import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
import org.forester.io.parsers.HmmPfamOutputParser;
-import org.forester.io.parsers.nexus.PaupLogParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.protein.ProteinId;
import org.forester.species.BasicSpecies;
import org.forester.species.Species;
-import org.forester.test.Test;
import org.forester.util.ForesterUtil;
@SuppressWarnings( "unused")
return false;
}
System.out.println( "OK." );
- System.out.print( " Overlap removal: " );
- if ( !TestSurfacing.testOverlapRemoval() ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
- System.out.print( " Engulfing overlap removal: " );
- if ( !TestSurfacing.testEngulfingOverlapRemoval() ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
System.out.print( " Binary domain combination: " );
if ( !TestSurfacing.testBinaryDomainCombination() ) {
System.out.println( "failed." );
return false;
}
System.out.println( "OK." );
- System.out.print( " Paup log parser: " );
- if ( !TestSurfacing.testPaupLogParser( test_dir ) ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
+
System.out.print( " Binary state matrix to gain loss matrix: " );
if ( !TestSurfacing.testBinaryStateMatrixToGainLossMatrix( test_dir ) ) {
System.out.println( "failed." );
final Domain F = new BasicDomain( "F", 1, 2, ( short ) 1, ( short ) 1, 0.01, -12 );
final Domain G = new BasicDomain( "G", 1, 2, ( short ) 1, ( short ) 1, 0.001, -12 );
final Domain X = new BasicDomain( "X", 1, 2, ( short ) 1, ( short ) 1, 0.0001, -12 );
- if ( !TestSurfacing.isEqual( X.getPerSequenceScore(), -12 ) ) {
- return false;
- }
final Protein mouse_1 = new BasicProtein( "1", "mouse", 0 );
final Protein rabbit_1 = new BasicProtein( "1", "rabbit", 0 );
final Protein ciona_1 = new BasicProtein( "1", "ciona", 0 );
final Domain F = new BasicDomain( "F", 1, 2, ( short ) 1, ( short ) 1, 0.01, -12 );
final Domain G = new BasicDomain( "G", 1, 2, ( short ) 1, ( short ) 1, 0.001, -12 );
final Domain X = new BasicDomain( "X", 1, 2, ( short ) 1, ( short ) 1, 0.0001, -12 );
- if ( !TestSurfacing.isEqual( X.getPerSequenceScore(), -12 ) ) {
- return false;
- }
final Protein mouse_1 = new BasicProtein( "1", "mouse", 0 );
final Protein rabbit_1 = new BasicProtein( "1", "rabbit", 0 );
final Protein ciona_1 = new BasicProtein( "1", "ciona", 0 );
private static boolean testBinaryDomainCombination() {
try {
- final BasicBinaryDomainCombination s0 = new BasicBinaryDomainCombination( "a", "a" );
- final BasicBinaryDomainCombination s1 = new BasicBinaryDomainCombination( "b", "a" );
- final BasicBinaryDomainCombination s2 = new BasicBinaryDomainCombination( "a", "b" );
- final BasicBinaryDomainCombination s3 = new BasicBinaryDomainCombination( "B", "A" );
- final BasicBinaryDomainCombination s4 = new BasicBinaryDomainCombination( "A", "B" );
- final BasicBinaryDomainCombination s5 = new BasicBinaryDomainCombination( "c", "a" );
- final BasicBinaryDomainCombination s6 = new BasicBinaryDomainCombination( "b", "c" );
- final BasicBinaryDomainCombination s7 = new BasicBinaryDomainCombination( "d", "a" );
- final BasicBinaryDomainCombination s8 = new BasicBinaryDomainCombination( "b", "d" );
- final BinaryDomainCombination s9 = BasicBinaryDomainCombination.createInstance( "z-z=a-aa" );
+ final BasicBinaryDomainCombination s0 = BasicBinaryDomainCombination.obtainInstance( "a", "a" );
+ final BasicBinaryDomainCombination s1 = BasicBinaryDomainCombination.obtainInstance( "b", "a" );
+ final BasicBinaryDomainCombination s2 = BasicBinaryDomainCombination.obtainInstance( "a", "b" );
+ final BasicBinaryDomainCombination s3 = BasicBinaryDomainCombination.obtainInstance( "B", "A" );
+ final BasicBinaryDomainCombination s4 = BasicBinaryDomainCombination.obtainInstance( "A", "B" );
+ final BasicBinaryDomainCombination s5 = BasicBinaryDomainCombination.obtainInstance( "c", "a" );
+ final BasicBinaryDomainCombination s6 = BasicBinaryDomainCombination.obtainInstance( "b", "c" );
+ final BasicBinaryDomainCombination s7 = BasicBinaryDomainCombination.obtainInstance( "d", "a" );
+ final BasicBinaryDomainCombination s8 = BasicBinaryDomainCombination.obtainInstance( "b", "d" );
+ final BinaryDomainCombination s9 = BasicBinaryDomainCombination.obtainInstance( "z-z=a-aa" );
if ( !s9.toString().equals( "a-aa=z-z" ) ) {
System.out.println( s9.toString() );
return false;
System.out.println( sorted.size() );
return false;
}
- final DirectedBinaryDomainCombination aa = new DirectedBinaryDomainCombination( "a", "a" );
- final DirectedBinaryDomainCombination ba = new DirectedBinaryDomainCombination( "b", "a" );
- final DirectedBinaryDomainCombination ab = new DirectedBinaryDomainCombination( "a", "b" );
- final DirectedBinaryDomainCombination bb = new DirectedBinaryDomainCombination( "b", "b" );
+ final DirectedBinaryDomainCombination aa = DirectedBinaryDomainCombination.obtainInstance( "a", "a" );
+ final DirectedBinaryDomainCombination ba = DirectedBinaryDomainCombination.obtainInstance( "b", "a" );
+ final DirectedBinaryDomainCombination ab = DirectedBinaryDomainCombination.obtainInstance( "a", "b" );
+ final DirectedBinaryDomainCombination bb = DirectedBinaryDomainCombination.obtainInstance( "b", "b" );
if ( !aa.equals( aa ) ) {
return false;
}
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" );
if ( cd0.toBinaryDomainCombinations().size() != 3 ) {
return false;
}
- final BasicBinaryDomainCombination s0 = new BasicBinaryDomainCombination( "key0", "a" );
- final BasicBinaryDomainCombination s1 = new BasicBinaryDomainCombination( "b", "key0" );
- final BasicBinaryDomainCombination s2 = new BasicBinaryDomainCombination( "key0", "c" );
- final BasicBinaryDomainCombination s3 = new BasicBinaryDomainCombination( "key0", "cc" );
- final BasicBinaryDomainCombination s4 = new BasicBinaryDomainCombination( "c", "key0" );
+ final BasicBinaryDomainCombination s0 = BasicBinaryDomainCombination.obtainInstance( "key0", "a" );
+ final BasicBinaryDomainCombination s1 = BasicBinaryDomainCombination.obtainInstance( "b", "key0" );
+ final BasicBinaryDomainCombination s2 = BasicBinaryDomainCombination.obtainInstance( "key0", "c" );
+ final BasicBinaryDomainCombination s3 = BasicBinaryDomainCombination.obtainInstance( "key0", "cc" );
+ final BasicBinaryDomainCombination s4 = BasicBinaryDomainCombination.obtainInstance( "c", "key0" );
if ( !cd0.toBinaryDomainCombinations().contains( s0 ) ) {
return false;
}
if ( cd1.toBinaryDomainCombinations().size() != 4 ) {
return false;
}
- final BasicBinaryDomainCombination kk = new BasicBinaryDomainCombination( "key1", "key1" );
+ final BasicBinaryDomainCombination kk = BasicBinaryDomainCombination.obtainInstance( "key1", "key1" );
if ( !cd1.toBinaryDomainCombinations().contains( kk ) ) {
return false;
}
if ( cd0.toBinaryDomainCombinations().size() != 3 ) {
return false;
}
- final BinaryDomainCombination s0 = new DirectedBinaryDomainCombination( "key0", "a" );
- final BinaryDomainCombination s1 = new DirectedBinaryDomainCombination( "b", "key0" );
- final BinaryDomainCombination s2 = new DirectedBinaryDomainCombination( "key0", "c" );
- final BinaryDomainCombination s3 = new DirectedBinaryDomainCombination( "key0", "cc" );
- final BinaryDomainCombination s4 = new DirectedBinaryDomainCombination( "a", "b" );
- final BinaryDomainCombination s5 = new DirectedBinaryDomainCombination( "b", "a" );
- final BinaryDomainCombination s6 = new DirectedBinaryDomainCombination( "key0", "b" );
- final BinaryDomainCombination s7 = new DirectedBinaryDomainCombination( "a", "key0" );
- final BinaryDomainCombination s8 = new DirectedBinaryDomainCombination( "c", "key0" );
+ final BinaryDomainCombination s0 = DirectedBinaryDomainCombination.obtainInstance( "key0", "a" );
+ final BinaryDomainCombination s1 = DirectedBinaryDomainCombination.obtainInstance( "b", "key0" );
+ final BinaryDomainCombination s2 = DirectedBinaryDomainCombination.obtainInstance( "key0", "c" );
+ final BinaryDomainCombination s3 = DirectedBinaryDomainCombination.obtainInstance( "key0", "cc" );
+ final BinaryDomainCombination s4 = DirectedBinaryDomainCombination.obtainInstance( "a", "b" );
+ final BinaryDomainCombination s5 = DirectedBinaryDomainCombination.obtainInstance( "b", "a" );
+ final BinaryDomainCombination s6 = DirectedBinaryDomainCombination.obtainInstance( "key0", "b" );
+ final BinaryDomainCombination s7 = DirectedBinaryDomainCombination.obtainInstance( "a", "key0" );
+ final BinaryDomainCombination s8 = DirectedBinaryDomainCombination.obtainInstance( "c", "key0" );
if ( !cd0.toBinaryDomainCombinations().contains( s0 ) ) {
return false;
}
if ( cd1.toBinaryDomainCombinations().size() != 4 ) {
return false;
}
- final BinaryDomainCombination kk = new DirectedBinaryDomainCombination( "key1", "key1" );
+ final BinaryDomainCombination kk = DirectedBinaryDomainCombination.obtainInstance( "key1", "key1" );
if ( !cd1.toBinaryDomainCombinations().contains( kk ) ) {
return false;
}
list_1.add( five_1 );
final GenomeWideCombinableDomains gwcd_1 = BasicGenomeWideCombinableDomains
.createInstance( list_1, false, new BasicSpecies( "1" ), DomainCombinationType.DIRECTED );
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "B" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "B" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "B", "A" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "B", "A" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "A" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "A", "A" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "C" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "C" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "C", "A" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "C", "A" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "B", "C" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "B",
+ "C" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "C", "X" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
+ "X" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "C", "Y" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
+ "Y" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "X" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "X" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "Y" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "Y" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "Y", "A" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
+ "A" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "X", "A" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "X", "A" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "C", "B" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "C", "B" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "X", "Y" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "X",
+ "Y" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "Y", "X" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
+ "X" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "Y" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "Y" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "A", "X" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
+ "X" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "Y", "C" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "Y", "C" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "M", "N" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
+ "N" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "N", "M" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
+ "M" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "N", "P" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
+ "P" ) ) ) {
return false;
}
- if ( !gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "M", "P" ) ) ) {
+ if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
+ "P" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "P", "N" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "P", "N" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "P", "M" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "P", "M" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "XX", "YY" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "XX",
+ "YY" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "YY", "XX" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "YY",
+ "XX" ) ) ) {
return false;
}
- if ( gwcd_1.toBinaryDomainCombinations().contains( new DirectedBinaryDomainCombination( "B", "B" ) ) ) {
+ if ( gwcd_1.toBinaryDomainCombinations()
+ .contains( DirectedBinaryDomainCombination.obtainInstance( "B", "B" ) ) ) {
return false;
}
