Merge branch 'features/sequenceFeatureRefactor' into develop

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 2928102..06f4b0f 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -792,6 +792,10 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     if (al != null && al.getHeight() > 0)
     {
+      if (title == null)
+      {
+        title = getDefaultRetrievalTitle();
+      }
       if (alignFrame == null)
       {
         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
@@ -804,10 +808,6 @@ public class SequenceFetcher extends JPanel implements Runnable
           // Alignments?
         }
 
-        if (title == null)
-        {
-          title = getDefaultRetrievalTitle();
-        }
         SequenceFeature[] sfs = null;
         List<SequenceI> alsqs;
         synchronized (alsqs = al.getSequences())
@@ -841,21 +841,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       else
       {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          alignFrame.viewport.getAlignment().addSequence(
-                  al.getSequenceAt(i)); // this
-          // also
-          // creates
-          // dataset
-          // sequence
-          // entries
-        }
-        alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
-                .getHeight());
-        alignFrame.viewport.getAlignment().getWidth();
-        alignFrame.viewport.firePropertyChange("alignment", null,
-                alignFrame.viewport.getAlignment().getSequences());
+        alignFrame.viewport.addAlignment(al, title);
       }
     }
     return al;