Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index a183794..122ad0f 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -46,13 +46,11 @@ public class GPCAPanel extends JInternalFrame
 {
   private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
 
-  protected JComboBox<String> xCombobox = new JComboBox<String>();
+  protected JComboBox<String> xCombobox = new JComboBox<>();
 
-  protected JComboBox<String> yCombobox = new JComboBox<String>();
+  protected JComboBox<String> yCombobox = new JComboBox<>();
 
-  protected JComboBox<String> zCombobox = new JComboBox<String>();
-
-  protected JMenu scoreModelMenu = new JMenu();
+  protected JComboBox<String> zCombobox = new JComboBox<>();
 
   protected JMenu viewMenu = new JMenu();
 
@@ -60,16 +58,15 @@ public class GPCAPanel extends JInternalFrame
 
   protected JMenu associateViewsMenu = new JMenu();
 
-  protected JMenu calcSettings = new JMenu();
-
-  protected JCheckBoxMenuItem nuclSetting = new JCheckBoxMenuItem();
-
-  protected JCheckBoxMenuItem protSetting = new JCheckBoxMenuItem();
-
   protected JLabel statusBar = new JLabel();
 
   protected JPanel statusPanel = new JPanel();
 
+  protected JMenuItem originalSeqData;
+
+  /**
+   * Constructor
+   */
   public GPCAPanel()
   {
     try
@@ -110,7 +107,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        zCombobox_actionPerformed(e);
+        doDimensionChange();
       }
     });
     yCombobox.setFont(VERDANA_12);
@@ -119,7 +116,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        yCombobox_actionPerformed(e);
+        doDimensionChange();
       }
     });
     xCombobox.setFont(VERDANA_12);
@@ -128,7 +125,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        xCombobox_actionPerformed(e);
+        doDimensionChange();
       }
     });
     JButton resetButton = new JButton();
@@ -139,7 +136,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        resetButton_actionPerformed(e);
+        resetButton_actionPerformed();
       }
     });
     JMenu fileMenu = new JMenu();
@@ -152,7 +149,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        eps_actionPerformed(e);
+        eps_actionPerformed();
       }
     });
     JMenuItem png = new JMenuItem("PNG");
@@ -161,7 +158,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        png_actionPerformed(e);
+        png_actionPerformed();
       }
     });
     JMenuItem outputValues = new JMenuItem();
@@ -171,7 +168,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        outputValues_actionPerformed(e);
+        outputValues_actionPerformed();
       }
     });
     JMenuItem outputPoints = new JMenuItem();
@@ -181,7 +178,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        outputPoints_actionPerformed(e);
+        outputPoints_actionPerformed();
       }
     });
     JMenuItem outputProjPoints = new JMenuItem();
@@ -192,7 +189,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        outputProjPoints_actionPerformed(e);
+        outputProjPoints_actionPerformed();
       }
     });
     JMenuItem print = new JMenuItem();
@@ -202,7 +199,7 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        print_actionPerformed(e);
+        print_actionPerformed();
       }
     });
     viewMenu.setText(MessageManager.getString("action.view"));
@@ -224,33 +221,13 @@ public class GPCAPanel extends JInternalFrame
       {
       }
     });
-    scoreModelMenu
-            .setText(MessageManager.getString("label.select_score_model"));
-    scoreModelMenu.addMenuListener(new MenuListener()
-    {
-      @Override
-      public void menuSelected(MenuEvent e)
-      {
-        scoreModel_menuSelected();
-      }
-
-      @Override
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      @Override
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
     showLabels.setText(MessageManager.getString("label.show_labels"));
     showLabels.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        showLabels_actionPerformed(e);
+        showLabels_actionPerformed();
       }
     });
     JMenuItem bgcolour = new JMenuItem();
@@ -260,47 +237,22 @@ public class GPCAPanel extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        bgcolour_actionPerformed(e);
+        bgcolour_actionPerformed();
       }
     });
-    JMenuItem originalSeqData = new JMenuItem();
+    originalSeqData = new JMenuItem();
     originalSeqData.setText(MessageManager.getString("label.input_data"));
     originalSeqData.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        originalSeqData_actionPerformed(e);
+        originalSeqData_actionPerformed();
       }
     });
     associateViewsMenu.setText(
             MessageManager.getString("label.associate_nodes_with"));
-    calcSettings.setText(MessageManager.getString("action.change_params"));
-    nuclSetting
-            .setText(MessageManager.getString("label.nucleotide_matrix"));
-    protSetting.setText(MessageManager.getString("label.protein_matrix"));
-    nuclSetting.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent arg0)
-      {
-        nuclSetting_actionPerfomed(arg0);
-      }
-    });
-    protSetting.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent arg0)
-      {
-        protSetting_actionPerfomed(arg0);
-      }
-    });
 
-    calcSettings.add(nuclSetting);
-    calcSettings.add(protSetting);
-    calcSettings.add(scoreModelMenu);
     statusPanel.setLayout(new GridLayout());
     statusBar.setFont(VERDANA_12);
     // statusPanel.setBackground(Color.lightGray);
@@ -321,7 +273,6 @@ public class GPCAPanel extends JInternalFrame
     JMenuBar jMenuBar1 = new JMenuBar();
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(viewMenu);
-    jMenuBar1.add(calcSettings);
     setJMenuBar(jMenuBar1);
     fileMenu.add(saveMenu);
     fileMenu.add(outputValues);
@@ -336,91 +287,51 @@ public class GPCAPanel extends JInternalFrame
     viewMenu.add(associateViewsMenu);
   }
 
-  protected void scoreModel_menuSelected()
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  protected void resetButton_actionPerformed(ActionEvent e)
+  protected void resetButton_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
-  protected void protSetting_actionPerfomed(ActionEvent arg0)
+  protected void outputPoints_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
-  protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+  protected void outputProjPoints_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
-  protected void outputPoints_actionPerformed(ActionEvent e)
+  protected void eps_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
-  protected void outputProjPoints_actionPerformed(ActionEvent e)
+  protected void png_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
-  protected void xCombobox_actionPerformed(ActionEvent e)
+  protected void outputValues_actionPerformed()
   {
   }
 
-  protected void yCombobox_actionPerformed(ActionEvent e)
+  protected void print_actionPerformed()
   {
   }
 
-  protected void zCombobox_actionPerformed(ActionEvent e)
+  protected void showLabels_actionPerformed()
   {
   }
 
-  public void eps_actionPerformed(ActionEvent e)
+  protected void bgcolour_actionPerformed()
   {
-
   }
 
-  public void png_actionPerformed(ActionEvent e)
+  protected void originalSeqData_actionPerformed()
   {
-
   }
 
-  public void outputValues_actionPerformed(ActionEvent e)
+  protected void viewMenu_menuSelected()
   {
-
   }
 
-  public void print_actionPerformed(ActionEvent e)
+  protected void doDimensionChange()
   {
-
-  }
-
-  public void showLabels_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void bgcolour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void originalSeqData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void viewMenu_menuSelected()
-  {
-
   }
 }