don't system.ext

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

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