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

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

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

        private int[] input1;
        private int[] input2;
        private int maxValue;
        
        public DifferenceSubstitutionMatrix(int[] input1,int[] input2) {
                this.input1 = input1;
                this.input2 = input2;
                this.maxValue = getMaxValue();
        }
        
        /* (non-Javadoc)
         * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
         */
        public double getDistance(int pos1, int pos2) {
                return maxValue - (input1[pos1] - input2[pos2]);
        }
        
        private int getMaxValue() {
                int max = input1[0];
                for (int i=0; i < input1.length; i++) {
                        if(input1[i] > max) {
                                max = input1[i];
                        }
                }
                for (int j=0; j < input2.length; j++) {
                        if(input2[j] > max) {
                                max = input2[j];
                        }
                }
                return max;
        }

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

        @Override
        public String info() {
                return "Max Value: " + maxValue;
        }

}