2 package org.forester.rio;
6 import org.forester.datastructures.IntMatrix;
7 import org.forester.io.parsers.nhx.NHXParser;
8 import org.forester.phylogeny.Phylogeny;
9 import org.forester.phylogeny.PhylogenyMethods;
10 import org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField;
11 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
12 import org.forester.phylogeny.factories.PhylogenyFactory;
13 import org.forester.rio.RIO.REROOTING;
14 import org.forester.sdi.SDIutil.ALGORITHM;
15 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
16 import org.forester.util.ForesterUtil;
18 public final class TestRIO {
20 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
21 + "test_data" + ForesterUtil.getFileSeparator();
23 public static void main( final String[] args ) {
24 if ( !testRIO_GSDIR() ) {
25 System.out.println( "testRIO GSDIR failed" );
28 System.out.println( "OK" );
32 public static boolean test() {
33 if ( !testRIO_GSDIR() ) {
39 private static boolean testRIO_GSDIR() {
41 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
42 final NHXParser nhx = new NHXParser();
43 nhx.setReplaceUnderscores( false );
44 nhx.setIgnoreQuotes( true );
45 nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
46 final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
47 + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
48 + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
49 final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
50 final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
51 final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
52 species_tree_1.setRooted( true );
53 PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
54 //Archaeopteryx.createApplication( species_trees_1 );
55 RIO rio = RIO.executeAnalysis( gene_trees_1,
58 REROOTING.BY_ALGORITHM,
62 if ( rio.getAnalyzedGeneTrees().length != 5 ) {
65 if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
68 if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
71 if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
74 IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
75 // System.out.println( m.toString() );
76 if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
79 if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
82 if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
85 if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
88 if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
91 if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
95 final Phylogeny[] gene_trees_2 = factory.create( gene_trees_1_str, nhx );
96 final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
97 final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
98 species_tree_2.setRooted( true );
99 PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
100 rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 );
101 m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
102 // System.out.println( m.toString() );
103 if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
106 if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
109 if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
112 if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
115 if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
118 if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
122 RIO r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode.run1.t" ),
123 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
125 REROOTING.BY_ALGORITHM,
131 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
134 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
137 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
140 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
143 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
146 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
149 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
150 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE,201,201,200,200,200,200" ) ) {
151 System.out.println( m.getRowAsString( 0, ',' ) );
154 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN,201,201,200,200,200,43" ) ) {
155 System.out.println( m.getRowAsString( 1, ',' ) );
158 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
159 System.out.println( m.getRowAsString( 2, ',' ) );
162 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_CIOSA,200,200,201,201,201,201" ) ) {
163 System.out.println( m.getRowAsString( 3, ',' ) );
166 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE,200,200,201,201,201,43" ) ) {
167 System.out.println( m.getRowAsString( 4, ',' ) );
170 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR,200,43,43,201,43,201" ) ) {
171 System.out.println( m.getRowAsString( 5, ',' ) );
175 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxid.run1.t" ),
176 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
178 REROOTING.BY_ALGORITHM,
184 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.ID ) {
187 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
190 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
193 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
196 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
199 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
202 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
203 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_45351,201,200,201,200,200,200" ) ) {
204 System.out.println( m.getRowAsString( 0, ',' ) );
208 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_10090,200,201,200,201,201,43" ) ) {
209 System.out.println( m.getRowAsString( 1, ',' ) );
213 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_9606,201,200,201,200,200,43" ) ) {
214 System.out.println( m.getRowAsString( 2, ',' ) );
217 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_51511,200,201,200,201,201,201" ) ) {
218 System.out.println( m.getRowAsString( 3, ',' ) );
221 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_7955,200,201,200,201,201,43" ) ) {
222 System.out.println( m.getRowAsString( 4, ',' ) );
225 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_8364,200,43,43,201,43,201" ) ) {
226 System.out.println( m.getRowAsString( 5, ',' ) );
229 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
230 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
232 REROOTING.BY_ALGORITHM,
238 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
241 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
244 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
247 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
250 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
253 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
256 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
257 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) {
258 System.out.println( m.getRowAsString( 0, ',' ) );
261 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) {
262 System.out.println( m.getRowAsString( 1, ',' ) );
265 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) {
266 System.out.println( m.getRowAsString( 2, ',' ) );
269 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) {
270 System.out.println( m.getRowAsString( 3, ',' ) );
273 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) {
274 System.out.println( m.getRowAsString( 4, ',' ) );
277 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) {
278 System.out.println( m.getRowAsString( 5, ',' ) );
282 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
283 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
291 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
294 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
297 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
300 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
303 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
306 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
309 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
310 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) {
311 System.out.println( m.getRowAsString( 0, ',' ) );
314 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) {
315 System.out.println( m.getRowAsString( 1, ',' ) );
318 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) {
319 System.out.println( m.getRowAsString( 2, ',' ) );
322 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) {
323 System.out.println( m.getRowAsString( 3, ',' ) );
326 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) {
327 System.out.println( m.getRowAsString( 4, ',' ) );
330 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) {
331 System.out.println( m.getRowAsString( 5, ',' ) );
335 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
336 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
339 "H2ZH97_Ciona_savignyi",
344 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
347 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
350 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
353 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
356 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
359 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
362 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
363 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) {
364 System.out.println( m.getRowAsString( 0, ',' ) );
367 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) {
368 System.out.println( m.getRowAsString( 1, ',' ) );
371 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) {
372 System.out.println( m.getRowAsString( 2, ',' ) );
375 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) {
376 System.out.println( m.getRowAsString( 3, ',' ) );
379 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) {
380 System.out.println( m.getRowAsString( 4, ',' ) );
383 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) {
384 System.out.println( m.getRowAsString( 5, ',' ) );
389 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
390 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
398 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
401 if ( r0.getAnalyzedGeneTrees().length != 10 ) {
404 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
407 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
410 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
413 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) {
416 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
417 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) {
418 System.out.println( m.getRowAsString( 0, ',' ) );
421 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) {
422 System.out.println( m.getRowAsString( 1, ',' ) );
425 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) {
426 System.out.println( m.getRowAsString( 2, ',' ) );
429 if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) {
430 System.out.println( m.getRowAsString( 3, ',' ) );
433 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) {
434 System.out.println( m.getRowAsString( 4, ',' ) );
437 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) {
438 System.out.println( m.getRowAsString( 5, ',' ) );
442 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ),
443 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
445 REROOTING.BY_ALGORITHM,
451 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
454 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
457 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) {
460 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) {
463 if ( r0.getRemovedGeneTreeNodes().size() != 3 ) {
466 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) {
469 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
470 if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) {
471 System.out.println( m.getRowAsString( 0, ',' ) );
474 if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) {
475 System.out.println( m.getRowAsString( 1, ',' ) );
478 if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) {
479 System.out.println( m.getRowAsString( 2, ',' ) );
484 r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ),
485 new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
487 REROOTING.BY_ALGORITHM,
493 if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
496 if ( r0.getAnalyzedGeneTrees().length != 201 ) {
499 if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
502 if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
505 if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
508 if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
511 m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
512 if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) {
513 System.out.println( m.getRowAsString( 0, ',' ) );
516 if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) {
517 System.out.println( m.getRowAsString( 1, ',' ) );
520 if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
521 System.out.println( m.getRowAsString( 2, ',' ) );
524 if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) {
525 System.out.println( m.getRowAsString( 3, ',' ) );
528 if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) {
529 System.out.println( m.getRowAsString( 4, ',' ) );
532 if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) {
533 System.out.println( m.getRowAsString( 5, ',' ) );
538 catch ( final Exception e ) {
539 e.printStackTrace( System.out );