source: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDsequenceStats.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.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.logging.Level;

import de.ugoe.cs.autoquest.eventcore.Event;
import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
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 CMDsequenceStats 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 = "sequences";
                double standarddev = 0.0;
                double mean = 0;
                double median = 0;
                double sum = 0;
                
                try {
                        sequencesName = (String) parameters.get(0);
                } catch (Exception e) {
                        throw new IllegalArgumentException();
                }

                Collection<List<Event>> sequences = new LinkedList<List<Event>>();
                Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
                if (obj != null) {
                
                        if (obj.getClass().equals(sequences.getClass())) {
                                sequences = (Collection<List<Event>>) obj;
                        }

                
                        Console.println("Number of sequences: " + sequences.size());
                        //Calculate the mean size
                        for(Iterator<List<Event>> iter = sequences.iterator();iter.hasNext();) {
                                sum += iter.next().size();
        
                        }
                        mean = sum/sequences.size();
                        
                        
                        //Calculate the median
                        List<List<Event>> list = new ArrayList<List<Event>>(sequences);
                        Collections.sort(list,new SizeComparator());
                        
                        Console.println("Mean size: " +mean);
                        Console.println("Median size: " + list.get(Math.round(list.size()/2)).size());
        
                }
        }

        class SizeComparator implements Comparator<List<Event>> {
            @Override
            public int compare(List<Event> a, List<Event> b) {
                return a.size() < b.size() ? -1 : a.size() == b.size() ? 0 : 1;
            }
        }
        /*
         * (non-Javadoc)
         * 
         * @see de.ugoe.cs.util.console.Command#help()
         */
        @Override
        public String help() {
                return "sequenceStats <sequence name>";
        }

}