X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=eafbf12f097e6a0a2615081a8026170140b75f17;hb=a6708aa208f1380c980dc51282b5380d9eda5470;hp=422f9a795a2850fdef1a6169fab21f788a2a1f42;hpb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 422f9a7..eafbf12 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
@@ -114,7 +115,6 @@ public class GAlignFrame
   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();
   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
@@ -125,6 +125,15 @@ public class GAlignFrame
 
   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();
+  JMenuItem dbRefs = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
   public GAlignFrame()
   {
 
@@ -896,6 +905,7 @@ 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)
@@ -987,6 +997,56 @@ 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);
+      }
+    });
+    dbRefs.setText("Fetch DB Refs");
+    dbRefs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        dbRefs_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -994,6 +1054,7 @@ 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 +1063,8 @@ 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();
@@ -1040,6 +1103,7 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
+    viewMenu.add(dbRefs);
     viewMenu.add(fetchSeqFeatures);
     viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
@@ -1075,10 +1139,7 @@ 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 +1151,42 @@ 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);
   }
 
   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)
   {
   }
@@ -1418,4 +1509,9 @@ public class GAlignFrame
   {
 
   }
+
+  public void dbRefs_actionPerformed(ActionEvent e)
+  {
+
+  }
 }