encountered_domains.add( line );
boolean found = false;
for( final PfamToGoMapping mapping : mappings ) {
- if ( mapping.getKey().getId().equals( line ) ) {
+ if ( mapping.getKey().equals( line ) ) {
System.out.println( mapping.getValue() );
found = true;
}
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
- + " to allow duplicates] <pfam2go file> <file with pfams>" );
+ + " to allow duplicates] <pfam2go file> <file with pfams>" );
System.out.println();
System.out.println();
}