JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / jbgui / GStructureViewer.java

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 7e1be58..bd0f1de 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,20 +20,74 @@
  */
 package jalview.jbgui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.util.MessageManager;
 
+import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
+import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 
-public class GStructureViewer extends JInternalFrame
+public abstract class GStructureViewer extends JInternalFrame implements
+        JalviewStructureDisplayI
 {
+  // private AAStructureBindingModel bindingModel;
+
+  protected JMenu savemenu = new JMenu();
+
+  protected JMenu viewMenu = new JMenu();
+
+  protected JMenu chainMenu = new JMenu();
+
+  protected JMenu viewerActionMenu = new JMenu();
+
+  protected JMenuItem alignStructs = new JMenuItem();
+
+  protected JMenuItem fitToWindow = new JMenuItem();
+
+  protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
+
+  protected JMenuItem helpItem = new JMenuItem();
+
+  protected JLabel statusBar = new JLabel();
+
+  protected JPanel statusPanel = new JPanel();
+
+  /**
+   * Constructor
+   */
   public GStructureViewer()
   {
     try
@@ -47,49 +101,81 @@ public class GStructureViewer extends JInternalFrame
 
   private void jbInit() throws Exception
   {
+    JMenuBar menuBar = new JMenuBar();
     this.setJMenuBar(menuBar);
+
+    JMenu fileMenu = new JMenu();
     fileMenu.setText(MessageManager.getString("action.file"));
+
     savemenu.setActionCommand(MessageManager.getString("action.save_image"));
     savemenu.setText(MessageManager.getString("action.save_as"));
+
+    JMenuItem pdbFile = new JMenuItem();
     pdbFile.setText(MessageManager.getString("label.pdb_file"));
     pdbFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         pdbFile_actionPerformed(actionEvent);
       }
     });
+
+    JMenuItem png = new JMenuItem();
     png.setText("PNG");
     png.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         png_actionPerformed(actionEvent);
       }
     });
+
+    JMenuItem eps = new JMenuItem();
     eps.setText("EPS");
     eps.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         eps_actionPerformed(actionEvent);
       }
     });
+
+    JMenuItem viewMapping = new JMenuItem();
     viewMapping.setText(MessageManager.getString("label.view_mapping"));
     viewMapping.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         viewMapping_actionPerformed(actionEvent);
       }
     });
     viewMenu.setText(MessageManager.getString("action.view"));
+
     chainMenu.setText(MessageManager.getString("action.show_chain"));
+
+    fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
+    fitToWindow.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        fitToWindow_actionPerformed();
+      }
+    });
+
+    JMenu colourMenu = new JMenu();
     colourMenu.setText(MessageManager.getString("label.colours"));
-    backGround.setText(MessageManager.getString("label.background_colour")
-            + "...");
+
+    JMenuItem backGround = new JMenuItem();
+    backGround
+            .setText(MessageManager.getString("action.background_colour"));
     backGround.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         backGround_actionPerformed(actionEvent);
@@ -99,6 +185,7 @@ public class GStructureViewer extends JInternalFrame
     seqColour.setText(MessageManager.getString("action.by_sequence"));
     seqColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         seqColour_actionPerformed(actionEvent);
@@ -107,6 +194,7 @@ public class GStructureViewer extends JInternalFrame
     chainColour.setText(MessageManager.getString("action.by_chain"));
     chainColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         chainColour_actionPerformed(actionEvent);
@@ -115,6 +203,7 @@ public class GStructureViewer extends JInternalFrame
     chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
     chargeColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         chargeColour_actionPerformed(actionEvent);
@@ -123,6 +212,7 @@ public class GStructureViewer extends JInternalFrame
     zappoColour.setText(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         zappoColour_actionPerformed(actionEvent);
@@ -131,6 +221,7 @@ public class GStructureViewer extends JInternalFrame
     taylorColour.setText(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         taylorColour_actionPerformed(actionEvent);
@@ -139,6 +230,7 @@ public class GStructureViewer extends JInternalFrame
     hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
     hydroColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         hydroColour_actionPerformed(actionEvent);
@@ -148,6 +240,7 @@ public class GStructureViewer extends JInternalFrame
             .getString("label.strand_propensity"));
     strandColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         strandColour_actionPerformed(actionEvent);
@@ -156,6 +249,7 @@ public class GStructureViewer extends JInternalFrame
     helixColour.setText(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         helixColour_actionPerformed(actionEvent);
@@ -164,6 +258,7 @@ public class GStructureViewer extends JInternalFrame
     turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         turnColour_actionPerformed(actionEvent);
@@ -172,6 +267,7 @@ public class GStructureViewer extends JInternalFrame
     buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         buriedColour_actionPerformed(actionEvent);
@@ -181,6 +277,7 @@ public class GStructureViewer extends JInternalFrame
             .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         purinePyrimidineColour_actionPerformed(actionEvent);
@@ -190,6 +287,7 @@ public class GStructureViewer extends JInternalFrame
     userColour.setText(MessageManager.getString("action.user_defined"));
     userColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         userColour_actionPerformed(actionEvent);
@@ -202,15 +300,19 @@ public class GStructureViewer extends JInternalFrame
             .getString("label.let_jmol_manage_structure_colours"));
     viewerColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         viewerColour_actionPerformed(actionEvent);
       }
     });
+
+    JMenu helpMenu = new JMenu();
     helpMenu.setText(MessageManager.getString("action.help"));
     helpItem.setText(MessageManager.getString("label.jmol_help"));
     helpItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         showHelp_actionPerformed(actionEvent);
@@ -220,6 +322,7 @@ public class GStructureViewer extends JInternalFrame
             .setText(MessageManager.getString("label.align_structures"));
     alignStructs.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         alignStructs_actionPerformed(actionEvent);
@@ -254,6 +357,8 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(viewerColour);
     colourMenu.add(backGround);
 
+    ButtonGroup colourButtons = new ButtonGroup();
+
     colourButtons.add(seqColour);
     colourButtons.add(chainColour);
     colourButtons.add(chargeColour);
@@ -264,80 +369,33 @@ public class GStructureViewer extends JInternalFrame
     colourButtons.add(strandColour);
     colourButtons.add(turnColour);
     colourButtons.add(buriedColour);
+    colourButtons.add(purinePyrimidineColour);
     colourButtons.add(userColour);
     colourButtons.add(viewerColour);
 
     helpMenu.add(helpItem);
     viewerActionMenu.add(alignStructs);
+
+    statusPanel.setLayout(new GridLayout());
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
   }
 
-  protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+  protected void fitToWindow_actionPerformed()
   {
   }
 
-  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  protected void highlightSelection_actionPerformed()
   {
   }
 
-  JMenuBar menuBar = new JMenuBar();
-
-  JMenu fileMenu = new JMenu();
-
-  JMenu savemenu = new JMenu();
-
-  JMenuItem pdbFile = new JMenuItem();
-
-  JMenuItem png = new JMenuItem();
-
-  JMenuItem eps = new JMenuItem();
-
-  JMenuItem viewMapping = new JMenuItem();
-
-  protected JMenu viewMenu = new JMenu();
-
-  protected JMenu chainMenu = new JMenu();
-
-  JMenu jMenu1 = new JMenu();
-
-  protected JMenu colourMenu = new JMenu();
-
-  protected JMenu viewerActionMenu = new JMenu();
-
-  protected JMenuItem alignStructs = new JMenuItem();
-
-  JMenuItem backGround = new JMenuItem();
-
-  protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
-
-  protected ButtonGroup colourButtons = new ButtonGroup();
-
-  JMenu helpMenu = new JMenu();
+  protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
 
-  protected JMenuItem helpItem = new JMenuItem();
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  {
+  }
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
@@ -428,4 +486,14 @@ public class GStructureViewer extends JInternalFrame
   {
 
   }
+
+  // {
+  // return bindingModel;
+  // }
+
+  // public void setBindingModel(AAStructureBindingModel bindingModel)
+  // {
+  // this.bindingModel = bindingModel;
+  // }
+
 }