// 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 java.io.BufferedWriter;
import java.io.File;
+import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.forester.io.parsers.FastaParser;
-import org.forester.util.ForesterUtil;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
+import org.forester.sequence.Sequence;
import org.forester.util.SystemCommandExecutor;
-public final class Mafft implements MsaInferrer {
+public final class Mafft extends MsaInferrer {
private final static String DEFAULT_PARAMETERS = "--maxiterate 1000 --localpair";
private String _error;
private int _exit_code;
private final String _path_to_prg;
-
-
public static MsaInferrer createInstance( final String path_to_prg ) throws IOException {
return new Mafft( path_to_prg );
}
-
-
private Mafft( final String path_to_prg ) throws IOException {
- if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
+ if ( !isInstalled( path_to_prg ) ) {
throw new IOException( "cannot execute MAFFT with \"" + path_to_prg + "\"" );
}
_path_to_prg = new String( path_to_prg );
}
@Override
- public Object clone() {
- throw new NoSuchMethodError();
- }
-
- @Override
public String getErrorDescription() {
return _error;
}
}
@Override
+ public Msa infer( final List<Sequence> 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 ) );
+ SequenceWriter.writeSeqs( seqs, writer, SEQ_FORMAT.FASTA, 100 );
+ writer.close();
+ final Msa msa = infer( file, opts );
+ file.delete();
+ return msa;
+ }
+
+ @Override
public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
init();
final List<String> my_opts = new ArrayList<String>();