png and eps output added

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index fa90a6e..44cb8b7 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -18,7 +18,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu fileMenu = new JMenu();\r
   protected JMenuItem closeMenuItem = new JMenuItem();\r
   protected JMenu editMenu = new JMenu();\r
-  protected JMenu fontMenu = new JMenu();\r
   protected JMenu viewMenu = new JMenu();\r
   protected JMenu colourMenu = new JMenu();\r
   protected JMenu calculateMenu = new JMenu();\r
@@ -33,9 +32,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
-  protected JMenuItem fontNameMenuItem = new JMenuItem();\r
-  protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
-  protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
@@ -68,22 +64,35 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem htmlMenuItem = new JMenuItem();\r
-  JMenuItem schemeKeyMenuItem = new JMenuItem();\r
   JMenuItem overviewMenuItem = new JMenuItem();\r
   protected JMenuItem undoMenuItem = new JMenuItem();\r
   protected JMenuItem redoMenuItem = new JMenuItem();\r
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\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 JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+  JMenuItem deleteGroups = new JMenuItem();\r
+  JMenuItem delete = new JMenuItem();\r
+  JMenuItem copy = new JMenuItem();\r
+  JMenuItem cut = new JMenuItem();\r
+  JMenu jMenu1 = new JMenu();\r
+  JMenuItem pasteNew = new JMenuItem();\r
+  JMenuItem pasteThis = new JMenuItem();\r
+  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+  JMenuItem createPNG = new JMenuItem();\r
+  protected JMenuItem font = new JMenuItem();\r
+  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+  JMenuItem epsFile = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
+\r
+\r
     try\r
     {\r
       jbInit();\r
@@ -133,6 +142,7 @@ public class GAlignFrame extends JInternalFrame
     colours.add(userDefinedColour);\r
     colours.add(PIDColour);\r
     colours.add(BLOSUM62Colour);\r
+    colours.add(nucleotideColour);\r
   }\r
   private void jbInit() throws Exception\r
   {\r
@@ -150,11 +160,11 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     editMenu.setText("Edit");\r
-    fontMenu.setText("Font");\r
     viewMenu.setText("View");\r
     colourMenu.setText("Colour");\r
     calculateMenu.setText("Calculate");\r
     alignMenu.setText("Web Service");\r
+    groupsMenuItem.setVisible(false);\r
     groupsMenuItem.setText("Groups");\r
     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -163,7 +173,7 @@ public class GAlignFrame extends JInternalFrame
         groupsMenuItem_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
@@ -171,7 +181,7 @@ 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
@@ -235,29 +245,6 @@ public class GAlignFrame extends JInternalFrame
         setGapCharMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fontNameMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    fontSizeMenuItem.setText("10");\r
-    fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fontSizeMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    fontStyleMenuItem.setText("Plain");\r
-    fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fontStyleMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     viewBoxesMenuItem.setText("Boxes");\r
     viewBoxesMenuItem.setState(true);\r
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -495,14 +482,6 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    schemeKeyMenuItem.setText("Colour Scheme Key");\r
-    schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        schemeKeyMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     overviewMenuItem.setText("Overview window");\r
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -548,7 +527,6 @@ public class GAlignFrame extends JInternalFrame
         noColourmenuItem_actionPerformed(e);\r
       }\r
     });\r
-    wrapMenuItem.setEnabled(false);\r
     wrapMenuItem.setText("Wrap alignment");\r
     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -557,14 +535,6 @@ 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
@@ -598,19 +568,121 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);\r
       }\r
     });\r
-    secondaryStructure.setSelected(true);\r
-    secondaryStructure.setText("Secondary Structure");\r
-    secondaryStructure.addActionListener(new ActionListener()\r
+    sequenceFeatures.setText("Sequence Features");\r
+    sequenceFeatures.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent actionEvent)\r
       {\r
-        secondaryStructure_actionPerformed(actionEvent);\r
+        sequenceFeatures_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
+    copy.setText("Copy");\r
+    copy.setMnemonic(KeyEvent.VK_C);\r
+\r
+    copy.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        copy_actionPerformed(e);\r
+      }\r
+    });\r
+    cut.setText("Cut");\r
+    cut.setMnemonic(KeyEvent.VK_X);\r
