From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 5 Apr 2016 17:14:42 +0000 (+0100)
Subject: JAL-2046 explicitly copy char[] when cloning sequence data for copy-constructor/deriv... 
X-Git-Tag: Release_2_10_0~249^2~31^2~11
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=52fca080c3cb048defbe2d3a6f44fff760365b51

JAL-2046 explicitly copy char[] when cloning sequence data for copy-constructor/deriveSequence

---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6f1b403..cb3ae70 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -25,6 +25,7 @@ import jalview.api.DBRefEntryI;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -216,8 +217,12 @@ public class Sequence extends ASequence implements SequenceI
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
-    initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+    {
+      char[] oseq = seq.getSequence();
+      initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+              seq.getStart(),
             seq.getEnd());
+    }
     description = seq.getDescription();
     sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
             seq.getSourceDBRef());