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gatk-3.8
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Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next(). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@513 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-23 20:16:26 +00:00
parent 998763950c
commit 282f1d88b8
1 changed files with 17 additions and 5 deletions
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22
java/src/org/broadinstitute/sting/gatk/iterators/ThreadedIterator.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.gatk.iterators;
import org.apache.log4j.Logger;
import java.util.Iterator;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
@ -18,11 +20,21 @@ public class ThreadedIterator<T> implements Iterator<T>, Runnable {
private int nOps = 0;
private final int printStateFreq = -1;
protected static Logger logger = Logger.getLogger(ThreadedIterator.class);
public void run() {
try {
while (it.hasNext()) {
queue.put(it.next());
printState("addNext");
// Spin loop...if queue has remaining capacity, add more elements.
// Otherwise, yield to the thread(s) waiting for the data.
if(queue.remainingCapacity() > 0 ) {
synchronized(this) {
queue.put(it.next());
printState("addNext");
}
}
else
Thread.yield();
}
} catch (InterruptedException ex) {
// bail out
@ -32,7 +44,7 @@ public class ThreadedIterator<T> implements Iterator<T>, Runnable {
public synchronized void printState(final String op) {
if ( printStateFreq != -1 && nOps++ % printStateFreq == 0 )
System.out.printf(" [%s] Queue has %d elements %d ops%n", op, queue.size(), nOps);
logger.info(String.format(" [%s] Queue has %d elements %d ops%n", op, queue.size(), nOps));
}
public ThreadedIterator(Iterator<T> it, int buffSize) {
@ -41,7 +53,7 @@ public class ThreadedIterator<T> implements Iterator<T>, Runnable {
new Thread(this).start();
}
public boolean hasNext() {
public synchronized boolean hasNext() {
return queue.peek() != null || it.hasNext();
}
@ -51,7 +63,7 @@ public class ThreadedIterator<T> implements Iterator<T>, Runnable {
return queue.poll(10, TimeUnit.SECONDS);
} catch (InterruptedException ex) {
// bail out
System.out.printf("ThreadedIterator next() timed out...%n");
logger.info("ThreadedIterator next() timed out...");
printState("getNext");
return null;
}