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() {
  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.AGRESSIVE );
  52             //
  53             final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
  54             final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
  55             final String species_trees_00_str = "(MOUSE,RAT);";
  56             final Phylogeny species_tree_00 = factory.create( species_trees_00_str, new NHXParser() )[ 0 ];
  57             species_tree_00.setRooted( true );
  58             PhylogenyMethods.transferNodeNameToField( species_tree_00, PhylogenyNodeField.TAXONOMY_CODE, true );
  59             RIO rio = RIO.executeAnalysis( gene_trees_00,
  60                                            species_tree_00,
  61                                            ALGORITHM.GSDIR,
  62                                            REROOTING.BY_ALGORITHM,
  63                                            "",
  64                                            true,
  65                                            false,
  66                                            true );
  67             if ( rio.getAnalyzedGeneTrees().length != 4 ) {
  68                 return false;
  69             }
  70             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
  71                 return false;
  72             }
  73             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
  74                 return false;
  75             }
  76             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
  77                 return false;
  78             }
  79             IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
  80             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE,4,4" ) ) {
  81                 System.out.println( m.toString() );
  82                 return false;
  83             }
  84             if ( !m.getRowAsString( 1, ',' ).equals( "RAT,4,4" ) ) {
  85                 System.out.println( m.toString() );
  86                 return false;
  87             }
  88             //
  89             final String gene_trees_000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
  90             final Phylogeny[] gene_trees_000 = factory.create( gene_trees_000_str, nhx );
  91             final String species_trees_000_str = "[&&NHX:S=MOUSE];";
  92             final Phylogeny species_tree_000 = factory.create( species_trees_000_str, new NHXParser() )[ 0 ];
  93             species_tree_000.setRooted( true );
  94             rio = RIO.executeAnalysis( gene_trees_000,
  95                                        species_tree_000,
  96                                        ALGORITHM.GSDIR,
  97                                        REROOTING.BY_ALGORITHM,
  98                                        "",
  99                                        true,
 100                                        false,
 101                                        true );
 102             if ( rio.getAnalyzedGeneTrees().length != 2 ) {
 103                 return false;
 104             }
 105             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 106                 return false;
 107             }
 108             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 109                 return false;
 110             }
 111             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 112                 return false;
 113             }
 114             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 115             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,2,0" ) ) {
 116                 System.out.println( m.toString() );
 117                 return false;
 118             }
 119             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,2" ) ) {
 120                 System.out.println( m.toString() );
 121                 return false;
 122             }
 123             //
 124             //
 125             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])";
 126             final Phylogeny[] gene_trees_0000 = factory.create( gene_trees_0000_str, nhx );
 127             final String species_trees_0000_str = "([&&NHX:S=MOUSE]);";
 128             final Phylogeny species_tree_0000 = factory.create( species_trees_0000_str, new NHXParser() )[ 0 ];
 129             species_tree_0000.setRooted( true );
 130             rio = RIO.executeAnalysis( gene_trees_0000,
 131                                        species_tree_0000,
 132                                        ALGORITHM.GSDIR,
 133                                        REROOTING.BY_ALGORITHM,
 134                                        "",
 135                                        true,
 136                                        false,
 137                                        true );
 138             if ( rio.getAnalyzedGeneTrees().length != 3 ) {
 139                 return false;
 140             }
 141             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 142                 return false;
 143             }
 144             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 145                 return false;
 146             }
 147             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 148                 return false;
 149             }
 150             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 151             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,3,0" ) ) {
 152                 System.out.println( m.toString() );
 153                 return false;
 154             }
 155             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,3" ) ) {
 156                 System.out.println( m.toString() );
 157                 return false;
 158             }
 159             //
 160             final String gene_trees_x_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
 161             final Phylogeny[] gene_trees_x = factory.create( gene_trees_x_str, nhx );
 162             final String species_trees_x_str = "[&&NHX:S=MOUSE];";
 163             final Phylogeny species_tree_x = factory.create( species_trees_x_str, new NHXParser() )[ 0 ];
 164             species_tree_x.setRooted( true );
 165             rio = RIO.executeAnalysis( gene_trees_x,
 166                                        species_tree_x,
 167                                        ALGORITHM.GSDIR,
 168                                        REROOTING.BY_ALGORITHM,
 169                                        "",
 170                                        true,
 171                                        false,
 172                                        true );
 173             if ( rio.getAnalyzedGeneTrees().length != 1 ) {
 174                 return false;
 175             }
 176             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 177                 return false;
 178             }
 179             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 180                 return false;
 181             }
 182             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 183                 return false;
 184             }
 185             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 186             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,0" ) ) {
 187                 System.out.println( m.toString() );
 188                 return false;
 189             }
 190             if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,1" ) ) {
 191                 System.out.println( m.toString() );
 192                 return false;
 193             }
 194             //
 195             final String gene_trees_xx_str = "(MOUSE1[&&NHX:S=MOUSE],RAT1[&&NHX:S=RAT])";
