// 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.msa;
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 Mafft 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( "__mafft_input_", ".fasta" );
file.deleteOnExit();
final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
_error = stderr.toString();
if ( _exit_code != 0 ) {
throw new IOException( "MAFFT program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
- + "\nError:\n" + stderr );
+ + "\nError:\n" + stderr );
}
final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {