From 7c1e9288401f2e32b91d46e20131b3e23769236c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 17 Jan 2005 14:17:22 +0000
Subject: [PATCH] SetSecondaryPanel

---
 src/jalview/jbgui/GAlignFrame.java     |   15 +++++++++++++++
 src/jalview/jbgui/GAlignmentPanel.java |   11 ++++++++++-
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6c216ec..fa90a6e 100755
--- 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();
   JMenu searchMenu = new JMenu();
   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
     try
@@ -597,6 +598,15 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
+    secondaryStructure.setSelected(true);
+    secondaryStructure.setText("Secondary Structure");
+    secondaryStructure.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        secondaryStructure_actionPerformed(actionEvent);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -638,6 +648,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(consensusGraphMenuItem);
     viewMenu.add(overviewMenuItem);
+    viewMenu.add(secondaryStructure);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(zappoColour);
@@ -974,4 +985,8 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  public void secondaryStructure_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
 }
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 4f6e29c..58957b3 100755
--- 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);
-- 
1.7.10.2