X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=3cda5adfbee3d3b4dbce6bcef26da0aa38b4132f;hb=381686a3389cb87bf0d4b5d075a439444e6d4263;hp=4c5cdfe7c4132aae4d9fb98fe64d8243da0f385e;hpb=de8ca844b40be7b588074f824eb0b6e067e39aad;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4c5cdfe..3cda5ad 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -99,20 +99,25 @@ 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();
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-  JMenuItem modifyPID = new JMenuItem();
-  JMenuItem modifyConservation = new JMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
+  protected JMenuItem modifyConservation = new JMenuItem();
   protected JMenu sortByTreeMenu = new JMenu();
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   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();
+  protected JMenuItem featureSettings = new JMenuItem();
+  public JCheckBoxMenuItem seqDBRef = new JCheckBoxMenuItem();
 
   public GAlignFrame()
   {
@@ -822,13 +827,14 @@ 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");
@@ -906,6 +912,49 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);
       }
     });
+    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);
+      }
+    });
+    seqDBRef.setState( jalview.bin.Cache.getDefault("SHOW_DBPREFIX",true));
+    seqDBRef.setText("Show Full Sequence Id");
+    seqDBRef.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        seqDBRef_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -913,6 +962,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
@@ -944,7 +994,8 @@ public class GAlignFrame
     viewMenu.add(font);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
-    viewMenu.add(fullSeqId);
+    viewMenu.add(seqDBRef);
+    viewMenu.add(seqLimits);
     viewMenu.add(scaleAbove);
     viewMenu.add(scaleLeft);
     viewMenu.add(scaleRight);
@@ -953,7 +1004,9 @@ 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 +1034,12 @@ 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);
@@ -1226,10 +1282,16 @@ 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)
   {
   }
@@ -1285,4 +1347,30 @@ public class GAlignFrame
   protected void ClustalRealign_actionPerformed(ActionEvent e)
   {
   }
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showTranslation_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void tabSelected()
+  {
+
+  }
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+
+  }
+
 }