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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 be0d082..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
@@ -141,9 +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
   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
@@ -384,7 +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
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|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
@@ -748,8 +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
@@ -939,6 +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
@@ -1088,7 +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
@@ -1098,7 +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
@@ -1160,11 +1180,52 @@ public class GAlignFrame
     });\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
@@ -1192,12 +1253,6 @@ public class GAlignFrame
     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
@@ -1205,24 +1260,13 @@ public class GAlignFrame
     editMenu.add(removeRedundancyMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(padGapsMenuitem);\r
-    searchMenu.add(findMenuItem);\r
     viewMenu.add(newView);\r
-    viewMenu.addSeparator();\r
-    viewMenu.add(font);\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
@@ -1230,6 +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
@@ -1264,6 +1309,7 @@ public class GAlignFrame
     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
@@ -1281,6 +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
@@ -1705,4 +1771,29 @@ public class GAlignFrame
   {\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