-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-package jalview.jbgui;\r
-\r
-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 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 JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem invertSequenceMenuItem = 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 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 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 JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem htmlMenuItem = 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 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 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
- 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(noColourmenuItem);\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(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(nucleotideColour);\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
- 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
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- selectAllSequenceMenuItem.setText("Select all");\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 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
- 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
- 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.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.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
- 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.setText("Percentage Identity");\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("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
- 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
- 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.setSelected(true);\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\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
- 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
- sequenceFeatures.setText("Sequence Features");\r
- sequenceFeatures.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\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(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(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(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
- editMenu.add(remove2RightMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(setGapCharMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.add(fullSeqId);\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(sequenceFeatures);\r
- colourMenu.add(applyToAllGroups);\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(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
- 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
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
- jMenu1.add(pasteNew);\r
- jMenu1.add(pasteThis);\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
-\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
-\r
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\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
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
-\r
- }\r
-\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
+/********************
+ * 2004 Jalview Reengineered
+ * Barton Group
+ * Dundee University
+ *
+ * AM Waterhouse
+ *******************/
+
+package jalview.jbgui;
+
+import javax.swing.*;
+import java.awt.event.*;
+import java.awt.*;
+
+public class GAlignFrame extends JInternalFrame
+{
+ protected JMenuBar alignFrameMenuBar = new JMenuBar();
+ protected JMenu fileMenu = new JMenu();
+ protected JMenuItem closeMenuItem = new JMenuItem();
+ protected JMenu editMenu = new JMenu();
+ protected JMenu viewMenu = new JMenu();
+ protected JMenu colourMenu = new JMenu();
+ protected JMenu calculateMenu = new JMenu();
+ protected JMenu alignMenu = new JMenu();
+ protected JMenuItem groupsMenuItem = new JMenuItem();
+ protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+ protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+ protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+ protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
+ protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+ protected JMenuItem remove2RightMenuItem = new JMenuItem();
+ protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+ protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+ protected JMenuItem setGapCharMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+ protected JMenuItem sortIDMenuItem = new JMenuItem();
+ protected JMenuItem sortGroupMenuItem = new JMenuItem();
+ protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
+ protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+ protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+ protected JMenuItem PCAMenuItem = new JMenuItem();
+ protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+ protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+ protected JMenuItem clustalAlignMenuItem = new JMenuItem();
+ BorderLayout borderLayout1 = new BorderLayout();
+ public JLabel statusBar = new JLabel();
+ protected JMenu saveAlignmentMenu = new JMenu();
+ protected JMenu outputTextboxMenu = new JMenu();
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ JMenuItem htmlMenuItem = new JMenuItem();
+ JMenuItem overviewMenuItem = new JMenuItem();
+ protected JMenuItem undoMenuItem = new JMenuItem();
+ protected JMenuItem redoMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+ JMenuItem printMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+ JMenuItem findMenuItem = new JMenuItem();
+ JMenu searchMenu = new JMenu();
+ protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ JMenuItem deleteGroups = new JMenuItem();
+ JMenuItem delete = new JMenuItem();
+ JMenuItem copy = new JMenuItem();
+ JMenuItem cut = new JMenuItem();
+ JMenu jMenu1 = new JMenu();
+ JMenuItem pasteNew = new JMenuItem();
+ JMenuItem pasteThis = new JMenuItem();
+ protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ JMenuItem createPNG = new JMenuItem();
+ protected JMenuItem font = new JMenuItem();
+ protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+ JMenuItem epsFile = new JMenuItem();
+ JMenuItem LoadtreeMenuItem = new JMenuItem();
+ public GAlignFrame()
+ {
+
+
+ try
+ {
+ jbInit();
+ setJMenuBar(alignFrameMenuBar);
+
+ JMenuItem item;
+ // dynamically fill save as menu with available formats
+ for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
+ item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
+ saveAlignmentMenu.add( item );
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAs_actionPerformed(e);
+ }
+ });
+
+ item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add( item );
+ }
+
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ ButtonGroup colours = new ButtonGroup();
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(nucleotideColour);
+ }
+ private void jbInit() throws Exception
+ {
+ fileMenu.setMnemonic('F');
+ fileMenu.setText("File");
+ saveAlignmentMenu.setMnemonic('L');
+ saveAlignmentMenu.setText("Save alignment to local file");
+ closeMenuItem.setMnemonic('C');
+ closeMenuItem.setText("Close");
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ closeMenuItem_actionPerformed(e);
+ }
+ });
+ editMenu.setText("Edit");
+ viewMenu.setText("View");
+ colourMenu.setText("Colour");
+ calculateMenu.setText("Calculate");
+ alignMenu.setText("Web Service");
+ groupsMenuItem.setVisible(false);
+ groupsMenuItem.setText("Groups");
+ groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groupsMenuItem_actionPerformed(e);
+ }
+ });
+ selectAllSequenceMenuItem.setText("Select all");
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ deselectAllSequenceMenuItem.setText("Clear selection");
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ invertSequenceMenuItem.setText("Invert sequence selection");
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ deselectAllColumnsMenuItem.setText("Deselect all columns");
+ deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllColumnsMenuItem_actionPerformed(e);
+ }
+ });
+ remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ });
+ remove2RightMenuItem.setText("Remove sequence -> right of selected column");
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ });
+ removeGappedColumnMenuItem.setText("Remove gapped columns");
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ });
+ removeAllGapsMenuItem.setText("Remove all gaps");
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ });
+ setGapCharMenuItem.setText("Set gap character to \".\"");
+ setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setGapCharMenuItem_actionPerformed(e);
+ }
+ });
+ viewBoxesMenuItem.setText("Boxes");
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewBoxesMenuItem_actionPerformed(e);
+ }
+ });
+ viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewTextMenuItem_actionPerformed(e);
+ }
+ });
+ sortPairwiseMenuItem.setText("Sort by pairwise identity");
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ sortIDMenuItem.setText("Sort by ID");
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortIDMenuItem_actionPerformed(e);
+ }
+ });
+ sortGroupMenuItem.setText("Sort by group");
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortGroupMenuItem_actionPerformed(e);
+ }
+ });
+ sortTreeOrderMenuItem.setText("Sort by tree order");
+ sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortTreeOrderMenuItem_actionPerformed(e);
+ }
+ });
+ removeRedundancyMenuItem.setText("Remove redundancy");
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ });
+ pairwiseAlignmentMenuItem.setText("Pairwise alignments");
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ PCAMenuItem.setText("Principal component analysis");
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PCAMenuItem_actionPerformed(e);
+ }
+ });
+ averageDistanceTreeMenuItem.setText("Average distance tree using PID");
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
+ clustalAlignMenuItem.setText("Clustal alignment");
+ clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalAlignMenuItem_actionPerformed(e);
+ }
+ });
+ this.getContentPane().setLayout(borderLayout1);
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+ statusBar.setText("Status bar");
+ outputTextboxMenu.setMnemonic('T');
+ outputTextboxMenu.setText("Output alignment via textbox");
+ clustalColour.setSelected(false);
+ clustalColour.setText("Clustalx colours");
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed(e);
+ }
+ });
+ zappoColour.setText("Zappo colour scheme");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed(e);
+ }
+ });
+ taylorColour.setText("Taylor colour scheme");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed(e);
+ }
+ });
+ hydrophobicityColour.setText("By hydrophobicity");
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText("Helix propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed(e);
+ }
+ });
+ strandColour.setText("Strand propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed(e);
+ }
+ });
+ turnColour.setText("Turn propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed(e);
+ }
+ });
+ buriedColour.setText("Buried index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed(e);
+ }
+ });
+ userDefinedColour.setText("User defined colours");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed(e);
+ }
+ });
+ BLOSUM62Colour.setText("BLOSUM62 score");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed(e);
+ }
+ });
+ avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ consensusGraphMenuItem.setActionCommand("");
+ consensusGraphMenuItem.setText("Consensus graph");
+ consensusGraphMenuItem.setState(true);
+ consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ consensusGraphMenuItem_actionPerformed(e);
+ }
+ });
+ colourTextMenuItem.setText("Colour text");
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+ htmlMenuItem.setText("Output as HTML");
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ htmlMenuItem_actionPerformed(e);
+ }
+ });
+ overviewMenuItem.setText("Overview window");
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ overviewMenuItem_actionPerformed(e);
+ }
+ });
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setMnemonic('Z');
+ undoMenuItem.setText("Undo");
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ undoMenuItem_actionPerformed(e);
+ }
+ });
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setMnemonic('0');
+ redoMenuItem.setText("Redo");
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ redoMenuItem_actionPerformed(e);
+ }
+ });
+ conservationMenuItem.setText("By conservation");
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
+ noColourmenuItem.setText("None");
+ noColourmenuItem.setSelected(true);
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed(e);
+ }
+ });
+ wrapMenuItem.setText("Wrap alignment");
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ wrapMenuItem_actionPerformed(e);
+ }
+ });
+ printMenuItem.setText("Print");
+ printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ printMenuItem_actionPerformed(e);
+ }
+ });
+ renderGapsMenuItem.setText("Render gaps");
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+ findMenuItem.setText("Find");
+ findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findMenuItem_actionPerformed(e);
+ }
+ });
+ searchMenu.setText("Search");
+
+ abovePIDThreshold.setText("Above PID threshold");
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ abovePIDThreshold_actionPerformed(e);
+ }
+ });
+ sequenceFeatures.setText("Sequence Features");
+ sequenceFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ sequenceFeatures_actionPerformed(actionEvent);
+ }
+ });
+ nucleotideColour.setText("Nucleotide colours");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+ deleteGroups.setSelected(false);
+ deleteGroups.setText("Delete all groups");
+ deleteGroups.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteGroups_actionPerformed(e);
+ }
+ });
+ copy.setText("Copy");
+ copy.setMnemonic(KeyEvent.VK_C);
+
+ copy.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(e);
+ }
+ });
+ cut.setText("Cut");
+ cut.setMnemonic(KeyEvent.VK_X);
+ cut.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed(e);
+ }
+ });
+ delete.setText("Delete");
+ delete.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ delete_actionPerformed(e);
+ }
+ });
+ jMenu1.setMnemonic('V');
+ jMenu1.setText("Paste");
+ pasteNew.setText("to new alignment");
+ pasteNew.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteNew_actionPerformed(e);
+ }
+ });
+ pasteThis.setText("add to this alignment");
+ pasteThis.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteThis_actionPerformed(e);
+ }
+ });
+ applyToAllGroups.setText("Apply colour to all groups");
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed(e);
+ }
+ });
+ createPNG.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createPNG_actionPerformed(e);
+ }
+ });
+ createPNG.setActionCommand("Save as PNG Image");
+ createPNG.setText("Save as PNG Image");
+ font.setText("Change Font");
+ font.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ font_actionPerformed(e);
+ }
+ });
+ fullSeqId.setText("Show full sequence id");
+ fullSeqId.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fullSeqId_actionPerformed(e);
+ }
+ });
+ epsFile.setText("Save as EPS file");
+ epsFile.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ epsFile_actionPerformed(e);
+ }
+ });
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+ LoadtreeMenuItem.setText("Load assocated tree");
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadtreeMenuItem_actionPerformed(e);
+ }
+ });
+ alignFrameMenuBar.add(fileMenu);
+ alignFrameMenuBar.add(editMenu);
+ alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(colourMenu);
+ alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(alignMenu);
+ fileMenu.add(saveAlignmentMenu);
+ fileMenu.add(outputTextboxMenu);
+ fileMenu.add(htmlMenuItem);
+ fileMenu.add(epsFile);
+ fileMenu.add(createPNG);
+ fileMenu.add(printMenuItem);
+ fileMenu.addSeparator();
+ fileMenu.add(LoadtreeMenuItem);
+ fileMenu.addSeparator();
+ fileMenu.add(closeMenuItem);
+ editMenu.add(copy);
+ editMenu.add(jMenu1);
+ editMenu.add(cut);
+ editMenu.add(delete);
+ editMenu.addSeparator();
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.addSeparator();
+ editMenu.add(deselectAllSequenceMenuItem);
+ editMenu.add(selectAllSequenceMenuItem);
+ editMenu.add(invertSequenceMenuItem);
+ editMenu.add(deleteGroups);
+ editMenu.add(groupsMenuItem);
+ editMenu.addSeparator();
+ editMenu.add(deselectAllColumnsMenuItem);
+ editMenu.add(remove2LeftMenuItem);
+ editMenu.add(remove2RightMenuItem);
+ editMenu.addSeparator();
+ editMenu.add(removeGappedColumnMenuItem);
+ editMenu.add(removeAllGapsMenuItem);
+ editMenu.add(setGapCharMenuItem);
+ searchMenu.add(findMenuItem);
+ viewMenu.add(font);
+ viewMenu.add(fullSeqId);
+ viewMenu.add(wrapMenuItem);
+ viewMenu.add(viewBoxesMenuItem);
+ viewMenu.add(viewTextMenuItem);
+ viewMenu.add(colourTextMenuItem);
+ viewMenu.add(renderGapsMenuItem);
+ viewMenu.add(consensusGraphMenuItem);
+ viewMenu.add(overviewMenuItem);
+ viewMenu.add(sequenceFeatures);
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(conservationMenuItem);
+ calculateMenu.add(sortPairwiseMenuItem);
+ calculateMenu.add(sortIDMenuItem);
+ calculateMenu.add(sortGroupMenuItem);
+ calculateMenu.add(sortTreeOrderMenuItem);
+ calculateMenu.add(removeRedundancyMenuItem);
+ calculateMenu.addSeparator();
+ calculateMenu.add(pairwiseAlignmentMenuItem);
+ calculateMenu.add(PCAMenuItem);
+ calculateMenu.addSeparator();
+ calculateMenu.add(averageDistanceTreeMenuItem);
+ calculateMenu.add(neighbourTreeMenuItem);
+ calculateMenu.add(avDistanceTreeBlosumMenuItem);
+ calculateMenu.add(njTreeBlosumMenuItem);
+ alignMenu.add(clustalAlignMenuItem);
+ this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+ jMenu1.add(pasteNew);
+ jMenu1.add(pasteThis);
+ }
+
+ protected void saveAs_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+
+
+ protected void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void groupsMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+
+
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+ protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void strandColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void printMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void findMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+
+ }
+
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void createPNG_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void font_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void fullSeqId_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void epsFile_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff