X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=8aa5159c513a23e422650bc3ed8b8e9cb15e2428;hb=fb4c54617dd9c5ac605853551478596902f34541;hp=f0e5e67163a615c31ffd64b536a771d1f940318a;hpb=a9ef2d2b865889e9f75faf8e14597c8f508d0ce1;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index f0e5e67..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
@@ -113,18 +114,29 @@ public class GAlignFrame
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
-  protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
-  //protected JTabbedPane tabbedPane = new JTabbedPane();
+  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();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  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()
   {
 
@@ -135,7 +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(
@@ -896,6 +908,7 @@ public class GAlignFrame
 
     jMenu2.setText("Export");
     padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -962,14 +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()
     {
@@ -979,7 +984,7 @@ public class GAlignFrame
       }
     });
     autoCalculate.setText("Autocalculate Consensus");
-    autoCalculate.setState(true);
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -987,6 +992,92 @@ public class GAlignFrame
         autoCalculate_actionPerformed(e);
       }
     });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        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);
@@ -994,6 +1085,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    fileMenu.add(addSequenceMenu);
     fileMenu.add(fetchSequence);
     fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
@@ -1002,6 +1094,8 @@ public class GAlignFrame
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
     fileMenu.add(associatedData);
     fileMenu.addSeparator();
@@ -1029,6 +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);
@@ -1040,7 +1138,6 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(fetchSeqFeatures);
     viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
@@ -1061,11 +1158,11 @@ public class GAlignFrame
     colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
-    colourMenu.add(annotationColour);
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1075,10 +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);
-  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    jMenu1.add(pasteNew);
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1090,12 +1184,46 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    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)
   {
   }
 
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -1404,17 +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)
   {
 
   }