X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureViewer.java;h=52f745d3e1375027b31df5c46a461b05b4a8eb87;hb=94379c810f9115b8564ee7bac46ed119218d5fd2;hp=b1b5200a249c4f19838ef482af31f4a6b3868515;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index b1b5200..52f745d 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,28 +1,101 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
 
-public class GStructureViewer extends JInternalFrame
+import java.awt.BorderLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Map;
+
+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 abstract class GStructureViewer extends JInternalFrame implements
+        JalviewStructureDisplayI
 {
+  // private AAStructureBindingModel bindingModel;
+
+  protected JMenu savemenu;
+
+  protected JMenu viewMenu;
+
+  protected JMenu colourMenu;
+
+  protected JMenu chainMenu;
+
+  protected JMenu viewerActionMenu;
+
+  protected JMenuItem alignStructs;
+
+  protected JMenuItem fitToWindow;
+
+  protected JRadioButtonMenuItem seqColour;
+
+  protected JRadioButtonMenuItem chainColour;
+
+  protected JRadioButtonMenuItem chargeColour;
+
+  protected JRadioButtonMenuItem zappoColour;
+
+  protected JRadioButtonMenuItem taylorColour;
+
+  protected JRadioButtonMenuItem hydroColour;
+
+  protected JRadioButtonMenuItem strandColour;
+
+  protected JRadioButtonMenuItem helixColour;
+
+  protected JRadioButtonMenuItem turnColour;
+
+  protected JRadioButtonMenuItem buriedColour;
+
+  protected JRadioButtonMenuItem nucleotideColour;
+
+  protected JRadioButtonMenuItem purinePyrimidineColour;
+
+  protected JRadioButtonMenuItem userColour;
+
+  protected JRadioButtonMenuItem viewerColour;
+
+  protected JMenuItem helpItem;
+
+  protected JLabel statusBar;
+
+  protected JPanel statusPanel;
+
+  /**
+   * Constructor
+   */
   public GStructureViewer()
   {
     try
@@ -36,192 +109,306 @@ public class GStructureViewer extends JInternalFrame
 
