X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=9d6467a05ac5b2dede3fd9101bedc1d8a0294c75;hb=e83f899e879e04af8f9baa9a495e2918a67f6a4f;hp=bc6ea866a778bc5325c3f9cd7eea234a568e5a17;hpb=c36a5cbdcbb1c099320e1454c1038327efa04efa;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bc6ea86..9d6467a 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -15,11 +15,12 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   OverviewPanel overviewPanel;
   SeqPanel   seqPanel;
   IdPanel    idPanel;
+  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   ScorePanel scorePanel;
 
-  public AlignmentPanel(AlignFrame af, AlignViewport av)
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
     this.av         = av;
@@ -27,7 +28,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanel         = new IdPanel   (av, this);
     scalePanel = new ScalePanel(av, this);
     scorePanel = new ScorePanel(av);
+    ssPanel = new SecondaryStructurePanel(av);
 
+    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
@@ -45,6 +48,24 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           RefreshPanels();
      }
    });
+
+   hscroll.setFocusable(false);
+   vscroll.setFocusable(false);
+   setFocusable(true);
+
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       if(evt.getKeyCode()==27)
+       {
+         av.setRubberbandGroup(null);
+         RefreshPanels();
+       }
+     }
+   });
+
+
   }
 
  public void highlightSearchResults(int [] results)
@@ -83,6 +104,12 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();
   }
 
+  public void setSecondaryStructureVisible(boolean b)
+  {
+    secondaryPanelHolder.setVisible(b);
+    RefreshPanels();
+  }
+
   public void setWrapAlignment(boolean wrap)
   {
       scalePanelHolder.setVisible(!wrap);
@@ -101,8 +128,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(av.getConservationSelected())
     {
 
-      Alignment al = (Alignment)av.getAlignment();
-      Conservation c = new Conservation("All",
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
                             ResidueProperties.propHash, 3, al.getSequences(), 0,
                             al.getWidth() );
 
@@ -113,13 +140,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        av.setGlobalColourScheme( ccs );
 
     }
-    seqPanel.seqCanvas.paintFlag = true;
-    repaint();
+
+    RefreshPanels();
   }
 
   public void RefreshPanels()
   {
-
+    requestFocus();
     invalidate();
     seqPanel.seqCanvas.paintFlag = true;
     idPanel.idCanvas.paintFlag = true;
@@ -131,6 +158,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     validate();
     repaint();
+
   }
 
   int hextent = 0;