X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;fp=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=eb33ce76b53a7dc671fc1bc28601b2447d312682;hb=bba03888565b5277a487f3186b6f6444477466e6;hp=a5f218e216d0feee95e5b28509c00dc532996976;hpb=7ac2996be1e7428d1651793c4a1b7e4091f221b9;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a5f218e..eb33ce7 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -840,9 +840,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          af.avc.markColumnsContainingFeatures(true, false, false,
-                  SequenceOntologyI.EXON);
-          af.getViewport().hideSelectedColumns();
+          hideIntronsIfPresent(af);
         }
 
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
@@ -867,6 +865,25 @@ public class SequenceFetcher extends JPanel implements Runnable
     return al;
   }
 
+  /**
+   * Hide columns not containing 'exon' features, provided there are exon
+   * features on the alignment
+   * 
+   * @param af
+   */
+  public void hideIntronsIfPresent(AlignFrame af)
+  {
+    boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
+            false,
+            SequenceOntologyI.EXON);
+    if (hasExons)
+    {
+      af.avc.markColumnsContainingFeatures(true, false, true,
+              SequenceOntologyI.EXON);
+      af.getViewport().hideSelectedColumns();
+    }
+  }
+
   void showErrorMessage(final String error)
   {
     resetDialog();