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package clump;
import java.util.Comparator;
import shared.Tools;
import stream.Read;
/** A minimal KmerComparator without the heavyweight auto-hashing methods of the original */
public abstract class KmerComparator2 implements Comparator<Read>{
@Override
public final int compare(Read a, Read b) {
final ReadKey keyA=(ReadKey)a.obj;
final ReadKey keyB=(ReadKey)b.obj;
int x=compare(keyA, keyB);
if(x==0){
x=compareSequence(a, b, 0);
}
return x==0 ? a.id.compareTo(b.id) : x;
}
//This gets overriden
public abstract int compare(ReadKey a, ReadKey b);
public static final int compareSequence(Read a, Read b, int depth){
int x=compareSequence(a.bases, b.bases);
if(x!=0){return x;}
if(a.mate!=null){x=compareSequence(a.mate.bases, b.mate.bases);}
if(x!=0){return x;}
return compareQuality(a, b);
}
public static final int compareSequence(final byte[] a, final byte[] b){
if(a==null || b==null){
if(a==null && b!=null){return 1;}
if(a!=null && b==null){return -1;}
return 0;
}
if(a.length!=b.length){
return b.length-a.length;
}
for(int i=0, lim=a.length; i<lim; i++){
int x=a[i]-b[i];
if(x!=0){return x;}
}
return 0;
}
//Not optimal, but fast. This function is probably not very important.
public static final int compareQuality(Read a, Read b){
if(a.quality==null){return 0;}
int qa=Tools.sumInt(a.quality);
int qb=Tools.sumInt(b.quality);
return qb-qa;
}
}
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