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package structures;
import java.util.concurrent.atomic.AtomicIntegerArray;
import shared.KillSwitch;
/**
* Atomic version
* @author Brian Bushnell
* @date Sep 20, 2014
*
*/
public class CoverageArray3A extends CoverageArray {
/**
*
*/
private static final long serialVersionUID = 98483952072098494L;
public static void main(String[] args){
//TODO
}
public CoverageArray3A(int chrom, int len){
super(chrom, len);
array=KillSwitch.allocAtomicInt(len);
minIndex=0;
maxIndex=len-1;
}
/**
* @param loc
*/
@Override
public void increment(int loc){
increment(loc, 1);
}
@Override
public void increment(int loc, int amt) {
int val=array.addAndGet(loc, (int)amt);
// assert(val>=0 || amt<0) : "Overflow!";
if(val<0 && amt>0){
if(!OVERFLOWED){
System.err.println("Note: Coverage capped at "+Integer.MAX_VALUE);
OVERFLOWED=true;
}
array.set(loc, Integer.MAX_VALUE);
}
}
@Override
public void incrementRangeSynchronized(int min, int max, int amt) {
incrementRange(min, max, amt);//Synchronized is not needed
}
@Override
public void incrementRange(int min, int max, int amt){
if(min<0){min=0;}
if(max>maxIndex){max=maxIndex;}
boolean over=false;
for(int loc=min; loc<=max; loc++){
int val=array.addAndGet(loc, (int)amt);
if(val<0 && amt>0){
over=true;
array.set(loc, Integer.MAX_VALUE);
}
}
if(over && !OVERFLOWED){
synchronized(CoverageArray3A.class){
if(!OVERFLOWED){
System.err.println("Note: Coverage capped at "+Integer.MAX_VALUE);
OVERFLOWED=true;
}
}
}
}
@Override
public void set(int loc, int val){
// if(loc<0 || loc>=maxIndex){return;}
array.set(loc, val);
}
@Override
public int get(int loc){
return loc<0 || loc>=array.length() ? 0 : array.get(loc);
}
@Override
public void resize(int newlen){
throw new RuntimeException("Resize: Unsupported.");
}
@Override
public String toString(){
StringBuilder sb=new StringBuilder();
sb.append('[');
for(int i=0; i<=length(); i++){
if(i>0){sb.append(", ");}
sb.append((int)array.get(i));
}
sb.append(']');
return sb.toString();
}
@Override
public int[] toArray() {
int[] array2=new int[length()];
for(int i=0; i<array2.length; i++) {
array2[i]=get(i);
}
return array2;
}
public final AtomicIntegerArray array;
// @Override
// public int length(){return maxIndex-minIndex+1;}
@Override
public int arrayLength(){return array.length();}
private static boolean OVERFLOWED=false;
}
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