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[jalview.git] / src / jalview / jbgui / GAlignFrame.java
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 7fb94f9..b5a0d30 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -88,7 +88,6 @@ public class GAlignFrame
   JMenuItem printMenuItem = new JMenuItem();\r
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem findMenuItem = new JMenuItem();\r
-  JMenu searchMenu = new JMenu();\r
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
@@ -96,7 +95,7 @@ public class GAlignFrame
   JMenuItem delete = new JMenuItem();\r
   JMenuItem copy = new JMenuItem();\r
   JMenuItem cut = new JMenuItem();\r
-  JMenu jMenu1 = new JMenu();\r
+  JMenu pasteMenu = new JMenu();\r
   JMenuItem pasteNew = new JMenuItem();\r
   JMenuItem pasteThis = new JMenuItem();\r
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
@@ -120,7 +119,6 @@ public class GAlignFrame
   protected JMenuItem showTranslation = new JMenuItem();\r
   public JMenuItem featureSettings = new JMenuItem();\r
   JMenuItem fetchSequence = new JMenuItem();\r
-  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
   JMenuItem annotationColour = new JMenuItem();\r
   JMenuItem associatedData = new JMenuItem();\r
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
@@ -142,8 +140,14 @@ public class GAlignFrame
   JMenuItem invertColSel = new JMenuItem();\r
   protected JTabbedPane tabbedPane = new JTabbedPane();\r
   JMenuItem save = new JMenuItem();\r
-  JMenuItem jMenuItem1 = new JMenuItem();\r
-  JMenuItem reload = new JMenuItem();\r
+  protected JMenuItem reload = new JMenuItem();\r
+  JMenuItem newView = new JMenuItem();\r
+  JMenuItem textColour = new JMenuItem();\r
+  JMenu formatMenu = new JMenu();\r
+  JMenu selectMenu = new JMenu();\r
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
+  protected JMenuItem gatherViews = new JMenuItem();\r
+  protected JMenuItem expandViews = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -171,6 +175,18 @@ public class GAlignFrame
     {\r
     }\r
 \r
+    if (!System.getProperty("os.name").startsWith("Mac"))\r
+    {\r
+      closeMenuItem.setMnemonic('C');\r
+      outputTextboxMenu.setMnemonic('T');\r
+      undoMenuItem.setMnemonic('Z');\r
+      redoMenuItem.setMnemonic('0');\r
+      copy.setMnemonic('C');\r
+      cut.setMnemonic('U');\r
+      pasteMenu.setMnemonic('P');\r
+      reload.setMnemonic('R');\r
+    }\r
+\r
 \r
     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
     {\r
@@ -319,9 +335,10 @@ public class GAlignFrame
       throws Exception\r
   {\r
     fileMenu.setText("File");\r
-    saveAs.setText("Save As ...");\r
+    saveAs.setText("Save As...");\r
     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
-        KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));\r
+        KeyEvent.VK_S,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     saveAs.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -329,7 +346,6 @@ public class GAlignFrame
         saveAs_actionPerformed(e);\r
       }\r
     });\r
-    closeMenuItem.setMnemonic('C');\r
     closeMenuItem.setText("Close");\r
     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
         event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
@@ -337,7 +353,7 @@ public class GAlignFrame
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        closeMenuItem_actionPerformed(e);\r
+        closeMenuItem_actionPerformed(false);\r
       }\r
     });\r
     editMenu.setText("Edit");\r
@@ -345,7 +361,7 @@ public class GAlignFrame
     colourMenu.setText("Colour");\r
     calculateMenu.setText("Calculate");\r
     webService.setText("Web Service");\r
-    selectAllSequenceMenuItem.setText("Select all");\r
+    selectAllSequenceMenuItem.setText("Select All");\r
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_A,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
@@ -372,7 +388,7 @@ public class GAlignFrame
     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_I,\r
-        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -414,7 +430,8 @@ public class GAlignFrame
     });\r
     removeAllGapsMenuItem.setText("Remove All Gaps");\r
     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
-        java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        java.awt.event.KeyEvent.VK_E,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -516,7 +533,6 @@ public class GAlignFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
     statusBar.setText("Status bar");\r
-    outputTextboxMenu.setMnemonic('T');\r
     outputTextboxMenu.setText("Output to Textbox");\r
     clustalColour.setText("Clustalx");\r
 \r
@@ -660,7 +676,6 @@ public class GAlignFrame
       }\r
     });\r
     undoMenuItem.setEnabled(false);\r
-    undoMenuItem.setMnemonic('Z');\r
     undoMenuItem.setText("Undo");\r
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_Z,\r
@@ -673,7 +688,6 @@ public class GAlignFrame
       }\r
     });\r
     redoMenuItem.setEnabled(false);\r
-    redoMenuItem.setMnemonic('0');\r
     redoMenuItem.setText("Redo");\r
     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
@@ -738,8 +752,6 @@ public class GAlignFrame
         findMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    searchMenu.setText("Search");\r
-\r
     abovePIDThreshold.setText("Above Identity Threshold");\r
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -778,7 +790,6 @@ public class GAlignFrame
     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_C,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
-    copy.setMnemonic(KeyEvent.VK_C);\r
 \r
     copy.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -791,7 +802,6 @@ public class GAlignFrame
     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_X,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
-    cut.setMnemonic(KeyEvent.VK_X);\r
     cut.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -809,12 +819,11 @@ public class GAlignFrame
         delete_actionPerformed(e);\r
       }\r
     });\r
-    jMenu1.setMnemonic('V');\r
-    jMenu1.setText("Paste");\r
+    pasteMenu.setText("Paste");\r
     pasteNew.setText("To New Alignment");\r
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_V,\r
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -823,6 +832,9 @@ public class GAlignFrame
       }\r
     });\r
     pasteThis.setText("Add To This Alignment");\r
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_V,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -929,6 +941,21 @@ public class GAlignFrame
     });\r
     sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
+    sort.addMenuListener(new MenuListener()\r
+    {\r
+      public void menuSelected(MenuEvent e)\r
+      {\r
+        buildTreeMenu();\r
+      }\r
+\r
+      public void menuDeselected(MenuEvent e)\r
+      {\r
+      }\r
+\r
+      public void menuCanceled(MenuEvent e)\r
+      {\r
+      }\r
+    });\r
     calculate.setText("Calculate Tree");\r
 \r
     jMenu2.setText("Export Image");\r
@@ -976,14 +1003,6 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);\r
       }\r
     });\r
-    smoothFont.setText("Smooth Fonts");\r
-    smoothFont.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        smoothFont_actionPerformed(e);\r
-      }\r
-    });\r
 \r
     annotationColour.setText("By Annotation...");\r
     annotationColour.addActionListener(new ActionListener()\r
@@ -1086,7 +1105,7 @@ public class GAlignFrame
         hideSelColumns_actionPerformed(e);\r
       }\r
     });\r
-    hiddenMarkers.setText("Hidden Markers");\r
+    hiddenMarkers.setText("Show Hidden Markers");\r
     hiddenMarkers.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -1096,7 +1115,10 @@ public class GAlignFrame
     });\r
     invertColSel.setText("Invert Column Selection");\r
     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
-        event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        event.KeyEvent.VK_I,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
+        |java.awt.event.KeyEvent.ALT_MASK,\r
+        false));\r
     invertColSel.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -1137,10 +1159,8 @@ public class GAlignFrame
         save_actionPerformed(e);\r
       }\r
     });\r
-    reload.setMnemonic('R');\r
+    reload.setEnabled(false);\r
     reload.setText("Reload");\r
-   // reload.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
-  //      KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     reload.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -1148,11 +1168,64 @@ public class GAlignFrame
         reload_actionPerformed(e);\r
       }\r
     });\r
+    newView.setText("New View");\r
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+    newView.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        newView_actionPerformed(e);\r
+      }\r
+    });\r
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
+                              +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
+    textColour.setText("Text Colour");\r
+    textColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        textColour_actionPerformed(e);\r
+      }\r
+    });\r
+    formatMenu.setText("Format");\r
+    selectMenu.setText("Select");\r
+    idRightAlign.setText("Right Align Sequence Id");\r
+    idRightAlign.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        idRightAlign_actionPerformed(e);\r
+      }\r
+    });\r
+    gatherViews.setEnabled(false);\r
+    gatherViews.setText("Gather Views");\r
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_G, 0, false));\r
+    gatherViews.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        gatherViews_actionPerformed(e);\r
+      }\r
+    });\r
+    expandViews.setEnabled(false);\r
+    expandViews.setText("Expand Views");\r
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_X, 0, false));\r
+    expandViews.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        expandViews_actionPerformed(e);\r
+      }\r
+    });\r
 \r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
-    alignFrameMenuBar.add(searchMenu);\r
+    alignFrameMenuBar.add(selectMenu);\r
     alignFrameMenuBar.add(viewMenu);\r
+    alignFrameMenuBar.add(formatMenu);\r
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
@@ -1177,15 +1250,9 @@ public class GAlignFrame
     editMenu.add(redoMenuItem);\r
     editMenu.add(cut);\r
     editMenu.add(copy);\r
-    editMenu.add(jMenu1);\r
+    editMenu.add(pasteMenu);\r
     editMenu.add(delete);\r
     editMenu.addSeparator();\r
-    editMenu.add(selectAllSequenceMenuItem);\r
-    editMenu.add(deselectAllSequenceMenuItem);\r
-    editMenu.add(invertSequenceMenuItem);\r
-    editMenu.add(invertColSel);\r
-    editMenu.add(deleteGroups);\r
-    editMenu.addSeparator();\r
     editMenu.add(remove2LeftMenuItem);\r
     editMenu.add(remove2RightMenuItem);\r
     editMenu.add(removeGappedColumnMenuItem);\r
@@ -1193,23 +1260,13 @@ public class GAlignFrame
     editMenu.add(removeRedundancyMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(padGapsMenuitem);\r
-    searchMenu.add(findMenuItem);\r
-    viewMenu.add(font);\r
-    viewMenu.add(smoothFont);\r
+    viewMenu.add(newView);\r
+    viewMenu.add(expandViews);\r
+    viewMenu.add(gatherViews);\r
     viewMenu.addSeparator();\r
     viewMenu.add(jMenu3);\r
     viewMenu.add(hideMenu);\r
-    viewMenu.add(hiddenMarkers);\r
     viewMenu.addSeparator();\r
-    viewMenu.add(wrapMenuItem);\r
-    viewMenu.add(seqLimits);\r
-    viewMenu.add(scaleAbove);\r
-    viewMenu.add(scaleLeft);\r
-    viewMenu.add(scaleRight);\r
-    viewMenu.add(viewBoxesMenuItem);\r
-    viewMenu.add(viewTextMenuItem);\r
-    viewMenu.add(colourTextMenuItem);\r
-    viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
     viewMenu.addSeparator();\r
     viewMenu.add(showSeqFeatures);\r
@@ -1217,6 +1274,7 @@ public class GAlignFrame
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
+    colourMenu.add(textColour);\r
     colourMenu.addSeparator();\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
@@ -1246,11 +1304,12 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);\r
     calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
-    webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
-    jMenu1.add(pasteThis);\r
+    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);\r
+    pasteMenu.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
+    sort.add(sortByTreeMenu);\r
     calculate.add(averageDistanceTreeMenuItem);\r
     calculate.add(neighbourTreeMenuItem);\r
     calculate.add(avDistanceTreeBlosumMenuItem);\r
@@ -1268,6 +1327,26 @@ public class GAlignFrame
     jMenu3.add(showAllSeqs);\r
     hideMenu.add(hideSelColumns);\r
     hideMenu.add(hideSelSequences);\r
+    formatMenu.add(font);\r
+    formatMenu.addSeparator();\r
+    formatMenu.add(wrapMenuItem);\r
+    formatMenu.add(scaleAbove);\r
+    formatMenu.add(scaleLeft);\r
+    formatMenu.add(scaleRight);\r
+    formatMenu.add(seqLimits);\r
+    formatMenu.add(idRightAlign);\r
+    formatMenu.add(hiddenMarkers);\r
+    formatMenu.add(viewBoxesMenuItem);\r
+    formatMenu.add(viewTextMenuItem);\r
+    formatMenu.add(colourTextMenuItem);\r
+    formatMenu.add(renderGapsMenuItem);\r
+    selectMenu.add(findMenuItem);\r
+    selectMenu.addSeparator();\r
+    selectMenu.add(selectAllSequenceMenuItem);\r
+    selectMenu.add(deselectAllSequenceMenuItem);\r
+    selectMenu.add(invertSequenceMenuItem);\r
+    selectMenu.add(invertColSel);\r
+    selectMenu.add(deleteGroups);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
@@ -1303,7 +1382,7 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void closeMenuItem_actionPerformed(ActionEvent e)\r
+  protected void closeMenuItem_actionPerformed(boolean b)\r
   {\r
   }\r
 \r
@@ -1687,4 +1766,34 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void newView_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void textColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void idRightAlign_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void expandViews_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void gatherViews_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void buildTreeMenu()\r
+  {\r
+\r
+  }\r
 }\r