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Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-05-14 15:17:32 +00:00
parent 5dda448ae0
commit 0215905bb6
2 changed files with 262 additions and 0 deletions
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111
java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java 100755
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@ -0,0 +1,111 @@
package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import java.util.Iterator;
/**
*
* User: aaron
* Date: May 13, 2009
* Time: 6:33:15 PM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date May 13, 2009
* <p/>
* Class StingSAMIteratorAdapter
* <p/>
* This class adapts other SAMRecord iterators to the StingSAMIterator
*/
public class StingSAMIteratorAdapter {
public static StingSAMIterator adapt(Iterator<SAMRecord> iter) {
return new PrivateStringSAMIterator(iter);
}
public static StingSAMIterator adapt(CloseableIterator<SAMRecord> iter) {
return new PrivateStringSAMCloseableIterator(iter);
}
}
/**
* this class wraps iterators<SAMRecord> in a StingSAMIterator, which means just adding the
* methods that implement the iterable<> interface and the close() method from CloseableIterator
*/
class PrivateStringSAMIterator implements StingSAMIterator {
private Iterator<SAMRecord> iter = null;
PrivateStringSAMIterator(Iterator<SAMRecord> iter) {
this.iter = iter;
}
public void close() {
// do nothing, we can't close the iterator anyway.
}
public boolean hasNext() {
return iter.hasNext();
}
public SAMRecord next() {
return iter.next();
}
public void remove() {
throw new UnsupportedOperationException("StingSAMIterator's don't allow remove()ing");
}
public Iterator<SAMRecord> iterator() {
return iter;
}
}
/**
* this class wraps closeable iterators<SAMRecord> in a StingSAMIterator, which means adding the
* methods that implement the iterable<> interface.
*/
class PrivateStringSAMCloseableIterator implements StingSAMIterator {
private CloseableIterator<SAMRecord> iter = null;
PrivateStringSAMCloseableIterator(CloseableIterator<SAMRecord> iter) {
this.iter = iter;
}
public void close() {
iter.close();
}
public boolean hasNext() {
return iter.hasNext();
}
public SAMRecord next() {
return iter.next();
}
public void remove() {
throw new UnsupportedOperationException("StingSAMIterator's don't allow remove()ing");
}
public Iterator<SAMRecord> iterator() {
return iter;
}
}

151
java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterTest.java 100755
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package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.BaseTest;
import static org.junit.Assert.assertEquals;
import org.junit.Test;
import java.util.Iterator;
/**
*
* User: aaron
* Date: May 13, 2009
* Time: 6:58:21 PM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date May 13, 2009
* <p/>
* Class StingSAMIteratorTest
* <p/>
* Tests the StingSAMIteratorAdapter class.
*/
public class StingSAMIteratorAdapterTest extends BaseTest {
class MyTestIterator implements Iterator<SAMRecord> {
public int count = 0;
public MyTestIterator() {
count = 0;
}
public boolean hasNext() {
if (count < 100) {
++count;
return true;
} else {
return false;
}
}
public SAMRecord next() {
return null;
}
public void remove() {
throw new UnsupportedOperationException("Unsupported");
}
}
class MyTestCloseableIterator implements CloseableIterator<SAMRecord> {
public int count = 0;
public MyTestCloseableIterator() {
count = 0;
}
public boolean hasNext() {
if (count < 100) {
++count;
return true;
} else {
return false;
}
}
public SAMRecord next() {
return null;
}
public void remove() {
throw new UnsupportedOperationException("Unsupported");
}
public void close() {
count = -1;
}
}
@Test
public void testNormalIterator() {
final int COUNT = 100;
MyTestIterator it = new MyTestIterator();
StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
int countCheck = 0;
while (samIt.hasNext()) {
samIt.next();
++countCheck;
//logger.warn("cnt = " + countCheck);
}
assertEquals(COUNT, countCheck);
assertEquals(COUNT, countCheck);
}
@Test
public void testCloseableIterator() {
final int COUNT = 100;
MyTestCloseableIterator it = new MyTestCloseableIterator();
StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
int countCheck = 0;
while (samIt.hasNext()) {
samIt.next();
++countCheck;
}
assertEquals(COUNT, countCheck);
}
@Test
public void testCloseOnCloseableIterator() {
final int COUNT = 100;
MyTestCloseableIterator it = new MyTestCloseableIterator();
StingSAMIterator samIt = StingSAMIteratorAdapter.adapt(it);
int countCheck = 0;
while (samIt.hasNext()) {
samIt.next();
++countCheck;
}
assertEquals(COUNT, countCheck);
// check to see that the count get's set to -1
samIt.close();
assertEquals(-1, it.count);
}
}