jpayne@68: package icecream;
jpayne@68: 
jpayne@68: import aligner.AlignmentResult;
jpayne@68: import shared.Shared;
jpayne@68: 
jpayne@68: public abstract class IceCreamAligner {
jpayne@68: 
jpayne@68: 	public static IceCreamAligner makeAligner(int bits){
jpayne@68: 		if(Shared.USE_JNI){
jpayne@68: 			return new IceCreamAlignerJNI();
jpayne@68: 		}else if(bits==32){
jpayne@68: 			return new IceCreamAlignerJava();
jpayne@68: 		}
jpayne@68: 		else{
jpayne@68: 			throw new RuntimeException(""+bits);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	/**
jpayne@68: 	 * @param query
jpayne@68: 	 * @param ref
jpayne@68: 	 * @param qstart
jpayne@68: 	 * @param rstart
jpayne@68: 	 * @param rstop
jpayne@68: 	 * @param minScore Quit early if score drops below this
jpayne@68: 	 * @param minRatio Don't return results if max score is less than this fraction of max possible score
jpayne@68: 	 * @return
jpayne@68: 	 */
jpayne@68: 	public abstract AlignmentResult alignForward(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
jpayne@68: 			final float minRatio);
jpayne@68: 
jpayne@68: 	/**
jpayne@68: 	 * @param query
jpayne@68: 	 * @param ref
jpayne@68: 	 * @param qstart
jpayne@68: 	 * @param rstart
jpayne@68: 	 * @param rstop
jpayne@68: 	 * @param minScore Quit early if score drops below this
jpayne@68: 	 * @param minRatio Don't return results if max score is less than this fraction of max possible score
jpayne@68: 	 * @return
jpayne@68: 	 */
jpayne@68: 	public abstract AlignmentResult alignForwardShort(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
jpayne@68: 			final float minRatio);
jpayne@68: 
jpayne@68: //	public static final int pointsMatch = 1;
jpayne@68: //	public static final int pointsSub = -1;
jpayne@68: //	public static final int pointsDel = -2;
jpayne@68: //	public static final int pointsIns = -2;
jpayne@68: 
jpayne@68: 	abstract long iters();
jpayne@68: 	abstract long itersShort();
jpayne@68: 
jpayne@68: }