JAL-2629 add non-functional HMMER menu

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index f7fe1b6..ea56bbb 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -67,6 +67,16 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu webService = new JMenu();
 
+  protected JMenu hmmerMenu = new JMenu();
+
+  protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
+
+  protected JMenuItem hmmAlign = new JMenuItem();
+
+  protected JMenuItem hmmSearch = new JMenuItem();
+
+  protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
+
   protected JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
@@ -113,7 +123,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
+  protected JMenuItem textColour;
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
@@ -193,13 +203,19 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -247,6 +263,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
+    initHMMERMenu();
 
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
@@ -287,6 +304,7 @@ public class GAlignFrame extends JInternalFrame
     JMenu calculateMenu = new JMenu(
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
+    hmmerMenu.setText(MessageManager.getString("action.hmmer"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
@@ -523,16 +541,6 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    JMenuItem PCAMenuItem = new JMenuItem(
-            MessageManager.getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -934,7 +942,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
+            MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1612,6 +1620,7 @@ public class GAlignFrame extends JInternalFrame
 
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -1699,6 +1708,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    alignFrameMenuBar.add(hmmerMenu);
 
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1801,7 +1811,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    // calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -1867,6 +1876,23 @@ public class GAlignFrame extends JInternalFrame
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
    */
+  protected void initHMMERMenu()
+  {
+    autoAlignSeqs = new JCheckBoxMenuItem(
+            MessageManager.getString("label.auto_align_seqs"));
+    hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
+    hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
+    hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
+    autoAlignSeqs.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
+      }
+    });
+
+  }
   protected void initColourMenu()
   {
     applyToAllGroups = new JCheckBoxMenuItem(
@@ -1880,8 +1906,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2282,10 +2308,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -2350,6 +2372,22 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void autoAlignSeqs_actionPerformed(boolean selected)
+  {
+  }
+
+  protected void hmmAlign_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void hmmBuild_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void hmmSearch_actionPerformed(ActionEvent e)
+  {
+  }
+
   public void createPNG(java.io.File f)
   {
   }
@@ -2661,4 +2699,22 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean complement)
   {
   }
+
+  protected void showInformationHistogram_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
 }