JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index f7fa6db..270acbe 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,22 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 jalview.util.MessageManager;
+
 import javax.swing.*;
 import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
@@ -37,10 +42,10 @@ public class GStructureViewer extends JInternalFrame
   private void jbInit() throws Exception
   {
     this.setJMenuBar(menuBar);
-    fileMenu.setText("File");
-    savemenu.setActionCommand("Save Image");
-    savemenu.setText("Save As");
-    pdbFile.setText("PDB File");
+    fileMenu.setText(MessageManager.getString("action.file"));
+    savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+    savemenu.setText(MessageManager.getString("action.save_as"));
+    pdbFile.setText(MessageManager.getString("label.pdb_file"));
     pdbFile.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -64,7 +69,7 @@ public class GStructureViewer extends JInternalFrame
         eps_actionPerformed(actionEvent);
       }
     });
-    viewMapping.setText("View Mapping");
+    viewMapping.setText(MessageManager.getString("label.view_mapping"));
     viewMapping.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -72,10 +77,10 @@ public class GStructureViewer extends JInternalFrame
         viewMapping_actionPerformed(actionEvent);
       }
     });
-    viewMenu.setText("View");
-    chainMenu.setText("Show Chain");
-    colourMenu.setText("Colours");
-    backGround.setText("Background Colour...");
+    viewMenu.setText(MessageManager.getString("action.view"));
+    chainMenu.setText(MessageManager.getString("action.show_chain"));
+    colourMenu.setText(MessageManager.getString("label.colours"));
+    backGround.setText(MessageManager.getString("label.background_colour") + "...");
     backGround.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -83,8 +88,8 @@ public class GStructureViewer extends JInternalFrame
         backGround_actionPerformed(actionEvent);
       }
     });
-    seqColour.setSelected(true);
-    seqColour.setText("By Sequence");
+    seqColour.setSelected(false);
+    seqColour.setText(MessageManager.getString("action.by_sequence"));
     seqColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -92,7 +97,7 @@ public class GStructureViewer extends JInternalFrame
         seqColour_actionPerformed(actionEvent);
       }
     });
-    chainColour.setText("By Chain");
+    chainColour.setText(MessageManager.getString("action.by_chain"));
     chainColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -100,7 +105,7 @@ public class GStructureViewer extends JInternalFrame
         chainColour_actionPerformed(actionEvent);
       }
     });
-    chargeColour.setText("Charge & Cysteine");
+    chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
     chargeColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -108,7 +113,7 @@ public class GStructureViewer extends JInternalFrame
         chargeColour_actionPerformed(actionEvent);
       }
     });
-    zappoColour.setText("Zappo");
+    zappoColour.setText(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -116,7 +121,7 @@ public class GStructureViewer extends JInternalFrame
         zappoColour_actionPerformed(actionEvent);
       }
     });
-    taylorColour.setText("Taylor");
+    taylorColour.setText(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -124,7 +129,7 @@ public class GStructureViewer extends JInternalFrame
         taylorColour_actionPerformed(actionEvent);
       }
     });
-    hydroColour.setText("Hydro");
+    hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
     hydroColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -132,7 +137,7 @@ public class GStructureViewer extends JInternalFrame
         hydroColour_actionPerformed(actionEvent);
       }
     });
-    strandColour.setText("Strand");
+    strandColour.setText(MessageManager.getString("label.strand_propensity"));
     strandColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -140,7 +145,7 @@ public class GStructureViewer extends JInternalFrame
         strandColour_actionPerformed(actionEvent);
       }
     });
-    helixColour.setText("Helix Propensity");
+    helixColour.setText(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -148,7 +153,7 @@ public class GStructureViewer extends JInternalFrame
         helixColour_actionPerformed(actionEvent);
       }
     });
-    turnColour.setText("Turn Propensity");
+    turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -156,7 +161,7 @@ public class GStructureViewer extends JInternalFrame
         turnColour_actionPerformed(actionEvent);
       }
     });
-    buriedColour.setText("Buried Index");
+    buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -164,7 +169,16 @@ public class GStructureViewer extends JInternalFrame
         buriedColour_actionPerformed(actionEvent);
       }
     });
-    userColour.setText("User Defined ...");
+    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        purinePyrimidineColour_actionPerformed(actionEvent);
+      }
+    });
+
+    userColour.setText(MessageManager.getString("action.user_defined"));
     userColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -172,8 +186,18 @@ public class GStructureViewer extends JInternalFrame
         userColour_actionPerformed(actionEvent);
       }
     });
-    helpMenu.setText("Help");
-    jmolHelp.setText("Jmol Help");
+    jmolColour.setSelected(false);
+    jmolColour.setText(MessageManager.getString("label.colour_with_jmol"));
+    jmolColour.setToolTipText(MessageManager.getString("label.let_jmol_manage_structure_colours"));
+    jmolColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolColour_actionPerformed(actionEvent);
+      }
+    });
+    helpMenu.setText(MessageManager.getString("action.help"));
+    jmolHelp.setText(MessageManager.getString("label.jmol_help"));
     jmolHelp.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -181,9 +205,20 @@ public class GStructureViewer extends JInternalFrame
         jmolHelp_actionPerformed(actionEvent);
       }
     });
+    alignStructs.setText(MessageManager.getString("label.align_structures"));
+    alignStructs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignStructs_actionPerformed(actionEvent);
+      }
+    });
+    jmolActionMenu.setText(MessageManager.getString("label.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);
@@ -202,7 +237,9 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(strandColour);
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
+    colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userColour);
+    colourMenu.add(jmolColour);
     colourMenu.add(backGround);
 
     colourButtons.add(seqColour);
@@ -216,8 +253,18 @@ public class GStructureViewer extends JInternalFrame
     colourButtons.add(turnColour);
     colourButtons.add(buriedColour);
     colourButtons.add(userColour);
-    
+    colourButtons.add(jmolColour);
+
     helpMenu.add(jmolHelp);
+    jmolActionMenu.add(alignStructs);
+  }
+
+  protected void jmolColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  {
   }
 
   JMenuBar menuBar = new JMenuBar();
@@ -234,13 +281,17 @@ public class GStructureViewer extends JInternalFrame
 
   JMenuItem viewMapping = new JMenuItem();
 
-  JMenu viewMenu = new JMenu();
+  protected JMenu viewMenu = new JMenu();
 
   protected JMenu chainMenu = new JMenu();
 
   JMenu jMenu1 = new JMenu();
 
-  JMenu colourMenu = new JMenu();
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenu jmolActionMenu = new JMenu();
+
+  protected JMenuItem alignStructs = new JMenuItem();
 
   JMenuItem backGround = new JMenuItem();
 
@@ -264,8 +315,12 @@ public class GStructureViewer extends JInternalFrame
 
   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();
@@ -342,6 +397,11 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {