+ *
+ * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
+ * domain with 0.3 is ignored
+ *
+ * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
+ *
+ *
+ * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
+ * ignored
+ *
+ * @param max_allowed_overlap
+ * maximal allowed overlap (inclusive) to be still considered not
+ * overlapping (zero or negative value to allow any overlap)
+ * @param remove_engulfed_domains
+ * to remove domains which are completely engulfed by coverage of
+ * domains with better support
+ * @param protein
+ * @return
+ */
+ public static Protein removeOverlappingDomains( final int max_allowed_overlap,
+ final boolean remove_engulfed_domains,
+ final Protein protein ) {
+ final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
+ .getSpeciesId(), protein.getLength() );
+ final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
+ final List<Boolean> covered_positions = new ArrayList<Boolean>();
+ for( final Domain domain : sorted ) {
+ if ( ( ( max_allowed_overlap < 0 ) || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
+ && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
+ final int covered_positions_size = covered_positions.size();
+ for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
+ covered_positions.add( false );
+ }
+ final int new_covered_positions_size = covered_positions.size();
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( i < new_covered_positions_size ) {
+ covered_positions.set( i, true );
+ }
+ else {
+ covered_positions.add( true );
+ }
+ }
+ pruned_protein.addProteinDomain( domain );
+ }
+ }
+ return pruned_protein;
+ }
+
+ /**
+ * Returns true is Domain domain falls in an uninterrupted stretch of
+ * covered positions.
+ *
+ * @param domain
+ * @param covered_positions
+ * @return
+ */
+ public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**