   private void jbInit() throws Exception
   {
+    JMenuBar menuBar = new JMenuBar();
     this.setJMenuBar(menuBar);
-    fileMenu.setText("File");
-    savemenu.setActionCommand("Save Image");
-    savemenu.setText("Save As");
-    pdbFile.setText("PDB File");
+
+    JMenu fileMenu = new JMenu();
+    fileMenu.setText(MessageManager.getString("action.file"));
+
+    savemenu = new JMenu();
+    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);
       }
     });
-    viewMapping.setText("View Mapping");
+
+    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("View");
-    chainMenu.setText("Show Chain");
-    colourMenu.setText("Colours");
-    backGround.setText("Background Colour...");
+
+    viewMenu = new JMenu();
+    viewMenu.setText(MessageManager.getString("action.view"));
+
+    chainMenu = new JMenu();
+    chainMenu.setText(MessageManager.getString("action.show_chain"));
+
+    fitToWindow = new JMenuItem();
+    fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
+    fitToWindow.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        fitToWindow_actionPerformed();
+      }
+    });
+
+    JMenu helpMenu = new JMenu();
+    helpMenu.setText(MessageManager.getString("action.help"));
+    helpItem = new JMenuItem();
+    helpItem.setText(MessageManager.getString("label.jmol_help"));
+    helpItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showHelp_actionPerformed(actionEvent);
+      }
+    });
+    alignStructs = new JMenuItem();
+    alignStructs
+            .setText(MessageManager.getString("label.align_structures"));
+    alignStructs.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignStructs_actionPerformed(actionEvent);
+      }
+    });
+
+    viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
+    viewerActionMenu.setVisible(false);
+    viewerActionMenu.add(alignStructs);
+    colourMenu = new JMenu();
+    buildColourMenu();
+    fileMenu.add(savemenu);
+    fileMenu.add(viewMapping);
+    savemenu.add(pdbFile);
+    savemenu.add(png);
+    savemenu.add(eps);
+    viewMenu.add(chainMenu);
+    helpMenu.add(helpItem);
+
+    menuBar.add(fileMenu);
+    menuBar.add(viewMenu);
+    menuBar.add(colourMenu);
+    menuBar.add(viewerActionMenu);
+    menuBar.add(helpMenu);
+
+    statusPanel = new JPanel();
+    statusPanel.setLayout(new GridLayout());
+    this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
+    statusBar = new JLabel();
+    statusPanel.add(statusBar, null);
+  }
+
+  /**
+   * Builds the colour menu
+   */
+  protected void buildColourMenu()
+  {
+    colourMenu.removeAll();
+    colourMenu.setText(MessageManager.getString("label.colours"));
+
+    JMenuItem backGround = new JMenuItem();
+    backGround
+            .setText(MessageManager.getString("action.background_colour"));
     backGround.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         backGround_actionPerformed(actionEvent);
       }
     });
+    seqColour = new JRadioButtonMenuItem();
     seqColour.setSelected(false);
-    seqColour.setText("By Sequence");
+    seqColour.setText(MessageManager.getString("action.by_sequence"));
     seqColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         seqColour_actionPerformed(actionEvent);
       }
     });
-    chainColour.setText("By Chain");
+    chainColour = new JRadioButtonMenuItem();
+    chainColour.setText(MessageManager.getString("action.by_chain"));
     chainColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         chainColour_actionPerformed(actionEvent);
       }
     });
-    chargeColour.setText("Charge & Cysteine");
+    chargeColour = new JRadioButtonMenuItem();
+    chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
     chargeColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         chargeColour_actionPerformed(actionEvent);
       }
     });
-    zappoColour.setText("Zappo");
+    zappoColour = new JRadioButtonMenuItem();
+    zappoColour.setText(MessageManager
+            .getString("label.colourScheme_zappo"));
     zappoColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         zappoColour_actionPerformed(actionEvent);
       }
     });
-    taylorColour.setText("Taylor");
+    taylorColour = new JRadioButtonMenuItem();
+    taylorColour.setText(MessageManager
+            .getString("label.colourScheme_taylor"));
     taylorColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         taylorColour_actionPerformed(actionEvent);
       }
     });
-    hydroColour.setText("Hydro");
+    hydroColour = new JRadioButtonMenuItem();
+    hydroColour.setText(MessageManager
+            .getString("label.colourScheme_hydrophobic"));
     hydroColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         hydroColour_actionPerformed(actionEvent);
       }
     });
-    strandColour.setText("Strand");
+    strandColour = new JRadioButtonMenuItem();
+    strandColour.setText(MessageManager
+            .getString("label.colourScheme_strand_propensity"));
     strandColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         strandColour_actionPerformed(actionEvent);
       }
     });
-    helixColour.setText("Helix Propensity");
+    helixColour = new JRadioButtonMenuItem();
+    helixColour.setText(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helixColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         helixColour_actionPerformed(actionEvent);
       }
     });
-    turnColour.setText("Turn Propensity");
+    turnColour = new JRadioButtonMenuItem();
+    turnColour.setText(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turnColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         turnColour_actionPerformed(actionEvent);
       }
     });
-    buriedColour.setText("Buried Index");
+    buriedColour = new JRadioButtonMenuItem();
+    buriedColour.setText(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buriedColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         buriedColour_actionPerformed(actionEvent);
       }
     });
-    purinePyrimidineColour.setText("Purine/Pyrimidine");
-    purinePyrimidineColour.addActionListener(new ActionListener()
+    nucleotideColour = new JRadioButtonMenuItem();
+    nucleotideColour.setText(MessageManager
+            .getString("label.colourScheme_nucleotide"));
+    nucleotideColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-    	  purinePyrimidineColour_actionPerformed(actionEvent);
+        nucleotideColour_actionPerformed(actionEvent);
       }
     });
-    
-    userColour.setText("User Defined ...");
-    userColour.addActionListener(new ActionListener()
+    purinePyrimidineColour = new JRadioButtonMenuItem();
+    purinePyrimidineColour.setText(MessageManager
+            .getString("label.colourScheme_purine/pyrimidine"));
+    purinePyrimidineColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        userColour_actionPerformed(actionEvent);
+        purinePyrimidineColour_actionPerformed(actionEvent);
       }
     });
-    jmolColour.setSelected(false);
-    jmolColour.setText("Colour with Jmol");
-    jmolColour.setToolTipText("Let Jmol manage structure colours.");
-    jmolColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        jmolColour_actionPerformed(actionEvent);
-      }
-    }
-    );
-    helpMenu.setText("Help");
-    jmolHelp.setText("Jmol Help");
-    jmolHelp.addActionListener(new ActionListener()
+    userColour = new JRadioButtonMenuItem();
+    userColour.setText(MessageManager.getString("action.user_defined"));
+    userColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        jmolHelp_actionPerformed(actionEvent);
+        userColour_actionPerformed(actionEvent);
       }
     });
-    alignStructs.setText("Align structures");
-    alignStructs.addActionListener(new ActionListener()
+    viewerColour = new JRadioButtonMenuItem();
+    viewerColour.setSelected(false);
+    viewerColour
+            .setText(MessageManager.getString("label.colour_with_jmol"));
+    viewerColour.setToolTipText(MessageManager
+            .getString("label.let_jmol_manage_structure_colours"));
+    viewerColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        alignStructs_actionPerformed(actionEvent);
+        viewerColour_actionPerformed(actionEvent);
       }
     });
-    jmolActionMenu.setText("Jmol");
-    menuBar.add(fileMenu);
-    menuBar.add(viewMenu);
-    menuBar.add(colourMenu);
-    menuBar.add(jmolActionMenu);
-    jmolActionMenu.setVisible(false);
-    menuBar.add(helpMenu);
-    fileMenu.add(savemenu);
-    fileMenu.add(viewMapping);
-    savemenu.add(pdbFile);
-    savemenu.add(png);
-    savemenu.add(eps);
-    viewMenu.add(chainMenu);
+
+    /*
+     * add colour buttons to a group so their selection
+     * is mutually exclusive
+     */
+    ButtonGroup colourButtons = new ButtonGroup();
 
     colourMenu.add(seqColour);
     colourMenu.add(chainColour);
@@ -234,8 +421,32 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(purinePyrimidineColour);
+
+    /*
+     * add any user-defined colours that are loaded
+     */
+    Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
+            .getUserColourSchemes();
+    if (userColourSchemes != null)
+    {
+      for (String schemeName : userColourSchemes.keySet())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+                schemeName);
+        radioItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent evt)
+          {
+            userColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.add(radioItem);
+        colourButtons.add(radioItem);
+      }
+    }
     colourMenu.add(userColour);
-    colourMenu.add(jmolColour);
+    colourMenu.add(viewerColour);
     colourMenu.add(backGround);
 
     colourButtons.add(seqColour);
@@ -248,81 +459,26 @@ public class GStructureViewer extends JInternalFrame
     colourButtons.add(strandColour);
     colourButtons.add(turnColour);
     colourButtons.add(buriedColour);
+    colourButtons.add(purinePyrimidineColour);
     colourButtons.add(userColour);
-    colourButtons.add(jmolColour);
-
-    helpMenu.add(jmolHelp);
-    jmolActionMenu.add(alignStructs);
+    colourButtons.add(viewerColour);
   }
 
-  protected void jmolColour_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 jmolActionMenu = 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 jmolColour = new JRadioButtonMenuItem();
-
-  protected ButtonGroup colourButtons = new ButtonGroup();
-
-  JMenu helpMenu = new JMenu();
+  protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
 
-  JMenuItem jmolHelp = new JMenuItem();
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  {
+  }
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
@@ -393,7 +549,12 @@ public class GStructureViewer extends JInternalFrame
   {
 
   }
-  
+
+  public void nucleotideColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
   public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
   {
 
@@ -409,8 +570,18 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed(ActionEvent actionEvent)
   {
 
   }
+
+  // {
+  // return bindingModel;
+  // }
+
+  // public void setBindingModel(AAStructureBindingModel bindingModel)
+  // {
+  // this.bindingModel = bindingModel;
+  // }
+
 }