From 0215905bb66eec6636405ab2d12468b00cc761f4 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 15:17:32 +0000
Subject: [PATCH] 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
---
 .../iterators/StingSAMIteratorAdapter.java    | 111 +++++++++++++
 .../StingSAMIteratorAdapterTest.java          | 151 ++++++++++++++++++
 2 files changed, 262 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
 create mode 100755 java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterTest.java

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java b/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
new file mode 100755
index 000000000..724d39b2f
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
@@ -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;
+    }
+}
+
diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterTest.java
new file mode 100755
index 000000000..5f022162b
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterTest.java
@@ -0,0 +1,151 @@
+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);
+    }
+}