X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FTestSurfacing.java;h=44c911511c5f33b2726f25bc31604b23ff054873;hb=07d2b6864846c6c95ec1d4f1b083c248ffbcc591;hp=8301b9b44944d693ba0a7f562e05342f6dbf98bd;hpb=757f42e63a33c5935b68af1d02a02c76d475fe79;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index 8301b9b..44c9115 100644 --- a/forester/java/src/org/forester/surfacing/TestSurfacing.java +++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java @@ -48,7 +48,16 @@ import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType; +import org.forester.protein.BasicDomain; +import org.forester.protein.BasicProtein; +import org.forester.protein.BinaryDomainCombination; +import org.forester.protein.BinaryDomainCombination.DomainCombinationType; +import org.forester.protein.Domain; +import org.forester.protein.DomainId; +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; @@ -351,10 +360,10 @@ public class TestSurfacing { if ( !TestSurfacing.isEqual( X.getPerSequenceScore(), -12 ) ) { return false; } - final Protein mouse_1 = new BasicProtein( "1", "mouse" ); - final Protein rabbit_1 = new BasicProtein( "1", "rabbit" ); - final Protein ciona_1 = new BasicProtein( "1", "ciona" ); - final Protein nemve_1 = new BasicProtein( "1", "nemve" ); + final Protein mouse_1 = new BasicProtein( "1", "mouse", 0 ); + final Protein rabbit_1 = new BasicProtein( "1", "rabbit", 0 ); + final Protein ciona_1 = new BasicProtein( "1", "ciona", 0 ); + final Protein nemve_1 = new BasicProtein( "1", "nemve", 0 ); mouse_1.addProteinDomain( A ); mouse_1.addProteinDomain( B ); mouse_1.addProteinDomain( C ); @@ -605,7 +614,7 @@ public class TestSurfacing { if ( sa2.getMaximalDifferenceInCounts() != 3 ) { return false; } - final Protein ciona_2 = new BasicProtein( "2", "ciona" ); + final Protein ciona_2 = new BasicProtein( "2", "ciona", 0 ); ciona_2.addProteinDomain( A ); ciona_2.addProteinDomain( A ); ciona_2.addProteinDomain( A ); @@ -618,7 +627,7 @@ public class TestSurfacing { ciona_2.addProteinDomain( F ); ciona_2.addProteinDomain( G ); ciona_2.addProteinDomain( X ); - final Protein ciona_3 = new BasicProtein( "3", "ciona" ); + final Protein ciona_3 = new BasicProtein( "3", "ciona", 0 ); ciona_3.addProteinDomain( A ); ciona_3.addProteinDomain( A ); ciona_3.addProteinDomain( A ); @@ -1067,10 +1076,10 @@ public class TestSurfacing { if ( !TestSurfacing.isEqual( X.getPerSequenceScore(), -12 ) ) { return false; } - final Protein mouse_1 = new BasicProtein( "1", "mouse" ); - final Protein rabbit_1 = new BasicProtein( "1", "rabbit" ); - final Protein ciona_1 = new BasicProtein( "1", "ciona" ); - final Protein nemve_1 = new BasicProtein( "1", "nemve" ); + final Protein mouse_1 = new BasicProtein( "1", "mouse", 0 ); + final Protein rabbit_1 = new BasicProtein( "1", "rabbit", 0 ); + final Protein ciona_1 = new BasicProtein( "1", "ciona", 0 ); + final Protein nemve_1 = new BasicProtein( "1", "nemve", 0 ); mouse_1.addProteinDomain( A ); mouse_1.addProteinDomain( D ); mouse_1.addProteinDomain( E ); @@ -1185,10 +1194,10 @@ public class TestSurfacing { try { final Domain A = new BasicDomain( "A", 1, 2, ( short ) 1, ( short ) 1, 0.15, -12 ); final Domain B = new BasicDomain( "B", 1, 2, ( short ) 1, ( short ) 1, 0.2, -12 ); - final Protein mouse_1 = new BasicProtein( "1", "mouse" ); - final Protein rabbit_1 = new BasicProtein( "1", "rabbit" ); - final Protein ciona_1 = new BasicProtein( "1", "ciona" ); - final Protein nemve_1 = new BasicProtein( "1", "nemve" ); + final Protein mouse_1 = new BasicProtein( "1", "mouse", 0 ); + final Protein rabbit_1 = new BasicProtein( "1", "rabbit", 0 ); + final Protein ciona_1 = new BasicProtein( "1", "ciona", 0 ); + final Protein nemve_1 = new BasicProtein( "1", "nemve", 0 ); mouse_1.addProteinDomain( A ); rabbit_1.addProteinDomain( A ); ciona_1.addProteinDomain( A ); @@ -1257,10 +1266,10 @@ public class TestSurfacing { if ( sims_ns.size() != 0 ) { return false; } - final Protein mouse_2 = new BasicProtein( "1", "mouse" ); - final Protein rabbit_2 = new BasicProtein( "1", "rabbit" ); - final Protein ciona_2 = new BasicProtein( "1", "ciona" ); - final Protein nemve_2 = new BasicProtein( "1", "nemve" ); + final Protein mouse_2 = new BasicProtein( "1", "mouse", 0 ); + final Protein rabbit_2 = new BasicProtein( "1", "rabbit", 0 ); + final Protein ciona_2 = new BasicProtein( "1", "ciona", 0 ); + final Protein nemve_2 = new BasicProtein( "1", "nemve", 0 ); mouse_2.addProteinDomain( A ); rabbit_2.addProteinDomain( A ); ciona_2.addProteinDomain( A ); @@ -1322,7 +1331,7 @@ public class TestSurfacing { final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 ); - final BasicProtein p = new BasicProtein( "p", "owl" ); + final BasicProtein p = new BasicProtein( "p", "owl", 0 ); p.addProteinDomain( B15 ); p.addProteinDomain( C50 ); p.addProteinDomain( A60 ); @@ -2151,11 +2160,11 @@ public class TestSurfacing { final GainLossStates L = GainLossStates.LOSS; final GainLossStates A = GainLossStates.UNCHANGED_ABSENT; final GainLossStates P = GainLossStates.UNCHANGED_PRESENT; - final Protein one_1 = new BasicProtein( "one", "1" ); - final Protein two_1 = new BasicProtein( "two", "1" ); - final Protein three_1 = new BasicProtein( "three", "1" ); - final Protein four_1 = new BasicProtein( "four", "1" ); - final Protein five_1 = new BasicProtein( "five", "1" ); + final Protein one_1 = new BasicProtein( "one", "1", 0 ); + final Protein two_1 = new BasicProtein( "two", "1", 0 ); + final Protein three_1 = new BasicProtein( "three", "1", 0 ); + final Protein four_1 = new BasicProtein( "four", "1", 0 ); + final Protein five_1 = new BasicProtein( "five", "1", 0 ); one_1.addProteinDomain( new BasicDomain( "B", 12, 14, ( short ) 1, ( short ) 4, 0.1, -12 ) ); one_1.addProteinDomain( new BasicDomain( "C", 13, 14, ( short ) 1, ( short ) 4, 0.1, -12 ) ); one_1.addProteinDomain( new BasicDomain( "A", 11, 12, ( short ) 1, ( short ) 4, 0.1, -12 ) ); @@ -2726,11 +2735,11 @@ public class TestSurfacing { private static boolean testDirectednessAndAdjacency() { try { - final Protein one_1 = new BasicProtein( "one", "1" ); - final Protein two_1 = new BasicProtein( "two", "1" ); - final Protein three_1 = new BasicProtein( "three", "1" ); - final Protein four_1 = new BasicProtein( "four", "1" ); - final Protein five_1 = new BasicProtein( "five", "1" ); + final Protein one_1 = new BasicProtein( "one", "1", 0 ); + final Protein two_1 = new BasicProtein( "two", "1", 0 ); + final Protein three_1 = new BasicProtein( "three", "1", 0 ); + final Protein four_1 = new BasicProtein( "four", "1", 0 ); + final Protein five_1 = new BasicProtein( "five", "1", 0 ); one_1.addProteinDomain( new BasicDomain( "B", 