X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FTestSurfacing.java;h=6e1e6dc8af9da79f7f785d69d4a47414197bc773;hb=97358f7a982d67831aedc14d5ab193727f6bdc83;hp=dabbb0640dfad012d01fff4d040e2c6190e4333c;hpb=3d68fcd1fc4272b56546f78f3cbd437237af5cfa;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index dabbb06..6e1e6dc 100644 --- a/forester/java/src/org/forester/surfacing/TestSurfacing.java +++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java @@ -57,7 +57,6 @@ 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") @@ -256,9 +255,6 @@ 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 ); @@ -313,17 +309,17 @@ public class TestSurfacing { cdc_list.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, true, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, false, true ); - final SortedSet sims = calc + final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, true, true ); - final Iterator sims_it = sims.iterator(); - final PrintableDomainSimilarity sa = sims_it.next(); + final Iterator sims_it = sims.iterator(); + final DomainSimilarity sa = sims_it.next(); if ( !sa.getDomainId().equals( "A" ) ) { return false; } @@ -364,7 +360,7 @@ public class TestSurfacing { if ( sa.getMaximalDifferenceInCounts() != 3 ) { return false; } - final PrintableDomainSimilarity sb = sims_it.next(); + final DomainSimilarity sb = sims_it.next(); if ( !sb.getDomainId().equals( "B" ) ) { return false; } @@ -398,7 +394,7 @@ public class TestSurfacing { if ( sb.getMaximalDifferenceInCounts() != 2 ) { return false; } - final PrintableDomainSimilarity sc = sims_it.next(); + final DomainSimilarity sc = sims_it.next(); if ( !sc.getDomainId().equals( "C" ) ) { return false; } @@ -464,17 +460,17 @@ public class TestSurfacing { cdc_list2.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, false, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, false, true ); - final SortedSet sims2 = calc2 + final SortedSet sims2 = calc2 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list2, false, true ); - final Iterator sims_it2 = sims2.iterator(); - final PrintableDomainSimilarity sa2 = sims_it2.next(); + final Iterator sims_it2 = sims2.iterator(); + final DomainSimilarity sa2 = sims_it2.next(); if ( !sa2.getDomainId().equals( "A" ) ) { return false; } @@ -552,17 +548,17 @@ public class TestSurfacing { cdc_list3.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, true, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, false, true ); - final SortedSet sims3 = calc3 + final SortedSet sims3 = calc3 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list3, false, true ); - final Iterator sims_it3 = sims3.iterator(); - final PrintableDomainSimilarity sa3 = sims_it3.next(); + final Iterator sims_it3 = sims3.iterator(); + final DomainSimilarity sa3 = sims_it3.next(); if ( !sa3.getDomainId().equals( "A" ) ) { return false; } @@ -596,17 +592,17 @@ public class TestSurfacing { cdc_list4.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, false, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, true, false, true ); - final SortedSet sims4 = calc4 + final SortedSet sims4 = calc4 .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list4, false, true ); - final Iterator sims_it4 = sims4.iterator(); - final PrintableDomainSimilarity sa4 = sims_it4.next(); + final Iterator sims_it4 = sims4.iterator(); + final DomainSimilarity sa4 = sims_it4.next(); if ( !sa4.getDomainId().equals( "A" ) ) { return false; } @@ -629,10 +625,10 @@ public class TestSurfacing { if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "X" ) != 3 ) { return false; } - final SortedSet sims4_d = calc4 + final SortedSet sims4_d = calc4 .calculateSimilarities( new DomainCountsBasedPairwiseSimilarityCalculator(), cdc_list4, false, true ); - final Iterator sims_it4_d = sims4_d.iterator(); - final PrintableDomainSimilarity sa4_d = sims_it4_d.next(); + final Iterator sims_it4_d = sims4_d.iterator(); + final DomainSimilarity sa4_d = sims_it4_d.next(); if ( !sa4_d.getDomainId().equals( "A" ) ) { return false; } @@ -653,13 +649,13 @@ public class TestSurfacing { if ( sa4_d.getN() != 6 ) { return false; } - final SortedSet sims4_p = calc4 + final SortedSet sims4_p = calc4 .calculateSimilarities( new ProteinCountsBasedPairwiseDomainSimilarityCalculator(), cdc_list4, false, true ); - final Iterator sims_it4_p = sims4_p.iterator(); - final PrintableDomainSimilarity sa4_p = sims_it4_p.next(); + final Iterator sims_it4_p = sims4_p.iterator(); + final DomainSimilarity sa4_p = sims_it4_p.next(); if ( !sa4_p.getDomainId().equals( "A" ) ) { return false; } @@ -708,10 +704,10 @@ public class TestSurfacing { cdc_list5.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, true, new BasicSpecies( "nemve" ) ) ); - final SortedSet sims5_d = calc4 + final SortedSet sims5_d = calc4 .calculateSimilarities( new DomainCountsBasedPairwiseSimilarityCalculator(), cdc_list5, false, true ); - final Iterator sims_it5_d = sims5_d.iterator(); - final PrintableDomainSimilarity sa5_d = sims_it5_d.next(); + final Iterator sims_it5_d = sims5_d.iterator(); + final DomainSimilarity sa5_d = sims_it5_d.next(); if ( sa5_d.getSpecies().size() != 4 ) { return false; } @@ -779,13 +775,13 @@ public class TestSurfacing { if ( sa5_d.getMaximalDifferenceInCounts() != 11 ) { return false; } - final SortedSet sims5_p = calc4 + final SortedSet sims5_p = calc4 .calculateSimilarities( new ProteinCountsBasedPairwiseDomainSimilarityCalculator(), cdc_list5, false, true ); - final Iterator sims_it5_p = sims5_p.iterator(); - final PrintableDomainSimilarity sa5_p = sims_it5_p.next(); + final Iterator sims_it5_p = sims5_p.iterator(); + final DomainSimilarity sa5_p = sims_it5_p.next(); if ( !sa5_p.getDomainId().equals( "A" ) ) { return false; } @@ -843,10 +839,10 @@ public class TestSurfacing { cdc_list6.