source: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java @ 1323

/**
 * 
 */
package de.ugoe.cs.autoquest.plugin.alignment.substitution;

/**
 * @author Ralph Krimmel
 *
 */
public class NearbySubstitutionMatrix implements SubstitutionMatrix {

        private int[] input1;
        private int[] input2;
        private int range;
        
        public NearbySubstitutionMatrix(int[] input1,int[] input2, int range) {
                this.input1 = input1;
                this.input2 = input2;
                this.range = range;
        }
        
        /* (non-Javadoc)
         * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
         */
        public double getDistance(int pos1, int pos2) {
                int difference = Math.abs(input1[pos1]-input2[pos2]); 
                if(difference < range) {
                        return range-difference;
                }
                else {
                        return -range;
                }
        }


        @Override
        public double getGapPenalty() {
                return -range-1;
        }

        @Override
        public String info() {
                return "Range: " + range;
        }

}