Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/IceCreamAligner.java @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@68 | 1 package icecream; |
| jpayne@68 | 2 |
| jpayne@68 | 3 import aligner.AlignmentResult; |
| jpayne@68 | 4 import shared.Shared; |
| jpayne@68 | 5 |
| jpayne@68 | 6 public abstract class IceCreamAligner { |
| jpayne@68 | 7 |
| jpayne@68 | 8 public static IceCreamAligner makeAligner(int bits){ |
| jpayne@68 | 9 if(Shared.USE_JNI){ |
| jpayne@68 | 10 return new IceCreamAlignerJNI(); |
| jpayne@68 | 11 }else if(bits==32){ |
| jpayne@68 | 12 return new IceCreamAlignerJava(); |
| jpayne@68 | 13 } |
| jpayne@68 | 14 else{ |
| jpayne@68 | 15 throw new RuntimeException(""+bits); |
| jpayne@68 | 16 } |
| jpayne@68 | 17 } |
| jpayne@68 | 18 |
| jpayne@68 | 19 /** |
| jpayne@68 | 20 * @param query |
| jpayne@68 | 21 * @param ref |
| jpayne@68 | 22 * @param qstart |
| jpayne@68 | 23 * @param rstart |
| jpayne@68 | 24 * @param rstop |
| jpayne@68 | 25 * @param minScore Quit early if score drops below this |
| jpayne@68 | 26 * @param minRatio Don't return results if max score is less than this fraction of max possible score |
| jpayne@68 | 27 * @return |
| jpayne@68 | 28 */ |
| jpayne@68 | 29 public abstract AlignmentResult alignForward(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore, |
| jpayne@68 | 30 final float minRatio); |
| jpayne@68 | 31 |
| jpayne@68 | 32 /** |
| jpayne@68 | 33 * @param query |
| jpayne@68 | 34 * @param ref |
| jpayne@68 | 35 * @param qstart |
| jpayne@68 | 36 * @param rstart |
| jpayne@68 | 37 * @param rstop |
| jpayne@68 | 38 * @param minScore Quit early if score drops below this |
| jpayne@68 | 39 * @param minRatio Don't return results if max score is less than this fraction of max possible score |
| jpayne@68 | 40 * @return |
| jpayne@68 | 41 */ |
| jpayne@68 | 42 public abstract AlignmentResult alignForwardShort(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore, |
| jpayne@68 | 43 final float minRatio); |
| jpayne@68 | 44 |
| jpayne@68 | 45 // public static final int pointsMatch = 1; |
| jpayne@68 | 46 // public static final int pointsSub = -1; |
| jpayne@68 | 47 // public static final int pointsDel = -2; |
| jpayne@68 | 48 // public static final int pointsIns = -2; |
| jpayne@68 | 49 |
| jpayne@68 | 50 abstract long iters(); |
| jpayne@68 | 51 abstract long itersShort(); |
| jpayne@68 | 52 |
| jpayne@68 | 53 } |