Watch out for - symbol lin jnet files

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index f32a350..4d73aa6 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -171,19 +171,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
             aa[selectedRow].visible = false;
 
-            if (aa[selectedRow].label.equals("Conservation"))
-            {
-                ap.av.showConservation = false;
-            }
-
             if (aa[selectedRow].label.equals("Quality"))
             {
-                ap.av.showQuality = false;
-            }
-
-            if (aa[selectedRow].label.equals("Consensus"))
-            {
-                ap.av.showIdentity = false;
+                ap.av.quality = null;
             }
 
             dif = aa[selectedRow].height * -1;
@@ -410,7 +400,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
       if (dseqs[0]==null) {
         dseqs[0] = new Sequence(sq);
-        dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence()));
+        dseqs[0].setSequence(
+            jalview.analysis.AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars,
+                sq.getSequenceAsString()));
+
         sq.setDatasetSequence(dseqs[0]);
       }
       Alignment ds=new Alignment(dseqs);