X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1cbe15c5dc274a5b6a56e0e49f50c2448d7311c2;hb=cb8ec179c020265666678572815ab056a024da22;hp=6f2119983c28cf6876d77ef5dabdd75ef03e8253;hpb=ee2c90ef919da121adf50b234730a9a0f484d4c5;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6f21199..1cbe15c 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -86,7 +86,7 @@ public class GAlignFrame
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -110,7 +110,7 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenu jMenu2 = new JMenu();
-  JMenuItem padGapsMenuitem = new JMenuItem();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
@@ -119,7 +119,12 @@ public class GAlignFrame
   JMenuItem fetchSequence = new JMenuItem();
   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
   JMenuItem annotationColour = new JMenuItem();
+  JMenuItem fetchSeqFeatures = new JMenuItem();
 
+
+
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
 
@@ -709,12 +714,12 @@ public class GAlignFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    sequenceFeatures.setText("Sequence Features");
-    sequenceFeatures.addActionListener(new ActionListener()
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        sequenceFeatures_actionPerformed(actionEvent);
+        showSeqFeatures_actionPerformed(actionEvent);
       }
     });
     nucleotideColour.setText("Nucleotide");
@@ -924,7 +929,6 @@ public class GAlignFrame
             tabSelected();
           }
         });*/
-    featureSettings.setEnabled(false);
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -933,7 +937,7 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText("Fetch Sequence...");
+    fetchSequence.setText("Fetch Sequence(s)...");
     fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -958,6 +962,31 @@ public class GAlignFrame
         annotationColour_actionPerformed(e);
       }
     });
+    fetchSeqFeatures.setText("Fetch Sequence Features");
+    fetchSeqFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSeqFeatures_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState(true);
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -966,6 +995,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
     fileMenu.add(fetchSequence);
+    fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(jMenu2);
@@ -973,6 +1003,7 @@ public class GAlignFrame
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -1009,13 +1040,13 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(sequenceFeatures);
+    viewMenu.add(fetchSeqFeatures);
+    viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
     colourMenu.addSeparator();
-    colourMenu.add(annotationColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -1034,7 +1065,7 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    colourMenu.addSeparator();
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1042,6 +1073,7 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
     webService.add(webServiceNoServices);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
@@ -1240,7 +1272,7 @@ public class GAlignFrame
   {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -1352,11 +1384,6 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
-  {
-
-  }
-
   public void featureSettings_actionPerformed(ActionEvent e)
   {
 
@@ -1376,4 +1403,19 @@ public class GAlignFrame
   {
 
   }
+
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
 }