forester/java/src/org/forester/rio/TestRIO.java

   1
   2 package org.forester.rio;
   3
   4 import java.io.File;
   5
   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;
  17
  18 public final class TestRIO {
  19
  20     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
  21                                                           + "test_data" + ForesterUtil.getFileSeparator();
  22
  23     public static void main( final String[] args ) {
  24         if ( !testRIO_GSDIR() ) {
  25             System.out.println( "testRIO GSDIR failed" );
  26         }
  27         if ( !testRIO_GSDIR_Iterating() ) {
  28             System.out.println( "testRIO GSDIR iterating failed" );
  29         }
  30         else {
  31             System.out.println( "OK" );
  32         }
  33     }
  34
  35     public static boolean test() {
  36         if ( !testRIO_GSDIR() ) {
  37             return false;
  38         }
  39         if ( !testRIO_GSDIR_Iterating() ) {
  40             return false;
  41         }
  42         return true;
  43     }
  44
  45     private static boolean testRIO_GSDIR_Iterating() {
  46         try {
  47             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  48             final NHXParser nhx = new NHXParser();
  49             nhx.setReplaceUnderscores( false );
  50             nhx.setIgnoreQuotes( true );
  51             nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
  52             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
  53                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
  54                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
  55             nhx.setSource( gene_trees_1_str );
  56             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
  57             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
  58             species_tree_1.setRooted( true );
  59             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
  60             //Archaeopteryx.createApplication( species_trees_1 );
  61             RIO rio = RIO.executeAnalysis( nhx,
  62                                            species_tree_1,
  63                                            ALGORITHM.GSDIR,
  64                                            REROOTING.BY_ALGORITHM,
  65                                            "",
  66                                            true,
  67                                            false );
  68             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
  69                 return false;
  70             }
  71             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
  72                 return false;
  73             }
  74             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
  75                 return false;
  76             }
  77             IntMatrix m = rio.getOrthologTable();
  78             //System.out.println( m.toString() );
  79             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
  80                 return false;
  81             }
  82             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
  83                 return false;
  84             }
  85             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
  86                 return false;
  87             }
  88             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
  89                 return false;
  90             }
  91             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
  92                 return false;
  93             }
  94             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
  95                 return false;
  96             }
  97             //
  98             final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
  99             final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
 100             species_tree_2.setRooted( true );
 101             PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
 102             rio = RIO.executeAnalysis( nhx, species_tree_2, ALGORITHM.GSDIR, REROOTING.BY_ALGORITHM, "", true, false );
 103             m = rio.getOrthologTable();
 104             // System.out.println( m.toString() );
 105             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 106                 return false;
 107             }
 108             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 109                 return false;
 110             }
 111             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
 112                 return false;
 113             }
 114             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
 115                 return false;
 116             }
 117             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
 118                 return false;
 119             }
 120             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 121                 return false;
 122             }
 123         }
 124         catch ( final Exception e ) {
 125             e.printStackTrace( System.out );
 126             return false;
 127         }
 128         return true;
 129     }
 130
 131     private static boolean testRIO_GSDIR() {
 132         try {
 133             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 134             final NHXParser nhx = new NHXParser();
 135             nhx.setReplaceUnderscores( false );
 136             nhx.setIgnoreQuotes( true );
 137             nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
 138             //
 139             final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
 140             final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
 141             final String species_trees_00_str = "(MOUSE,RAT);";
 142             final Phylogeny species_tree_00 = factory.create( species_trees_00_str, new NHXParser() )[ 0 ];
 143             species_tree_00.setRooted( true );
 144             PhylogenyMethods.transferNodeNameToField( species_tree_00, PhylogenyNodeField.TAXONOMY_CODE, true );
 145             RIO rio = RIO.executeAnalysis( gene_trees_00,
 146                                            species_tree_00,
 147                                            ALGORITHM.GSDIR,
 148                                            REROOTING.BY_ALGORITHM,
 149                                            "",
 150                                            true,
 151                                            false );
 152             if ( rio.getAnalyzedGeneTrees().length != 4 ) {
 153                 return false;
 154             }
 155             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 156                 return false;
 157             }
 158             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 159                 return false;
 160             }
 161             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 162                 return false;
 163             }
 164             IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 165             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE,4,4" ) ) {
 166                 System.out.println( m.toString() );
 167                 return false;
 168             }
 169             if ( !m.getRowAsString( 1, ',' ).equals( "RAT,4,4" ) ) {
 170                 System.out.println( m.toString() );
 171                 return false;
 172             }
 173             //
 174             final String gene_trees_000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
 175             final Phylogeny[] gene_trees_000 = factory.create( gene_trees_000_str, nhx );
 176             final String species_trees_000_str = "[&&NHX:S=MOUSE];";
 177             final Phylogeny species_tree_000 = factory.create( species_trees_000_str, new NHXParser() )[ 0 ];
 178             species_tree_000.setRooted( true );
 179             rio = RIO.executeAnalysis( gene_trees_000,
 180                                        species_tree_000,
 181                                        ALGORITHM.GSDIR,
 182                                        REROOTING.BY_ALGORITHM,
 183                                        "",
 184                                        true,
 185                                        false );
 186             if ( rio.getAnalyzedGeneTrees().length != 2 ) {
 187                 return false;
 188             }
 189             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 190                 return false;
 191             }
 192             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 193                 return false;
 194             }
 195             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 196                 return false;
 197             }
 198             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 199             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,2,0" ) ) {
 200                 System.out.println( m.toString() );
 201                 return false;
 202             }
 203             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,2" ) ) {
 204                 System.out.println( m.toString() );
 205                 return false;
 206             }
 207             //
 208             //
 209             final String gene_trees_0000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
 210             final Phylogeny[] gene_trees_0000 = factory.create( gene_trees_0000_str, nhx );
 211             final String species_trees_0000_str = "([&&NHX:S=MOUSE]);";
 212             final Phylogeny species_tree_0000 = factory.create( species_trees_0000_str, new NHXParser() )[ 0 ];
 213             species_tree_0000.setRooted( true );
 214             rio = RIO.executeAnalysis( gene_trees_0000,
 215                                        species_tree_0000,
 216                                        ALGORITHM.GSDIR,
 217                                        REROOTING.BY_ALGORITHM,
 218                                        "",
 219                                        true,
 220                                        false );
 221             if ( rio.getAnalyzedGeneTrees().length != 3 ) {
 222                 return false;
 223             }
 224             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 225                 return false;
 226             }
 227             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 228                 return false;
 229             }
 230             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 231                 return false;
 232             }
 233             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 234             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,3,0" ) ) {
 235                 System.out.println( m.toString() );
 236                 return false;
 237             }
 238             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,3" ) ) {
 239                 System.out.println( m.toString() );
 240                 return false;
 241             }
 242             //
 243             final String gene_trees_x_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
 244             final Phylogeny[] gene_trees_x = factory.create( gene_trees_x_str, nhx );
 245             final String species_trees_x_str = "[&&NHX:S=MOUSE];";
 246             final Phylogeny species_tree_x = factory.create( species_trees_x_str, new NHXParser() )[ 0 ];
 247             species_tree_x.setRooted( true );
 248             rio = RIO.executeAnalysis( gene_trees_x,
 249                                        species_tree_x,
 250                                        ALGORITHM.GSDIR,
 251                                        REROOTING.BY_ALGORITHM,
 252                                        "",
 253                                        true,
 254                                        false );
 255             if ( rio.getAnalyzedGeneTrees().length != 1 ) {
 256                 return false;
 257             }
 258             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 259                 return false;
 260             }
 261             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 262                 return false;
 263             }
 264             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 265                 return false;
 266             }
 267             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 268             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,0" ) ) {
 269                 System.out.println( m.toString() );
 270                 return false;
 271             }
 272             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,1" ) ) {
 273                 System.out.println( m.toString() );
 274                 return false;
 275             }
 276             //
 277             final String gene_trees_xx_str = "(MOUSE1[&&NHX:S=MOUSE],RAT1[&&NHX:S=RAT])";
 278             final Phylogeny[] gene_trees_xx = factory.create( gene_trees_xx_str, nhx );
 279             final String species_trees_xx_str = "([&&NHX:S=MOUSE],[&&NHX:S=RAT]);";
 280             final Phylogeny species_tree_xx = factory.create( species_trees_xx_str, new NHXParser() )[ 0 ];
 281             species_tree_xx.setRooted( true );
 282             rio = RIO.executeAnalysis( gene_trees_xx,
 283                                        species_tree_xx,
 284                                        ALGORITHM.GSDIR,
 285                                        REROOTING.BY_ALGORITHM,
 286                                        "",
 287                                        true,
 288                                        false );
 289             if ( rio.getAnalyzedGeneTrees().length != 1 ) {
 290                 return false;
 291             }
 292             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 293                 return false;
 294             }
 295             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 296                 return false;
 297             }
 298             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 299                 return false;
 300             }
 301             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 302             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,1" ) ) {
 303                 System.out.println( m.toString() );
 304                 return false;
 305             }
 306             if ( !m.getRowAsString( 1, ',' ).equals( "RAT1,1,1" ) ) {
 307                 System.out.println( m.toString() );
 308                 return false;
 309             }
 310             //
 311             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
 312                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
 313                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
 314             final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
 315             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
 316             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
 317             species_tree_1.setRooted( true );
 318             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
 319             rio = RIO.executeAnalysis( gene_trees_1,
 320                                        species_tree_1,
 321                                        ALGORITHM.GSDIR,
 322                                        REROOTING.BY_ALGORITHM,
 323                                        "",
 324                                        true,
 325                                        false );
 326             if ( rio.getAnalyzedGeneTrees().length != 5 ) {
 327                 return false;
 328             }
 329             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 330                 return false;
 331             }
 332             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 333                 return false;
 334             }
 335             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 336                 return false;
 337             }
 338             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 339             // System.out.println( m.toString() );
 340             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 341                 return false;
 342             }
 343             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 344                 return false;
 345             }
 346             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
 347                 return false;
 348             }
 349             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
 350                 return false;
 351             }
 352             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
 353                 return false;
 354             }
 355             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 356                 return false;
 357             }
 358             //
 359             final Phylogeny[] gene_trees_2 = factory.create( gene_trees_1_str, nhx );
 360             final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
 361             final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
 362             species_tree_2.setRooted( true );
 363             PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
 364             rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 );
 365             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 366             // System.out.println( m.toString() );
 367             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 368                 return false;
 369             }
 370             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 371                 return false;
 372             }
 373             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
 374                 return false;
 375             }
 376             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
 377                 return false;
 378             }
 379             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
 380                 return false;
 381             }
 382             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 383                 return false;
 384             }
 385             //
 386             RIO r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode.run1.t" ),
 387                                           new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 388                                           ALGORITHM.GSDIR,
 389                                           REROOTING.BY_ALGORITHM,
 390                                           "",
 391                                           -1,
 392                                           -1,
 393                                           true,
 394                                           false );
 395             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 396                 return false;
 397             }
 398             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 399                 return false;
 400             }
 401             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 402                 return false;
 403             }
 404             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 405                 return false;
 406             }
 407             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 408                 return false;
 409             }
 410             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 411                 return false;
 412             }
 413             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 414             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE,201,201,200,200,200,200" ) ) {
 415                 System.out.println( m.getRowAsString( 0, ',' ) );
 416                 return false;
 417             }
 418             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN,201,201,200,200,200,43" ) ) {
 419                 System.out.println( m.getRowAsString( 1, ',' ) );
 420                 return false;
 421             }
 422             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
 423                 System.out.println( m.getRowAsString( 2, ',' ) );
 424                 return false;
 425             }
 426             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_CIOSA,200,200,201,201,201,201" ) ) {
 427                 System.out.println( m.getRowAsString( 3, ',' ) );
 428                 return false;
 429             }
 430             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE,200,200,201,201,201,43" ) ) {
 431                 System.out.println( m.getRowAsString( 4, ',' ) );
 432                 return false;
 433             }
 434             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR,200,43,43,201,43,201" ) ) {
 435                 System.out.println( m.getRowAsString( 5, ',' ) );
 436                 return false;
 437             }
 438             //
 439             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxid.run1.t" ),
 440                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 441                                       ALGORITHM.GSDIR,
 442                                       REROOTING.BY_ALGORITHM,
 443                                       "",
 444                                       -1,
 445                                       -1,
 446                                       true,
 447                                       false );
 448             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.ID ) {
 449                 return false;
 450             }
 451             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 452                 return false;
 453             }
 454             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 455                 return false;
 456             }
 457             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 458                 return false;
 459             }
 460             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 461                 return false;
 462             }
 463             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 464                 return false;
 465             }
 466             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 467             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_45351,201,200,201,200,200,200" ) ) {
 468                 System.out.println( m.getRowAsString( 0, ',' ) );
 469                 return false;
 470             }
 471             //mouse
 472             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_10090,200,201,200,201,201,43" ) ) {
 473                 System.out.println( m.getRowAsString( 1, ',' ) );
 474                 return false;
 475             }
 476             //human
 477             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_9606,201,200,201,200,200,43" ) ) {
 478                 System.out.println( m.getRowAsString( 2, ',' ) );
 479                 return false;
 480             }
 481             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_51511,200,201,200,201,201,201" ) ) {
 482                 System.out.println( m.getRowAsString( 3, ',' ) );
 483                 return false;
 484             }
 485             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_7955,200,201,200,201,201,43" ) ) {
 486                 System.out.println( m.getRowAsString( 4, ',' ) );
 487                 return false;
 488             }
 489             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_8364,200,43,43,201,43,201" ) ) {
 490                 System.out.println( m.getRowAsString( 5, ',' ) );
 491                 return false;
 492             }
 493             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 494                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 495                                       ALGORITHM.GSDIR,
 496                                       REROOTING.BY_ALGORITHM,
 497                                       "",
 498                                       -1,
 499                                       -1,
 500                                       true,
 501                                       false );
 502             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 503                 return false;
 504             }
 505             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 506                 return false;
 507             }
 508             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 509                 return false;
 510             }
 511             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 512                 return false;
 513             }
 514             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 515                 return false;
 516             }
 517             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 518                 return false;
 519             }
 520             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 521             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) {
 522                 System.out.println( m.getRowAsString( 0, ',' ) );
 523                 return false;
 524             }
 525             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) {
 526                 System.out.println( m.getRowAsString( 1, ',' ) );
 527                 return false;
 528             }
 529             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) {
 530                 System.out.println( m.getRowAsString( 2, ',' ) );
 531                 return false;
 532             }
 533             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) {
 534                 System.out.println( m.getRowAsString( 3, ',' ) );
 535                 return false;
 536             }
 537             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) {
 538                 System.out.println( m.getRowAsString( 4, ',' ) );
 539                 return false;
 540             }
 541             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) {
 542                 System.out.println( m.getRowAsString( 5, ',' ) );
 543                 return false;
 544             }
 545             //
 546             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 547                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 548                                       ALGORITHM.GSDIR,
 549                                       REROOTING.MIDPOINT,
 550                                       "",
 551                                       -1,
 552                                       -1,
 553                                       true,
 554                                       false );
 555             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 556                 return false;
 557             }
 558             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 559                 return false;
 560             }
 561             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 562                 return false;
 563             }
 564             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 565                 return false;
 566             }
 567             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 568                 return false;
 569             }
 570             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
 571                 return false;
 572             }
 573             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 574             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) {
 575                 System.out.println( m.getRowAsString( 0, ',' ) );
 576                 return false;
 577             }
 578             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) {
 579                 System.out.println( m.getRowAsString( 1, ',' ) );
 580                 return false;
 581             }
 582             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) {
 583                 System.out.println( m.getRowAsString( 2, ',' ) );
 584                 return false;
 585             }
 586             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) {
 587                 System.out.println( m.getRowAsString( 3, ',' ) );
 588                 return false;
 589             }
 590             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) {
 591                 System.out.println( m.getRowAsString( 4, ',' ) );
 592                 return false;
 593             }
 594             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) {
 595                 System.out.println( m.getRowAsString( 5, ',' ) );
 596                 return false;
 597             }
 598             //
 599             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 600                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 601                                       ALGORITHM.GSDIR,
 602                                       REROOTING.OUTGROUP,
 603                                       "H2ZH97_Ciona_savignyi",
 604                                       -1,
 605                                       -1,
 606                                       true,
 607                                       false );
 608             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 609                 return false;
 610             }
 611             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 612                 return false;
 613             }
 614             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 615                 return false;
 616             }
 617             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 618                 return false;
 619             }
 620             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 621                 return false;
 622             }
 623             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
 624                 return false;
 625             }
 626             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 627             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) {
 628                 System.out.println( m.getRowAsString( 0, ',' ) );
 629                 return false;
 630             }
 631             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) {
 632                 System.out.println( m.getRowAsString( 1, ',' ) );
 633                 return false;
 634             }
 635             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) {
 636                 System.out.println( m.getRowAsString( 2, ',' ) );
 637                 return false;
 638             }
 639             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) {
 640                 System.out.println( m.getRowAsString( 3, ',' ) );
 641                 return false;
 642             }
 643             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) {
 644                 System.out.println( m.getRowAsString( 4, ',' ) );
 645                 return false;
 646             }
 647             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) {
 648                 System.out.println( m.getRowAsString( 5, ',' ) );
 649                 return false;
 650             }
 651             //
 652             //
 653             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 654                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 655                                       ALGORITHM.GSDIR,
 656                                       REROOTING.NONE,
 657                                       null,
 658                                       10,
 659                                       19,
 660                                       true,
 661                                       false );
 662             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 663                 return false;
 664             }
 665             if ( r0.getAnalyzedGeneTrees().length != 10 ) {
 666                 return false;
 667             }
 668             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 669                 return false;
 670             }
 671             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 672                 return false;
 673             }
 674             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 675                 return false;
 676             }
 677             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) {
 678                 return false;
 679             }
 680             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 681             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) {
 682                 System.out.println( m.getRowAsString( 0, ',' ) );
 683                 return false;
 684             }
 685             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) {
 686                 System.out.println( m.getRowAsString( 1, ',' ) );
 687                 return false;
 688             }
 689             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) {
 690                 System.out.println( m.getRowAsString( 2, ',' ) );
 691                 return false;
 692             }
 693             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) {
 694                 System.out.println( m.getRowAsString( 3, ',' ) );
 695                 return false;
 696             }
 697             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) {
 698                 System.out.println( m.getRowAsString( 4, ',' ) );
 699                 return false;
 700             }
 701             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) {
 702                 System.out.println( m.getRowAsString( 5, ',' ) );
 703                 return false;
 704             }
 705             //
 706             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ),
 707                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 708                                       ALGORITHM.GSDIR,
 709                                       REROOTING.BY_ALGORITHM,
 710                                       "",
 711                                       -1,
 712                                       -1,
 713                                       true,
 714                                       false );
 715             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 716                 return false;
 717             }
 718             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 719                 return false;
 720             }
 721             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) {
 722                 return false;
 723             }
 724             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) {
 725                 return false;
 726             }
 727             if ( r0.getRemovedGeneTreeNodes().size() != 3 ) {
 728                 return false;
 729             }
 730             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) {
 731                 return false;
 732             }
 733             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 734             if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) {
 735                 System.out.println( m.getRowAsString( 0, ',' ) );
 736                 return false;
 737             }
 738             if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) {
 739                 System.out.println( m.getRowAsString( 1, ',' ) );
 740                 return false;
 741             }
 742             if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) {
 743                 System.out.println( m.getRowAsString( 2, ',' ) );
 744                 return false;
 745             }
 746             //
 747             //
 748             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ),
 749                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 750                                       ALGORITHM.GSDIR,
 751                                       REROOTING.BY_ALGORITHM,
 752                                       "",
 753                                       -1,
 754                                       -1,
 755                                       true,
 756                                       false );
 757             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 758                 return false;
 759             }
 760             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 761                 return false;
 762             }
 763             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 764                 return false;
 765             }
 766             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 767                 return false;
 768             }
 769             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 770                 return false;
 771             }
 772             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 773                 return false;
 774             }
 775             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 776             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) {
 777                 System.out.println( m.getRowAsString( 0, ',' ) );
 778                 return false;
 779             }
 780             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) {
 781                 System.out.println( m.getRowAsString( 1, ',' ) );
 782                 return false;
 783             }
 784             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
 785                 System.out.println( m.getRowAsString( 2, ',' ) );
 786                 return false;
 787             }
 788             if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) {
 789                 System.out.println( m.getRowAsString( 3, ',' ) );
 790                 return false;
 791             }
 792             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) {
 793                 System.out.println( m.getRowAsString( 4, ',' ) );
 794                 return false;
 795             }
 796             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) {
 797                 System.out.println( m.getRowAsString( 5, ',' ) );
 798                 return false;
 799             }
 800             //
 801         }
 802         catch ( final Exception e ) {
 803             e.printStackTrace( System.out );
 804             return false;
 805         }
 806         return true;
 807     }
 808 }