import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
}
else {
try {
- final List<Sequence> seqs = FastaParser.parse( new FileInputStream( infile ) );
+ final List<MolecularSequence> seqs = FastaParser.parse( new FileInputStream( infile ) );
final Map<String, Short> names = new HashMap<String, Short>();
int duplicates = 0;
- for( final Sequence seq : seqs ) {
+ for( final MolecularSequence seq : seqs ) {
if ( procSeq( infile.toString(), names, seq ) ) {
++duplicates;
}
}
}
- private static boolean procSeq( final String infile, final Map<String, Short> names, final Sequence seq ) {
+ private static boolean procSeq( final String infile, final Map<String, Short> names, final MolecularSequence seq ) {
boolean duplicate = false;
final String name = seq.getIdentifier();
if ( !names.containsKey( name ) ) {