import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.surfacing.SurfacingUtil;
import org.forester.util.ForesterUtil;
import org.forester.protein.Protein;
import org.forester.surfacing.SurfacingUtil;
import org.forester.util.ForesterUtil;
private static final ReturnType RETURN_TYPE_DEFAULT = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
private static final boolean IGNORE_DUFS_DEFAULT = false;
private static final int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
private static final ReturnType RETURN_TYPE_DEFAULT = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
private static final boolean IGNORE_DUFS_DEFAULT = false;
private static final int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
private final FilterType _filter_type;
private final File _input_file;
private final String _species;
private final FilterType _filter_type;
private final File _input_file;
private final String _species;
private int _domains_ignored_due_to_e_value;
private int _domains_ignored_due_to_individual_score_cutoff;
private int _domains_stored;
private int _domains_ignored_due_to_e_value;
private int _domains_ignored_due_to_individual_score_cutoff;
private int _domains_stored;
private long _time;
private int _domains_ignored_due_to_negative_domain_filter;
private Map<String, Integer> _domains_ignored_due_to_negative_domain_filter_counts_map;
private long _time;
private int _domains_ignored_due_to_negative_domain_filter;
private Map<String, Integer> _domains_ignored_due_to_negative_domain_filter_counts_map;
private void addProtein( final List<Protein> proteins, final Protein current_protein ) {
if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
private void addProtein( final List<Protein> proteins, final Protein current_protein ) {
if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
for( final Domain d : current_protein.getProteinDomains() ) {
domain_ids_in_protein.add( d.getDomainId() );
}
for( final Domain d : current_protein.getProteinDomains() ) {
domain_ids_in_protein.add( d.getDomainId() );
}
setDomainsEncountered( 0 );
setProteinsEncountered( 0 );
setProteinsIgnoredDueToFilter( 0 );
setDomainsEncountered( 0 );
setProteinsEncountered( 0 );
setProteinsIgnoredDueToFilter( 0 );
ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), id );
++_domains_ignored_due_to_virus_like_id;
}
ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), id );
++_domains_ignored_due_to_virus_like_id;
}
++_domains_ignored_due_to_negative_domain_filter;
ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), id );
}
++_domains_ignored_due_to_negative_domain_filter;
ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), id );
}