// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
import org.forester.go.OBOparser;
import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
-import org.forester.protein.DomainId;
public class pfam2go_extractor {
}
final SortedSet<String> pfams = new TreeSet<String>();
for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
- final DomainId domain_id = pfam_to_go_mapping.getKey();
+ final String domain_id = pfam_to_go_mapping.getKey();
final GoId go_id = pfam_to_go_mapping.getValue();
final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
supers.add( go_id );
private static void printHelp() {
System.out.println();
System.out.println( PRG_NAME
- + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
+ + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
System.out.println();
}
}