b" );
1491 m5.setIdentifier( 2, "c" );
1492 m5.setIdentifier( 3, "d" );
1493 m5.setIdentifier( 4, "e" );
1494 m5.setIdentifier( 5, "f" );
1495 m5.setCharacter( 0, "0" );
1496 m5.setState( "a", "0", PRESENT );
1497 m5.setState( "b", "0", ABSENT );
1498 m5.setState( "c", "0", PRESENT );
1499 m5.setState( "d", "0", ABSENT );
1500 m5.setState( "e", "0", PRESENT );
1501 m5.setState( "f", "0", ABSENT );
1502 fitch5.setReturnInternalStates( true );
1503 fitch5.setReturnGainLossMatrix( true );
1504 fitch5.execute( p5, m5 );
1505 final CharacterStateMatrix<GainLossStates> gl_m_5 = fitch5.getGainLossMatrix();
1506 if ( fitch5.getCost() != 3 ) {
1509 if ( fitch5.getTotalLosses() != 2 ) {
1512 if ( fitch5.getTotalGains() != 1 ) {
1515 if ( fitch5.getTotalUnchanged() != 8 ) {
1518 if ( gl_m_5.getState( "abcde", "0" ) != GAIN ) {
1521 if ( gl_m_5.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1524 if ( gl_m_5.getState( "b", "0" ) != LOSS ) {
1527 if ( gl_m_5.getState( "d", "0" ) != LOSS ) {
1530 if ( gl_m_5.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1533 final FitchParsimony<BinaryStates> fitch6 = new FitchParsimony<BinaryStates>();
1534 final PhylogenyFactory factory6 = ParserBasedPhylogenyFactory.getInstance();
1535 final String p6_str = "(((a,b)ab,((c,d)cd,e)cde)abcde,f)r";
1536 final Phylogeny p6 = factory6.create( p6_str, new NHXParser() )[ 0 ];
1537 final CharacterStateMatrix<BinaryStates> m6 = new BasicCharacterStateMatrix<BinaryStates>( 6, 1 );
1538 m6.setIdentifier( 0, "a" );
1539 m6.setIdentifier( 1, "b" );
1540 m6.setIdentifier( 2, "c" );
1541 m6.setIdentifier( 3, "d" );
1542 m6.setIdentifier( 4, "e" );
1543 m6.setIdentifier( 5, "f" );
1544 m6.setCharacter( 0, "0" );
1545 m6.setState( "a", "0", PRESENT );
1546 m6.setState( "b", "0", ABSENT );
1547 m6.setState( "c", "0", PRESENT );
1548 m6.setState( "d", "0", PRESENT );
1549 m6.setState( "e", "0", ABSENT );
1550 m6.setState( "f", "0", PRESENT );
1551 fitch6.setReturnInternalStates( true );
1552 fitch6.setReturnGainLossMatrix( true );
1553 fitch6.execute( p6, m6 );
1554 final CharacterStateMatrix<GainLossStates> gl_m_6 = fitch6.getGainLossMatrix();
1555 if ( fitch6.getCost() != 2 ) {
1558 if ( fitch6.getTotalLosses() != 2 ) {
1561 if ( fitch6.getTotalGains() != 0 ) {
1564 if ( fitch6.getTotalUnchanged() != 9 ) {
1567 if ( gl_m_6.getState( "abcde", "0" ) != UNCHANGED_PRESENT ) {
1570 if ( gl_m_6.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1573 if ( gl_m_6.getState( "b", "0" ) != LOSS ) {
1576 if ( gl_m_6.getState( "e", "0" ) != LOSS ) {
1579 final FitchParsimony<BinaryStates> fitch7 = new FitchParsimony<BinaryStates>();
1580 final PhylogenyFactory factory7 = ParserBasedPhylogenyFactory.getInstance();
1581 final String p7_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1582 final Phylogeny p7 = factory7.create( p7_str, new NHXParser() )[ 0 ];
1583 final CharacterStateMatrix<BinaryStates> m7 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1584 m7.setIdentifier( 0, "a" );
1585 m7.setIdentifier( 1, "b" );
1586 m7.setIdentifier( 2, "c" );
1587 m7.setIdentifier( 3, "d" );
1588 m7.setIdentifier( 4, "e" );
1589 m7.setIdentifier( 5, "f" );
1590 m7.setIdentifier( 6, "g" );
1591 m7.setIdentifier( 7, "h" );
1592 m7.setCharacter( 0, "0" );
1593 m7.setState( "a", "0", PRESENT );
1594 m7.setState( "b", "0", ABSENT );
1595 m7.setState( "c", "0", PRESENT );
1596 m7.setState( "d", "0", ABSENT );
1597 m7.setState( "e", "0", PRESENT );
1598 m7.setState( "f", "0", ABSENT );
1599 m7.setState( "g", "0", PRESENT );
1600 m7.setState( "h", "0", ABSENT );
1601 fitch7.setReturnInternalStates( true );
1602 fitch7.setReturnGainLossMatrix( true );
1603 fitch7.execute( p7, m7 );
1604 final CharacterStateMatrix<GainLossStates> gl_m_7 = fitch7.getGainLossMatrix();
1605 if ( fitch7.getCost() != 4 ) {
1608 if ( fitch7.getTotalLosses() != 0 ) {
1611 if ( fitch7.getTotalGains() != 4 ) {
1614 if ( fitch7.getTotalUnchanged() != 11 ) {
1617 if ( gl_m_7.getState( "a", "0" ) != GAIN ) {
1620 if ( gl_m_7.getState( "c", "0" ) != GAIN ) {
1623 if ( gl_m_7.getState( "e", "0" ) != GAIN ) {
1626 if ( gl_m_7.getState( "g", "0" ) != GAIN ) {
1629 if ( gl_m_7.getState( "r", "0" ) != UNCHANGED_ABSENT ) {
1632 fitch7.setReturnInternalStates( true );
1633 fitch7.setReturnGainLossMatrix( true );
1634 fitch7.setUseLast( true );
1635 fitch7.execute( p7, m7 );
1636 final CharacterStateMatrix<GainLossStates> gl_m_71 = fitch7.getGainLossMatrix();
1637 if ( fitch7.getCost() != 4 ) {
1640 if ( fitch7.getTotalLosses() != 4 ) {
1643 if ( fitch7.getTotalGains() != 0 ) {
1646 if ( fitch7.getTotalUnchanged() != 11 ) {
1649 if ( gl_m_71.getState( "b", "0" ) != LOSS ) {
1652 if ( gl_m_71.getState( "d", "0" ) != LOSS ) {
1655 if ( gl_m_71.getState( "f", "0" ) != LOSS ) {
1658 if ( gl_m_71.getState( "h", "0" ) != LOSS ) {
1661 if ( gl_m_71.getState( "r", "0" ) != UNCHANGED_PRESENT ) {
1664 final FitchParsimony<BinaryStates> fitch8 = new FitchParsimony<BinaryStates>();
1665 final PhylogenyFactory factory8 = ParserBasedPhylogenyFactory.getInstance();
1666 final String p8_str = "(((a,b)ab,(c,d)cd)abcd,((e,f)ef,(g,h)gh)efgh)r";
1667 final Phylogeny p8 = factory8.create( p8_str, new NHXParser() )[ 0 ];
1668 final CharacterStateMatrix<BinaryStates> m8 = new BasicCharacterStateMatrix<BinaryStates>( 8, 1 );
1669 m8.setIdentifier( 0, "a" );
1670 m8.setIdentifier( 1, "b" );
1671 m8.setIdentifier( 2, "c" );
1672 m8.setIdentifier( 3, "d" );
1673 m8.setIdentifier( 4, "e" );
1674 m8.setIdentifier( 5, "f" );
1675 m8.setIdentifier( 6, "g" );
1676 m8.setIdentifier( 7, "h" );
1677 m8.setCharacter( 0, "0" );
1678 m8.setState( "a", "0", PRESENT );
1679 m8.setState( "b", "0", PRESENT );
1680 m8.setState( "c", "0", PRESENT );
1681 m8.setState( "d", "0", ABSENT );
1682 m8.setState( "e", "0", ABSENT );
1683 m8.setState( "f", "0", ABSENT );
1684 m8.setState( "g", "0", ABSENT );
1685 m8.setState( "h", "0", ABSENT );
1686 fitch8.setReturnInternalStates( true );
1687 fitch8.setReturnGainLossMatrix( true );
1688 fitch8.execute( p8, m8 );
1689 final CharacterStateMatrix<GainLossStates> gl_m_8 = fitch8.getGainLossMatrix();
1690 if ( fitch8.getCost() != 2 ) {
1693 if ( fitch8.getTotalLosses() != 1 ) {
1696 if ( fitch8.getTotalGains() != 1 ) {
1699 if ( fitch8.getTotalUnchanged() != 13 ) {
1702 if ( gl_m_8.getState( "d", "0" ) != LOSS ) {
1705 if ( gl_m_8.getState( "abcd", "0" ) != GAIN ) {
1708 final FitchParsimony<BinaryStates> fitch9 = new FitchParsimony<BinaryStates>();
1709 final PhylogenyFactory factory9 = ParserBasedPhylogenyFactory.getInstance();
1710 final String p9_str = "(((a,b)ab,c)abc,d)abcd";
1711 final Phylogeny p9 = factory9.create( p9_str, new NHXParser() )[ 0 ];
1712 final CharacterStateMatrix<BinaryStates> m9 = new BasicCharacterStateMatrix<BinaryStates>( 4, 1 );
1713 m9.setIdentifier( 0, "a" );
1714 m9.setIdentifier( 1, "b" );
1715 m9.setIdentifier( 2, "c" );
1716 m9.setIdentifier( 3, "d" );
1717 m9.setCharacter( 0, "0" );
1718 m9.setState( "a", "0", PRESENT );
1719 m9.setState( "b", "0", ABSENT );
1720 m9.setState( "c", "0", PRESENT );
1721 m9.setState( "d", "0", ABSENT );
1722 fitch9.setReturnInternalStates( true );
1723 fitch9.setReturnGainLossMatrix( true );
1724 fitch9.setUseLast( false );
1725 fitch9.execute( p9, m9 );
1726 final CharacterStateMatrix<GainLossStates> gl_m_9a = fitch9.getGainLossMatrix();
1727 if ( fitch9.getCost() != 2 ) {
1730 if ( fitch9.getTotalLosses() != 1 ) {
1733 if ( fitch9.getTotalGains() != 1 ) {
1736 if ( fitch9.getTotalUnchanged() != 5 ) {
1739 if ( gl_m_9a.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1742 if ( gl_m_9a.getState( "b", "0" ) != LOSS ) {
1745 if ( gl_m_9a.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1748 if ( gl_m_9a.getState( "d", "0" ) != UNCHANGED_ABSENT ) {
1751 if ( gl_m_9a.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1754 if ( gl_m_9a.getState( "abc", "0" ) != GAIN ) {
1757 if ( gl_m_9a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1760 fitch9.setUseLast( true );
1761 fitch9.execute( p9, m9 );
1762 final CharacterStateMatrix<GainLossStates> gl_m_9b = fitch9.getGainLossMatrix();
1763 if ( fitch9.getCost() != 2 ) {
1766 if ( fitch9.getTotalLosses() != 2 ) {
1769 if ( fitch9.getTotalGains() != 0 ) {
1772 if ( fitch9.getTotalUnchanged() != 5 ) {
1775 if ( gl_m_9b.getState( "a", "0" ) != UNCHANGED_PRESENT ) {
1778 if ( gl_m_9b.getState( "b", "0" ) != LOSS ) {
1781 if ( gl_m_9b.getState( "c", "0" ) != UNCHANGED_PRESENT ) {
1784 if ( gl_m_9b.getState( "d", "0" ) != LOSS ) {
1787 if ( gl_m_9b.getState( "ab", "0" ) != UNCHANGED_PRESENT ) {
1790 if ( gl_m_9b.getState( "abc", "0" ) != UNCHANGED_PRESENT ) {
1793 if ( gl_m_9b.getState( "abcd", "0" ) != UNCHANGED_PRESENT ) {
1796 fitch9.setUseLast( false );
1797 fitch9.setRandomize( true );
1798 fitch9.setRandomNumberSeed( 8722445 );
1799 fitch9.execute( p9, m9 );
1800 fitch9.getGainLossMatrix();
1801 if ( fitch9.getCost() != 2 ) {
1804 if ( fitch9.getTotalLosses() != 1 ) {
1807 if ( fitch9.getTotalGains() != 1 ) {
1810 if ( fitch9.getTotalUnchanged() != 5 ) {
1813 final FitchParsimony<BinaryStates> fitch10 = new FitchParsimony<BinaryStates>();
1814 final PhylogenyFactory factory10 = ParserBasedPhylogenyFactory.getInstance();
1815 final String p10_str = "((((a,b)ab,c)abc,d)abcd,e)abcde";
1816 final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
1817 final CharacterStateMatrix<BinaryStates> m10 = new BasicCharacterStateMatrix<BinaryStates>( 5, 1 );
1818 m10.setIdentifier( 0, "a" );
1819 m10.setIdentifier( 1, "b" );
1820 m10.setIdentifier( 2, "c" );
1821 m10.setIdentifier( 3, "d" );
1822 m10.setIdentifier( 4, "e" );
1823 m10.setCharacter( 0, "0" );
1824 m10.setState( "a", "0", PRESENT );
1825 m10.setState( "b", "0", ABSENT );
1826 m10.setState( "c", "0", ABSENT );
1827 m10.setState( "d", "0", PRESENT );
1828 m10.setState( "e", "0", ABSENT );
1829 fitch10.setReturnInternalStates( true );
1830 fitch10.setReturnGainLossMatrix( true );
1831 fitch10.setUseLast( false );
1832 fitch10.execute( p10, m10 );
1833 final CharacterStateMatrix<GainLossStates> gl_m_10a = fitch10.getGainLossMatrix();
1834 if ( fitch10.getCost() != 2 ) {
1837 if ( fitch10.getTotalLosses() != 0 ) {
1840 if ( fitch10.getTotalGains() != 2 ) {
1843 if ( fitch10.getTotalUnchanged() != 7 ) {
1846 if ( gl_m_10a.getState( "a", "0" ) != GAIN ) {
1849 if ( gl_m_10a.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1852 if ( gl_m_10a.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1855 if ( gl_m_10a.getState( "d", "0" ) != GAIN ) {
1858 if ( gl_m_10a.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1861 if ( gl_m_10a.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1864 if ( gl_m_10a.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1867 if ( gl_m_10a.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1870 if ( gl_m_10a.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1873 fitch10.setUseLast( true );
1874 fitch10.execute( p10, m10 );
1875 final CharacterStateMatrix<GainLossStates> gl_m_10b = fitch10.getGainLossMatrix();
1876 if ( fitch10.getCost() != 2 ) {
1879 if ( fitch10.getTotalLosses() != 0 ) {
1882 if ( fitch10.getTotalGains() != 2 ) {
1885 if ( fitch10.getTotalUnchanged() != 7 ) {
1888 if ( gl_m_10b.getState( "a", "0" ) != GAIN ) {
1891 if ( gl_m_10b.getState( "b", "0" ) != UNCHANGED_ABSENT ) {
1894 if ( gl_m_10b.getState( "c", "0" ) != UNCHANGED_ABSENT ) {
1897 if ( gl_m_10b.getState( "d", "0" ) != GAIN ) {
1900 if ( gl_m_10b.getState( "e", "0" ) != UNCHANGED_ABSENT ) {
1903 if ( gl_m_10b.getState( "ab", "0" ) != UNCHANGED_ABSENT ) {
1906 if ( gl_m_10b.getState( "abc", "0" ) != UNCHANGED_ABSENT ) {
1909 if ( gl_m_10b.getState( "abcd", "0" ) != UNCHANGED_ABSENT ) {
1912 if ( gl_m_10b.getState( "abcde", "0" ) != UNCHANGED_ABSENT ) {
1916 catch ( final Exception e ) {
1917 e.printStackTrace( System.out );
1923 private static boolean testNeighborJoining() {
1925 NeighborJoining nj = NeighborJoining.createInstance();
1926 final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
1927 m0.setIdentifier( 0, "A" );
1928 m0.setIdentifier( 1, "B" );
1929 m0.setIdentifier( 2, "C" );
1930 m0.setIdentifier( 3, "D" );
1931 m0.setRow( "5 ", 1 );
1932 m0.setRow( "3 6 ", 2 );
1933 m0.setRow( "7.5 10.5 5.5", 3 );
1934 final Phylogeny p0 = nj.execute( m0 );
1935 p0.reRoot( p0.getNode( "D" ) );
1936 if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) {
1939 if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
1942 if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
1945 if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
1948 if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
1951 if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) {
1954 nj = NeighborJoining.createInstance();
1955 final BasicSymmetricalDistanceMatrix m00 = new BasicSymmetricalDistanceMatrix( 4 );
1956 m00.setIdentifier( 0, "A" );
1957 m00.setIdentifier( 1, "B" );
1958 m00.setIdentifier( 2, "C" );
1959 m00.setIdentifier( 3, "D" );
1960 m00.setRow( "2.01 ", 1 );
1961 m00.setRow( "3 3.01 ", 2 );
1962 m00.setRow( "3.01 3.02 1.01", 3 );
1963 final Phylogeny p00 = nj.execute( m00 );
1964 p00.reRoot( p00.getNode( "D" ) );
1965 if ( isUnequal( p00.getNode( "A" ).getDistanceToParent(), 1 ) ) {
1968 if ( isUnequal( p00.getNode( "B" ).getDistanceToParent(), 1.01 ) ) {
1971 if ( isUnequal( p00.getNode( "C" ).getDistanceToParent(), 0.5 ) ) {
