X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=8aa5159c513a23e422650bc3ed8b8e9cb15e2428;hb=fb4c54617dd9c5ac605853551478596902f34541;hp=eafbf12f097e6a0a2615081a8026170140b75f17;hpb=4d85e896a94bc9fe9a8476473a5f2358979a0627;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index eafbf12..8aa5159 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -114,15 +114,11 @@ public class GAlignFrame
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
-  protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
+  protected JMenuItem showTranslation = new JMenuItem();
   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();
   JMenu addSequenceMenu = new JMenu();
@@ -131,9 +127,16 @@ public class GAlignFrame
   JMenuItem addFromURL = new JMenuItem();
   JMenuItem exportAnnotations = new JMenuItem();
   JMenuItem exportFeatures = new JMenuItem();
-  JMenuItem dbRefs = new JMenuItem();
   protected JPanel statusPanel = new JPanel();
   GridLayout gridLayout1 = new GridLayout();
+  JMenu jMenu3 = new JMenu();
+  JMenuItem showAllSeqs = new JMenuItem();
+  JMenuItem showAllColumns = new JMenuItem();
+  JMenu jMenu4 = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+
   public GAlignFrame()
   {
 
@@ -144,7 +147,7 @@ public class GAlignFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
       {
         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
                              elementAt(
@@ -972,14 +975,6 @@ 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()
     {
@@ -1038,15 +1033,51 @@ public class GAlignFrame
         exportAnnotations_actionPerformed(e);
       }
     });
-    dbRefs.setText("Fetch DB Refs");
-    dbRefs.addActionListener(new ActionListener()
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        dbRefs_actionPerformed(e);
+        showAllSeqs_actionPerformed(e);
       }
     });
-    statusPanel.setLayout(gridLayout1);
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    jMenu4.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Hidden Markers");
+    hiddenMarkers.setState(true);
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -1092,6 +1123,10 @@ public class GAlignFrame
     viewMenu.add(font);
     viewMenu.add(smoothFont);
     viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(jMenu4);
+    viewMenu.add(hiddenMarkers);
+    viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
     viewMenu.add(seqLimits);
     viewMenu.add(scaleAbove);
@@ -1103,8 +1138,6 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(dbRefs);
-    viewMenu.add(fetchSeqFeatures);
     viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
@@ -1156,6 +1189,10 @@ public class GAlignFrame
     addSequenceMenu.add(addFromURL);
     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
+    jMenu3.add(showAllColumns);
+    jMenu3.add(showAllSeqs);
+    jMenu4.add(hideSelColumns);
+    jMenu4.add(hideSelSequences);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
@@ -1495,22 +1532,53 @@ public class GAlignFrame
 
   }
 
-  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void associatedData_actionPerformed(ActionEvent e)
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void autoCalculate_actionPerformed(ActionEvent e)
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void findPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void enterPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void dbRefs_actionPerformed(ActionEvent e)
+  public void pdbFile_actionPerformed(ActionEvent e)
   {
 
   }