X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1cbe15c5dc274a5b6a56e0e49f50c2448d7311c2;hb=cb8ec179c020265666678572815ab056a024da22;hp=bb69a54dba0d2ed06b16a5c5dfc07176f43b68c2;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bb69a54..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();
@@ -110,14 +110,21 @@ 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();
   //protected JTabbedPane tabbedPane = new JTabbedPane();
   public JMenuItem featureSettings = new JMenuItem();
   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()
   {
 
@@ -707,12 +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");
@@ -830,7 +837,7 @@ public class GAlignFrame
       }
     });
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Assocated Tree");
+    LoadtreeMenuItem.setText("Load Associated Tree");
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -922,7 +929,6 @@ public class GAlignFrame
             tabSelected();
           }
         });*/
-    featureSettings.setEnabled(false);
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -931,7 +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)
@@ -939,6 +945,48 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);
       }
     });
+    smoothFont.setText("Smooth Fonts");
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        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);
@@ -947,6 +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);
@@ -954,6 +1003,7 @@ public class GAlignFrame
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -977,6 +1027,7 @@ public class GAlignFrame
     editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
+    viewMenu.add(smoothFont);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
     viewMenu.add(seqLimits);
@@ -989,7 +1040,8 @@ 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);
@@ -1013,6 +1065,7 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1020,6 +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);
@@ -1218,7 +1272,7 @@ public class GAlignFrame
   {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -1330,17 +1384,37 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void featureSettings_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }