From 98558735e9208afa98bb155bd5350ad0a680ca24 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 11 Oct 2017 16:17:13 +0100
Subject: [PATCH] JAL-2772 check array bounds for sequence access

---
 src/jalview/datamodel/Sequence.java      |    4 +++-
 test/jalview/datamodel/SequenceTest.java |   32 ++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 796937d..2ee412b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1827,7 +1827,9 @@ public class Sequence extends ASequence implements SequenceI
      * and we may have included adjacent or enclosing features;
      * remove any that are not enclosing, non-contact features
      */
-    if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
+    boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+            && Comparison.isGap(sequence[toColumn - 1]);
+    if (endPos > this.end || endColumnIsGapped)
     {
       ListIterator<SequenceFeature> it = result.listIterator();
       while (it.hasNext())
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6844072..23e8cf7 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1672,4 +1672,36 @@ public class SequenceTest
     assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
     assertEquals(new Range(8, 13), sq.findPositions(1, 99));
   }
+
+  @Test(groups = { "Functional" })
+  public void testFindFeatures_largeEndPos()
+  {
+    /*
+     * imitate a PDB sequence where end is larger than end position
+     */
+    SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+    sq.createDatasetSequence();
+  
+    assertTrue(sq.findFeatures(1, 9).isEmpty());
+    // should be no array bounds exception - JAL-2772
+    assertTrue(sq.findFeatures(1, 15).isEmpty());
+  
+    // add feature on BCD
+    SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+            null);
+    sq.addSequenceFeature(sfBCD);
+  
+    // no features in columns 1-2 (-A)
+    List<SequenceFeature> found = sq.findFeatures(1, 2);
+    assertTrue(found.isEmpty());
+  
+    // columns 1-6 (-ABC--) includes BCD
+    found = sq.findFeatures(1, 6);
+    assertEquals(1, found.size());
+    assertTrue(found.contains(sfBCD));
+
+    // columns 10-11 (--) should find nothing
+    found = sq.findFeatures(10, 11);
+    assertEquals(0, found.size());
+  }
 }
-- 
1.7.10.2