private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
+ "test_data" + ForesterUtil.getFileSeparator();
+ public static void main( final String[] args ) {
+ if ( !testRIO_GSDIR() ) {
+ System.out.println( "testRIO GSDIR failed" );
+ }
+ else {
+ System.out.println( "OK" );
+ }
+ }
+
public static boolean test() {
if ( !testRIO_GSDIR() ) {
return false;
species_tree_1.setRooted( true );
PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
//Archaeopteryx.createApplication( species_trees_1 );
- RIO rio = new RIO( gene_trees_1, species_tree_1, ALGORITHM.GSDIR, REROOTING.BY_ALGORITHM, "", true, false );
+ RIO rio = RIO.executeAnalysis( gene_trees_1,
+ species_tree_1,
+ ALGORITHM.GSDIR,
+ REROOTING.BY_ALGORITHM,
+ "",
+ true,
+ false );
if ( rio.getAnalyzedGeneTrees().length != 5 ) {
return false;
}
final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
species_tree_2.setRooted( true );
PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
- rio = new RIO( gene_trees_2, species_tree_2, ALGORITHM.GSDIR, REROOTING.BY_ALGORITHM, null, true, false );
+ rio = RIO.executeAnalysis( gene_trees_2, species_tree_2 );
m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
// System.out.println( m.toString() );
if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
}
return true;
}
-
- public static void main( final String[] args ) {
- if ( !testRIO_GSDIR() ) {
- System.out.println( "testRIO GSDIR failed" );
- }
- else {
- System.out.println( "OK" );
- }
- }
}
\ No newline at end of file