Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/IceCreamAligner.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package icecream;
2
3 import aligner.AlignmentResult;
4 import shared.Shared;
5
6 public abstract class IceCreamAligner {
7
8 public static IceCreamAligner makeAligner(int bits){
9 if(Shared.USE_JNI){
10 return new IceCreamAlignerJNI();
11 }else if(bits==32){
12 return new IceCreamAlignerJava();
13 }
14 else{
15 throw new RuntimeException(""+bits);
16 }
17 }
18
19 /**
20 * @param query
21 * @param ref
22 * @param qstart
23 * @param rstart
24 * @param rstop
25 * @param minScore Quit early if score drops below this
26 * @param minRatio Don't return results if max score is less than this fraction of max possible score
27 * @return
28 */
29 public abstract AlignmentResult alignForward(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
30 final float minRatio);
31
32 /**
33 * @param query
34 * @param ref
35 * @param qstart
36 * @param rstart
37 * @param rstop
38 * @param minScore Quit early if score drops below this
39 * @param minRatio Don't return results if max score is less than this fraction of max possible score
40 * @return
41 */
42 public abstract AlignmentResult alignForwardShort(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
43 final float minRatio);
44
45 // public static final int pointsMatch = 1;
46 // public static final int pointsSub = -1;
47 // public static final int pointsDel = -2;
48 // public static final int pointsIns = -2;
49
50 abstract long iters();
51 abstract long itersShort();
52
53 }