source: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java

/*
 * 
 */
package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;

import java.util.ArrayList;

import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;

// TODO: Auto-generated Javadoc
/**
 * The Interface AlignmentAlgorithm.
 */
public interface AlignmentAlgorithm {

        /**
         * Align.
         *
         * @param input1 the input1
         * @param input2 the input2
         * @param submat the submat
         * @param threshold the threshold
         */
        void align(NumberSequence input1, NumberSequence input2,
                        SubstitutionMatrix submat, float threshold);

        /**
         * Gets the alignment.
         *
         * @return the alignment
         */
        public abstract ArrayList<NumberSequence> getAlignment();

        /**
         * Get the alignment score between the two input strings.
         *
         * @return the alignment score
         */
        public abstract double getAlignmentScore();

        /**
         * Gets the matches.
         *
         * @return the matches
         */
        public abstract ArrayList<Match> getMatches();

        /**
         * Gets the max score.
         *
         * @return the max score
         */
        public double getMaxScore();

        /**
         * Prints the alignment.
         */
        public abstract void printAlignment();

        /**
         * Prints the dp matrix.
         */
        public abstract void printDPMatrix();

}