// 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.IOException;
import java.util.List;
-public interface MsaInferrer {
+import org.forester.sequence.Sequence;
+import org.forester.util.SystemCommandExecutor;
- public String getErrorDescription();
+public abstract class MsaInferrer {
- public int getExitCode();
+ public abstract String getErrorDescription();
- public Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
+ public abstract int getExitCode();
+
+ public static boolean isInstalled( final String path_to_prg ) {
+ return SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) );
+ }
+
+ @Override
+ public Object clone() {
+ throw new NoSuchMethodError();
+ }
+
+ public abstract Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
+
+ public abstract Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException;
}