--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/IceCreamAligner.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,53 @@
+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();
+
+}
\ No newline at end of file