From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 11 May 2018 11:19:52 +0000 (+0100)
Subject: JAL-2986 corrected findIndex for out of range residue value
X-Git-Tag: Release_2_11_0~38
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d716c9b072f989bef39c6eba038f779ce98396a8;p=jalview.git

JAL-2986 corrected findIndex for out of range residue value
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 59c3fb1..33de452 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -445,7 +445,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public Vector<PDBEntry> getAllPDBEntries()
   {
-    return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+    return pdbIds == null ? new Vector<>() : pdbIds;
   }
 
   /**
@@ -815,7 +815,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param curs
    * @return
    */
-  protected int findIndex(int pos, SequenceCursor curs)
+  protected int findIndex(final int pos, SequenceCursor curs)
   {
     if (!isValidCursor(curs))
     {
@@ -841,10 +841,15 @@ public class Sequence extends ASequence implements SequenceI
     while (newPos != pos)
     {
       col += delta; // shift one column left or right
-      if (col < 0 || col == sequence.length)
+      if (col < 0)
       {
         break;
       }
+      if (col == sequence.length)
+      {
+        col--; // return last column if we failed to reach pos
+        break;
+      }
       if (!Comparison.isGap(sequence[col]))
       {
         newPos += delta;
@@ -852,7 +857,14 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     col++; // convert back to base 1
-    updateCursor(pos, col, curs.firstColumnPosition);
+
+    /*
+     * only update cursor if we found the target position
+     */
+    if (newPos == pos)
+    {
+      updateCursor(pos, col, curs.firstColumnPosition);
+    }
 
     return col;
   }