From 2606e67cf1cc412ed240c6c47a617a78d0c229b8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Oct 2010 14:40:42 +0000
Subject: [PATCH] Reverting Matt's change from yesterday which I accidentally
 blew away when trying to cope with the stupid svn update issues we've been
 plagued with recently.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4495 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/sam/GATKSAMRecord.java        | 77 +++++++++++++++++++
 1 file changed, 77 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index ad557471a..dc56c3775 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -1,8 +1,10 @@
 package org.broadinstitute.sting.utils.sam;
 
+import java.lang.reflect.Method;
 import java.util.*;
 
 import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 /**
@@ -16,6 +18,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
  *   if they are ever modified externally then one must also invoke the
  *   setReadGroup() method here to ensure that the cache is kept up-to-date.
  *
+ * 13 Oct 2010 - mhanna - this class is fundamentally flawed: it uses a decorator
+ *                        pattern to wrap a heavyweight object, which can lead
+ *                        to heinous side effects if the wrapping is not carefully
+ *                        done.  Hopefully SAMRecord will become an interface and
+ *                        this will eventually be fixed.
  */
 public class GATKSAMRecord extends SAMRecord {
 
@@ -327,6 +334,76 @@ public class GATKSAMRecord extends SAMRecord {
 
     public void setValidationStringency(net.sf.samtools.SAMFileReader.ValidationStringency validationStringency) { mRecord.setValidationStringency(validationStringency); }
 
+    public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
+
+    public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
+
+    public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }
+
+    public Byte getByteAttribute(final String tag) { return mRecord.getByteAttribute(tag); }
+
+    public String getStringAttribute(final String tag) { return mRecord.getStringAttribute(tag); }
+
+    public Character getCharacterAttribute(final String tag) { return mRecord.getCharacterAttribute(tag); }
+
+    public Float getFloatAttribute(final String tag) { return mRecord.getFloatAttribute(tag); }
+
+    public byte[] getByteArrayAttribute(final String tag) { return mRecord.getByteArrayAttribute(tag); }
+
+    protected Object getAttribute(final short tag) {
+        Object attribute;
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("getAttribute",Short.TYPE);
+            method.setAccessible(true);
+            attribute = method.invoke(mRecord,tag);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke getAttribute method",ex);
+        }
+        return attribute;
+    }
+
+    public void setAttribute(final String tag, final Object value) { mRecord.setAttribute(tag,value); }
+
+    protected void setAttribute(final short tag, final Object value) {
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("setAttribute",Short.TYPE,Object.class);
+            method.setAccessible(true);
+            method.invoke(mRecord,tag,value);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke setAttribute method",ex);
+        }
+    }
+
+    public void clearAttributes() { mRecord.clearAttributes(); }
+
+    protected void setAttributes(final SAMBinaryTagAndValue attributes) {
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("setAttributes",SAMBinaryTagAndValue.class);
+            method.setAccessible(true);
+            method.invoke(mRecord,attributes);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke setAttributes method",ex);
+        }
+   }
+
+    protected SAMBinaryTagAndValue getBinaryAttributes() {
+        SAMBinaryTagAndValue binaryAttributes;
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("getBinaryAttributes");
+            method.setAccessible(true);
+            binaryAttributes = (SAMBinaryTagAndValue)method.invoke(mRecord);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke getBinaryAttributes method",ex);
+        }
+        return binaryAttributes;
+    }
+
+    public List<SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
+
     public SAMFileHeader getHeader() { return mRecord.getHeader(); }
 
     public void setHeader(SAMFileHeader samFileHeader) { mRecord.setHeader(samFileHeader); }