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change order of menuitems
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4410880..a74c5e7 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -16,7 +16,6 @@ public class GAlignFrame extends JInternalFrame
 {\r
   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
   protected JMenu fileMenu = new JMenu();\r
-  protected JMenuItem saveAsPostscriptMenuItem = new JMenuItem();\r
   protected JMenuItem closeMenuItem = new JMenuItem();\r
   protected JMenu editMenu = new JMenu();\r
   protected JMenu fontMenu = new JMenu();\r
@@ -25,13 +24,9 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu calculateMenu = new JMenu();\r
   protected JMenu alignMenu = new JMenu();\r
   protected JMenuItem groupsMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
-  protected JMenuItem deleteSelectedMenuItem = new JMenuItem();\r
-  protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
-  protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
@@ -65,13 +60,11 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
-  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem htmlMenuItem = new JMenuItem();\r
@@ -80,10 +73,21 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem undoMenuItem = new JMenuItem();\r
   protected JMenuItem redoMenuItem = new JMenuItem();\r
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-  JMenuItem noColourmenuItem = new JMenuItem();\r
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
+  JMenuItem pdbTest = new JMenuItem();\r
+  JMenuItem printMenuItem = new JMenuItem();\r
+  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
+  JMenuItem findMenuItem = new JMenuItem();\r
+  JMenu searchMenu = new JMenu();\r
+  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+  protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();\r
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+  JMenuItem deleteGroups = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
+\r
+\r
     try\r
     {\r
       jbInit();\r
@@ -121,6 +125,7 @@ public class GAlignFrame extends JInternalFrame
     }\r
 \r
     ButtonGroup colours = new ButtonGroup();\r
+    colours.add(noColourmenuItem);\r
     colours.add(clustalColour);\r
     colours.add(zappoColour);\r
     colours.add(taylorColour);\r
@@ -129,10 +134,10 @@ public class GAlignFrame extends JInternalFrame
     colours.add(strandColour);\r
     colours.add(turnColour);\r
     colours.add(buriedColour);\r
-    colours.add(abovePIDColour);\r
     colours.add(userDefinedColour);\r
     colours.add(PIDColour);\r
     colours.add(BLOSUM62Colour);\r
+    colours.add(nucleotideColour);\r
   }\r
   private void jbInit() throws Exception\r
   {\r
@@ -140,15 +145,6 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.setText("File");\r
     saveAlignmentMenu.setMnemonic('L');\r
     saveAlignmentMenu.setText("Save alignment to local file");\r
-    saveAsPostscriptMenuItem.setMnemonic('P');\r
-    saveAsPostscriptMenuItem.setText("Save alignment as postscript");\r
-    saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        saveAsPostscriptMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     closeMenuItem.setMnemonic('C');\r
     closeMenuItem.setText("Close");\r
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -172,15 +168,7 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    groupEditingMenuItem.setText("Group editing mode");\r
-    groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupEditingMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    selectAllSequenceMenuItem.setText("Select all sequences");\r
+    selectAllSequenceMenuItem.setText("Select all");\r
     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -188,7 +176,7 @@ public class GAlignFrame extends JInternalFrame
         selectAllSequenceMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
+    deselectAllSequenceMenuItem.setText("Clear selection");\r
     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -204,30 +192,6 @@ public class GAlignFrame extends JInternalFrame
         invertSequenceMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    deleteSelectedMenuItem.setText("Delete selected sequences");\r
-    deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        deleteSelectedMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
-    moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        moveSelectedMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
-    copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        copySelectedMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -268,7 +232,7 @@ public class GAlignFrame extends JInternalFrame
         removeAllGapsMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    setGapCharMenuItem.setText("Set gap character to \"-\"");\r
+    setGapCharMenuItem.setText("Set gap character to \".\"");\r
     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -405,7 +369,6 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText("Status bar");\r
     outputTextboxMenu.setMnemonic('T');\r
     outputTextboxMenu.setText("Output alignment via textbox");\r
-    clustalColour.setEnabled(false);\r
     clustalColour.setSelected(false);\r
     clustalColour.setText("Clustalx colours");\r
     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
@@ -415,7 +378,6 @@ public class GAlignFrame extends JInternalFrame
         clustalColour_actionPerformed(e);\r
       }\r
     });\r
-    zappoColour.setSelected(true);\r
     zappoColour.setText("Zappo colour scheme");\r
     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -472,15 +434,6 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);\r
       }\r
     });\r
-    abovePIDColour.setEnabled(false);\r
-    abovePIDColour.setText("Above PID threshold only");\r
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        abovePIDColour_actionPerformed(e);\r
-      }\r
-    });\r
     userDefinedColour.setText("User defined colours");\r
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -489,8 +442,7 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);\r
       }\r
     });\r
-    PIDColour.setEnabled(false);\r
-    PIDColour.setText("By PID");\r
+    PIDColour.setText("Percentage Identity");\r
     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -498,7 +450,7 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);\r
       }\r
     });\r
-    BLOSUM62Colour.setText("By BLOSUM62 score");\r
+    BLOSUM62Colour.setText("BLOSUM62 score");\r
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -522,15 +474,6 @@ public class GAlignFrame extends JInternalFrame
         njTreeBlosumMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    conservationColourIncMenuItem.setEnabled(false);\r
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        conservationColourIncMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     consensusGraphMenuItem.setActionCommand("");\r
     consensusGraphMenuItem.setText("Consensus graph");\r
     consensusGraphMenuItem.setState(true);\r
@@ -602,6 +545,7 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     noColourmenuItem.setText("None");\r
+    noColourmenuItem.setSelected(true);\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -618,32 +562,95 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    pdbTest.setText("PDB Test Viewer");\r
+    pdbTest.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pdbTest_actionPerformed(e);\r
+      }\r
+    });\r
+    printMenuItem.setText("Print");\r
+    printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        printMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    renderGapsMenuItem.setText("Render gaps");\r
+    renderGapsMenuItem.setState(true);\r
+    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        renderGapsMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    findMenuItem.setText("Find");\r
+    findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        findMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    searchMenu.setText("Search");\r
+\r
+    abovePIDThreshold.setText("Above PID threshold");\r
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
+      public void actionPerformed(ActionEvent e) {\r
+        abovePIDThreshold_actionPerformed(e);\r
+      }\r
+    });\r
+    secondaryStructure.setSelected(true);\r
+    secondaryStructure.setText("Secondary Structure");\r
+    secondaryStructure.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent actionEvent)\r
+      {\r
+        secondaryStructure_actionPerformed(actionEvent);\r
+      }\r
+    });\r
+    nucleotideColour.setText("Nucleotide colours");\r
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        nucleotideColour_actionPerformed(e);\r
+      }\r
+    });\r
+    deleteGroups.setSelected(false);\r
+    deleteGroups.setText("Delete all groups");\r
+    deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        deleteGroups_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
+    alignFrameMenuBar.add(searchMenu);\r
     alignFrameMenuBar.add(fontMenu);\r
     alignFrameMenuBar.add(viewMenu);\r
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(alignMenu);\r
     fileMenu.add(saveAlignmentMenu);\r
-    fileMenu.add(saveAsPostscriptMenuItem);\r
     fileMenu.add(outputTextboxMenu);\r
     fileMenu.add(htmlMenuItem);\r
+    fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
     editMenu.add(undoMenuItem);\r
     editMenu.add(redoMenuItem);\r
     editMenu.addSeparator();\r
-    editMenu.add(groupsMenuItem);\r
-    editMenu.add(groupEditingMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(deselectAllSequenceMenuItem);\r
+    editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(invertSequenceMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(copySelectedMenuItem);\r
-    editMenu.add(moveSelectedMenuItem);\r
-    editMenu.add(deleteSelectedMenuItem);\r
+    editMenu.add(deleteGroups);\r
+    editMenu.add(groupsMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(deselectAllColumnsMenuItem);\r
     editMenu.add(remove2LeftMenuItem);\r
@@ -652,16 +659,18 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeGappedColumnMenuItem);\r
     editMenu.add(removeAllGapsMenuItem);\r
     editMenu.add(setGapCharMenuItem);\r
+    searchMenu.add(findMenuItem);\r
     fontMenu.add(fontNameMenuItem);\r
     fontMenu.add(fontSizeMenuItem);\r
     fontMenu.add(fontStyleMenuItem);\r
-    fontMenu.addSeparator();\r
-    fontMenu.add(colourTextMenuItem);\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(viewBoxesMenuItem);\r
     viewMenu.add(viewTextMenuItem);\r
+    viewMenu.add(colourTextMenuItem);\r
+    viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(consensusGraphMenuItem);\r
     viewMenu.add(overviewMenuItem);\r
+    viewMenu.add(secondaryStructure);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(zappoColour);\r
@@ -671,15 +680,14 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(strandColour);\r
     colourMenu.add(turnColour);\r
     colourMenu.add(buriedColour);\r
+    colourMenu.add(nucleotideColour);\r
     colourMenu.add(userDefinedColour);\r
-    colourMenu.addSeparator();\r
-    colourMenu.add(conservationMenuItem);\r
-    colourMenu.add(conservationColourIncMenuItem);\r
-    colourMenu.addSeparator();\r
-    colourMenu.add(abovePIDColour);\r
     colourMenu.add(PIDColour);\r
     colourMenu.add(BLOSUM62Colour);\r
     colourMenu.addSeparator();\r
+    colourMenu.add(abovePIDThreshold);\r
+    colourMenu.add(conservationMenuItem);\r
+    colourMenu.addSeparator();\r
     colourMenu.add(schemeKeyMenuItem);\r
     calculateMenu.add(sortPairwiseMenuItem);\r
     calculateMenu.add(sortIDMenuItem);\r
@@ -695,6 +703,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
     calculateMenu.add(njTreeBlosumMenuItem);\r
     alignMenu.add(clustalAlignMenuItem);\r
+    alignMenu.add(pdbTest);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
   }\r
 \r
@@ -715,10 +724,6 @@ public class GAlignFrame extends JInternalFrame
 \r
 \r
 \r
-  protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
 \r
   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
@@ -742,10 +747,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -762,20 +763,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -965,46 +952,76 @@ public class GAlignFrame extends JInternalFrame
   }\r
 \r
 \r
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
 \r
- }\r
+  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void PIDColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  {\r
 \r
+  }\r
 \r
-  protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+  }\r
+\r
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  protected void PIDColour_actionPerformed(ActionEvent e)\r
+  protected void pdbTest_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  protected void printMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  protected void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
+\r
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+\r
+  }\r
+\r
+  public void secondaryStructure_actionPerformed(ActionEvent actionEvent)\r
   {\r
 \r
   }\r
 \r
+  protected void nucleotideColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void deleteGroups_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
 }\r