-/********************
- * 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 webService = new JMenu();
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();
- protected JMenuItem remove2RightMenuItem = new JMenuItem();
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
- protected JMenuItem removeAllGapsMenuItem = 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 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 annotationPanelMenuItem = 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();
- JMenuItem jpred = new JMenuItem();
- protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- JMenuItem modifyPID = new JMenuItem();
- JMenuItem modifyConservation = new JMenuItem();
- protected JMenu sortByTreeMenu = new JMenu();
- JMenu jMenu2 = new JMenu();
- JMenu sort = new JMenu();
- JMenu calculate = new JMenu();
- JMenuItem preferences = new JMenuItem();
- JMenuItem msaAlignMenuItem = 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");
- 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");
- webService.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select all");
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- selectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- deselectAllSequenceMenuItem.setText("Deselect All");
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
- getKeyStroke(java.awt.event.
- KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deselectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- invertSequenceMenuItem.setText("Invert Selection");
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- invertSequenceMenuItem_actionPerformed(e);
- }
- });
- remove2LeftMenuItem.setText("Remove Left");
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- remove2LeftMenuItem_actionPerformed(e);
- }
- });
- remove2RightMenuItem.setText("Remove Right");
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- remove2RightMenuItem_actionPerformed(e);
- }
- });
- removeGappedColumnMenuItem.setText("Remove Empty 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);
- }
- });
- 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("Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortPairwiseMenuItem_actionPerformed(e);
- }
- });
- sortIDMenuItem.setText("ID");
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortIDMenuItem_actionPerformed(e);
- }
- });
- sortGroupMenuItem.setText("Group");
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortGroupMenuItem_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 Using % Identity...");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
- 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 to Textbox");
- clustalColour.setSelected(false);
- clustalColour.setText("Clustalx");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed(e);
- }
- });
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setText("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...");
- 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 using BLOSUM62...");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Show Annotations");
- annotationPanelMenuItem.setState(true);
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotationPanelMenuItem_actionPerformed(e);
- }
- });
- colourTextMenuItem.setText("Colour Text");
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- colourTextMenuItem_actionPerformed(e);
- }
- });
- htmlMenuItem.setText("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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
- 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");
- 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("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_actionPerformed(e);
- }
- });
- findMenuItem.setText("Find...");
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- findMenuItem_actionPerformed(e);
- }
- });
- searchMenu.setText("Search");
-
- abovePIDThreshold.setText("Above Identity 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");
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed(e);
- }
- });
- deleteGroups.setSelected(false);
- deleteGroups.setText("Undefine groups");
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deleteGroups_actionPerformed(e);
- }
- });
- copy.setText("Copy");
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
- copy.setMnemonic(KeyEvent.VK_C);
-
- copy.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- copy_actionPerformed(e);
- }
- });
- cut.setText("Cut");
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
- 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
- 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("PNG");
- font.setText("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("EPS");
- 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);
- }
- });
- jpred.setText("JPred...");
- jpred.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- jpred_actionPerformed(e);
- }
- });
- scaleAbove.setVisible(false);
- scaleAbove.setText("Scale Above");
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- scaleAbove_actionPerformed(e);
- }
- });
- scaleLeft.setVisible(false);
- scaleLeft.setSelected(true);
- scaleLeft.setText("Scale Left");
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- scaleLeft_actionPerformed(e);
- }
- });
- scaleRight.setVisible(false);
- scaleRight.setSelected(true);
- scaleRight.setText("Scale Right");
- scaleRight.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- scaleRight_actionPerformed(e);
- }
- });
- modifyPID.setText("Modify Identity Threshold...");
- modifyPID.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- modifyPID_actionPerformed(e);
- }
- });
- modifyConservation.setText("Modify Conservation Threshold...");
- modifyConservation.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
- sortByTreeMenu.setText("Tree Order");
- jMenu2.setText("Save as");
- sort.setText("Sort");
- calculate.setText("Calculate Tree");
- preferences.setText("Preferences...");
- preferences.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- preferences_actionPerformed(e);
- }
- });
- msaAlignMenuItem.setText("Muscle Alignment...");
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
- msaAlignMenuItem_actionPerformed(e);
- }
- });
- alignFrameMenuBar.add(fileMenu);
- alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
- alignFrameMenuBar.add(viewMenu);
- alignFrameMenuBar.add(colourMenu);
- alignFrameMenuBar.add(calculateMenu);
- fileMenu.add(saveAlignmentMenu);
- fileMenu.add(jMenu2);
- fileMenu.add(outputTextboxMenu);
- fileMenu.add(printMenuItem);
- fileMenu.addSeparator();
- fileMenu.add(LoadtreeMenuItem);
- fileMenu.addSeparator();
- fileMenu.add(closeMenuItem);
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.add(cut);
- editMenu.add(copy);
- editMenu.add(jMenu1);
- editMenu.add(delete);
- editMenu.addSeparator();
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
- editMenu.add(remove2LeftMenuItem);
- editMenu.add(remove2RightMenuItem);
- editMenu.add(removeGappedColumnMenuItem);
