import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.DomainId;
import org.forester.protein.Protein;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.DomainId;
import org.forester.protein.Protein;
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 Set<DomainId> _filter;
private final FilterType _filter_type;
private final File _input_file;
private final Set<DomainId> _filter;
private final FilterType _filter_type;
private final File _input_file;
else if ( isIgnoreVirusLikeIds()
&& ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
|| uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )
else if ( isIgnoreVirusLikeIds()
&& ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
|| uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )