Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 579da08..6148d86 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -64,17 +64,20 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+@SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu webService = new JMenu();
+  public JMenu webService = new JMenu();// BH 2019 was protected, but not
+                                        // sufficient for AlignFrame thread run
+    // JBP - followed suite for these other service related GUI elements.
+    // TODO: check we really need these to be public
+  public JMenu hmmerMenu = new JMenu();
 
-  protected JMenu hmmerMenu = new JMenu();
-
-  protected JMenuItem webServiceNoServices;
+  public JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
@@ -82,7 +85,9 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  protected JLabel statusBar = new JLabel();
+  public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+                                          // sufficient for
+                                          // AlignFrame.printWriter
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -210,6 +215,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
+  protected JMenuItem openFeatureSettings;
+
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
@@ -222,6 +229,10 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+
+      // for Web-page embedding using id=align-frame-div
+      setName("jalview-alignment");
+
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
@@ -235,7 +246,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            outputText_actionPerformed(e);
+            outputText_actionPerformed(e.getActionCommand());
           }
         });
 
@@ -246,7 +257,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!Platform.isAMac())
+    if (Platform.allowMnemonics()) // was "not mac and not JS"
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -270,7 +281,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveAs_actionPerformed(e);
+        saveAs_actionPerformed();
       }
     };
   
@@ -1031,7 +1042,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        copy_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
@@ -1044,7 +1055,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -1056,7 +1067,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        delete_actionPerformed();
       }
     });
   
@@ -1302,8 +1313,8 @@ public class GAlignFrame extends JInternalFrame
     /*
      * Translate as cDNA with sub-menu of translation tables
      */
-    showTranslation.setText(MessageManager
-            .getString("label.translate_cDNA"));
+    showTranslation
+            .setText(MessageManager.getString("label.translate_cDNA"));
     boolean first = true;
     for (final GeneticCodeI table : GeneticCodes.getInstance()
             .getCodeTables())
@@ -1372,8 +1383,8 @@ public class GAlignFrame extends JInternalFrame
         runGroovy_actionPerformed();
       }
     });
-  
-    JMenuItem openFeatureSettings = new JMenuItem(
+
+    openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
@@ -1383,6 +1394,10 @@ public class GAlignFrame extends JInternalFrame
         featureSettings_actionPerformed(e);
       }
     });
+
+    /*
+     * add sub-menu of database we can fetch from
+     */
     JMenuItem fetchSequence = new JMenuItem(
             MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
@@ -1390,7 +1405,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fetchSequence_actionPerformed(e);
+        fetchSequence_actionPerformed();
       }
     });
   
@@ -1411,7 +1426,8 @@ public class GAlignFrame extends JInternalFrame
         }
       }
     });
-    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf = new JMenuItem(
+            MessageManager.getString("label.load_vcf_file"));
     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
     loadVcf.addActionListener(new ActionListener()
     {
@@ -1817,8 +1833,11 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(webService);
-    alignFrameMenuBar.add(hmmerMenu);
+    if (!Platform.isJS())
+    {
+      alignFrameMenuBar.add(webService);
+      alignFrameMenuBar.add(hmmerMenu);
+    }
   
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1836,7 +1855,10 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    fileMenu.add(loadVcf);
+    if (!Platform.isJS())
+    {
+      fileMenu.add(loadVcf);
+    }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
   
@@ -1936,17 +1958,25 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    calculateMenu.addSeparator();
-    calculateMenu.add(runGroovy);
-  
+    if (!Platform.isJS())
+    {
+      calculateMenu.addSeparator();
+      calculateMenu.add(runGroovy);
+    }
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    exportImageMenu.add(htmlMenuItem);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(htmlMenuItem);
+    }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
-    exportImageMenu.add(createBioJS);
-    exportImageMenu.add(createSVG);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(createBioJS);
+      exportImageMenu.add(createSVG);
+    }
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -2448,7 +2478,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(String formatName)
   {
   }
 
@@ -2622,15 +2652,15 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void copy_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed()
   {
   }
 
-  protected void cut_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed()
   {
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed()
   {
   }
 
@@ -2745,7 +2775,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed()
   {
   }
 
@@ -2773,7 +2803,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
 
   }