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 b759d64..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();
@@ -129,7 +139,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -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
@@ -523,36 +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);
-      }
-    });
-    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem neighbourTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -563,27 +551,6 @@ public class GAlignFrame extends JInternalFrame
     outputTextboxMenu.setText(MessageManager
             .getString("label.out_to_textbox"));
 
-
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_blosum62"));
-    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText(MessageManager
             .getString("label.show_annotations"));
@@ -1203,7 +1170,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1240,8 +1207,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree.setText(MessageManager
+            .getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
@@ -1741,6 +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);
@@ -1843,7 +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);
@@ -1905,16 +1872,27 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
-  protected void configureSelectMenu()
-  {
-    // TODO Auto-generated method stub
-
-  }
-
   /**
    * 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(
@@ -2330,26 +2308,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
@@ -2410,6 +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)
   {
   }
@@ -2634,7 +2612,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }
@@ -2721,4 +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
+
+  }
 }