X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=8aa5159c513a23e422650bc3ed8b8e9cb15e2428;hb=fb4c54617dd9c5ac605853551478596902f34541;hp=5a404eb255c71b6fc45d5e8a96f0eeb4768d6fd7;hpb=3e52a9c5f970c4ea43a648296893a2aa58ebd137;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a404eb..8aa5159 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;
 
 import jalview.schemes.*;
+import java.awt.BorderLayout;
 
 public class GAlignFrame
     extends JInternalFrame
@@ -113,15 +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();
@@ -130,6 +127,16 @@ public class GAlignFrame
   JMenuItem addFromURL = new JMenuItem();
   JMenuItem exportAnnotations = new JMenuItem();
   JMenuItem exportFeatures = 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()
   {
 
@@ -140,7 +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(
@@ -968,14 +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()
     {
@@ -1034,6 +1033,51 @@ public class GAlignFrame
         exportAnnotations_actionPerformed(e);
       }
     });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    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);
@@ -1079,6 +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);
@@ -1090,7 +1138,6 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(fetchSeqFeatures);
     viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
@@ -1125,9 +1172,7 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);
     calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1142,6 +1187,12 @@ public class GAlignFrame
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     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)
@@ -1481,17 +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 pdbFile_actionPerformed(ActionEvent e)
   {
 
   }