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