source: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java @ 1543

//   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.util.Collection;
import java.util.LinkedList;
import java.util.List;

import de.ugoe.cs.autoquest.eventcore.Event;
import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SequenceGenerator;
import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
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 Ralph Krimmel
 * @version 1.0
 */
public class CMDbinaryAlignment implements Command {

        /*
         * (non-Javadoc)
         * 
         * @see de.ugoe.cs.util.console.Command#run(java.util.List)
         */
        @SuppressWarnings("unchecked")
        public void run(List<Object> parameters) {
                String sequencesName = "numberSequences";
                String substitutionName = "substitutionMatrix";
                String algorithm = "smithwaterman";
                try {
                        sequencesName = (String) parameters.get(0);
                        substitutionName = (String) parameters.get(1);
                        if (parameters.size() > 2) {
                                algorithm = (String) parameters.get(2);
                        }
                } catch (Exception e) {
                        throw new IllegalArgumentException();
                }

                SimpleSequenceGenerator gen;
                Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
                if (obj != null) {
                        if (obj instanceof SimpleSequenceGenerator) {
                                gen = (SimpleSequenceGenerator) obj;
                                Console.println("Number of sequences: " + gen.sequenceCount());

                                int[] seq1 = gen.get(0).getSequence();
                                int[] seq2 = gen.get(0).getSequence();
                                
                                ObjectDistanceSubstitionMatrix submat = new
                                ObjectDistanceSubstitionMatrix();
                                submat.generate(sequences);
                                // SmithWaterman sw = new SmithWaterman(seq1, seq2,
                                // new NearbySubstitutionMatrix(seq1, seq2, 10));
                                // sw.printDPMatrix();
                                // System.out.println();
                                // sw.printAlignments();
                                // sw.getMatches();
                                System.out.println("foo");

                        } else {
                                Console.printerr("No number sequences generated. Please run the generateNumberSequences before.");
                                
                        }

                                        }

        }

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

}