// final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>();
// 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 } } );
final GenomeWideCombinableDomains gwcd_1 = BasicGenomeWideCombinableDomains
.createInstance( list_1, false, new BasicSpecies( "1" ), DomainCombinationType.DIRECTED_ADJACTANT );
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "B" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "B" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "B", "A" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "B", "A" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "A" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "A" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "C" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "C" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "C", "A" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "C", "A" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "B", "C" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "B", "C" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "C", "X" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "C", "X" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "C", "Y" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "C", "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "X", "Y" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "X", "Y" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "X" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "X" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "Y" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "Y" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "Y", "A" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "Y", "A" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "X", "A" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "X", "A" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "C", "B" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "C", "B" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "X", "Y" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "X", "Y" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "Y", "X" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "Y", "X" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "Y" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "Y" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "A", "X" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "A", "X" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "Y", "C" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "Y", "C" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "M", "N" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "M", "N" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "N", "M" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "N", "M" ) ) ) {
return false;
}
if ( !gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "N", "P" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "N", "P" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "M", "P" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "M", "P" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "P", "N" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "P", "N" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "P", "M" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "P", "M" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "XX", "YY" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "XX", "YY" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "YY", "XX" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "YY", "XX" ) ) ) {
return false;
}
if ( gwcd_1.toBinaryDomainCombinations()
- .contains( new AdjactantDirectedBinaryDomainCombination( "B", "B" ) ) ) {
+ .contains( AdjactantDirectedBinaryDomainCombination.obtainInstance( "B", "B" ) ) ) {
return false;
}
}
if ( shared_i.size() != 3 ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "a" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "a" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "c" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "c" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "d" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "d" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "e" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "e" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "c" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "c" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "d" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "d" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "e" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "e" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "c", "d" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "d" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "c", "e" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "e" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "d", "e" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "d", "e" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "e", "f" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "e", "f" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "g", "h" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "g", "h" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "i" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "i" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "a", "l" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "l" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "i" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "i" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "b", "l" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "l" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "c", "i" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "i" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "c", "l" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "l" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "i", "l" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "i", "l" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "i", "f" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "i", "f" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "m", "n" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "m", "n" ) ) ) {
return false;
}
- if ( !a_ni.contains( new BasicBinaryDomainCombination( "j", "k" ) ) ) {
+ if ( !a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "j", "k" ) ) ) {
return false;
}
- if ( a_ni.contains( new BasicBinaryDomainCombination( "a", "g" ) ) ) {
+ if ( a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "g" ) ) ) {
return false;
}
- if ( a_ni.contains( new BasicBinaryDomainCombination( "a", "m" ) ) ) {
+ if ( a_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "m" ) ) ) {
return false;
}
- if ( a_i.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( a_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( a_i.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( a_i.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( a_i.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( a_i.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( !shared_ni.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( !shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( !shared_ni.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( !shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
- if ( !shared_ni.contains( new BasicBinaryDomainCombination( "a", "c" ) ) ) {
+ if ( !shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "c" ) ) ) {
return false;
}
- if ( !shared_ni.contains( new BasicBinaryDomainCombination( "b", "c" ) ) ) {
+ if ( !shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "c" ) ) ) {
return false;
}
- if ( !shared_ni.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( !shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( shared_ni.contains( new BasicBinaryDomainCombination( "m", "n" ) ) ) {
+ if ( shared_ni.contains( BasicBinaryDomainCombination.obtainInstance( "m", "n" ) ) ) {
return false;
}
- if ( shared_i.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( !shared_i.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( !shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
- if ( !shared_i.contains( new BasicBinaryDomainCombination( "a", "c" ) ) ) {
+ if ( !shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "c" ) ) ) {
return false;
}
- if ( !shared_i.contains( new BasicBinaryDomainCombination( "b", "c" ) ) ) {
+ if ( !shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "b", "c" ) ) ) {
return false;
}
- if ( shared_i.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( shared_i.contains( new BasicBinaryDomainCombination( "m", "n" ) ) ) {
+ if ( shared_i.contains( BasicBinaryDomainCombination.obtainInstance( "m", "n" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "a", "d" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "d" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "a", "e" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "e" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "b", "d" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "d" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "b", "e" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "e" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "c", "d" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "d" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "c", "e" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "e" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "d", "e" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "d", "e" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "e", "f" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "e", "f" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "g", "h" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "g", "h" ) ) ) {
return false;
}
- if ( !s_0_ni.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( !s_0_ni.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "a", "d" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "d" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "a", "e" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "e" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "b", "d" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "b", "d" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "b", "e" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "b", "e" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "c", "d" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "c", "d" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "c", "e" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "c", "e" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "d", "e" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "d", "e" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "e", "f" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "e", "f" ) ) ) {
return false;
}
- if ( !s_0_i.contains( new BasicBinaryDomainCombination( "g", "h" ) ) ) {
+ if ( !s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "g", "h" ) ) ) {
return false;
}
- if ( s_0_i.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( s_0_i.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "a", "i" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "i" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "a", "l" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "l" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "b", "i" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "i" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "b", "l" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "b", "l" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "c", "i" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "i" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "c", "l" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "c", "l" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "l", "i" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "l", "i" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "i", "f" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "i", "f" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "m", "n" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "m", "n" ) ) ) {
return false;
}
- if ( !s_1_ni.contains( new BasicBinaryDomainCombination( "j", "k" ) ) ) {
+ if ( !s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "j", "k" ) ) ) {
return false;
}
