From f7593435eb38af416a90013ca72c75e15a128b34 Mon Sep 17 00:00:00 2001
From: weisburd <weisburd@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 2 Jul 2010 21:01:36 +0000
Subject: [PATCH] Implemented decodeLoc(..)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3713 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../annotator/AnnotatorInputTableCodec.java         | 12 +++++++++---
 .../annotator/AnnotatorInputTableFeature.java       | 13 +++++++++++++
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
index 66d52d1b5..ace7c0d56 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
@@ -75,11 +75,17 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
         return null;  // TODO: do we want the header to be a concrete type?
     }
 
-    // todo -- probably worth implementing for performance reasons
+    @Override
     public Feature decodeLoc(String line) {
-        return decode(line);
+        int tabIndex = line.indexOf(DELIMITER);
+        if(tabIndex <= 0) {
+            throw new CodecLineParsingException("Couldn't parse GenomeLoc out the following line because line.indexOf(DELIMITER) returned " + tabIndex + ".\nLine: " + line);
+        }
+        GenomeLoc loc = GenomeLocParser.parseGenomeLoc(line.substring(0, tabIndex));
+        return new AnnotatorInputTableFeature(loc.getContig(), (int) loc.getStart(), (int) loc.getStop());
     }
-    
+
+
     /**
      * Parses the line into an AnnotatorInputTableFeature object.
      *
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
index 5b1c6a2dd..cb3f91ed9 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
@@ -60,6 +60,19 @@ public class AnnotatorInputTableFeature implements Feature {
 
 
 
+    /**
+     * Constructor.
+     * @param chr The chromosome name.
+     * @param start
+     * @param end
+     */
+    public AnnotatorInputTableFeature(String chr, int start, int end) {
+        this.chr = chr;
+        this.start = start;
+        this.end = end;
+    }
+
+
     /**
      * Constructor.
      * @param columnNames  The column names as parsed out of the file header.