From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 4 Oct 2013 14:03:52 +0000 (+0100)
Subject: fix for JAL-1380 and efficiency todo for JAL-1381
X-Git-Tag: Jalview_2_9~200^2~22
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=507800557a9b27cc6e1a3f831cbb7d18c9d173d0;p=jalview.git

fix for JAL-1380 and efficiency todo for JAL-1381
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 580c850..fa063ff 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -707,6 +707,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
+      j=sequence.length;
     }
     else
     {
@@ -715,6 +716,9 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence, j, tmp, i, sequence.length - j);
     }
     boolean createNewDs = false;
+    // TODO: take a look at the new dataset creation validation method below -
+    // this could become time comsuming for large sequences - consider making it
+    // more efficient
     for (int s = i; s < j; s++)
     {
       if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)