 196             final Phylogeny[] gene_trees_xx = factory.create( gene_trees_xx_str, nhx );
 197             final String species_trees_xx_str = "([&&NHX:S=MOUSE],[&&NHX:S=RAT]);";
 198             final Phylogeny species_tree_xx = factory.create( species_trees_xx_str, new NHXParser() )[ 0 ];
 199             species_tree_xx.setRooted( true );
 200             rio = RIO.executeAnalysis( gene_trees_xx,
 201                                        species_tree_xx,
 202                                        ALGORITHM.GSDIR,
 203                                        REROOTING.BY_ALGORITHM,
 204                                        "",
 205                                        true,
 206                                        false,
 207                                        true );
 208             if ( rio.getAnalyzedGeneTrees().length != 1 ) {
 209                 return false;
 210             }
 211             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
 212                 return false;
 213             }
 214             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 215                 return false;
 216             }
 217             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 218                 return false;
 219             }
 220             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 221             if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,1" ) ) {
 222                 System.out.println( m.toString() );
 223                 return false;
 224             }
 225             if ( !m.getRowAsString( 1, ',' ).equals( "RAT1,1,1" ) ) {
 226                 System.out.println( m.toString() );
 227                 return false;
 228             }
 229             //
 230             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
 231                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
 232                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
 233             final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
 234             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
 235             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
 236             species_tree_1.setRooted( true );
 237             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
 238             rio = RIO.executeAnalysis( gene_trees_1,
 239                                        species_tree_1,
 240                                        ALGORITHM.GSDIR,
 241                                        REROOTING.BY_ALGORITHM,
 242                                        "",
 243                                        true,
 244                                        false,
 245                                        true );
 246             if ( rio.getAnalyzedGeneTrees().length != 5 ) {
 247                 return false;
 248             }
 249             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 250                 return false;
 251             }
 252             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 253                 return false;
 254             }
 255             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 256                 return false;
 257             }
 258             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 259             // System.out.println( m.toString() );
 260             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 261                 return false;
 262             }
 263             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 264                 return false;
 265             }
 266             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
 267                 return false;
 268             }
 269             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
 270                 return false;
 271             }
 272             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
 273                 return false;
 274             }
 275             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 276                 return false;
 277             }
 278             //
 279             final Phylogeny[] gene_trees_2 = factory.create( gene_trees_1_str, nhx );
 280             final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
 281             final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
 282             species_tree_2.setRooted( true );
 283             PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
 284             rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 );
 285             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 286             // System.out.println( m.toString() );
 287             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 288                 return false;
 289             }
 290             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 291                 return false;
 292             }
 293             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
 294                 return false;
 295             }
 296             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
 297                 return false;
 298             }
 299             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
 300                 return false;
 301             }
 302             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 303                 return false;
 304             }
 305             //
 306             RIO r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode.run1.t" ),
 307                                           new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 308                                           ALGORITHM.GSDIR,
 309                                           REROOTING.BY_ALGORITHM,
 310                                           "",
 311                                           -1,
 312                                           -1,
 313                                           true,
 314                                           false,
 315                                           true );
 316             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 317                 return false;
 318             }
 319             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 320                 return false;
 321             }
 322             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 323                 return false;
 324             }
 325             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 326                 return false;
 327             }
 328             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 329                 return false;
 330             }
 331             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 332                 return false;
 333             }
 334             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 335             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE,201,201,200,200,200,200" ) ) {
 336                 System.out.println( m.getRowAsString( 0, ',' ) );
 337                 return false;
 338             }
 339             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN,201,201,200,200,200,43" ) ) {
 340                 System.out.println( m.getRowAsString( 1, ',' ) );
 341                 return false;
 342             }
 343             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
 344                 System.out.println( m.getRowAsString( 2, ',' ) );
 345                 return false;
 346             }
 347             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_CIOSA,200,200,201,201,201,201" ) ) {
 348                 System.out.println( m.getRowAsString( 3, ',' ) );
 349                 return false;
 350             }
 351             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE,200,200,201,201,201,43" ) ) {
 352                 System.out.println( m.getRowAsString( 4, ',' ) );
 353                 return false;
 354             }
 355             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR,200,43,43,201,43,201" ) ) {
 356                 System.out.println( m.getRowAsString( 5, ',' ) );
 357                 return false;
 358             }
 359             //
 360             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxid.run1.t" ),
 361                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 362                                       ALGORITHM.GSDIR,
 363                                       REROOTING.BY_ALGORITHM,
 364                                       "",
 365                                       -1,
 366                                       -1,
 367                                       true,
 368                                       false,
 369                                       true );
 370             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.ID ) {
 371                 return false;
 372             }
 373             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 374                 return false;
 375             }
 376             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 377                 return false;
 378             }
 379             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 380                 return false;
 381             }
 382             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 383                 return false;
 384             }
 385             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 386                 return false;
 387             }
 388             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 389             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_45351,201,200,201,200,200,200" ) ) {
 390                 System.out.println( m.getRowAsString( 0, ',' ) );
 391                 return false;
 392             }
 393             //mouse
 394             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_10090,200,201,200,201,201,43" ) ) {
 395                 System.out.println( m.getRowAsString( 1, ',' ) );
 396                 return false;
 397             }
 398             //human
 399             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_9606,201,200,201,200,200,43" ) ) {
 400                 System.out.println( m.getRowAsString( 2, ',' ) );
 401                 return false;
 402             }
 403             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_51511,200,201,200,201,201,201" ) ) {
 404                 System.out.println( m.getRowAsString( 3, ',' ) );
 405                 return false;
 406             }
 407             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_7955,200,201,200,201,201,43" ) ) {
 408                 System.out.println( m.getRowAsString( 4, ',' ) );
 409                 return false;
 410             }
 411             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_8364,200,43,43,201,43,201" ) ) {
 412                 System.out.println( m.getRowAsString( 5, ',' ) );
 413                 return false;
 414             }
 415             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 416                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 417                                       ALGORITHM.GSDIR,
 418                                       REROOTING.BY_ALGORITHM,
 419                                       "",
 420                                       -1,
 421                                       -1,
 422                                       true,
 423                                       false,
 424                                       true );
 425             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 426                 return false;
 427             }
 428             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 429                 return false;
 430             }
 431             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 432                 return false;
 433             }
 434             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 435                 return false;
 436             }
 437             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 438                 return false;
 439             }
 440             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 441                 return false;
 442             }
 443             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 444             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) {
 445                 System.out.println( m.getRowAsString( 0, ',' ) );
 446                 return false;
 447             }
 448             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) {
 449                 System.out.println( m.getRowAsString( 1, ',' ) );
 450                 return false;
 451             }
 452             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) {
 453                 System.out.println( m.getRowAsString( 2, ',' ) );
 454                 return false;
 455             }
 456             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) {
 457                 System.out.println( m.getRowAsString( 3, ',' ) );
 458                 return false;
 459             }
 460             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) {
 461                 System.out.println( m.getRowAsString( 4, ',' ) );
 462                 return false;
 463             }
 464             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) {
 465                 System.out.println( m.getRowAsString( 5, ',' ) );
 466                 return false;
 467             }
 468             //
 469             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 470                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 471                                       ALGORITHM.GSDIR,
 472                                       REROOTING.MIDPOINT,
 473                                       "",
 474                                       -1,
 475                                       -1,
 476                                       true,
 477                                       false,
 478                                       true );
 479             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 480                 return false;
 481             }
 482             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 483                 return false;
 484             }
 485             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 486                 return false;
 487             }
 488             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 489                 return false;
 490             }
 491             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 492                 return false;
 493             }
 494             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
 495                 return false;
 496             }
 497             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 498             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) {
 499                 System.out.println( m.getRowAsString( 0, ',' ) );
 500                 return false;
 501             }
 502             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) {
 503                 System.out.println( m.getRowAsString( 1, ',' ) );