+    cut.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        cut_actionPerformed(e);\r
+      }\r
+    });\r
+    delete.setText("Delete");\r
+    delete.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        delete_actionPerformed(e);\r
+      }\r
+    });\r
+    jMenu1.setMnemonic('V');\r
+    jMenu1.setText("Paste");\r
+    pasteNew.setText("to new alignment");\r
+    pasteNew.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pasteNew_actionPerformed(e);\r
+      }\r
+    });\r
+    pasteThis.setText("add to this alignment");\r
+    pasteThis.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pasteThis_actionPerformed(e);\r
+      }\r
+    });\r
+    applyToAllGroups.setText("Apply colour to all groups");\r
+    applyToAllGroups.setState(true);\r
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        applyToAllGroups_actionPerformed(e);\r
+      }\r
+    });\r
+    createPNG.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        createPNG_actionPerformed(e);\r
+      }\r
+    });\r
+    createPNG.setActionCommand("Save as PNG Image");\r
+    createPNG.setText("Save as PNG Image");\r
+    font.setText("Change Font");\r
+    font.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        font_actionPerformed(e);\r
+      }\r
+    });\r
+    fullSeqId.setText("Show full sequence id");\r
+    fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        fullSeqId_actionPerformed(e);\r
+      }\r
+    });\r
+    epsFile.setText("Save as EPS file");\r
+    epsFile.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        epsFile_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
@@ -618,17 +690,24 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(outputTextboxMenu);\r
     fileMenu.add(htmlMenuItem);\r
+    fileMenu.add(epsFile);\r
+    fileMenu.add(createPNG);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
+    editMenu.add(copy);\r
+    editMenu.add(jMenu1);\r
+    editMenu.add(cut);\r
+    editMenu.add(delete);\r
+    editMenu.addSeparator();\r
     editMenu.add(undoMenuItem);\r
     editMenu.add(redoMenuItem);\r
     editMenu.addSeparator();\r
-    editMenu.add(groupsMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(deselectAllSequenceMenuItem);\r
+    editMenu.add(selectAllSequenceMenuItem);\r
     editMenu.add(invertSequenceMenuItem);\r
+    editMenu.add(deleteGroups);\r
+    editMenu.add(groupsMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(deselectAllColumnsMenuItem);\r
     editMenu.add(remove2LeftMenuItem);\r
@@ -638,9 +717,8 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);\r
     editMenu.add(setGapCharMenuItem);\r
     searchMenu.add(findMenuItem);\r
-    fontMenu.add(fontNameMenuItem);\r
-    fontMenu.add(fontSizeMenuItem);\r
-    fontMenu.add(fontStyleMenuItem);\r
+    viewMenu.add(font);\r
+    viewMenu.add(fullSeqId);\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(viewBoxesMenuItem);\r
     viewMenu.add(viewTextMenuItem);\r
@@ -648,7 +726,8 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(consensusGraphMenuItem);\r
     viewMenu.add(overviewMenuItem);\r
-    viewMenu.add(secondaryStructure);\r
+    viewMenu.add(sequenceFeatures);\r
+    colourMenu.add(applyToAllGroups);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(zappoColour);\r
@@ -658,14 +737,13 @@ 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.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
     calculateMenu.add(sortGroupMenuItem);\r
@@ -680,8 +758,9 @@ 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
+    jMenu1.add(pasteNew);\r
+    jMenu1.add(pasteThis);\r
   }\r
 \r
   protected void saveAs_actionPerformed(ActionEvent e)\r
@@ -772,20 +851,8 @@ public class GAlignFrame extends JInternalFrame
   }\r
 \r
 \r
-  protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
 \r
-  }\r
 \r
-  protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -945,10 +1012,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -960,10 +1023,6 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  protected void pdbTest_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
 \r
   protected void printMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -985,8 +1044,72 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
-  public void secondaryStructure_actionPerformed(ActionEvent actionEvent)\r
+  public void sequenceFeatures_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
+ protected void copy_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
+\r
+\r
+  protected void cut_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void delete_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void pasteNew_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void pasteThis_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void createPNG_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void font_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void fullSeqId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  protected void epsFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
+\r
 }\r