Check if featuresDisplayed is null

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 422f9a7..eafbf12 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;\r
 \r
 import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
 \r
 public class GAlignFrame\r
     extends JInternalFrame\r
@@ -114,7 +115,6 @@ public class GAlignFrame
   protected ButtonGroup colours = new ButtonGroup();\r
   JMenuItem vamsasStore = new JMenuItem();\r
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
-  //protected JTabbedPane tabbedPane = new JTabbedPane();\r
   public JMenuItem featureSettings = new JMenuItem();\r
   JMenuItem fetchSequence = new JMenuItem();\r
   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
@@ -125,6 +125,15 @@ public class GAlignFrame
 \r
   JMenuItem associatedData = new JMenuItem();\r
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
+  JMenu addSequenceMenu = new JMenu();\r
+  JMenuItem addFromFile = new JMenuItem();\r
+  JMenuItem addFromText = new JMenuItem();\r
+  JMenuItem addFromURL = new JMenuItem();\r
+  JMenuItem exportAnnotations = new JMenuItem();\r
+  JMenuItem exportFeatures = new JMenuItem();\r
+  JMenuItem dbRefs = new JMenuItem();\r
+  protected JPanel statusPanel = new JPanel();\r
+  GridLayout gridLayout1 = new GridLayout();\r
   public GAlignFrame()\r
   {\r
 \r
@@ -896,6 +905,7 @@ public class GAlignFrame
 \r
     jMenu2.setText("Export");\r
     padGapsMenuitem.setText("Pad Gaps");\r
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -987,6 +997,56 @@ public class GAlignFrame
         autoCalculate_actionPerformed(e);\r
       }\r
     });\r
+    addSequenceMenu.setText("Add Sequences");\r
+    addFromFile.setText("From File");\r
+    addFromFile.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromFile_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromText.setText("From Textbox");\r
+    addFromText.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromText_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromURL.setText("From URL");\r
+    addFromURL.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromURL_actionPerformed(e);\r
+      }\r
+    });\r
+    exportFeatures.setText("Export Features...");\r
+    exportFeatures.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportFeatures_actionPerformed(e);\r
+      }\r
+    });\r
+    exportAnnotations.setText("Export Annotations...");\r
+    exportAnnotations.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportAnnotations_actionPerformed(e);\r
+      }\r
+    });\r
+    dbRefs.setText("Fetch DB Refs");\r
+    dbRefs.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        dbRefs_actionPerformed(e);\r
+      }\r
+    });\r
+    statusPanel.setLayout(gridLayout1);\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -994,6 +1054,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
+    fileMenu.add(addSequenceMenu);\r
     fileMenu.add(fetchSequence);\r
     fileMenu.addSeparator();\r
     fileMenu.add(vamsasStore);\r
@@ -1002,6 +1063,8 @@ public class GAlignFrame
     fileMenu.add(outputTextboxMenu);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
+    fileMenu.add(exportFeatures);\r
+    fileMenu.add(exportAnnotations);\r
     fileMenu.add(LoadtreeMenuItem);\r
     fileMenu.add(associatedData);\r
     fileMenu.addSeparator();\r
@@ -1040,6 +1103,7 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
     viewMenu.addSeparator();\r
+    viewMenu.add(dbRefs);\r
     viewMenu.add(fetchSeqFeatures);\r
     viewMenu.add(showSeqFeatures);\r
     viewMenu.add(featureSettings);\r
@@ -1075,10 +1139,7 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);\r
     calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
-    webService.add(webServiceNoServices);\r
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
-    jMenu1.add(pasteNew);\r
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
@@ -1090,12 +1151,42 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);\r
     jMenu2.add(epsFile);\r
     jMenu2.add(createPNG);\r
+    addSequenceMenu.add(addFromFile);\r
+    addSequenceMenu.add(addFromText);\r
+    addSequenceMenu.add(addFromURL);\r
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+    statusPanel.add(statusBar, null);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
+  public void addFromFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromText_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromURL_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportFeatures_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportAnnotations_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
   {\r
   }\r
@@ -1418,4 +1509,9 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void dbRefs_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r