Adding an iterator that bounds the number of reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java

@@ -0,0 +1,105 @@
+package org.broadinstitute.sting.gatk.iterators;
+
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CloseableIterator;
+
+import java.util.Iterator;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 14, 2009
+ * Time: 5:27:31 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 Apr 14, 2009
+ * <p/>
+ * Class BoundedReadIterator
+ * <p/>
+ * This class implements a read iterator that is bounded by the number of reads
+ * it will produce over the iteration.
+ */
+public class BoundedReadIterator implements CloseableIterator<SAMRecord>, Iterable<SAMRecord> {
+
+    // the genome loc we're bounding
+    final private long readCount;
+    private long currentCount = 0;
+    // the iterator we want to decorate
+    private CloseableIterator<SAMRecord> iterator;
+
+    // are we open
+    private boolean isOpen = false;
+    /**
+     * constructor
+     * @param iter
+     * @param readCount
+     */
+    public BoundedReadIterator(CloseableIterator<SAMRecord> iter, long readCount) {
+        if (iter != null) {
+            isOpen = true;
+            this.iterator = iter;
+        }
+        this.readCount = readCount;
+    }
+
+
+    /**
+     * Do we have a next? If the iterator has a read and we're not over the read
+     * count, then yes
+     * @return
+     */
+    public boolean hasNext() {
+        if (isOpen && iterator.hasNext() && currentCount < readCount) {
+            return true;
+        } else {
+            if (isOpen) {
+                close();
+            }
+            return false;
+        }
+    }
+
+    /**
+     * get the next SAMRecord
+     * @return SAMRecord representing the next read
+     */
+    public SAMRecord next() {
+        if (!isOpen) {
+            throw new UnsupportedOperationException("You cannot call next on a closed iterator");
+        }
+        ++currentCount;
+        return iterator.next();
+    }
+
+    /**
+     * this is unsupported on SAMRecord iterators
+     */
+    public void remove() {
+        throw new UnsupportedOperationException("You cannot use an iterator to remove a SAMRecord");
+    }
+
+    /**
+     * close the iterator
+     */
+    public void close() {
+        isOpen = false;
+        iterator.close();
+    }
+
+    public Iterator<SAMRecord> iterator() {
+        return this;
+    }
+}