- final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
- }
- try {
- final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
- final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
- domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
- if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
- ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
- "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
- }
- domain_id_to_go_ids_count = parser.getMappingCount();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ final String error1 = ForesterUtil.isReadableFile( pfam_to_go_file );
+ if ( !ForesterUtil.isEmpty( error1 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error1 );
+ }
+ Map<String, List<GoId>> domain_id_to_go_ids_map = null;
+ int domain_id_to_go_ids_count = 0;
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+ if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
+ "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );