Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 23c3de7..5fa37e3 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -708,6 +708,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
+      j=sequence.length;
     }
     else
     {
@@ -716,6 +717,9 @@ 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)