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 63d7c53..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;
@@ -217,7 +207,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           SequenceI cons=av.getConsensusSeq();
           if (cons!=null)
             copy_annotseqtoclipboard(cons);
-          
+
         }
 
         ap.annotationPanel.adjustPanelHeight();
@@ -387,8 +377,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           cbmi.addActionListener(new ActionListener()
               {public void actionPerformed(ActionEvent e)
                {
-                 ap.av.setIgnoreGapsConsensus(cbmi.getState());
-                 ap.repaint();
+                 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
                }
               });
           pop.add(cbmi);
@@ -411,7 +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);
@@ -442,7 +435,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                             region[1]});
         }
       }
-      
+
       Desktop.jalviewClipboard = new Object[]{ seqs,
           ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
           hiddenColumns};