 504                 return false;
 505             }
 506             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) {
 507                 System.out.println( m.getRowAsString( 2, ',' ) );
 508                 return false;
 509             }
 510             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) {
 511                 System.out.println( m.getRowAsString( 3, ',' ) );
 512                 return false;
 513             }
 514             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) {
 515                 System.out.println( m.getRowAsString( 4, ',' ) );
 516                 return false;
 517             }
 518             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) {
 519                 System.out.println( m.getRowAsString( 5, ',' ) );
 520                 return false;
 521             }
 522             //
 523             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 524                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 525                                       ALGORITHM.GSDIR,
 526                                       REROOTING.OUTGROUP,
 527                                       "H2ZH97_Ciona_savignyi",
 528                                       -1,
 529                                       -1,
 530                                       true,
 531                                       false,
 532                                       true );
 533             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 534                 return false;
 535             }
 536             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 537                 return false;
 538             }
 539             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 540                 return false;
 541             }
 542             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 543                 return false;
 544             }
 545             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 546                 return false;
 547             }
 548             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
 549                 return false;
 550             }
 551             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 552             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) {
 553                 System.out.println( m.getRowAsString( 0, ',' ) );
 554                 return false;
 555             }
 556             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) {
 557                 System.out.println( m.getRowAsString( 1, ',' ) );
 558                 return false;
 559             }
 560             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) {
 561                 System.out.println( m.getRowAsString( 2, ',' ) );
 562                 return false;
 563             }
 564             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) {
 565                 System.out.println( m.getRowAsString( 3, ',' ) );
 566                 return false;
 567             }
 568             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) {
 569                 System.out.println( m.getRowAsString( 4, ',' ) );
 570                 return false;
 571             }
 572             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) {
 573                 System.out.println( m.getRowAsString( 5, ',' ) );
 574                 return false;
 575             }
 576             //
 577             //
 578             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
 579                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 580                                       ALGORITHM.GSDIR,
 581                                       REROOTING.NONE,
 582                                       null,
 583                                       10,
 584                                       19,
 585                                       true,
 586                                       false,
 587                                       true );
 588             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
 589                 return false;
 590             }
 591             if ( r0.getAnalyzedGeneTrees().length != 10 ) {
 592                 return false;
 593             }
 594             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 595                 return false;
 596             }
 597             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 598                 return false;
 599             }
 600             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 601                 return false;
 602             }
 603             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) {
 604                 return false;
 605             }
 606             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 607             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) {
 608                 System.out.println( m.getRowAsString( 0, ',' ) );
 609                 return false;
 610             }
 611             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) {
 612                 System.out.println( m.getRowAsString( 1, ',' ) );
 613                 return false;
 614             }
 615             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) {
 616                 System.out.println( m.getRowAsString( 2, ',' ) );
 617                 return false;
 618             }
 619             if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) {
 620                 System.out.println( m.getRowAsString( 3, ',' ) );
 621                 return false;
 622             }
 623             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) {
 624                 System.out.println( m.getRowAsString( 4, ',' ) );
 625                 return false;
 626             }
 627             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) {
 628                 System.out.println( m.getRowAsString( 5, ',' ) );
 629                 return false;
 630             }
 631             //
 632             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ),
 633                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 634                                       ALGORITHM.GSDIR,
 635                                       REROOTING.BY_ALGORITHM,
 636                                       "",
 637                                       -1,
 638                                       -1,
 639                                       true,
 640                                       false,
 641                                       true );
 642             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 643                 return false;
 644             }
 645             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 646                 return false;
 647             }
 648             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) {
 649                 return false;
 650             }
 651             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) {
 652                 return false;
 653             }
 654             if ( r0.getRemovedGeneTreeNodes().size() != 3 ) {
 655                 return false;
 656             }
 657             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) {
 658                 return false;
 659             }
 660             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 661             if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) {
 662                 System.out.println( m.getRowAsString( 0, ',' ) );
 663                 return false;
 664             }
 665             if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) {
 666                 System.out.println( m.getRowAsString( 1, ',' ) );
 667                 return false;
 668             }
 669             if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) {
 670                 System.out.println( m.getRowAsString( 2, ',' ) );
 671                 return false;
 672             }
 673             //
 674             //
 675             r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ),
 676                                       new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
 677                                       ALGORITHM.GSDIR,
 678                                       REROOTING.BY_ALGORITHM,
 679                                       "",
 680                                       -1,
 681                                       -1,
 682                                       true,
 683                                       false,
 684                                       true );
 685             if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 686                 return false;
 687             }
 688             if ( r0.getAnalyzedGeneTrees().length != 201 ) {
 689                 return false;
 690             }
 691             if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 692                 return false;
 693             }
 694             if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
 695                 return false;
 696             }
 697             if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
 698                 return false;
 699             }
 700             if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
 701                 return false;
 702             }
 703             m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
 704             if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) {
 705                 System.out.println( m.getRowAsString( 0, ',' ) );
 706                 return false;
 707             }
 708             if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) {
 709                 System.out.println( m.getRowAsString( 1, ',' ) );
 710                 return false;
 711             }
 712             if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
 713                 System.out.println( m.getRowAsString( 2, ',' ) );
 714                 return false;
 715             }
 716             if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) {
 717                 System.out.println( m.getRowAsString( 3, ',' ) );
 718                 return false;
 719             }
 720             if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) {
 721                 System.out.println( m.getRowAsString( 4, ',' ) );
 722                 return false;
 723             }
 724             if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) {
 725                 System.out.println( m.getRowAsString( 5, ',' ) );
 726                 return false;
 727             }
 728             //
 729         }
 730         catch ( final Exception e ) {
 731             e.printStackTrace( System.out );
 732             return false;
 733         }
 734         return true;
 735     }
 736
 737     private static boolean testRIO_GSDIR_Iterating() {
 738         try {
 739             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 740             final NHXParser nhx = new NHXParser();
 741             nhx.setReplaceUnderscores( false );
 742             nhx.setIgnoreQuotes( true );
 743             nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
 744             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
 745                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
 746                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
 747             nhx.setSource( gene_trees_1_str );
 748             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
 749             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
 750             species_tree_1.setRooted( true );
 751             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
 752             //Archaeopteryx.createApplication( species_trees_1 );
 753             RIO rio = RIO.executeAnalysis( nhx,
 754                                            species_tree_1,
 755                                            ALGORITHM.GSDIR,
 756                                            REROOTING.BY_ALGORITHM,
 757                                            "",
 758                                            true,
 759                                            false,
 760                                            true );
 761             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
 762                 return false;
 763             }
 764             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
 765                 return false;
 766             }
 767             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
 768                 return false;
 769             }
 770             IntMatrix m = rio.getOrthologTable();
 771             //System.out.println( m.toString() );
 772             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 773                 return false;
 774             }
 775             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 776                 return false;
 777             }
 778             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
 779                 return false;
 780             }
 781             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
 782                 return false;
 783             }
 784             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
 785                 return false;
 786             }
 787             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 788                 return false;
 789             }
 790             //
 791             final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
 792             final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
 793             species_tree_2.setRooted( true );
 794             PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
 795             rio = RIO.executeAnalysis( nhx,
 796                                        species_tree_2,
 797                                        ALGORITHM.GSDIR,
 798                                        REROOTING.BY_ALGORITHM,
 799                                        "",
 800                                        true,
 801                                        false,
 802                                        true );
 803             m = rio.getOrthologTable();
 804             // System.out.println( m.toString() );
 805             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 806                 return false;
 807             }
 808             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 809                 return false;
 810             }
 811             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
 812                 return false;
 813             }
 814             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
 815                 return false;
 816             }
 817             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
 818                 return false;
 819             }
 820             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 821                 return false;
 822             }
 823         }
 824         catch ( final Exception e ) {
 825             e.printStackTrace( System.out );
 826             return false;
 827         }
 828         return true;
 829     }
 830 }