jpayne@68: package clump;
jpayne@68: 
jpayne@68: import java.util.Random;
jpayne@68: 
jpayne@68: import shared.Tools;
jpayne@68: import stream.Read;
jpayne@68: 
jpayne@68: public class Hasher {
jpayne@68: 
jpayne@68: 	private static synchronized long[][] makeCodes2(int modes){
jpayne@68: 		long[][] r=makeCodes(128, modes);
jpayne@68: 		
jpayne@68: 		for(int i=0; i<26; i++){
jpayne@68: 			char c=(char)('A'+i);
jpayne@68: 			r[Tools.toLowerCase(c)]=r[c];
jpayne@68: 		}
jpayne@68: 		return r;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static synchronized long[][] makeCodes(int symbols, int modes){
jpayne@68: 		Random randy=new Random(1);
jpayne@68: 		long[][] r=new long[symbols][modes];
jpayne@68: 		for(int i=0; i<symbols; i++){
jpayne@68: 			for(int j=0; j<modes; j++){
jpayne@68: 				r[i][j]=randy.nextLong();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return r;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static long hash(byte[] bases){
jpayne@68: 		long code=bases.length;
jpayne@68: 		for(int i=0; i<bases.length; i++){
jpayne@68: 			byte b=bases[i];
jpayne@68: 			int mode=(int)(code&31);
jpayne@68: 			assert(hashcodes[b]!=null) : "Invalid sequence character: '"+(char)b+"'";
jpayne@68: 			code=code^hashcodes[b][mode];
jpayne@68: 			code=Long.rotateLeft(code, 1);
jpayne@68: 		}
jpayne@68: 		return code;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final long hash(Read r){
jpayne@68: 		return hash(r.bases);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final long hashPair(Read r){
jpayne@68: 		long a=hash(r);
jpayne@68: 		if(r.mate==null){return a;}
jpayne@68: 		long b=hash(r.mate);
jpayne@68: 		return a^Long.rotateLeft(b, 1);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final boolean equalsPaired(Read a, Read b){
jpayne@68: 		return equals(a, b) && equals(a.mate, b.mate);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final boolean equals(Read a, Read b){
jpayne@68: 		if(a==b){return true;}
jpayne@68: 		if(a==null || b==null){
jpayne@68: 			assert(a!=null || b!=null);
jpayne@68: 			return false;
jpayne@68: 		}
jpayne@68: 		if(a.length()!=b.length()){return false;}
jpayne@68: 		if(a.length()==0){return true;}
jpayne@68: 		byte[] ab=a.bases, bb=b.bases;
jpayne@68: 		for(int i=0; i<ab.length; i++){
jpayne@68: 			if(ab[i]!=bb[i]){return false;}
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static final long[][] hashcodes=makeCodes2(32);
jpayne@68: 	
jpayne@68: }