From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 14 Sep 2017 10:00:07 +0000 (+0100)
Subject: JAL-2541 length check in deleteChars (redoing lost commit 4a4bc78)
X-Git-Tag: Release_2_11_1_0~98^2~23^2~14
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=043dab77c998532aa84020699d5525832713905d;p=jalview.git

JAL-2541 length check in deleteChars (redoing lost commit 4a4bc78)
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 80de543..6aaa68b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1159,9 +1159,9 @@ public class Sequence extends ASequence implements SequenceI
     // the very large sequence case
     int eindex = -1, sindex = -1;
     boolean ecalc = false, scalc = false;
-    for (int s = i; s < j; s++)
+    for (int s = i; s < j && s < sequence.length; s++)
     {
-      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      if (!Comparison.isGap(sequence[s]))
       {
         if (createNewDs)
         {
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index cc3c090..5584999 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -548,6 +548,21 @@ public class SequenceTest
     assertEquals(1, sq.getStart());
     assertEquals(4, sq.getEnd());
     assertNull(PA.getValue(sq, "datasetSequence"));
+
+    /*
+     * delete more positions than there are
+     */
+    sq = new Sequence("test/8-11", "ABCD");
+    sq.deleteChars(0, 99);
+    assertEquals("", sq.getSequenceAsString());
+    assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
+    assertEquals(11, sq.getEnd());
+
+    sq = new Sequence("test/8-11", "----");
+    sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
+    assertEquals("", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(11, sq.getEnd());
   }
 
   @Test(groups = { "Functional" })