From cd91e365f4a4f0dfb75a2455e80dc3447f676e22 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 23 Jan 2013 14:13:21 -0500
Subject: [PATCH] Optimize getCurrentContigLength and getLocForOffset in
 ActivityProfile

---
 .../sting/utils/activeregion/ActivityProfile.java    | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
index ab9095106..80484e12f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
@@ -49,6 +49,12 @@ public class ActivityProfile {
     protected GenomeLoc regionStartLoc = null;
     protected GenomeLoc regionStopLoc = null;
 
+    /**
+     * A cached value of the regionStartLoc contig length, to make calls to
+     * getCurrentContigLength efficient
+     */
+    protected int contigLength = -1;
+
     /**
      * Create a new empty ActivityProfile
      * @param parser the parser we can use to create genome locs, cannot be null
@@ -155,7 +161,7 @@ public class ActivityProfile {
         if ( start < 0 || start > getCurrentContigLength() ) {
             return null;
         } else {
-            return parser.createGenomeLoc(regionStartLoc.getContig(), start);
+            return parser.createGenomeLoc(regionStartLoc.getContig(), regionStartLoc.getContigIndex(), start, start);
         }
     }
 
@@ -166,8 +172,7 @@ public class ActivityProfile {
     @Requires("regionStartLoc != null")
     @Ensures("result > 0")
     private int getCurrentContigLength() {
-        // TODO -- fix performance problem with getContigInfo
-        return parser.getContigInfo(regionStartLoc.getContig()).getSequenceLength();
+        return contigLength;
     }
 
     // --------------------------------------------------------------------------------
@@ -190,6 +195,7 @@ public class ActivityProfile {
         if ( regionStartLoc == null ) {
             regionStartLoc = loc;
             regionStopLoc = loc;
+            contigLength = parser.getContigInfo(regionStartLoc.getContig()).getSequenceLength();
         } else {
             // TODO -- need to figure out where to add loc as the regions will be popping off the front
             if ( regionStopLoc.getStart() != loc.getStart() - 1 )