JAL-1528 bug fixes and adjustments to Chimera interface

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

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index f6c4e05..7e1be58 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -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
 {
@@ -189,24 +195,25 @@ public class GStructureViewer extends JInternalFrame
         userColour_actionPerformed(actionEvent);
       }
     });
-    jmolColour.setSelected(false);
-    jmolColour.setText(MessageManager.getString("label.colour_with_jmol"));
-    jmolColour.setToolTipText(MessageManager
+    viewerColour.setSelected(false);
+    viewerColour
+            .setText(MessageManager.getString("label.colour_with_jmol"));
+    viewerColour.setToolTipText(MessageManager
             .getString("label.let_jmol_manage_structure_colours"));
-    jmolColour.addActionListener(new ActionListener()
+    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
@@ -218,12 +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);
@@ -244,7 +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);
@@ -258,13 +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)
   {
   }
 
@@ -294,7 +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();
 
@@ -324,13 +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)
   {
@@ -417,7 +424,7 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  public void showHelp_actionPerformed(ActionEvent actionEvent)
   {
 
   }