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, false, new BasicSpecies( "nemve" ) ) ); - final SortedSet sims6_d = calc4 + final SortedSet sims6_d = calc4 .calculateSimilarities( new DomainCountsBasedPairwiseSimilarityCalculator(), cdc_list6, false, true ); - final Iterator sims_it6_d = sims6_d.iterator(); - final PrintableDomainSimilarity sa6_d = sims_it6_d.next(); + final Iterator sims_it6_d = sims6_d.iterator(); + final DomainSimilarity sa6_d = sims_it6_d.next(); if ( sa6_d.getSpecies().size() != 4 ) { return false; } @@ -914,13 +910,13 @@ public class TestSurfacing { if ( sa6_d.getMaximalDifferenceInCounts() != 11 ) { return false; } - final SortedSet sims6_p = calc4 + final SortedSet sims6_p = calc4 .calculateSimilarities( new ProteinCountsBasedPairwiseDomainSimilarityCalculator(), cdc_list6, false, true ); - final Iterator sims_it6_p = sims6_p.iterator(); - final PrintableDomainSimilarity sa6_p = sims_it6_p.next(); + final Iterator sims_it6_p = sims6_p.iterator(); + final DomainSimilarity sa6_p = sims_it6_p.next(); if ( !sa6_p.getDomainId().equals( "A" ) ) { return false; } @@ -982,9 +978,6 @@ 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 ); @@ -1028,17 +1021,17 @@ public class TestSurfacing { cdc_list.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, true, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, false, true ); - final SortedSet sims = calc + final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, true, false ); - final Iterator sims_it = sims.iterator(); - final PrintableDomainSimilarity sa = sims_it.next(); + final Iterator sims_it = sims.iterator(); + final DomainSimilarity sa = sims_it.next(); if ( !sa.getDomainId().equals( "A" ) ) { return false; } @@ -1069,7 +1062,7 @@ public class TestSurfacing { if ( sa.getMaximalDifferenceInCounts() != 0 ) { return false; } - final PrintableDomainSimilarity sb = sims_it.next(); + final DomainSimilarity sb = sims_it.next(); if ( !sb.getDomainId().equals( "B" ) ) { return false; } @@ -1079,13 +1072,13 @@ public class TestSurfacing { if ( !sb.getSpecies().contains( new BasicSpecies( "rabbit" ) ) ) { return false; } - final SortedSet sims2 = calc + final SortedSet sims2 = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, true, true ); - final Iterator sims_it2 = sims2.iterator(); - final PrintableDomainSimilarity sa2 = sims_it2.next(); + final Iterator sims_it2 = sims2.iterator(); + final DomainSimilarity sa2 = sims_it2.next(); if ( !sa2.getDomainId().equals( "D" ) ) { return false; } @@ -1137,11 +1130,11 @@ public class TestSurfacing { cdc_list.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve, true, new BasicSpecies( "nemve" ) ) ); - final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( PrintableDomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, + final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID, false, false, true ); - final SortedSet sims = calc + final SortedSet sims = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, false, @@ -1149,8 +1142,8 @@ public class TestSurfacing { if ( sims.size() != 1 ) { return false; } - final Iterator sims_it = sims.iterator(); - final PrintableDomainSimilarity sa = sims_it.next(); + final Iterator sims_it = sims.iterator(); + final DomainSimilarity sa = sims_it.next(); if ( !sa.getDomainId().equals( "A" ) ) { return false; } @@ -1169,7 +1162,7 @@ public class TestSurfacing { if ( !sa.getSpecies().contains( new BasicSpecies( "rabbit" ) ) ) { return false; } - final SortedSet sims_ns = calc + final SortedSet sims_ns = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list, true, @@ -1211,7 +1204,7 @@ public class TestSurfacing { cdc_list2.add( BasicGenomeWideCombinableDomains.createInstance( protein_list_nemve2, true, new BasicSpecies( "nemve" ) ) ); - final SortedSet sims2 = calc + final SortedSet sims2 = calc .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(), cdc_list2, true, @@ -1229,16 +1222,16 @@ 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 +1277,10 @@ 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 +1315,7 @@ 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 +1470,11 @@ 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 +1520,7 @@ 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 +1705,15 @@ 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 +1771,7 @@ 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 +1820,112 @@ 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 +1941,7 @@ 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 +2423,115 @@ 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 +2840,256 @@ 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 +3206,43 @@ 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 +3313,43 @@ 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 +3426,12 @@ 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 +3476,7 @@ 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 +4414,128 @@ 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 +4549,7 @@ 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 +4626,8 @@ 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 +4707,6 @@ 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 +4718,7 @@ 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 +4736,6 @@ 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 +4755,6 @@ 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 +4775,6 @@ 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 +4796,6 @@ 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 +4816,6 @@ 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 +4834,6 @@ 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 +4855,6 @@ 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 +4877,6 @@ 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 );