import java.util.TreeMap;
import java.util.TreeSet;
-import org.forester.surfacing.BasicDomain;
-import org.forester.surfacing.BasicProtein;
-import org.forester.surfacing.Domain;
-import org.forester.surfacing.DomainId;
-import org.forester.surfacing.Protein;
+import org.forester.protein.BasicDomain;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.Domain;
+import org.forester.protein.DomainId;
+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 boolean IGNORE_REPLACED_RRMS = false;
private final Set<DomainId> _filter;
private final FilterType _filter_type;
private final File _input_file;
addProtein( proteins, current_protein );
}
if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
- current_protein = new BasicProtein( query, getSpecies() );
+ current_protein = new BasicProtein( query, getSpecies(), qlen );
}
else {
throw new IllegalArgumentException( "unknown return type" );
else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
++_domains_ignored_due_to_duf;
}
+ else if ( IGNORE_REPLACED_RRMS
+ && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id
+ .contains( "RRM_6" ) ) ) {
+ }
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 )