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=3a79d7bc56e0997858558db40466df611d77909e;hpb=08a92c65e8b969a3ce2a4b511055cd6029357831;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index 3a79d7b..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") @@ -147,18 +145,6 @@ public class TestSurfacing { 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." ); @@ -189,12 +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." ); @@ -268,9 +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 ); @@ -327,7 +305,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, - false ); + false, + true ); final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, @@ -477,7 +456,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, - false ); + false, + true ); final SortedSet sims2 = calc2 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list2, @@ -564,7 +544,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, - false ); + false, + true ); final SortedSet sims3 = calc3 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list3, @@ -607,7 +588,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, true, - false ); + false, + true ); final SortedSet sims4 = calc4 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list4, @@ -990,9 +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 ); @@ -1038,7 +1017,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, - false ); + false, + true ); final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, @@ -1146,7 +1126,8 @@ public class TestSurfacing { new BasicSpecies( "nemve" ) ) ); final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, - false ); + false, + true ); final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, @@ -1235,16 +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; @@ -1290,10 +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; } @@ -1328,7 +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" ); @@ -1483,11 +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; } @@ -1533,7 +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; } @@ -1718,15 +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; } @@ -1784,7 +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; } @@ -1833,85 +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(); @@ -1927,7 +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 } } ); @@ -2409,115 +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; } } @@ -2826,256 +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(), @@ -3192,36 +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 ); @@ -3292,36 +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 ); @@ -3398,10 +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(), @@ -3446,7 +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 ); @@ -4163,105 +4187,6 @@ public class TestSurfacing { 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 covered = new ArrayList(); - 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 ); @@ -4483,128 +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; } } @@ -4618,7 +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 ); @@ -4695,14 +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 ); @@ -4782,9 +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 ); @@ -4796,7 +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 ); @@ -4814,7 +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 ); @@ -4834,7 +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 ); @@ -4855,7 +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 ); @@ -4877,7 +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 ); @@ -4898,7 +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 ); @@ -4917,7 +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 ); @@ -4939,7 +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 ); @@ -4962,7 +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 ); @@ -4993,160 +4901,6 @@ public class TestSurfacing { 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 covered = new ArrayList(); - 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; @@ -5672,73 +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; - } + }