JAL-1620 version bump and release notes

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

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 270acbe..904d75c 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -22,9 +22,15 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import javax.swing.*;
-import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
 
 public class GStructureViewer extends JInternalFrame
 {
@@ -80,7 +86,8 @@ public class GStructureViewer extends JInternalFrame
     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.setText(MessageManager.getString("label.background_colour")
+            + "...");
     backGround.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -137,7 +144,8 @@ public class GStructureViewer extends JInternalFrame
         hydroColour_actionPerformed(actionEvent);
       }
     });
-    strandColour.setText(MessageManager.getString("label.strand_propensity"));
+    strandColour.setText(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -169,7 +177,8 @@ public class GStructureViewer extends JInternalFrame
         buriedColour_actionPerformed(actionEvent);
       }
     });
-    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour.setText(MessageManager
+            .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -186,26 +195,29 @@ public class GStructureViewer extends JInternalFrame
         userColour_actionPerformed(actionEvent);
       }
     });
-    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()
+    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()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        jmolColour_actionPerformed(actionEvent);
+        viewerColour_actionPerformed(actionEvent);
       }
     });
     helpMenu.setText(MessageManager.getString("action.help"));
-    jmolHelp.setText(MessageManager.getString("label.jmol_help"));
-    jmolHelp.addActionListener(new ActionListener()
+    helpItem.setText(MessageManager.getString("label.jmol_help"));
+    helpItem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        jmolHelp_actionPerformed(actionEvent);
+        showHelp_actionPerformed(actionEvent);
       }
     });
-    alignStructs.setText(MessageManager.getString("label.align_structures"));
+    alignStructs
+            .setText(MessageManager.getString("label.align_structures"));
     alignStructs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -213,12 +225,12 @@ public class GStructureViewer extends JInternalFrame
         alignStructs_actionPerformed(actionEvent);
       }
     });
-    jmolActionMenu.setText(MessageManager.getString("label.jmol"));
+    viewerActionMenu.setText(MessageManager.getString("label.jmol"));
     menuBar.add(fileMenu);
     menuBar.add(viewMenu);
     menuBar.add(colourMenu);
-    menuBar.add(jmolActionMenu);
-    jmolActionMenu.setVisible(false);
+    menuBar.add(viewerActionMenu);
+    viewerActionMenu.setVisible(false);
     menuBar.add(helpMenu);
     fileMenu.add(savemenu);
     fileMenu.add(viewMapping);
@@ -239,7 +251,7 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userColour);
-    colourMenu.add(jmolColour);
+    colourMenu.add(viewerColour);
     colourMenu.add(backGround);
 
     colourButtons.add(seqColour);
@@ -253,13 +265,13 @@ public class GStructureViewer extends JInternalFrame
     colourButtons.add(turnColour);
     colourButtons.add(buriedColour);
     colourButtons.add(userColour);
-    colourButtons.add(jmolColour);
+    colourButtons.add(viewerColour);
 
-    helpMenu.add(jmolHelp);
-    jmolActionMenu.add(alignStructs);
+    helpMenu.add(helpItem);
+    viewerActionMenu.add(alignStructs);
   }
 
-  protected void jmolColour_actionPerformed(ActionEvent actionEvent)
+  protected void viewerColour_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -271,7 +283,7 @@ public class GStructureViewer extends JInternalFrame
 
   JMenu fileMenu = new JMenu();
 
-  JMenu savemenu = new JMenu();
+  protected JMenu savemenu = new JMenu();
 
   JMenuItem pdbFile = new JMenuItem();
 
@@ -289,7 +301,7 @@ public class GStructureViewer extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JMenu jmolActionMenu = new JMenu();
+  protected JMenu viewerActionMenu = new JMenu();
 
   protected JMenuItem alignStructs = new JMenuItem();
 
@@ -319,13 +331,13 @@ public class GStructureViewer extends JInternalFrame
 
   protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
 
-  protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
 
   protected ButtonGroup colourButtons = new ButtonGroup();
 
   JMenu helpMenu = new JMenu();
 
-  JMenuItem jmolHelp = new JMenuItem();
+  protected JMenuItem helpItem = new JMenuItem();
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
@@ -412,7 +424,7 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed(ActionEvent actionEvent)
   {
 
   }