Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/Hasher.java @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 68:5028fdace37b |
|---|---|
| 1 package clump; | |
| 2 | |
| 3 import java.util.Random; | |
| 4 | |
| 5 import shared.Tools; | |
| 6 import stream.Read; | |
| 7 | |
| 8 public class Hasher { | |
| 9 | |
| 10 private static synchronized long[][] makeCodes2(int modes){ | |
| 11 long[][] r=makeCodes(128, modes); | |
| 12 | |
| 13 for(int i=0; i<26; i++){ | |
| 14 char c=(char)('A'+i); | |
| 15 r[Tools.toLowerCase(c)]=r[c]; | |
| 16 } | |
| 17 return r; | |
| 18 } | |
| 19 | |
| 20 private static synchronized long[][] makeCodes(int symbols, int modes){ | |
| 21 Random randy=new Random(1); | |
| 22 long[][] r=new long[symbols][modes]; | |
| 23 for(int i=0; i<symbols; i++){ | |
| 24 for(int j=0; j<modes; j++){ | |
| 25 r[i][j]=randy.nextLong(); | |
| 26 } | |
| 27 } | |
| 28 return r; | |
| 29 } | |
| 30 | |
| 31 public static long hash(byte[] bases){ | |
| 32 long code=bases.length; | |
| 33 for(int i=0; i<bases.length; i++){ | |
| 34 byte b=bases[i]; | |
| 35 int mode=(int)(code&31); | |
| 36 assert(hashcodes[b]!=null) : "Invalid sequence character: '"+(char)b+"'"; | |
| 37 code=code^hashcodes[b][mode]; | |
| 38 code=Long.rotateLeft(code, 1); | |
| 39 } | |
| 40 return code; | |
| 41 } | |
| 42 | |
| 43 public static final long hash(Read r){ | |
| 44 return hash(r.bases); | |
| 45 } | |
| 46 | |
| 47 public static final long hashPair(Read r){ | |
| 48 long a=hash(r); | |
| 49 if(r.mate==null){return a;} | |
| 50 long b=hash(r.mate); | |
| 51 return a^Long.rotateLeft(b, 1); | |
| 52 } | |
| 53 | |
| 54 public static final boolean equalsPaired(Read a, Read b){ | |
| 55 return equals(a, b) && equals(a.mate, b.mate); | |
| 56 } | |
| 57 | |
| 58 public static final boolean equals(Read a, Read b){ | |
| 59 if(a==b){return true;} | |
| 60 if(a==null || b==null){ | |
| 61 assert(a!=null || b!=null); | |
| 62 return false; | |
| 63 } | |
| 64 if(a.length()!=b.length()){return false;} | |
| 65 if(a.length()==0){return true;} | |
| 66 byte[] ab=a.bases, bb=b.bases; | |
| 67 for(int i=0; i<ab.length; i++){ | |
| 68 if(ab[i]!=bb[i]){return false;} | |
| 69 } | |
| 70 return true; | |
| 71 } | |
| 72 | |
| 73 private static final long[][] hashcodes=makeCodes2(32); | |
| 74 | |
| 75 } |