X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=f4212970fb8677f0cd971a8d4e7e2af2b32d5e1c;hb=dd6a434e05eef33808d4cda23dd2c6f8d10a4630;hp=f4095d03ed42c22b2ca5d5c2710b495a3fc0154c;hpb=5ac7843efbf08ac78859912b6b3df19cb2b99279;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index f4095d0..f421297 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,7 +21,6 @@ package jalview.jbgui;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import javax.swing.event.*;
 
 import jalview.schemes.*;
 
@@ -99,7 +98,7 @@ public class GAlignFrame
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
   JMenuItem createPNG = new JMenuItem();
   protected JMenuItem font = new JMenuItem();
-  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
   JMenuItem epsFile = new JMenuItem();
   JMenuItem LoadtreeMenuItem = new JMenuItem();
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -113,6 +112,11 @@ public class GAlignFrame
   JMenu jMenu2 = new JMenu();
   JMenuItem padGapsMenuitem = new JMenuItem();
   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();
 
   public GAlignFrame()
   {
@@ -471,21 +475,6 @@ public class GAlignFrame
     });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    alignFrameMenuBar.addAncestorListener(new AncestorListener()
-    {
-      public void ancestorAdded(AncestorEvent event)
-      {
-        alignFrameMenuBar_ancestorAdded(event);
-      }
-
-      public void ancestorRemoved(AncestorEvent event)
-      {
-      }
-
-      public void ancestorMoved(AncestorEvent event)
-      {
-      }
-    });
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
@@ -822,13 +811,14 @@ public class GAlignFrame
         font_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show Full Sequence ID");
-    fullSeqId.setState(true);
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+    seqLimits.setText("Show Sequence Limits");
+    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+    seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fullSeqId_actionPerformed(e);
+        seqLimit_actionPerformed(e);
       }
     });
     epsFile.setText("EPS");
@@ -840,7 +830,7 @@ 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)
@@ -906,6 +896,49 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);
       }
     });
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStore_actionPerformed(e);
+      }
+    });
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showTranslation_actionPerformed(e);
+      }
+    });
+
+   /* tabbedPane.addChangeListener(new ChangeListener()
+        {
+          public void stateChanged(ChangeEvent ece)
+          {
+
+            tabSelected();
+          }
+        });*/
+    featureSettings.setEnabled(false);
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        featureSettings_actionPerformed(e);
+      }
+    });
+    fetchSequence.setText("Fetch Sequence...");
+    fetchSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSequence_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -913,6 +946,8 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    fileMenu.add(fetchSequence);
+    fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
@@ -944,7 +979,7 @@ public class GAlignFrame
     viewMenu.add(font);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
-    viewMenu.add(fullSeqId);
+    viewMenu.add(seqLimits);
     viewMenu.add(scaleAbove);
     viewMenu.add(scaleLeft);
     viewMenu.add(scaleRight);
@@ -953,7 +988,9 @@ public class GAlignFrame
     viewMenu.add(colourTextMenuItem);
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
+    viewMenu.addSeparator();
     viewMenu.add(sequenceFeatures);
+    viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
@@ -981,9 +1018,12 @@ public class GAlignFrame
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
+    calculateMenu.addSeparator();
+    calculateMenu.add(showTranslation);
     webServiceNoServices=new JMenuItem("<No Services>");
     webService.add(webServiceNoServices);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
     jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
@@ -1110,10 +1150,6 @@ public class GAlignFrame
   {
   }
 
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
   }
@@ -1226,10 +1262,16 @@ public class GAlignFrame
   {
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  protected void seqLimit_actionPerformed(ActionEvent e)
   {
   }
 
+  public void seqDBRef_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
   public void createEPS(java.io.File f)
   {
   }
@@ -1262,27 +1304,44 @@ public class GAlignFrame
   {
   }
 
-  protected void preferences_actionPerformed(ActionEvent e)
+
+
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  public void vamsasLoad_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  public void tabSelected()
+  {
+
+  }
+
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
+
   }
 }