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