return false;
}
System.out.println( "OK." );
- System.out.print( " Overlap removal: " );
- if ( !TestSurfacing.testOverlapRemoval() ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
- System.out.print( " Engulfing overlap removal: " );
- if ( !TestSurfacing.testEngulfingOverlapRemoval() ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
System.out.print( " Binary domain combination: " );
if ( !TestSurfacing.testBinaryDomainCombination() ) {
System.out.println( "failed." );
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims2 = calc2
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list2,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims3 = calc3
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list3,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
true,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims4 = calc4
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list4,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,
return true;
}
- private static boolean testEngulfingOverlapRemoval() {
- try {
- final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
- final List<Boolean> covered = new ArrayList<Boolean>();
- covered.add( true ); // 0
- covered.add( false ); // 1
- covered.add( true ); // 2
- covered.add( false ); // 3
- covered.add( true ); // 4
- covered.add( true ); // 5
- covered.add( false ); // 6
- covered.add( true ); // 7
- covered.add( true ); // 8
- if ( SurfacingUtil.isEngulfed( d0, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d1, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d2, covered ) ) {
- return false;
- }
- if ( !SurfacingUtil.isEngulfed( d3, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d4, covered ) ) {
- return false;
- }
- if ( SurfacingUtil.isEngulfed( d5, covered ) ) {
- return false;
- }
- if ( !SurfacingUtil.isEngulfed( d6, covered ) ) {
- return false;
- }
- final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
- final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
- final Protein abc = new BasicProtein( "abc", "nemve", 0 );
- abc.addProteinDomain( a );
- abc.addProteinDomain( b );
- abc.addProteinDomain( c );
- final Protein abc_r1 = SurfacingUtil.removeOverlappingDomains( 3, false, abc );
- final Protein abc_r2 = SurfacingUtil.removeOverlappingDomains( 3, true, abc );
- if ( abc.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
- return false;
- }
- if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
- return false;
- }
- final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
- final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
- final Protein def = new BasicProtein( "def", "nemve", 0 );
- def.addProteinDomain( d );
- def.addProteinDomain( e );
- def.addProteinDomain( f );
- final Protein def_r1 = SurfacingUtil.removeOverlappingDomains( 5, false, def );
- final Protein def_r2 = SurfacingUtil.removeOverlappingDomains( 5, true, def );
- if ( def.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( def_r1.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( def_r2.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
- return false;
- }
- if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testGenomeWideCombinableDomains() {
try {
final Domain a = new BasicDomain( "a", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
return true;
}
- private static boolean testOverlapRemoval() {
- try {
- final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
- final List<Boolean> covered = new ArrayList<Boolean>();
- covered.add( true ); // 0
- covered.add( false ); // 1
- covered.add( true ); // 2
- covered.add( false ); // 3
- covered.add( true ); // 4
- covered.add( true ); // 5
- covered.add( false ); // 6
- covered.add( true ); // 7
- covered.add( true ); // 8
- if ( SurfacingUtil.calculateOverlap( d0, covered ) != 3 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d1, covered ) != 2 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d2, covered ) != 6 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d3, covered ) != 0 ) {
- return false;
- }
- if ( SurfacingUtil.calculateOverlap( d4, covered ) != 2 ) {
- return false;
- }
- final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
- final Protein ab = new BasicProtein( "ab", "varanus", 0 );
- ab.addProteinDomain( a );
- ab.addProteinDomain( b );
- final Protein ab_s0 = SurfacingUtil.removeOverlappingDomains( 3, false, ab );
- if ( ab.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
- return false;
- }
- final Protein ab_s1 = SurfacingUtil.removeOverlappingDomains( 4, false, ab );
- if ( ab.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
- return false;
- }
- final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain d = new BasicDomain( "d",
- ( short ) 10000,
- ( short ) 10500,
- ( short ) 1,
- ( short ) 1,
- 0.0000001,
- 1 );
- final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Protein cde = new BasicProtein( "cde", "varanus", 0 );
- cde.addProteinDomain( c );
- cde.addProteinDomain( d );
- cde.addProteinDomain( e );
- final Protein cde_s0 = SurfacingUtil.removeOverlappingDomains( 0, false, cde );
- if ( cde.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
- return false;
- }
- final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
- final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
- final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
- fghi.addProteinDomain( f );
- fghi.addProteinDomain( g );
- fghi.addProteinDomain( h );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i );
- fghi.addProteinDomain( i2 );
- final Protein fghi_s0 = SurfacingUtil.removeOverlappingDomains( 10, false, fghi );
- if ( fghi.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
- return false;
- }
- final Protein fghi_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, fghi );
- if ( fghi.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
- final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
- final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
- final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
- final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
- final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
- final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
- final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
- jklm.addProteinDomain( j );
- jklm.addProteinDomain( k );
- jklm.addProteinDomain( l );
- jklm.addProteinDomain( m );
- jklm.addProteinDomain( m0 );
- jklm.addProteinDomain( m1 );
- jklm.addProteinDomain( m2 );
- final Protein jklm_s0 = SurfacingUtil.removeOverlappingDomains( 10, false, jklm );
- if ( jklm.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
- return false;
- }
- final Protein jklm_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, jklm );
- if ( jklm.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
- return false;
- }
- final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
- final Protein od = new BasicProtein( "od", "varanus", 0 );
- od.addProteinDomain( only );
- final Protein od_s0 = SurfacingUtil.removeOverlappingDomains( 0, false, od );
- if ( od.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- if ( od_s0.getNumberOfProteinDomains() != 1 ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testParsimony() {
try {
final BinaryStates X = BinaryStates.PRESENT;
git://source.jalview.org / jalview.git / blobdiff