SetSecondaryPanel

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6c216ec..fa90a6e 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -81,6 +81,7 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem findMenuItem = new JMenuItem();\r
   JMenu searchMenu = new JMenu();\r
   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+  protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -597,6 +598,15 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);\r
       }\r
     });\r
+    secondaryStructure.setSelected(true);\r
+    secondaryStructure.setText("Secondary Structure");\r
+    secondaryStructure.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        secondaryStructure_actionPerformed(actionEvent);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -638,6 +648,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(consensusGraphMenuItem);\r
     viewMenu.add(overviewMenuItem);\r
+    viewMenu.add(secondaryStructure);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(zappoColour);\r
@@ -974,4 +985,8 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  public void secondaryStructure_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+\r
+  }\r
 }\r

diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 4f6e29c..58957b3 100755 (executable)
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -33,6 +33,10 @@ public class GAlignmentPanel extends JPanel
   BorderLayout borderLayout7 = new BorderLayout();
   JPanel jPanel1 = new JPanel();
   FlowLayout flowLayout1 = new FlowLayout();
+  JPanel jPanel3 = new JPanel();
+  protected JPanel secondaryPanelHolder = new JPanel();
+  BorderLayout borderLayout8 = new BorderLayout();
+  BorderLayout borderLayout9 = new BorderLayout();
 
   public GAlignmentPanel()
   {
@@ -78,12 +82,17 @@ public class GAlignmentPanel extends JPanel
     jPanel1.setLayout(flowLayout1);
     flowLayout1.setHgap(0);
     flowLayout1.setVgap(0);
-    sequenceHolderPanel.add(scorePanelHolder, BorderLayout.SOUTH);
+    jPanel3.setLayout(borderLayout9);
+    secondaryPanelHolder.setBackground(Color.cyan);
+    secondaryPanelHolder.setLayout(borderLayout8);
     sequenceHolderPanel.add(scalePanelHolder,  BorderLayout.NORTH);
     sequenceHolderPanel.add(seqPanelHolder,  BorderLayout.CENTER);
     this.add(jPanel2, BorderLayout.CENTER);
     jPanel2.add(sequenceHolderPanel, BorderLayout.CENTER);
     seqPanelHolder.add(vscroll, BorderLayout.EAST);
+    sequenceHolderPanel.add(jPanel3,  BorderLayout.SOUTH);
+    jPanel3.add(scorePanelHolder, BorderLayout.CENTER);
+    jPanel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
     this.add(idPanelHolder, BorderLayout.WEST);
     idPanelHolder.add(idSpaceFillerPanel1,  BorderLayout.NORTH);
     idPanelHolder.add(idSpaceFillerPanel,  BorderLayout.SOUTH);