@SuppressWarnings( "unused")
public final class Test {
- private final static boolean PERFORM_DB_TESTS = true;
+ private final static boolean PERFORM_DB_TESTS = false;
private final static double ZERO_DIFF = 1.0E-9;
private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "test_data"
if ( ForesterUtil.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 Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -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 );
if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
return false;
}
- if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
+ if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
return false;
}
final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
return false;
}
- if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
+ if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
+ return false;
+ }
+ if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
return false;
}
final Protein p1 = proteins.get( 0 );
if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
- return false;
- }
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
- return false;
- }
if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
return false;
}