JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d742eaa..f46779b 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -658,6 +658,11 @@ public class DBRefFetcher implements Runnable
         // unknownSequences.remove(sequence);
         int absEnd = absStart + nonGapped.length();
         absStart += 1;
+        if (!trimDatasetSeqs) {
+          // insert full length sequence from record
+          sequence.setSequence(entry.getSequenceAsString());
+          sequence.setStart(entry.getStart());
+        }
         if (updateRefFrame)
         {
           // finally, update local sequence reference frame if we're allowed
@@ -665,9 +670,6 @@ public class DBRefFetcher implements Runnable
             // just fix start/end
             sequence.setStart(absStart);
             sequence.setEnd(absEnd);
-          } else {
-            // insert full length sequence from record
-            sequence.setSequence(entry.getSequenceAsString());
           }
           // search for alignment sequences to update coordinate frame for
           for (int alsq = 0; alsq < alseqs.length; alsq++)