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;
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 );
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 );
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 );
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 );
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 );
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 );
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 );
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 ) );
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 ) );
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 );
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 );
true,
new BasicSpecies( "human" ),
null,
- DomainCombinationType.BASIC );
+ DomainCombinationType.BASIC,
+ null,
+ null );
cd = cdcc2.get( new DomainId( "A" ) );
if ( cd.getKeyDomainCount() != 9 ) {
return false;
-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 );
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 );
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 );
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 );
}
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 );
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 );
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 );
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 );
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 ) {
// 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<Protein> one_list = new ArrayList<Protein>();
// 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<Protein> one_list = new ArrayList<Protein>();
git://source.jalview.org / jalview.git / blobdiff