- if ( s_1_ni.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( s_1_ni.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "a", "i" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "i" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "a", "l" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "l" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "b", "i" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "b", "i" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "b", "l" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "b", "l" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "c", "i" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "c", "i" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "c", "l" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "c", "l" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "l", "i" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "l", "i" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "i", "f" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "i", "f" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "m", "n" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "m", "n" ) ) ) {
return false;
}
- if ( !s_1_i.contains( new BasicBinaryDomainCombination( "j", "k" ) ) ) {
+ if ( !s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "j", "k" ) ) ) {
return false;
}
- if ( s_1_i.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( s_1_i.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
if ( !isEqual( calc_ni.calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore(),
return false;
}
if ( !calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "v", "u" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "v", "u" ) ) ) {
return false;
}
if ( !calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "w", "v" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "v" ) ) ) {
return false;
}
if ( !calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "w", "x" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "x" ) ) ) {
return false;
}
- if ( !calc_u.getSharedBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "u" ) ) ) {
+ if ( !calc_u.getSharedBinaryDomainCombinations()
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "u" ) ) ) {
return false;
}
- if ( !calc_u.getSharedBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "z", "y" ) ) ) {
+ if ( !calc_u.getSharedBinaryDomainCombinations()
+ .contains( BasicBinaryDomainCombination.obtainInstance( "z", "y" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "v", "u" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
+ "u" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "v" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "v" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "x" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "x" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "u" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "u" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "z", "y" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
+ "y" ) ) ) {
return false;
}
calc_u.setAllowDomainsToBeIgnored( true );
return false;
}
if ( calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "v", "u" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "v", "u" ) ) ) {
return false;
}
if ( !calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "w", "v" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "v" ) ) ) {
return false;
}
if ( !calc_u.getBinaryDomainCombinationsSpecificToGenome0()
- .contains( new BasicBinaryDomainCombination( "w", "x" ) ) ) {
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "x" ) ) ) {
return false;
}
- if ( calc_u.getSharedBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "u" ) ) ) {
+ if ( calc_u.getSharedBinaryDomainCombinations()
+ .contains( BasicBinaryDomainCombination.obtainInstance( "w", "u" ) ) ) {
return false;
}
- if ( !calc_u.getSharedBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "z", "y" ) ) ) {
+ if ( !calc_u.getSharedBinaryDomainCombinations()
+ .contains( BasicBinaryDomainCombination.obtainInstance( "z", "y" ) ) ) {
return false;
}
- if ( calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "v", "u" ) ) ) {
+ if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
+ "u" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "v" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "v" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "x" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "x" ) ) ) {
return false;
}
- if ( calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "w", "u" ) ) ) {
+ if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
+ "u" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "z", "y" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
+ "y" ) ) ) {
return false;
}
calc_u.setAllowDomainsToBeIgnored( false );
if ( calc_u.getAllBinaryDomainCombinations().size() != 1 ) {
return false;
}
- if ( !calc_u.getSharedBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "y", "z" ) ) ) {
+ if ( !calc_u.getSharedBinaryDomainCombinations()
+ .contains( BasicBinaryDomainCombination.obtainInstance( "y", "z" ) ) ) {
return false;
}
- if ( !calc_u.getAllBinaryDomainCombinations().contains( new BasicBinaryDomainCombination( "z", "y" ) ) ) {
+ if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
+ "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 );
return true;
}
- private static boolean testEngulfingOverlapRemoval() {
- try {
- final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
- final List<Boolean> covered = new ArrayList<Boolean>();
- covered.add( true ); // 0
- covered.add( false ); // 1
- covered.add( true ); // 2
- covered.add( false ); // 3
- covered.add( true ); // 4
- covered.add( true ); // 5
- covered.add( false ); // 6
- covered.add( true ); // 7
- covered.add( true ); // 8
- if ( SurfacingUtil.isEngulfed( d0, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d1, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d2, covered ) ) {
- return false;
- }
- if ( !SurfacingUtil.isEngulfed( d3, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d4, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d5, covered ) ) {
- return false;
- }
- if ( !SurfacingUtil.isEngulfed( d6, covered ) ) {
- return false;
- }
- final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
- final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
- final Protein abc = new BasicProtein( "abc", "nemve", 0 );
- abc.addProteinDomain( a );
- abc.addProteinDomain( b );
- abc.addProteinDomain( c );
- final Protein abc_r1 = SurfacingUtil.removeOverlappingDomains( 3, false, abc );
- final Protein abc_r2 = SurfacingUtil.removeOverlappingDomains( 3, true, abc );
- if ( abc.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
- return false;
- }
- if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
- return false;
- }
- final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
- final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
- final Protein def = new BasicProtein( "def", "nemve", 0 );
- def.addProteinDomain( d );
- def.addProteinDomain( e );
- def.addProteinDomain( f );
- final Protein def_r1 = SurfacingUtil.removeOverlappingDomains( 5, false, def );
- final Protein def_r2 = SurfacingUtil.removeOverlappingDomains( 5, true, def );
- if ( def.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( def_r1.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( def_r2.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testGenomeWideCombinableDomains() {
try {
final Domain a = new BasicDomain( "a", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
if ( bc0.size() != 15 ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "b", "a" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "b", "a" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "a", "c" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "c" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "a", "d" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "d" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "a", "e" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "e" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "b", "c" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "b", "c" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "b", "d" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "b", "d" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "b", "e" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "b", "e" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "c", "d" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "c", "d" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "c", "e" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "c", "e" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "d", "e" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "d", "e" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "e", "f" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "e", "f" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( !bc0.contains( new BasicBinaryDomainCombination( "g", "h" ) ) ) {
+ if ( !bc0.contains( BasicBinaryDomainCombination.obtainInstance( "g", "h" ) ) ) {
return false;
}
- if ( bc0.contains( new BasicBinaryDomainCombination( "f", "a" ) ) ) {
+ if ( bc0.contains( BasicBinaryDomainCombination.obtainInstance( "f", "a" ) ) ) {
return false;
}
- if ( bc0.contains( new BasicBinaryDomainCombination( "f", "b" ) ) ) {
+ if ( bc0.contains( BasicBinaryDomainCombination.obtainInstance( "f", "b" ) ) ) {
return false;
}
- if ( bc0.contains( new BasicBinaryDomainCombination( "a", "h" ) ) ) {
+ if ( bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "h" ) ) ) {
return false;
}
- if ( bc0.contains( new BasicBinaryDomainCombination( "a", "g" ) ) ) {
+ if ( bc0.contains( BasicBinaryDomainCombination.obtainInstance( "a", "g" ) ) ) {
return false;
}
final SortedSet<BinaryDomainCombination> bc1 = eel_ignore.toBinaryDomainCombinations();
if ( bc1.size() != 12 ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "a", "a" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "a" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "a", "b" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "b" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "b", "a" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "b", "a" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "a", "c" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "c" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "a", "d" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "d" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "a", "e" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "e" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "b", "c" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "b", "c" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "b", "d" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "b", "d" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "b", "e" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "b", "e" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "c", "d" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "c", "d" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "c", "e" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "c", "e" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "d", "e" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "d", "e" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "e", "f" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "e", "f" ) ) ) {
return false;
}
- if ( !bc1.contains( new BasicBinaryDomainCombination( "g", "h" ) ) ) {
+ if ( !bc1.contains( BasicBinaryDomainCombination.obtainInstance( "g", "h" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "e", "e" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "e", "e" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "f", "f" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "f", "f" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "f", "a" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "f", "a" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "f", "b" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "f", "b" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "a", "g" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "a", "g" ) ) ) {
return false;
}
- if ( bc1.contains( new BasicBinaryDomainCombination( "b", "g" ) ) ) {
+ if ( bc1.contains( BasicBinaryDomainCombination.obtainInstance( "b", "g" ) ) ) {
return false;
}
}
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 );
if ( uba_domain.getTo() != 57 ) {
return false;
}
