final BinaryStates O = BinaryStates.ABSENT;
try {
final CharacterStateMatrix<BinaryStates> binary_states_matrix_0 = new BasicCharacterStateMatrix<BinaryStates>( 7,
- 6 );
+ 6 );
binary_states_matrix_0.setIdentifier( 0, "A" );
binary_states_matrix_0.setIdentifier( 1, "B" );
binary_states_matrix_0.setIdentifier( 2, "C" );
final GenomeWideCombinableDomains gwcd_1 = BasicGenomeWideCombinableDomains
.createInstance( list_1, false, new BasicSpecies( "1" ), DomainCombinationType.DIRECTED );
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "B" ) ) ) {
+ "B" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "C" ) ) ) {
+ "C" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "B",
- "C" ) ) ) {
+ "C" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
- "X" ) ) ) {
+ "X" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
- "Y" ) ) ) {
+ "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "X" ) ) ) {
+ "X" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "Y" ) ) ) {
+ "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
- "A" ) ) ) {
+ "A" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "X",
- "Y" ) ) ) {
+ "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
- "X" ) ) ) {
+ "X" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "Y" ) ) ) {
+ "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
- "X" ) ) ) {
+ "X" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
- "N" ) ) ) {
+ "N" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
- "M" ) ) ) {
+ "M" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
- "P" ) ) ) {
+ "P" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
- "P" ) ) ) {
+ "P" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
return false;
}
if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "XX",
- "YY" ) ) ) {
+ "YY" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "YY",
- "XX" ) ) ) {
+ "XX" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
// if ( matrix_bc.getState( 0, 0 ) != X ) {
// return false;
// }
- //
+ //
//
// final BasicCharacterStateMatrix<BinaryStates> dm = new BasicCharacterStateMatrix<BinaryStates>( new BinaryStates[][] {
// { X, X, X, X, X, X }, { X, X, X, X, X, X } } );
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
- "u" ) ) ) {
+ "u" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "v" ) ) ) {
+ "v" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "x" ) ) ) {
+ "x" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "u" ) ) ) {
+ "u" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
- "y" ) ) ) {
+ "y" ) ) ) {
return false;
}
calc_u.setAllowDomainsToBeIgnored( true );
return false;
}
if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
- "u" ) ) ) {
+ "u" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "v" ) ) ) {
+ "v" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "x" ) ) ) {
+ "x" ) ) ) {
return false;
}
if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
- "u" ) ) ) {
+ "u" ) ) ) {
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
- "y" ) ) ) {
+ "y" ) ) ) {
return false;
}
calc_u.setAllowDomainsToBeIgnored( false );
return false;
}
if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
- "y" ) ) ) {
+ "y" ) ) ) {
return false;
}
if ( !isEqual( calc_u.calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore(),
private static boolean testDomainCombinationCounting( final File test_dir ) {
try {
final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" );
+ + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" );
parser.setEValueMaximum( 0.2 );
parser.setIgnoreDufs( true );
parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
private static boolean testHmmPfamOutputParser( final File test_dir ) {
try {
final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" );
+ + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" );
parser.setEValueMaximum( 0.2 );
parser.setIgnoreDufs( true );
parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
return false;
}
final HmmPfamOutputParser parser2 = new HmmPfamOutputParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" );
+ + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" );
parser2.setEValueMaximum( 0.2 );
parser2.setIgnoreDufs( true );
parser2.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
private static boolean testHmmPfamOutputParserWithFilter( final File test_dir ) {
try {
HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator()
- + "hmmpfam_output3" ), "human", "ls" );
+ + "hmmpfam_output3" ), "human", "ls" );
parser.setEValueMaximum( 0.2 );
parser.setIgnoreDufs( true );
parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );