From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 21 Apr 2014 15:06:30 +0000 (+0100)
Subject: JAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set.
X-Git-Tag: Jalview_2_9~198^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9f80616357f04492852a963a610f98657c63533;p=jalview.git

JAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set.
---

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d742eaa..84eba02 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -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++)