- if ( !Test.isEqual( uba_domain.getPerSequenceEvalue(), 0.00084 ) ) {
- return false;
- }
- if ( !Test.isEqual( uba_domain.getPerSequenceScore(), 23.2 ) ) {
- 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 );
if ( uba_domain2.getTo() != 57 ) {
return false;
}
- if ( !Test.isEqual( uba_domain2.getPerSequenceEvalue(), 0.00084 ) ) {
- return false;
- }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
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 );
filter.add( "strange" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "strange" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "C" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "X" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN );
parser.setEValueMaximum( 0.2 );
filter.add( "C" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "UIM" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "UIM" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
filter.add( "C" );
parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
"human",
- "ls",
filter,
HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN );
parser.setEValueMaximum( 0.2 );
return true;
}
- private static boolean testOverlapRemoval() {
- try {
- final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final List<Boolean> covered = new ArrayList<Boolean>();
- covered.add( true ); // 0
- covered.add( false ); // 1
- covered.add( true ); // 2
- covered.add( false ); // 3
- covered.add( true ); // 4
- covered.add( true ); // 5
- covered.add( false ); // 6
- covered.add( true ); // 7
- covered.add( true ); // 8
- if ( SurfacingUtil.calculateOverlap( d0, covered ) != 3 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d1, covered ) != 2 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d2, covered ) != 6 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d3, covered ) != 0 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d4, covered ) != 2 ) {
- return false;
- }
- final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Protein ab = new BasicProtein( "ab", "varanus", 0 );
- ab.addProteinDomain( a );
- ab.addProteinDomain( b );
- final Protein ab_s0 = SurfacingUtil.removeOverlappingDomains( 3, false, ab );
- if ( ab.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
- return false;
- }
- final Protein ab_s1 = SurfacingUtil.removeOverlappingDomains( 4, false, ab );
- if ( ab.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain d = new BasicDomain( "d",
- ( short ) 10000,
- ( short ) 10500,
- ( short ) 1,
- ( short ) 1,
- 0.0000001,
- 1 );
- final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Protein cde = new BasicProtein( "cde", "varanus", 0 );
- cde.addProteinDomain( c );
- cde.addProteinDomain( d );
- cde.addProteinDomain( e );
- final Protein cde_s0 = SurfacingUtil.removeOverlappingDomains( 0, false, cde );
- if ( cde.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
- final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
- final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
- fghi.addProteinDomain( f );
- fghi.addProteinDomain( g );
- fghi.addProteinDomain( h );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i2 );
- final Protein fghi_s0 = SurfacingUtil.removeOverlappingDomains( 10, false, fghi );
- if ( fghi.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
- return false;
- }
- final Protein fghi_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, fghi );
- if ( fghi.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
- final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
- final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
- final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
- final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
- jklm.addProteinDomain( j );
- jklm.addProteinDomain( k );
- jklm.addProteinDomain( l );
- jklm.addProteinDomain( m );
- jklm.addProteinDomain( m0 );
- jklm.addProteinDomain( m1 );
- jklm.addProteinDomain( m2 );
- final Protein jklm_s0 = SurfacingUtil.removeOverlappingDomains( 10, false, jklm );
- if ( jklm.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
- return false;
- }
- final Protein jklm_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, jklm );
- if ( jklm.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
- final Protein od = new BasicProtein( "od", "varanus", 0 );
- od.addProteinDomain( only );
- final Protein od_s0 = SurfacingUtil.removeOverlappingDomains( 0, false, od );
- if ( od.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( od_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testParsimony() {
try {
final BinaryStates X = BinaryStates.PRESENT;
return true;
}
- private static boolean testPaupLogParser( final File test_dir ) {
- try {
- final PaupLogParser parser = new PaupLogParser();
- parser.setSource( new File( test_dir + ForesterUtil.getFileSeparator() + "paup_log_test_1" ) );
- final CharacterStateMatrix<BinaryStates> matrix = parser.parse();
- if ( matrix.getNumberOfIdentifiers() != 8 ) {
- return false;
- }
- if ( !matrix.getIdentifier( 0 ).equals( "MOUSE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 1 ).equals( "NEMVE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 2 ).equals( "MONBE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 3 ).equals( "DICDI" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 4 ).equals( "ARATH" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 5 ).equals( "6" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 6 ).equals( "7" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 7 ).equals( "8" ) ) {
- return false;
- }
- if ( matrix.getNumberOfCharacters() != ( 66 + 66 + 28 ) ) {
- return false;
- }
- if ( matrix.getState( 0, 4 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 0, 5 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 1, 5 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 154 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 7, 155 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 156 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 157 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 7, 158 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 159 ) != BinaryStates.ABSENT ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
+
}
git://source.jalview.org / jalview.git / blobdiff