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

   1
   2 package org.forester.rio;
   3
   4 import org.forester.datastructures.IntMatrix;
   5 import org.forester.io.parsers.nhx.NHXParser;
   6 import org.forester.phylogeny.Phylogeny;
   7 import org.forester.phylogeny.PhylogenyMethods;
   8 import org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField;
   9 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  10 import org.forester.phylogeny.factories.PhylogenyFactory;
  11 import org.forester.rio.RIO.REROOTING;
  12 import org.forester.sdi.SDIutil.ALGORITHM;
  13 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
  14 import org.forester.util.ForesterUtil;
  15
  16 public final class TestRIO {
  17
  18     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
  19                                                           + "test_data" + ForesterUtil.getFileSeparator();
  20
  21     public static void main( final String[] args ) {
  22         if ( !testRIO_GSDIR() ) {
  23             System.out.println( "testRIO GSDIR failed" );
  24         }
  25         else {
  26             System.out.println( "OK" );
  27         }
  28     }
  29
  30     public static boolean test() {
  31         if ( !testRIO_GSDIR() ) {
  32             return false;
  33         }
  34         return true;
  35     }
  36
  37     private static boolean testRIO_GSDIR() {
  38         try {
  39             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  40             final NHXParser nhx = new NHXParser();
  41             nhx.setReplaceUnderscores( false );
  42             nhx.setIgnoreQuotes( true );
  43             nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
  44             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
  45                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
  46                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
  47             final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
  48             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
  49             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
  50             species_tree_1.setRooted( true );
  51             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
  52             //Archaeopteryx.createApplication( species_trees_1 );
  53             RIO rio = RIO.executeAnalysis( gene_trees_1,
  54                                            species_tree_1,
  55                                            ALGORITHM.GSDIR,
  56                                            REROOTING.BY_ALGORITHM,
  57                                            "",
  58                                            true,
  59                                            false );
  60             if ( rio.getAnalyzedGeneTrees().length != 5 ) {
  61                 return false;
  62             }
  63             if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
  64                 return false;
  65             }
  66             if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
  67                 return false;
  68             }
  69             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
  70                 return false;
  71             }
  72             IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
  73             // System.out.println( m.toString() );
  74             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
  75                 return false;
  76             }
  77             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
  78                 return false;
  79             }
  80             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
  81                 return false;
  82             }
  83             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
  84                 return false;
  85             }
  86             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
  87                 return false;
  88             }
  89             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
  90                 return false;
  91             }
  92             //
  93             final Phylogeny[] gene_trees_2 = factory.create( gene_trees_1_str, nhx );
  94             final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
  95             final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
  96             species_tree_2.setRooted( true );
  97             PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
  98             rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 );
  99             m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 100             // System.out.println( m.toString() );
 101             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
 102                 return false;
 103             }
 104             if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
 105                 return false;
 106             }
 107             if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
 108                 return false;
 109             }
 110             if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
 111                 return false;
 112             }
 113             if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
 114                 return false;
 115             }
 116             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
 117                 return false;
 118             }
 119         }
 120         catch ( final Exception e ) {
 121             e.printStackTrace( System.out );
 122             return false;
 123         }
 124         return true;
 125     }
 126 }