12, 14, ( short ) 1, ( short ) 4, 0.1, -12 ) ); one_1.addProteinDomain( new BasicDomain( "C", 13, 14, ( short ) 1, ( short ) 4, 0.1, -12 ) ); one_1.addProteinDomain( new BasicDomain( "A", 11, 12, ( short ) 1, ( short ) 4, 0.1, -12 ) ); @@ -2891,21 +2900,21 @@ public class TestSurfacing { final Domain l = new BasicDomain( "l", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain m = new BasicDomain( "m", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain n = new BasicDomain( "n", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); - final Protein eel_0 = new BasicProtein( "0", "eel" ); - final Protein eel_1 = new BasicProtein( "1", "eel" ); - final Protein eel_2 = new BasicProtein( "2", "eel" ); - final Protein eel_3 = new BasicProtein( "3", "eel" ); - final Protein eel_4 = new BasicProtein( "4", "eel" ); - final Protein eel_5 = new BasicProtein( "5", "eel" ); - final Protein eel_6 = new BasicProtein( "6", "eel" ); - final Protein rat_0 = new BasicProtein( "0", "rat" ); - final Protein rat_1 = new BasicProtein( "1", "rat" ); - final Protein rat_2 = new BasicProtein( "2", "rat" ); - final Protein rat_3 = new BasicProtein( "3", "rat" ); - final Protein rat_4 = new BasicProtein( "4", "rat" ); - final Protein rat_5 = new BasicProtein( "5", "rat" ); - final Protein rat_6 = new BasicProtein( "6", "rat" ); - final Protein rat_7 = new BasicProtein( "7", "rat" ); + final Protein eel_0 = new BasicProtein( "0", "eel", 0 ); + final Protein eel_1 = new BasicProtein( "1", "eel", 0 ); + final Protein eel_2 = new BasicProtein( "2", "eel", 0 ); + final Protein eel_3 = new BasicProtein( "3", "eel", 0 ); + final Protein eel_4 = new BasicProtein( "4", "eel", 0 ); + final Protein eel_5 = new BasicProtein( "5", "eel", 0 ); + final Protein eel_6 = new BasicProtein( "6", "eel", 0 ); + final Protein rat_0 = new BasicProtein( "0", "rat", 0 ); + final Protein rat_1 = new BasicProtein( "1", "rat", 0 ); + final Protein rat_2 = new BasicProtein( "2", "rat", 0 ); + final Protein rat_3 = new BasicProtein( "3", "rat", 0 ); + final Protein rat_4 = new BasicProtein( "4", "rat", 0 ); + final Protein rat_5 = new BasicProtein( "5", "rat", 0 ); + final Protein rat_6 = new BasicProtein( "6", "rat", 0 ); + final Protein rat_7 = new BasicProtein( "7", "rat", 0 ); eel_1.addProteinDomain( a ); eel_2.addProteinDomain( a ); eel_2.addProteinDomain( b ); @@ -3445,11 +3454,11 @@ public class TestSurfacing { final Domain x = new BasicDomain( "x", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain y = new BasicDomain( "y", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain z = new BasicDomain( "z", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); - final Protein a_0 = new BasicProtein( "0", "a" ); - final Protein a_1 = new BasicProtein( "1", "a" ); - final Protein a_2 = new BasicProtein( "2", "a" ); - final Protein b_0 = new BasicProtein( "0", "b" ); - final Protein b_1 = new BasicProtein( "1", "b" ); + final Protein a_0 = new BasicProtein( "0", "a", 0 ); + final Protein a_1 = new BasicProtein( "1", "a", 0 ); + final Protein a_2 = new BasicProtein( "2", "a", 0 ); + final Protein b_0 = new BasicProtein( "0", "b", 0 ); + final Protein b_1 = new BasicProtein( "1", "b", 0 ); a_0.addProteinDomain( u ); a_0.addProteinDomain( v ); a_0.addProteinDomain( w ); @@ -4100,7 +4109,9 @@ public class TestSurfacing { true, new BasicSpecies( "human" ), null, - DomainCombinationType.BASIC ); + DomainCombinationType.BASIC, + null, + null ); cd = cdcc2.get( new DomainId( "A" ) ); if ( cd.getKeyDomainCount() != 9 ) { return false; @@ -4431,7 +4442,7 @@ public class TestSurfacing { -0.111 ); final Domain H7 = new BasicDomain( "H7", ( short ) 700, ( short ) 800, ( short ) 5, ( short ) 5, 0.7, -12 ); final Domain H8 = new BasicDomain( "H7", ( short ) 700, ( short ) 800, ( short ) 5, ( short ) 200, 0.7, -12 ); - final Protein protein = new BasicProtein( "00", "bat" ); + final Protein protein = new BasicProtein( "00", "bat", 0 ); protein.addProteinDomain( H5 ); protein.addProteinDomain( H2 ); protein.addProteinDomain( H7 ); @@ -4614,7 +4625,7 @@ public class TestSurfacing { 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" ); + final Protein abc = new BasicProtein( "abc", "nemve", 0 ); abc.addProteinDomain( a ); abc.addProteinDomain( b ); abc.addProteinDomain( c ); @@ -4638,7 +4649,7 @@ public class TestSurfacing { 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" ); + final Protein def = new BasicProtein( "def", "nemve", 0 ); def.addProteinDomain( d ); def.addProteinDomain( e ); def.addProteinDomain( f ); @@ -4681,13 +4692,13 @@ public class TestSurfacing { final Domain g = new BasicDomain( "g", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain h = new BasicDomain( "h", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); final Domain x = new BasicDomain( "x", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 ); - final Protein eel_0 = new BasicProtein( "0", "eel" ); - final Protein eel_1 = new BasicProtein( "1", "eel" ); - final Protein eel_2 = new BasicProtein( "2", "eel" ); - final Protein eel_3 = new BasicProtein( "3", "eel" ); - final Protein eel_4 = new BasicProtein( "4", "eel" ); - final Protein eel_5 = new BasicProtein( "5", "eel" ); - final Protein eel_6 = new BasicProtein( "6", "eel" ); + final Protein eel_0 = new BasicProtein( "0", "eel", 0 ); + final Protein eel_1 = new BasicProtein( "1", "eel", 0 ); + final Protein eel_2 = new BasicProtein( "2", "eel", 0 ); + final Protein eel_3 = new BasicProtein( "3", "eel", 0 ); + final Protein eel_4 = new BasicProtein( "4", "eel", 0 ); + final Protein eel_5 = new BasicProtein( "5", "eel", 0 ); + final Protein eel_6 = new BasicProtein( "6", "eel", 0 ); eel_1.addProteinDomain( a ); eel_2.addProteinDomain( a ); eel_2.addProteinDomain( b ); @@ -5435,7 +5446,7 @@ public class TestSurfacing { } 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" ); + final Protein ab = new BasicProtein( "ab", "varanus", 0 ); ab.addProteinDomain( a ); ab.addProteinDomain( b ); final Protein ab_s0 = SurfacingUtil.removeOverlappingDomains( 3, false, ab ); @@ -5464,7 +5475,7 @@ public class TestSurfacing { 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" ); + final Protein cde = new BasicProtein( "cde", "varanus", 0 ); cde.addProteinDomain( c ); cde.addProteinDomain( d ); cde.addProteinDomain( e ); @@ -5480,7 +5491,7 @@ public class TestSurfacing { 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" ); + final Protein fghi = new BasicProtein( "fghi", "varanus", 0 ); fghi.addProteinDomain( f ); fghi.addProteinDomain( g ); fghi.addProteinDomain( h ); @@ -5512,7 +5523,7 @@ public class TestSurfacing { 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" ); + final