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