1974 if ( isUnequal( p00.getNode( "D" ).getDistanceToParent(), 0.255 ) ) {
1977 if ( isUnequal( p00.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) {
1980 if ( isUnequal( p00.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.255 ) ) {
1983 BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
1985 m.setRow( "4 7", 2 );
1986 m.setRow( "7 10 7", 3 );
1987 m.setRow( "6 9 6 5", 4 );
1988 m.setRow( "8 11 8 9 8", 5 );
1989 m.setIdentifier( 0, "A" );
1990 m.setIdentifier( 1, "B" );
1991 m.setIdentifier( 2, "C" );
1992 m.setIdentifier( 3, "D" );
1993 m.setIdentifier( 4, "E" );
1994 m.setIdentifier( 5, "F" );
1995 nj = NeighborJoining.createInstance();
1996 final Phylogeny p1 = nj.execute( m );
1997 p1.reRoot( p1.getNode( "F" ) );
1998 if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
2001 if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) {
2004 if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) {
2007 if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) {
2010 if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) {
2013 if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) {
2016 if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) {
2019 if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) {
2022 if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) {
2025 if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) {
2028 if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) {
2031 if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) {
2034 m = new BasicSymmetricalDistanceMatrix( 7 );
2035 m.setIdentifier( 0, "Bovine" );
2036 m.setIdentifier( 1, "Mouse" );
2037 m.setIdentifier( 2, "Gibbon" );
2038 m.setIdentifier( 3, "Orang" );
2039 m.setIdentifier( 4, "Gorilla" );
2040 m.setIdentifier( 5, "Chimp" );
2041 m.setIdentifier( 6, "Human" );
2042 m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
2043 m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
2044 m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
2045 m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
2046 m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
2047 m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
2048 m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
2049 nj = NeighborJoining.createInstance( false, 6 );
2050 final Phylogeny p2 = nj.execute( m );
2051 p2.reRoot( p2.getNode( "Bovine" ) );
2052 if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
2055 if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) {
2058 if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) {
2061 if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) {
2064 if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) {
2067 if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) {
2070 if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) {
2073 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) {
2076 if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) {
2079 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) {
2082 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) {
2085 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(),
2089 if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
2090 .getDistanceToParent(), 0.458845 ) ) {
2093 m = new BasicSymmetricalDistanceMatrix( 4 );
2094 m.setIdentifier( 0, "A" );
2095 m.setIdentifier( 1, "B" );
2096 m.setIdentifier( 2, "C" );
2097 m.setIdentifier( 3, "D" );
2098 m.setRow( "0.00 0.95 0.17 0.98", 0 );
2099 m.setRow( "0.95 0.00 1.02 1.83", 1 );
2100 m.setRow( "0.17 1.02 0.00 1.01", 2 );
2101 m.setRow( "0.98 1.83 1.01 0.00", 3 );
2102 final Phylogeny p3 = nj.execute( m );
2103 p3.reRoot( p3.getNode( "C" ) );
2104 if ( isUnequal( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) {
2107 if ( isUnequal( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) {
2110 if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.05 ) ) {
2113 if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) {
2116 if ( isUnequal( p3.getNode( "A" ).getParent().getDistanceToParent(), 0.02 ) ) {
2119 if ( isUnequal( p3.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.05 ) ) {
2123 // timeNeighborJoining();
2126 catch ( final Exception e ) {
2127 e.printStackTrace( System.out );
2133 private static boolean testSymmetricalDistanceMatrixParser() {
2135 final String l = ForesterUtil.getLineSeparator();
2136 StringBuffer source = new StringBuffer();
2137 source.append( " 4" + l );
2138 source.append( "A 0 0 0 0" + l );
2139 source.append( "B 1 0 0 0" + l );
2140 source.append( "C 2 4 0 0" + l );
2141 source.append( "D 3 5 6 0" + l );
2143 source.append( " 4" + l );
2144 source.append( "A 0 11 12 13" + l );
2145 source.append( "B 11 0 14 15" + l );
2146 source.append( "C 12 14 0 16" + l );
2147 source.append( "D 13 15 16 0" + l );
2150 source.append( " " + l );
2151 source.append( " 4" + l );
2152 source.append( " A 0 " + l );
2153 source.append( " B 21 0" + l );
2154 source.append( " C 22 24 0 " + l );
2155 source.append( " # 2 222 2 2 " + l );
2156 source.append( " D 23 25 26 0" + l );
2159 source.append( " " + l );
2160 final SymmetricalDistanceMatrixParser p0 = SymmetricalDistanceMatrixParser.createInstance();
2161 final DistanceMatrix[] ma0 = p0.parse( source.toString() );
2162 if ( ma0.length != 3 ) {
2165 if ( !isEqual( ma0[ 0 ].getValue( 0, 0 ), 0 ) ) {
2168 if ( !isEqual( ma0[ 0 ].getValue( 1, 0 ), 1 ) ) {
2171 if ( !isEqual( ma0[ 0 ].getValue( 2, 0 ), 2 ) ) {
2174 if ( !isEqual( ma0[ 0 ].getValue( 3, 0 ), 3 ) ) {
2177 if ( !isEqual( ma0[ 0 ].getValue( 0, 1 ), 1 ) ) {
2180 if ( !isEqual( ma0[ 0 ].getValue( 1, 1 ), 0 ) ) {
2183 if ( !isEqual( ma0[ 0 ].getValue( 2, 1 ), 4 ) ) {
2186 if ( !isEqual( ma0[ 0 ].getValue( 3, 1 ), 5 ) ) {
2189 if ( !isEqual( ma0[ 1 ].getValue( 0, 0 ), 0 ) ) {
2192 if ( !isEqual( ma0[ 1 ].getValue( 1, 0 ), 11 ) ) {
2195 if ( !isEqual( ma0[ 1 ].getValue( 2, 0 ), 12 ) ) {
2198 if ( !isEqual( ma0[ 1 ].getValue( 3, 0 ), 13 ) ) {
2201 if ( !isEqual( ma0[ 1 ].getValue( 0, 1 ), 11 ) ) {
2204 if ( !isEqual( ma0[ 1 ].getValue( 1, 1 ), 0 ) ) {
2207 if ( !isEqual( ma0[ 1 ].getValue( 2, 1 ), 14 ) ) {
2210 if ( !isEqual( ma0[ 1 ].getValue( 3, 1 ), 15 ) ) {
2213 if ( !isEqual( ma0[ 2 ].getValue( 0, 0 ), 0 ) ) {
2216 if ( !isEqual( ma0[ 2 ].getValue( 1, 0 ), 21 ) ) {
2219 if ( !isEqual( ma0[ 2 ].getValue( 2, 0 ), 22 ) ) {
2222 if ( !isEqual( ma0[ 2 ].getValue( 3, 0 ), 23 ) ) {
2225 if ( !isEqual( ma0[ 2 ].getValue( 0, 1 ), 21 ) ) {
2228 if ( !isEqual( ma0[ 2 ].getValue( 1, 1 ), 0 ) ) {
2231 if ( !isEqual( ma0[ 2 ].getValue( 2, 1 ), 24 ) ) {
2234 if ( !isEqual( ma0[ 2 ].getValue( 3, 1 ), 25 ) ) {
2237 source = new StringBuffer();
2238 source.append( "A 0 0 0 0" + l );
2239 source.append( "B 1 0 0 0" + l );
2240 source.append( "C 2 4 0 0" + l );
2241 source.append( "D 3 5 6 0" + l );
2242 source.append( " " + l );
2243 source.append( "A 0 11 12 13" + l );
2244 source.append( "B 11 0 14 15" + l );
2245 source.append( "C 12 14 0 16" + l );
2246 source.append( "D 13 15 16 0" + l );
2248 source.append( " A 0 " + l );
2249 source.append( " B 21 0" + l );
2250 source.append( " C 22 24 0 " + l );
2251 source.append( " # 2 222 2 2 " + l );
2252 source.append( " D 23 25 26 0" + l );
2253 final DistanceMatrix[] ma1 = p0.parse( source.toString() );
2254 if ( ma1.length != 3 ) {
2257 if ( !isEqual( ma1[ 0 ].getValue( 0, 0 ), 0 ) ) {
2260 if ( !isEqual( ma1[ 0 ].getValue( 1, 0 ), 1 ) ) {
2263 if ( !isEqual( ma1[ 0 ].getValue( 2, 0 ), 2 ) ) {
2266 if ( !isEqual( ma1[ 0 ].getValue( 3, 0 ), 3 ) ) {
2269 if ( !isEqual( ma1[ 0 ].getValue( 0, 1 ), 1 ) ) {
2272 if ( !isEqual( ma1[ 0 ].getValue( 1, 1 ), 0 ) ) {
2275 if ( !isEqual( ma1[ 0 ].getValue( 2, 1 ), 4 ) ) {
2278 if ( !isEqual( ma1[ 0 ].getValue( 3, 1 ), 5 ) ) {
2281 if ( !isEqual( ma1[ 1 ].getValue( 0, 0 ), 0 ) ) {
2284 if ( !isEqual( ma1[ 1 ].getValue( 1, 0 ), 11 ) ) {
2287 if ( !isEqual( ma1[ 1 ].getValue( 2, 0 ), 12 ) ) {
2290 if ( !isEqual( ma1[ 1 ].getValue( 3, 0 ), 13 ) ) {
2293 if ( !isEqual( ma1[ 1 ].getValue( 0, 1 ), 11 ) ) {
2296 if ( !isEqual( ma1[ 1 ].getValue( 1, 1 ), 0 ) ) {
2299 if ( !isEqual( ma1[ 1 ].getValue( 2, 1 ), 14 ) ) {
2302 if ( !isEqual( ma1[ 1 ].getValue( 3, 1 ), 15 ) ) {
2305 if ( !isEqual( ma1[ 2 ].getValue( 0, 0 ), 0 ) ) {
2308 if ( !isEqual( ma1[ 2 ].getValue( 1, 0 ), 21 ) ) {
2311 if ( !isEqual( ma1[ 2 ].getValue( 2, 0 ), 22 ) ) {
2314 if ( !isEqual( ma1[ 2 ].getValue( 3, 0 ), 23 ) ) {
2317 if ( !isEqual( ma1[ 2 ].getValue( 0, 1 ), 21 ) ) {
2320 if ( !isEqual( ma1[ 2 ].getValue( 1, 1 ), 0 ) ) {
2323 if ( !isEqual( ma1[ 2 ].getValue( 2, 1 ), 24 ) ) {
2326 if ( !isEqual( ma1[ 2 ].getValue( 3, 1 ), 25 ) ) {
2329 source = new StringBuffer();
2330 source.append( "A 0" + l );
2331 source.append( "B 10 0" + l );
2332 final DistanceMatrix[] ma2 = p0.parse( source.toString() );
2333 if ( ma2.length != 1 ) {
2336 if ( !isEqual( ma2[ 0 ].getValue( 0, 1 ), 10 ) ) {
2339 source = new StringBuffer();
2340 source.append( " " + l );
2341 source.append( "#" + l );
2342 final DistanceMatrix[] ma3 = p0.parse( source.toString() );
2343 if ( ma3.length != 0 ) {
2346 source = new StringBuffer();
2347 source.append( " " + l );
2348 source.append( "A 0 11 12 13" + l );
2349 source.append( "B 0 14 15" + l );
2350 source.append( "C 0 16" + l );
2351 source.append( "D 0" + l );
2353 source.append( "A 0 21 22 23" + l );
2354 source.append( "B 0 24 25" + l );
2355 source.append( "C 0 26" + l );
2356 source.append( "D 0" + l );
2357 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2358 final DistanceMatrix[] ma4 = p0.parse( source );
2359 if ( ma4.length != 2 ) {
2362 if ( !isEqual( ma4[ 0 ].getValue( 0, 0 ), 0 ) ) {
2365 if ( !isEqual( ma4[ 0 ].getValue( 1, 0 ), 11 ) ) {
2368 if ( !isEqual( ma4[ 0 ].getValue( 2, 0 ), 12 ) ) {
2371 if ( !isEqual( ma4[ 0 ].getValue( 3, 0 ), 13 ) ) {
2374 if ( !isEqual( ma4[ 0 ].getValue( 0, 1 ), 11 ) ) {
2377 if ( !isEqual( ma4[ 0 ].getValue( 1, 1 ), 0 ) ) {
2380 if ( !isEqual( ma4[ 0 ].getValue( 2, 1 ), 14 ) ) {
2383 if ( !isEqual( ma4[ 0 ].getValue( 3, 1 ), 15 ) ) {
2386 if ( !isEqual( ma4[ 0 ].getValue( 0, 2 ), 12 ) ) {
2389 if ( !isEqual( ma4[ 0 ].getValue( 1, 2 ), 14 ) ) {
2392 if ( !isEqual( ma4[ 0 ].getValue( 2, 2 ), 0 ) ) {
2395 if ( !isEqual( ma4[ 0 ].getValue( 3, 2 ), 16 ) ) {
2398 if ( !isEqual( ma4[ 0 ].getValue( 0, 3 ), 13 ) ) {
2401 if ( !isEqual( ma4[ 0 ].getValue( 1, 3 ), 15 ) ) {
2404 if ( !isEqual( ma4[ 0 ].getValue( 2, 3 ), 16 ) ) {
2407 if ( !isEqual( ma4[ 0 ].getValue( 3, 3 ), 0 ) ) {
2410 source = new StringBuffer();
2411 source.append( " 4 " + l );
2412 source.append( "A 0 11 12 13" + l );
2413 source.append( "B 0 14 15" + l );
2414 source.append( "C 0 16" + l );
2415 source.append( "D 0" + l );
2416 source.append( " 4" + l );
2417 source.append( "A 0 21 22 23" + l );
2418 source.append( "B 0 24 25" + l );
2419 source.append( "C 0 26" + l );
2420 source.append( "D 0" + l );
2421 source.append( " " + l );
2422 source.append( " 4" + l );
2423 source.append( "A 0 21 22 23" + l );
2424 source.append( "B 0 24 25" + l );
2425 source.append( "C 0 26" + l );
2426 source.append( "D 0" + l );
2428 source.append( "A 0 21 22 23" + l );
2429 source.append( "B 0 24 25" + l );
2430 source.append( "C 0 26" + l );
2431 source.append( "D 0" + l );
2432 p0.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
2433 final DistanceMatrix[] ma5 = p0.parse( source );
2434 if ( ma5.length != 4 ) {
2437 if ( !isEqual( ma5[ 0 ].getValue( 0, 0 ), 0 ) ) {
2440 if ( !isEqual( ma5[ 0 ].getValue( 1, 0 ), 11 ) ) {
2443 if ( !isEqual( ma5[ 0 ].getValue( 2, 0 ), 12 ) ) {
2446 if ( !isEqual( ma5[ 0 ].getValue( 3, 0 ), 13 ) ) {
2449 if ( !isEqual( ma5[ 0 ].getValue( 0, 1 ), 11 ) ) {
2452 if ( !isEqual( ma5[ 0 ].getValue( 1, 1 ), 0 ) ) {
2455 if ( !isEqual( ma5[ 0 ].getValue( 2, 1 ), 14 ) ) {
2458 if ( !isEqual( ma5[ 0 ].getValue( 3, 1 ), 15 ) ) {
2461 if ( !isEqual( ma5[ 0 ].getValue( 0, 2 ), 12 ) ) {
2464 if ( !isEqual( ma5[ 0 ].getValue( 1, 2 ), 14 ) ) {
2467 if ( !isEqual( ma5[ 0 ].getValue( 2, 2 ), 0 ) ) {
2470 if ( !isEqual( ma5[ 0 ].getValue( 3, 2 ), 16 ) ) {
2473 if ( !isEqual( ma5[ 0 ].getValue( 0, 3 ), 13 ) ) {
2476 if ( !isEqual( ma5[ 0 ].getValue( 1, 3 ), 15 ) ) {
2479 if ( !isEqual( ma5[ 0 ].getValue( 2, 3 ), 16 ) ) {
2482 if ( !isEqual( ma5[ 0 ].getValue( 3, 3 ), 0 ) ) {
2486 catch ( final Exception e ) {
2487 e.printStackTrace( System.out );
2493 private static void timeNeighborJoining() {
2494 final NeighborJoining nj = NeighborJoining.createInstance();
2495 for( int n = 3; n <= 10; ++n ) {
2496 final int x = ( int ) Math.pow( 2, n );
2497 final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
2498 mt.randomize( new Date().getTime() );
2499 // for( int i = 0; i < mt.getSize(); i++ ) {
2500 // mt.setIdentifier( i, i + "i" );
2502 // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
2503 final long start_time = new Date().getTime();
2505 System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
2507 final NeighborJoiningX njx = NeighborJoiningX.createInstance();
2508 for( int n = 3; n <= 10; ++n ) {
2509 final int x = ( int ) Math.pow( 2, n );
2510 final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
2511 mt.randomize( new Date().getTime() );
2512 // for( int i = 0; i < mt.getSize(); i++ ) {
2513 // mt.setIdentifier( i, i + "i" );
2515 // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
2516 final long start_time = new Date().getTime();
2518 System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );