From a3b3c4269d29f085e573cbeb731f3fb5dfb7b0c9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 2 May 2007 12:19:55 +0000
Subject: [PATCH] checks for negative start column in restrict

---
 src/jalview/datamodel/AlignmentAnnotation.java |    8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index cc4308d..3ed84a3 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -357,12 +357,18 @@ Loading...
    */
   public void restrict(int startRes, int endRes)
   {
+    if (startRes<0)
+      startRes=0;
+    if (startRes>=annotations.length)
+      startRes = annotations.length-1;
+    if (endRes>=annotations.length)
+      endRes = annotations.length-1;
     if (annotations==null)
       return;
     Annotation[] temp = new Annotation[endRes-startRes+1];
     if (startRes<annotations.length)
     {
-      System.arraycopy(annotations, startRes, temp, 0, Math.min(endRes, annotations.length-1)-startRes+1);
+      System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
     }
     if (sequenceRef!=null) {
       // Clip the mapping, if it exists.
-- 
1.7.10.2