Protein jklm = new BasicProtein( "jklm", "varanus", 0 ); jklm.addProteinDomain( j ); jklm.addProteinDomain( k ); jklm.addProteinDomain( l ); @@ -5538,7 +5549,7 @@ public class TestSurfacing { 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" ); + final Protein od = new BasicProtein( "od", "varanus", 0 ); od.addProteinDomain( only ); final Protein od_s0 = SurfacingUtil.removeOverlappingDomains( 0, false, od ); if ( od.getNumberOfProteinDomains() != 1 ) { @@ -5592,58 +5603,58 @@ public class TestSurfacing { // 2 a b c e f g i n o // 3 a b d e f g j p q // 4 a b d p r - final Protein aa1 = new BasicProtein( "aa1", "one" ); + final Protein aa1 = new BasicProtein( "aa1", "one", 0 ); aa1.addProteinDomain( a ); aa1.addProteinDomain( a ); - final Protein ab1 = new BasicProtein( "ab1", "one" ); + final Protein ab1 = new BasicProtein( "ab1", "one", 0 ); ab1.addProteinDomain( a ); ab1.addProteinDomain( b ); - final Protein ac1 = new BasicProtein( "ac1", "one" ); + final Protein ac1 = new BasicProtein( "ac1", "one", 0 ); ac1.addProteinDomain( a ); ac1.addProteinDomain( c ); - final Protein efgh1 = new BasicProtein( "efgh1", "one" ); + final Protein efgh1 = new BasicProtein( "efgh1", "one", 0 ); efgh1.addProteinDomain( e ); efgh1.addProteinDomain( f ); efgh1.addProteinDomain( g ); efgh1.addProteinDomain( h ); - final Protein lm1 = new BasicProtein( "lm1", "one" ); + final Protein lm1 = new BasicProtein( "lm1", "one", 0 ); lm1.addProteinDomain( l ); lm1.addProteinDomain( m ); - final Protein ab2 = new BasicProtein( "ab2", "two" ); + final Protein ab2 = new BasicProtein( "ab2", "two", 0 ); ab2.addProteinDomain( a ); ab2.addProteinDomain( b ); - final Protein ac2 = new BasicProtein( "ac2", "two" ); + final Protein ac2 = new BasicProtein( "ac2", "two", 0 ); ac2.addProteinDomain( a ); ac2.addProteinDomain( c ); - final Protein efgi2 = new BasicProtein( "efgi2", "two" ); + final Protein efgi2 = new BasicProtein( "efgi2", "two", 0 ); efgi2.addProteinDomain( e ); efgi2.addProteinDomain( f ); efgi2.addProteinDomain( g ); efgi2.addProteinDomain( i ); - final Protein no2 = new BasicProtein( "no2", "two" ); + final Protein no2 = new BasicProtein( "no2", "two", 0 ); no2.addProteinDomain( n ); no2.addProteinDomain( o ); - final Protein ab3 = new BasicProtein( "ab3", "three" ); + final Protein ab3 = new BasicProtein( "ab3", "three", 0 ); ab3.addProteinDomain( a ); ab3.addProteinDomain( b ); - final Protein ad3 = new BasicProtein( "ad3", "three" ); + final Protein ad3 = new BasicProtein( "ad3", "three", 0 ); ad3.addProteinDomain( a ); ad3.addProteinDomain( d ); - final Protein efgj3 = new BasicProtein( "efgj3", "three" ); + final Protein efgj3 = new BasicProtein( "efgj3", "three", 0 ); efgj3.addProteinDomain( e ); efgj3.addProteinDomain( f ); efgj3.addProteinDomain( g ); efgj3.addProteinDomain( j ); - final Protein pq3 = new BasicProtein( "pq3", "three" ); + final Protein pq3 = new BasicProtein( "pq3", "three", 0 ); pq3.addProteinDomain( p ); pq3.addProteinDomain( q ); - final Protein ab4 = new BasicProtein( "ab4", "four" ); + final Protein ab4 = new BasicProtein( "ab4", "four", 0 ); ab4.addProteinDomain( a ); ab4.addProteinDomain( b ); - final Protein ad4 = new BasicProtein( "ad4", "four" ); + final Protein ad4 = new BasicProtein( "ad4", "four", 0 ); ad4.addProteinDomain( a ); ad4.addProteinDomain( d ); - final Protein pr4 = new BasicProtein( "pr4", "four" ); + final Protein pr4 = new BasicProtein( "pr4", "four", 0 ); pr4.addProteinDomain( p ); pr4.addProteinDomain( r ); final List one_list = new ArrayList(); @@ -5875,58 +5886,58 @@ public class TestSurfacing { // 2 a b c e f g i n o // 3 a b d e f g j p q // 4 a b d p r - final Protein aa1 = new BasicProtein( "aa1", "one" ); + final Protein aa1 = new BasicProtein( "aa1", "one", 0 ); aa1.addProteinDomain( a ); aa1.addProteinDomain( a ); - final Protein ab1 = new BasicProtein( "ab1", "one" ); + final Protein ab1 = new BasicProtein( "ab1", "one", 0 ); ab1.addProteinDomain( a ); ab1.addProteinDomain( b ); - final Protein ac1 = new BasicProtein( "ac1", "one" ); + final Protein ac1 = new BasicProtein( "ac1", "one", 0 ); ac1.addProteinDomain( a ); ac1.addProteinDomain( c ); - final Protein efgh1 = new BasicProtein( "efgh1", "one" ); + final Protein efgh1 = new BasicProtein( "efgh1", "one", 0 ); efgh1.addProteinDomain( e ); efgh1.addProteinDomain( f ); efgh1.addProteinDomain( g ); efgh1.addProteinDomain( h ); - final Protein lm1 = new BasicProtein( "lm1", "one" ); + final Protein lm1 = new BasicProtein( "lm1", "one", 0 ); lm1.addProteinDomain( l ); lm1.addProteinDomain( m ); - final Protein ab2 = new BasicProtein( "ab2", "two" ); + final Protein ab2 = new BasicProtein( "ab2", "two", 0 ); ab2.addProteinDomain( a ); ab2.addProteinDomain( b ); - final Protein ac2 = new BasicProtein( "ac2", "two" ); + final Protein ac2 = new BasicProtein( "ac2", "two", 0 ); ac2.addProteinDomain( a ); ac2.addProteinDomain( c ); - final Protein efgi2 = new BasicProtein( "efgi2", "two" ); + final Protein efgi2 = new BasicProtein( "efgi2", "two", 0 ); efgi2.addProteinDomain( e ); efgi2.addProteinDomain( f ); efgi2.addProteinDomain( g ); efgi2.addProteinDomain( i ); - final Protein no2 = new BasicProtein( "no2", "two" ); + final Protein no2 = new BasicProtein( "no2", "two", 0 ); no2.addProteinDomain( n ); no2.addProteinDomain( o ); - final Protein ab3 = new BasicProtein( "ab3", "three" ); + final Protein ab3 = new BasicProtein( "ab3", "three", 0 ); ab3.addProteinDomain( a ); ab3.addProteinDomain( b ); - final Protein ad3 = new BasicProtein( "ad3", "three" ); + final Protein ad3 = new BasicProtein( "ad3", "three", 0 ); ad3.addProteinDomain( a ); ad3.addProteinDomain( d ); - final Protein efgj3 = new BasicProtein( "efgj3", "three" ); + final Protein efgj3 = new BasicProtein( "efgj3", "three", 0 ); efgj3.addProteinDomain( e ); efgj3.addProteinDomain( f ); efgj3.addProteinDomain( g ); efgj3.addProteinDomain( j ); - final Protein pq3 = new BasicProtein( "pq3", "three" ); + final Protein pq3 = new BasicProtein( "pq3", "three", 0 ); pq3.addProteinDomain( p ); pq3.addProteinDomain( q ); - final Protein ab4 = new BasicProtein( "ab4", "four" ); + final Protein ab4 = new BasicProtein( "ab4", "four", 0 ); ab4.addProteinDomain( a ); ab4.addProteinDomain( b ); - final Protein ad4 = new BasicProtein( "ad4", "four" ); + final Protein ad4 = new BasicProtein( "ad4", "four", 0 ); ad4.addProteinDomain( a ); ad4.addProteinDomain( d ); - final Protein pr4 = new BasicProtein( "pr4", "four" ); + final Protein pr4 = new BasicProtein( "pr4", "four", 0 ); pr4.addProteinDomain( p ); pr4.addProteinDomain( r ); final List one_list = new ArrayList();