- editMenu.add(removeAllGapsMenuItem);
- editMenu.add(removeRedundancyMenuItem);
- editMenu.addSeparator();
- editMenu.add(preferences);
-
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.add(fullSeqId);
- viewMenu.addSeparator();
- viewMenu.add(wrapMenuItem);
- viewMenu.add(scaleAbove);
- viewMenu.add(scaleLeft);
- viewMenu.add(scaleRight);
- viewMenu.addSeparator();
- viewMenu.add(viewBoxesMenuItem);
- viewMenu.add(viewTextMenuItem);
- viewMenu.add(colourTextMenuItem);
- viewMenu.add(renderGapsMenuItem);
- viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(sequenceFeatures);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.add(noColourmenuItem);
- colourMenu.addSeparator();
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- 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.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
- calculateMenu.addSeparator();
- calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
- calculateMenu.addSeparator();
- calculateMenu.add(webService);
- webService.add(clustalAlignMenuItem);
- webService.add(jpred);
- webService.add(msaAlignMenuItem);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- sort.add(sortIDMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- }
-
- 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 selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void invertSequenceMenuItem_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 wrapMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void annotationPanelMenuItem_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 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) {
-
- }
-
- protected void jpred_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void scaleAbove_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void scaleLeft_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void scaleRight_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void modifyPID_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void modifyConservation_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void preferences_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
-
- }
-
-}
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+package jalview.jbgui;\r
+\r
+import jalview.gui.Preferences;\r
+\r
+import jalview.schemes.ColourSchemeProperty;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+import javax.swing.event.AncestorEvent;\r
+import javax.swing.event.AncestorListener;\r
+\r
+\r
+public class GAlignFrame extends JInternalFrame {\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 webService = new JMenu();\r
+ protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem invertSequenceMenuItem = 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 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 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 JMenuItem saveAlignmentMenu = new JMenuItem();\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 annotationPanelMenuItem = 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
+ JMenuItem LoadtreeMenuItem = new JMenuItem();\r
+ JMenuItem jpred = new JMenuItem();\r
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
+ JMenuItem modifyPID = new JMenuItem();\r
+ JMenuItem modifyConservation = new JMenuItem();\r
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenuItem msaAlignMenuItem = new JMenuItem();\r
+ JMenu jMenu2 = new JMenu();\r
+ JMenuItem padGapsMenuitem = new JMenuItem();\r
+ JMenuItem ClustalRealign = new JMenuItem();\r
+\r
+ public GAlignFrame() {\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
+ noColourmenuItem.setSelected(true);\r
+\r
+ String defaultColour = Preferences.defaultColour;\r
+\r
+ if (defaultColour != null) {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+\r
+ switch (index) {\r
+ case ColourSchemeProperty.CLUSTAL:\r
+ clustalColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BLOSUM:\r
+ BLOSUM62Colour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.PID:\r
+ PIDColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.ZAPPO:\r
+ zappoColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HYDROPHOBIC:\r
+ hydrophobicityColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HELIX:\r
+ helixColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.STRAND:\r
+ strandColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TURN:\r
+ turnColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BURIED:\r
+ buriedColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.NUCLEOTIDE:\r
+ nucleotideColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.USER_DEFINED:\r
+ userDefinedColour.setSelected(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ try {\r
+ jbInit();\r
+ setJMenuBar(alignFrameMenuBar);\r
+\r
+ JMenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
+ item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ fileMenu.setMnemonic('F');\r
+ fileMenu.setText("File");\r
+ saveAlignmentMenu.setMnemonic('L');\r
+ saveAlignmentMenu.setText("Save As");\r
+ saveAlignmentMenu.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveAlignmentMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ closeMenuItem.setMnemonic('C');\r
+ closeMenuItem.setText("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ viewMenu.setText("View");\r
+ colourMenu.setText("Colour");\r
+ calculateMenu.setText("Calculate");\r
+ webService.setText("Web Service");\r
+ selectAllSequenceMenuItem.setText("Select all");\r
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_A,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setText("Deselect All");\r
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setText("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setText("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setText("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setText("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setText("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewTextMenuItem.setText("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setText("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setText("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setText("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setText("Principal Component Analysis...");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setText(\r
+ "Average Distance Using % Identity...");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ clustalAlignMenuItem.setText("Clustal Alignment...");\r
+ clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
+ public void ancestorAdded(AncestorEvent event) {\r
+ alignFrameMenuBar_ancestorAdded(event);\r
+ }\r
+\r
+ public void ancestorRemoved(AncestorEvent event) {\r
+ }\r
+\r
+ public void ancestorMoved(AncestorEvent event) {\r
+ }\r
+ });\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 to Textbox");\r
+ clustalColour.setText("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setText("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setText("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setText("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setText("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setText("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setText("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62...");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ colourTextMenuItem.setText("Colour Text");\r
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ colourTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ htmlMenuItem.setText("HTML");\r
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ htmlMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ overviewMenuItem.setText("Overview Window...");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setMnemonic('Z');\r
+ undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\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
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setText("By Conservation");\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setText("Wrap");\r
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ wrapMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenuItem.setText("Print");\r
+ printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ printMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setText("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ renderGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setText("Search");\r
+\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ sequenceFeatures.setText("Sequence Features");\r
+ sequenceFeatures.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent actionEvent) {\r
+ sequenceFeatures_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ nucleotideColour.setText("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setText("Undefine groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_C,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ copy.setMnemonic(KeyEvent.VK_C);\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setText("Cut");\r
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_X,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ cut.setMnemonic(KeyEvent.VK_X);\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setMnemonic('V');\r
+ jMenu1.setText("Paste");\r
+ pasteNew.setText("To New Alignment");\r
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\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
+ public void actionPerformed(ActionEvent e) {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ createPNG_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.setActionCommand("Save As PNG Image");\r
+ createPNG.setText("PNG");\r
+ font.setText("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setText("Show Full Sequence ID");\r
+ fullSeqId.setState(true);\r
+ fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fullSeqId_actionPerformed(e);\r
+ }\r
+ });\r
+ epsFile.setText("EPS");\r
+ epsFile.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ epsFile_actionPerformed(e);\r
+ }\r
+ });\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Assocated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ LoadtreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jpred.setText("JPred...");\r
+ jpred.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ jpred_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleAbove_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleLeft.setVisible(false);\r
+ scaleLeft.setSelected(true);\r
+ scaleLeft.setText("Scale Left");\r
+ scaleLeft.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleLeft_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleRight.setVisible(false);\r
+ scaleRight.setSelected(true);\r
+ scaleRight.setText("Scale Right");\r
+ scaleRight.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleRight_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ calculate.setText("Calculate Tree");\r
+ msaAlignMenuItem.setText("Muscle Alignment...");\r
+ msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ msaAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu2.setText("Export");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ ClustalRealign.setText("Clustal Realign...");\r
+ ClustalRealign.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ClustalRealign_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
+ fileMenu.add(saveAlignmentMenu);\r
+ fileMenu.add(jMenu2);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(printMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(jMenu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ editMenu.addSeparator();\r
+ editMenu.add(padGapsMenuitem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\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.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(webService);\r
+ webService.add(clustalAlignMenuItem);\r
+ webService.add(msaAlignMenuItem);\r
+ webService.add(jpred);\r
+ webService.add(ClustalRealign);\r
+ this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ jMenu1.add(pasteNew);\r
+ jMenu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ jMenu2.add(htmlMenuItem);\r
+ jMenu2.add(epsFile);\r
+ jMenu2.add(createPNG);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void clustalColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void zappoColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void taylorColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void helixColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void strandColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void turnColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void buriedColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void PIDColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void printMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void findMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
+ }\r
+\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void deleteGroups_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void copy_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void cut_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void delete_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void createPNG_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void font_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void fullSeqId_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void epsFile_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void jpred_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void scaleAbove_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void scaleLeft_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void preferences_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
+ }\r
+\r
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void ClustalRealign_actionPerformed(ActionEvent e) {\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff