A Flauss reccommends

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 53c0bf6..7370995 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -14,6 +14,8 @@ import java.awt.*;
 \r
 import jalview.gui.Preferences;\r
 import jalview.schemes.ColourSchemeProperty;\r
+import javax.swing.event.AncestorListener;\r
+import javax.swing.event.AncestorEvent;\r
 \r
 public class GAlignFrame extends JInternalFrame\r
 {\r
@@ -45,7 +47,7 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   public JLabel statusBar = new JLabel();\r
-  protected JMenu saveAlignmentMenu = new JMenu();\r
+  protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
   protected JMenu outputTextboxMenu = new JMenu();\r
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
@@ -96,10 +98,10 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem modifyPID = new JMenuItem();\r
   JMenuItem modifyConservation = new JMenuItem();\r
   protected JMenu sortByTreeMenu = new JMenu();\r
-  JMenu jMenu2 = new JMenu();\r
   JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
   JMenuItem msaAlignMenuItem = new JMenuItem();\r
+  JMenu jMenu2 = new JMenu();\r
   public GAlignFrame()\r
   {\r
     ButtonGroup colours = new ButtonGroup();\r
@@ -148,16 +150,6 @@ public class GAlignFrame extends JInternalFrame
       // dynamically fill save as menu with available formats\r
       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
         item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
-        saveAlignmentMenu.add( item );\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            saveAs_actionPerformed(e);\r
-          }\r
-        });\r
-\r
-        item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
         item.addActionListener(new java.awt.event.ActionListener()\r
         {\r
           public void actionPerformed(ActionEvent e)\r
@@ -181,7 +173,14 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.setMnemonic('F');\r
     fileMenu.setText("File");\r
     saveAlignmentMenu.setMnemonic('L');\r
-    saveAlignmentMenu.setText("Save");\r
+    saveAlignmentMenu.setText("Save As");\r
+    saveAlignmentMenu.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        saveAlignmentMenu_actionPerformed(e);\r
+      }\r
+    });\r
     closeMenuItem.setMnemonic('C');\r
     closeMenuItem.setText("Close");\r
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -275,7 +274,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortPairwiseMenuItem.setText("Pairwise Identity");\r
+    sortPairwiseMenuItem.setText("By Pairwise Identity");\r
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -283,7 +282,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortIDMenuItem.setText("ID");\r
+    sortIDMenuItem.setText("By ID");\r
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -291,7 +290,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    sortGroupMenuItem.setText("Group");\r
+    sortGroupMenuItem.setText("By Group");\r
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -349,6 +348,21 @@ public class GAlignFrame extends JInternalFrame
     });\r
     this.getContentPane().setLayout(borderLayout1);\r
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+    alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
+    {\r
+      public void ancestorAdded(AncestorEvent event)\r
+      {\r
+        alignFrameMenuBar_ancestorAdded(event);\r
+      }\r
+\r
+      public void ancestorRemoved(AncestorEvent event)\r
+      {\r
+      }\r
+\r
+      public void ancestorMoved(AncestorEvent event)\r
+      {\r
+      }\r
+    });\r
     statusBar.setBackground(Color.white);\r
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
@@ -569,7 +583,7 @@ public class GAlignFrame extends JInternalFrame
     });\r
     searchMenu.setText("Search");\r
 \r
-    abovePIDThreshold.setText("Above Identity threshold");\r
+    abovePIDThreshold.setText("Above Identity Threshold");\r
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
       public void actionPerformed(ActionEvent e) {\r
         abovePIDThreshold_actionPerformed(e);\r
@@ -666,7 +680,7 @@ public class GAlignFrame extends JInternalFrame
         createPNG_actionPerformed(e);\r
       }\r
     });\r
-    createPNG.setActionCommand("Save as PNG Image");\r
+    createPNG.setActionCommand("Save As PNG Image");\r
     createPNG.setText("PNG");\r
     font.setText("Font...");\r
     font.addActionListener(new java.awt.event.ActionListener()\r
@@ -753,8 +767,7 @@ public class GAlignFrame extends JInternalFrame
         modifyConservation_actionPerformed(e);\r
       }\r
     });\r
-    sortByTreeMenu.setText("Tree Order");\r
-    jMenu2.setText("Save as");\r
+    sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
     calculate.setText("Calculate Tree");\r
     msaAlignMenuItem.setText("Muscle Alignment...");\r
@@ -763,6 +776,7 @@ public class GAlignFrame extends JInternalFrame
         msaAlignMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    jMenu2.setText("Export");\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -844,22 +858,17 @@ public class GAlignFrame extends JInternalFrame
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
-    jMenu2.add(htmlMenuItem);\r
-    jMenu2.add(epsFile);\r
-    jMenu2.add(createPNG);\r
     sort.add(sortIDMenuItem);\r
-    sort.add(sortGroupMenuItem);\r
     sort.add(sortByTreeMenu);\r
+    sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
     calculate.add(averageDistanceTreeMenuItem);\r
     calculate.add(neighbourTreeMenuItem);\r
     calculate.add(avDistanceTreeBlosumMenuItem);\r
     calculate.add(njTreeBlosumMenuItem);\r
-  }\r
-\r
-  protected void saveAs_actionPerformed(ActionEvent e)\r
-  {\r
-\r
+    jMenu2.add(htmlMenuItem);\r
+    jMenu2.add(epsFile);\r
+    jMenu2.add(createPNG);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
@@ -1218,4 +1227,14 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  public void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+  {\r
+\r
+  }\r
+\r
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
 }\r