source: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java @ 1314

//   Copyright 2012 Georg-August-Universität Göttingen, Germany
//
//   Licensed under the Apache License, Version 2.0 (the "License");
//   you may not use this file except in compliance with the License.
//   You may obtain a copy of the License at
//
//       http://www.apache.org/licenses/LICENSE-2.0
//
//   Unless required by applicable law or agreed to in writing, software
//   distributed under the License is distributed on an "AS IS" BASIS,
//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
//   See the License for the specific language governing permissions and
//   limitations under the License.

package de.ugoe.cs.autoquest.plugin.alignment.commands;

import java.io.File;
import java.io.FilenameFilter;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.logging.Level;

import de.ugoe.cs.autoquest.CommandHelpers;
import de.ugoe.cs.autoquest.eventcore.Event;
import de.ugoe.cs.autoquest.plugin.alignment.NearbySubstitutionMatrix;
import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
import de.ugoe.cs.autoquest.plugin.alignment.DifferenceSubstitutionMatrix;
import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator;
import de.ugoe.cs.util.console.Command;
import de.ugoe.cs.util.console.Console;
import de.ugoe.cs.util.console.GlobalDataContainer;

/**
 * <p>
 * Command to generate a binary alignment of two sequences
 * </p>
 * 
 * @author Steffen Herbold
 * @version 1.0
 */
public class CMDbinaryAlignment implements Command {

        /*
         * (non-Javadoc)
         * 
         * @see de.ugoe.cs.util.console.Command#run(java.util.List)
         */
        @Override
        public void run(List<Object> parameters) {
                String sequencesName;
                String algorithm;
                try {
                        sequencesName = (String) parameters.get(0);
                        if (parameters.size() > 1) {
                                algorithm = (String) parameters.get(1);
                        }
                } catch (Exception e) {
                        throw new IllegalArgumentException();
                }

                Collection<List<Event>> sequences = new LinkedList<List<Event>>();
                sequences = (Collection<List<Event>>) GlobalDataContainer.getInstance()
                                .getData(sequencesName);
                Console.println("Number of sequences: " + sequences.size());
                for (Iterator<List<Event>> it = sequences.iterator(); it.hasNext();) {
                        List<Event> ev = it.next();
                        RandomSequenceGenerator randgen1 = new RandomSequenceGenerator(1,
                                        80, 3000);
                        RandomSequenceGenerator randgen2 = new RandomSequenceGenerator(1,
                                        80, 3000);
                        
                        int[] seq1 = randgen1.generate(ev);
                        int[] seq2 = randgen2.generate(ev);
                        SmithWaterman sw = new SmithWaterman(seq1, seq2,
                                        new NearbySubstitutionMatrix(seq1, seq2,10));

                        //sw.printDPMatrix();
                        System.out.println();
                        //sw.printAlignments();
                        sw.getMatches();
                        Console.println("Number of events in sequence: " + ev.size());
                }

        }

        /*
         * (non-Javadoc)
         * 
         * @see de.ugoe.cs.util.console.Command#help()
         */
        @Override
        public String help() {
                return "binaryAlignment <sequencesName> {<algorithm>}";
        }

}