JAL-1466 import full length sequence to dataset sequence or trim it to local sequence...

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index a156b2c..d742eaa 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -577,6 +577,7 @@ public class DBRefFetcher implements Runnable
         // mappings are made (but content matches retrieved set)
         boolean updateRefFrame = sequence.getDBRef() == null
                 || sequence.getDBRef().length == 0;
+        // TODO:
         // verify sequence against the entry sequence
 
         String nonGapped = AlignSeq.extractGaps("-. ",
@@ -660,8 +661,14 @@ public class DBRefFetcher implements Runnable
         if (updateRefFrame)
         {
           // finally, update local sequence reference frame if we're allowed
-          sequence.setStart(absStart);
-          sequence.setEnd(absEnd);
+          if (trimDatasetSeqs) {
+            // 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++)
           {