import org.forester.io.parsers.FastaParser;
import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.SystemCommandExecutor;
public final class ClustalOmega extends MsaInferrer {
}
@Override
- public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+ public Msa infer( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException {
final File file = File.createTempFile( "__clustalo_input_", ".fasta" );
file.deleteOnExit();
final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );