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package var2;
//This class is not currently thought to be used
/** Allows simpler hashing, without complete alleles. */
public class VarKey implements Comparable<VarKey> {
public static VarKey toVarKey(Var v){
if(v.type==Var.INS){
return new VarKey(v.scafnum, v.start, v.allele.length, v.type, v.allele[0]);
}else if(v.type==Var.DEL){
return new VarKey(v.scafnum, v.start, v.reflen(), v.type, 0);
}
return new VarKey(v.scafnum, v.start, v.reflen(), v.type, v.allele[0]);
}
public VarKey(int scafNum_, int start_, int length_, int type_, int allele_){
scafNum=scafNum_;
start=start_;
length=length_;
type=type_;
allele=allele_;
}
@Override
public int hashCode(){
return scafNum^Integer.rotateLeft(start, 4)^Integer.rotateRight(start, 18)^Integer.rotateLeft(type, 8)^Integer.rotateLeft(allele, 12);
}
@Override
public boolean equals(Object b){
return equals((VarKey)b);
}
public boolean equals(VarKey b){
if(b==null){return false;}
return scafNum==b.scafNum && start==b.start && length==b.length && type==b.type && allele==b.allele;
}
@Override
public int compareTo(VarKey b){
if(b==null){return -1;}
if(scafNum!=b.scafNum){return scafNum-b.scafNum;}
if(start!=b.start){return start-b.start;}
if(length!=b.length){return length-b.length;}
if(type!=b.type){return type-b.type;}
if(allele!=b.allele){return allele-b.allele;}
return 0;
}
int scafNum;
int start;
int length;
int type;
//0 for DEL, otherwise first letter of allele
int allele;
}
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