// $Id:
// forester -- software libraries and applications
// for genomics and evolutionary biology research.
//
// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester

package org.forester.msa;

import java.io.File;
import java.io.IOException;
import java.util.List;

import org.forester.sequence.MolecularSequence;
import org.forester.util.SystemCommandExecutor;

public abstract class MsaInferrer {

    public abstract String getErrorDescription();

    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<MolecularSequence> seqs, final List<String> opts ) throws IOException,
    InterruptedException;
}