JAL-2629 suppress 'Add Database' menu option in favour of file chooser argument

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 663f544..e71d548 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -72,26 +72,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu hmmerMenu = new JMenu();
 
-  protected JMenu hmmAlign = new JMenu();
-
-  protected JMenuItem hmmAlignRun = new JMenuItem();
-
-  protected JMenuItem hmmAlignSettings = new JMenuItem();
-
-  protected JMenu hmmSearch = new JMenu();
-
-  protected JMenuItem hmmSearchRun = new JMenuItem();
-
-  protected JMenuItem hmmSearchSettings = new JMenuItem();
-
-  protected JMenuItem addDatabase = new JMenuItem();
-
-  protected JMenu hmmBuild = new JMenu();
-
-  protected JMenuItem hmmBuildRun = new JMenuItem();
-
-  protected JMenuItem hmmBuildSettings = new JMenuItem();
-
   protected JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
@@ -172,6 +152,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -278,7 +260,6 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-    initHMMERMenu();
   
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
@@ -320,19 +301,8 @@ 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"));
-    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
-    hmmerMenu.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmerMenu_actionPerformed(e);
-      }
-    });
-    hmmerMenu.add(hmmBuild);
-    hmmerMenu.add(hmmAlign);
-    hmmerMenu.add(hmmSearch);
+
+    initHMMERMenu();
 
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
@@ -1378,6 +1348,16 @@ public class GAlignFrame extends JInternalFrame
         }
       }
     });
+    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+    loadVcf.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadVcf_actionPerformed();
+      }
+    });
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
     autoCalculate.setState(
@@ -1745,81 +1725,6 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
-    hmmBuildRun.setText(MessageManager.formatMessage(
-            "label.action_with_default_settings", "hmmbuild"));
-    hmmBuildRun.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmBuildRun_actionPerformed();
-      }
-    });
-    hmmBuildSettings.setText(
-            MessageManager.getString("label.edit_settings_and_run"));
-    hmmBuildSettings.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmBuildSettings_actionPerformed();
-      }
-    });
-    hmmAlignRun.setText(MessageManager.formatMessage(
-            "label.action_with_default_settings", "hmmalign"));
-    hmmAlignRun.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmAlignRun_actionPerformed();
-      }
-    });
-    hmmAlignSettings.setText(
-            MessageManager.getString("label.edit_settings_and_run"));
-    hmmAlignSettings.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmAlignSettings_actionPerformed();
-      }
-    });
-    hmmSearchRun.setText(MessageManager.formatMessage(
-            "label.action_with_default_settings", "hmmsearch"));
-    hmmSearchRun.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmSearchRun_actionPerformed();
-      }
-    });
-    addDatabase.setText(MessageManager.getString("label.add_database"));
-    addDatabase.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        try
-        {
-          addDatabase_actionPerformed();
-        } catch (IOException e1)
-        {
-          e1.printStackTrace();
-        }
-      }
-    });
-    hmmSearchSettings.setText(
-            MessageManager.getString("label.edit_settings_and_run"));
-    hmmSearchSettings.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hmmSearchSettings_actionPerformed();
-      }
-    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -1856,6 +1761,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
+    fileMenu.add(loadVcf);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
   
@@ -2001,40 +1907,123 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
-  public void hmmerMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
   /**
-   * Constructs the entries on the HMMER menu (does not add them to the menu).
+   * Constructs the entries on the HMMER menu
    */
   protected void initHMMERMenu()
   {
-    hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
-    hmmAlignSettings = new JMenuItem(
-            MessageManager.getString("label.edit_settings_and_run"));
-    hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
-            "label.action_with_default_settings", "hmmalign"));
-    hmmAlign.add(hmmAlignSettings);
-    hmmAlign.add(hmmAlignRun);
-    hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
-    hmmBuildSettings = new JMenuItem(
+    /*
+     * hmmbuild
+     */
+    JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+    JMenuItem hmmBuildSettings = new JMenuItem(
             MessageManager.getString("label.edit_settings_and_run"));
-    hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+    hmmBuildSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(false);
+      }
+    });
+    JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
             "label.action_with_default_settings", "hmmbuild"));
-    hmmBuild.add(hmmBuildSettings);
+    hmmBuildRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(true);
+      }
+    });
     hmmBuild.add(hmmBuildRun);
-    hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
-    hmmSearchSettings = new JMenuItem(
+    hmmBuild.add(hmmBuildSettings);
+
+    /*
+     * hmmalign
+     */
+    JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+    JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlignRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(true);
+      }
+    });
+    JMenuItem hmmAlignSettings = new JMenuItem(
             MessageManager.getString("label.edit_settings_and_run"));
-    hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+    hmmAlignSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(false);
+      }
+    });
+    hmmAlign.add(hmmAlignRun);
+    hmmAlign.add(hmmAlignSettings);
+
+    /*
+     * hmmsearch
+     */
+    JMenu hmmSearch = new JMenu(
+            MessageManager.getString("label.hmmsearch"));
+    JMenuItem hmmSearchSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(false);
+      }
+    });
+    JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
             "label.action_with_default_settings", "hmmsearch"));
-    addDatabase = new JMenuItem(
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(true);
+      }
+    });
+    JMenuItem addDatabase = new JMenuItem(
             MessageManager.getString("label.add_database"));
-    hmmSearch.add(hmmSearchSettings);
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
     hmmSearch.add(hmmSearchRun);
-    hmmSearch.add(addDatabase);
+    hmmSearch.add(hmmSearchSettings);
+    // hmmSearch.add(addDatabase);
+
+    /*
+     * top level menu
+     */
+    hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmSearch);
+
+  }
+
+  protected void loadVcf_actionPerformed()
+  {
   }
 
   /**
@@ -2521,11 +2510,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void hmmBuildRun_actionPerformed()
+  protected void hmmBuild_actionPerformed(boolean withDefaults)
   {
   }
 
-  protected void hmmSearchRun_actionPerformed()
+  protected void hmmSearch_actionPerformed(boolean withDefaults)
   {
   }
 
@@ -2534,19 +2523,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void hmmAlignRun_actionPerformed()
-  {
-  }
-
-  protected void hmmBuildSettings_actionPerformed()
-  {
-  }
-
-  protected void hmmSearchSettings_actionPerformed()
-  {
-  }
-
-  protected void hmmAlignSettings_actionPerformed()
+  protected void hmmAlign_actionPerformed(boolean withDefaults)
   {
   }
 
@@ -2862,20 +2839,4 @@ 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)
-  {
-
-  }
-
-  protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
-  {
-
-  }
 }