-import javax.swing.*;\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-\r
-public class GAlignFrame extends JInternalFrame\r
-{\r
- protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
- 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
- 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
- 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
- protected JMenuItem sortIDMenuItem = new JMenuItem();\r
- protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
- protected JMenuItem PCAMenuItem = new JMenuItem();\r
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public JLabel statusBar = new JLabel();\r
- protected JMenu saveAlignmentMenu = new JMenu();\r
- protected JMenu outputTextboxMenu = new JMenu();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- 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
- 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
- JMenuItem noColourmenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem pdbTest = new JMenuItem();\r
- JMenuItem printMenuItem = new JMenuItem();\r
- public GAlignFrame()\r
- {\r
- try\r
- {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- JMenuItem item;\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().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.FormatProperties.getFormats().elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add( item );\r
- }\r
-\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- 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
- }\r
- private void jbInit() throws Exception\r
- {\r
- fileMenu.setMnemonic('F');\r
- fileMenu.setText("File");\r
- saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save alignment to local file");\r
- closeMenuItem.setMnemonic('C');\r
- closeMenuItem.setText("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- closeMenuItem_actionPerformed(e);\r
- }\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.setText("Groups");\r
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setText("Invert sequence selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllColumnsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setText("Remove gapped columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setText("Remove all gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- setGapCharMenuItem.setText("Set gap character to \"-\"");\r
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewBoxesMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewTextMenuItem.setText("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setText("Sort by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setText("Sort by group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortTreeOrderMenuItem.setText("Sort by tree order");\r
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortTreeOrderMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setText("Remove redundancy");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setText("Principal component analysis");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- clustalAlignMenuItem.setText("Clustal alignment");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- 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 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
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor colour scheme");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("By hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setEnabled(false);\r
- PIDColour.setText("By PID");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("By BLOSUM62 score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- consensusGraphMenuItem_actionPerformed(e);\r
- }\r
- });\r
- colourTextMenuItem.setText("Colour text");\r
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- colourTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- htmlMenuItem.setText("Output as HTML");\r
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- public void actionPerformed(ActionEvent e)\r
- {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
- undoMenuItem.setText("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\r
- redoMenuItem.setText("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setEnabled(false);\r
- wrapMenuItem.setText("Wrap alignment");\r
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- 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
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\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(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(invertSequenceMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(copySelectedMenuItem);\r
- editMenu.add(moveSelectedMenuItem);\r
- editMenu.add(deleteSelectedMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(deselectAllColumnsMenuItem);\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(setGapCharMenuItem);\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(consensusGraphMenuItem);\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\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(schemeKeyMenuItem);\r
- calculateMenu.add(sortPairwiseMenuItem);\r
- calculateMenu.add(sortIDMenuItem);\r
- calculateMenu.add(sortGroupMenuItem);\r
- calculateMenu.add(sortTreeOrderMenuItem);\r
- calculateMenu.add(removeRedundancyMenuItem);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(averageDistanceTreeMenuItem);\r
- calculateMenu.add(neighbourTreeMenuItem);\r
- 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
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\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
-\r
- }\r