// Copyright (C) 2009 Christian M. Zmasek
// Copyright (C) 2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// 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.surfacing.DomainId;
+import org.forester.protein.DomainId;
public class pfam2go_extractor {
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 );
- for( int i = 0; i < queries.length; ++i ) {
- if ( supers.contains( queries[ i ] ) ) {
+ for( final GoId querie : queries ) {
+ if ( supers.contains( querie ) ) {
pfams.add( domain_id.toString() );
}
}