X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FTestSurfacing.java;h=72141d22cee47970d132b5f4f16b4e3943f19244;hb=3d5864a39739960c126f2ab5585162fd52d1f47d;hp=168b6a47a89fd461bf25dc5fc0fc0b09fe2f4d27;hpb=0898ccf757a9e1b3c10f0a8ad51829eb809d3062;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index 168b6a4..72141d2 100644 --- a/forester/java/src/org/forester/surfacing/TestSurfacing.java +++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java @@ -42,7 +42,6 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix; 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; @@ -57,7 +56,6 @@ import org.forester.protein.Protein; 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") @@ -177,12 +175,7 @@ public class TestSurfacing { 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." ); @@ -256,9 +249,6 @@ public class TestSurfacing { 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 ); @@ -982,9 +972,6 @@ public class TestSurfacing { 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 ); @@ -1229,16 +1216,16 @@ public class TestSurfacing { 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; @@ -1284,10 +1271,10 @@ public class TestSurfacing { 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; } @@ -1322,7 +1309,7 @@ public class TestSurfacing { final BinaryStates O = BinaryStates.ABSENT; try { final CharacterStateMatrix binary_states_matrix_0 = new BasicCharacterStateMatrix( 7, - 6 ); + 6 ); binary_states_matrix_0.setIdentifier( 0, "A" ); binary_states_matrix_0.setIdentifier( 1, "B" ); binary_states_matrix_0.setIdentifier( 2, "C" ); @@ -1477,11 +1464,11 @@ public class TestSurfacing { 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; } @@ -1527,7 +1514,7 @@ public class TestSurfacing { 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; } @@ -1712,15 +1699,15 @@ public class TestSurfacing { 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; } @@ -1778,7 +1765,7 @@ public class TestSurfacing { 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; } @@ -1827,85 +1814,112 @@ public class TestSurfacing { 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 gwcd_list = new ArrayList(); @@ -1921,7 +1935,7 @@ public class TestSurfacing { // if ( matrix_bc.getState( 0, 0 ) != X ) { // return false; // } - // + // // // final BasicCharacterStateMatrix dm = new BasicCharacterStateMatrix( new BinaryStates[][] { // { X, X, X, X, X, X }, { X, X, X, X, X, X } } ); @@ -2403,115 +2417,115 @@ public class TestSurfacing { 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; } } @@ -2820,256 +2834,256 @@ public class TestSurfacing { 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(), @@ -3186,36 +3200,43 @@ public class TestSurfacing { 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 ); @@ -3286,36 +3307,43 @@ public class TestSurfacing { 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 ); @@ -3392,10 +3420,12 @@ public class TestSurfacing { 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(), @@ -3440,7 +3470,7 @@ public class TestSurfacing { 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 ); @@ -4378,128 +4408,128 @@ public class TestSurfacing { 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 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; } } @@ -4513,7 +4543,7 @@ public class TestSurfacing { 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 ); @@ -4590,14 +4620,8 @@ public class TestSurfacing { 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 ); @@ -4677,9 +4701,6 @@ public class TestSurfacing { 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 ); @@ -4691,7 +4712,7 @@ public class TestSurfacing { 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 ); @@ -4709,7 +4730,6 @@ public class TestSurfacing { 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 ); @@ -4729,7 +4749,6 @@ public class TestSurfacing { 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 ); @@ -4750,7 +4769,6 @@ public class TestSurfacing { 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 ); @@ -4772,7 +4790,6 @@ public class TestSurfacing { 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 ); @@ -4793,7 +4810,6 @@ public class TestSurfacing { 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 ); @@ -4812,7 +4828,6 @@ public class TestSurfacing { 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 ); @@ -4834,7 +4849,6 @@ public class TestSurfacing { 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 ); @@ -4857,7 +4871,6 @@ public class TestSurfacing { 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 ); @@ -5413,73 +5426,5 @@ public class TestSurfacing { 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 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; - } + }