X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=2c99170e4450b56100073545896a002946c79da8;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=18df6ce17fb86dd654d293bdcceb885c58892d21;hpb=03ba271b19ac384a6d7fdad31a3a3bc6b0cc0006;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 18df6ce..2c99170 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,1056 +1,1599 @@ -/******************** - * 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 fontMenu = 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 JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem(); - protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); - protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); - protected JMenuItem invertSequenceMenuItem = new JMenuItem(); - protected JMenuItem deleteSelectedMenuItem = new JMenuItem(); - protected JMenuItem moveSelectedMenuItem = new JMenuItem(); - protected JMenuItem copySelectedMenuItem = 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 JMenuItem fontNameMenuItem = new JMenuItem(); - protected JMenuItem fontSizeMenuItem = new JMenuItem(); - protected JMenuItem fontStyleMenuItem = 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 abovePIDColour = 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 JMenuItem conservationColourIncMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - JMenuItem htmlMenuItem = new JMenuItem(); - JMenuItem schemeKeyMenuItem = new JMenuItem(); - JMenuItem overviewMenuItem = new JMenuItem(); - protected JMenuItem undoMenuItem = new JMenuItem(); - protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - JMenuItem noColourmenuItem = new JMenuItem(); - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); - JMenuItem pdbTest = new JMenuItem(); - JMenuItem printMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); - JMenuItem findMenuItem = 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(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - } - 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"); - fontMenu.setText("Font"); - viewMenu.setText("View"); - colourMenu.setText("Colour"); - calculateMenu.setText("Calculate"); - alignMenu.setText("Web Service"); - groupsMenuItem.setText("Groups"); - groupsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupsMenuItem_actionPerformed(e); - } - }); - groupEditingMenuItem.setText("Group editing mode"); - groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupEditingMenuItem_actionPerformed(e); - } - }); - selectAllSequenceMenuItem.setText("Select all sequences"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - selectAllSequenceMenuItem_actionPerformed(e); - } - }); - deselectAllSequenceMenuItem.setText("Clear sequence 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); - } - }); - deleteSelectedMenuItem.setText("Delete selected sequences"); - deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSelectedMenuItem_actionPerformed(e); - } - }); - moveSelectedMenuItem.setText("Move selected sequences to new alignment"); - moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveSelectedMenuItem_actionPerformed(e); - } - }); - copySelectedMenuItem.setText("Copy selected sequences to new alignment"); - copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copySelectedMenuItem_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); - } - }); - fontNameMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontNameMenuItem_actionPerformed(e); - } - }); - fontSizeMenuItem.setText("10"); - fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontSizeMenuItem_actionPerformed(e); - } - }); - fontStyleMenuItem.setText("Plain"); - fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontStyleMenuItem_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.setEnabled(false); - clustalColour.setSelected(false); - clustalColour.setText("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setSelected(true); - 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); - } - }); - abovePIDColour.setEnabled(false); - abovePIDColour.setText("Above PID threshold only"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); - userDefinedColour.setText("User defined colours"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour.setEnabled(false); - PIDColour.setText("By PID"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour.setText("By 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); - } - }); - conservationColourIncMenuItem.setEnabled(false); - conservationColourIncMenuItem.setText("Conservation Colour Increment"); - conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationColourIncMenuItem_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); - } - }); - schemeKeyMenuItem.setText("Colour Scheme Key"); - schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - schemeKeyMenuItem_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.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); - wrapMenuItem.setEnabled(false); - wrapMenuItem.setText("Wrap alignment"); - wrapMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - wrapMenuItem_actionPerformed(e); - } - }); - pdbTest.setText("PDB Test Viewer"); - pdbTest.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pdbTest_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); - } - }); - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(fontMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(alignMenu); - fileMenu.add(saveAlignmentMenu); - fileMenu.add(outputTextboxMenu); - fileMenu.add(htmlMenuItem); - fileMenu.add(printMenuItem); - fileMenu.addSeparator(); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.addSeparator(); - editMenu.add(groupsMenuItem); - editMenu.add(groupEditingMenuItem); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.addSeparator(); - editMenu.add(copySelectedMenuItem); - editMenu.add(moveSelectedMenuItem); - editMenu.add(deleteSelectedMenuItem); - editMenu.addSeparator(); - editMenu.add(deselectAllColumnsMenuItem); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.addSeparator(); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(setGapCharMenuItem); - editMenu.addSeparator(); - editMenu.add(findMenuItem); - fontMenu.add(fontNameMenuItem); - fontMenu.add(fontSizeMenuItem); - fontMenu.add(fontStyleMenuItem); - viewMenu.add(wrapMenuItem); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(consensusGraphMenuItem); - viewMenu.add(overviewMenuItem); - 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(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(conservationColourIncMenuItem); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(PIDColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.addSeparator(); - colourMenu.add(schemeKeyMenuItem); - 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); - alignMenu.add(pdbTest); - this.getContentPane().add(statusBar, BorderLayout.SOUTH); - } - - 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 groupEditingMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void moveSelectedMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void copySelectedMenuItem_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 fontNameMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void fontSizeMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void fontStyleMenuItem_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 conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - - } - - - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - - } - - protected void PIDColour_actionPerformed(ActionEvent e) - { - - } - - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - - } - - protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void pdbTest_actionPerformed(ActionEvent e) - { - - } - - protected void printMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void findMenuItem_actionPerformed(ActionEvent e) - { - - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.jbgui; + +import java.awt.*; +import java.awt.event.*; +import javax.swing.*; + +import jalview.schemes.*; +import java.awt.BorderLayout; + +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 webServiceNoServices; + 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(); + public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + public 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 JMenuItem saveAlignmentMenu = new JMenuItem(); + 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(); + public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + JMenuItem htmlMenuItem = new JMenuItem(); + JMenuItem overviewMenuItem = new JMenuItem(); + protected JMenuItem undoMenuItem = new JMenuItem(); + protected JMenuItem redoMenuItem = new JMenuItem(); + public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + JMenuItem printMenuItem = new JMenuItem(); + public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + JMenuItem findMenuItem = new JMenuItem(); + JMenu searchMenu = new JMenu(); + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeatures = 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(); + public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + JMenuItem createPNG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); + public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + JMenuItem epsFile = new JMenuItem(); + JMenuItem LoadtreeMenuItem = new JMenuItem(); + public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + protected JMenu sortByTreeMenu = new JMenu(); + protected JMenu sort = new JMenu(); + JMenu calculate = new JMenu(); + JMenu jMenu2 = new JMenu(); + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JMenuItem showTranslation = new JMenuItem(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); + JMenuItem annotationColour = new JMenuItem(); + JMenuItem associatedData = new JMenuItem(); + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); + JMenu addSequenceMenu = new JMenu(); + JMenuItem addFromFile = new JMenuItem(); + JMenuItem addFromText = new JMenuItem(); + JMenuItem addFromURL = new JMenuItem(); + JMenuItem exportAnnotations = new JMenuItem(); + JMenuItem exportFeatures = new JMenuItem(); + protected JPanel statusPanel = new JPanel(); + GridLayout gridLayout1 = new GridLayout(); + JMenu jMenu3 = new JMenu(); + JMenuItem showAllSeqs = new JMenuItem(); + JMenuItem showAllColumns = new JMenuItem(); + JMenu jMenu4 = new JMenu(); + JMenuItem hideSelSequences = new JMenuItem(); + JMenuItem hideSelColumns = new JMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + JMenuItem invertColSel = new JMenuItem(); + + public GAlignFrame() + { + + + try + { + jbInit(); + setJMenuBar(alignFrameMenuBar); + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + { + JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] ); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + } + catch (Exception e) + { + } + + + if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours. + nextElement().toString()); + radioItem.setName("USER_DEFINED"); + radioItem.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) + { + radioItem.removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop, + "Remove from default list?", + "Remove user defined colour", + JOptionPane.YES_NO_OPTION); + if(option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText()); + colourMenu.remove(radioItem); + } + else + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + } + } + }); + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.insert(radioItem, 15); + colours.add(radioItem); + } + } + 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); + + setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); + + + } + + public void setColourSelected(String defaultColour) + { + + if (defaultColour != null) + { + int index = ColourSchemeProperty.getColourIndexFromName(defaultColour); + + switch (index) + { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; + case ColourSchemeProperty.CLUSTAL: + clustalColour.setSelected(true); + + break; + + case ColourSchemeProperty.BLOSUM: + BLOSUM62Colour.setSelected(true); + + break; + + case ColourSchemeProperty.PID: + PIDColour.setSelected(true); + + break; + + case ColourSchemeProperty.ZAPPO: + zappoColour.setSelected(true); + + break; + + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + + case ColourSchemeProperty.HYDROPHOBIC: + hydrophobicityColour.setSelected(true); + + break; + + case ColourSchemeProperty.HELIX: + helixColour.setSelected(true); + + break; + + case ColourSchemeProperty.STRAND: + strandColour.setSelected(true); + + break; + + case ColourSchemeProperty.TURN: + turnColour.setSelected(true); + + break; + + case ColourSchemeProperty.BURIED: + buriedColour.setSelected(true); + + break; + + case ColourSchemeProperty.NUCLEOTIDE: + nucleotideColour.setSelected(true); + + break; + + case ColourSchemeProperty.USER_DEFINED: + userDefinedColour.setSelected(true); + + break; + } + } + + } + + private void jbInit() + throws Exception + { + fileMenu.setMnemonic('F'); + fileMenu.setText("File"); + saveAlignmentMenu.setMnemonic('L'); + saveAlignmentMenu.setText("Save As"); + saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); + saveAlignmentMenu.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveAlignmentMenu_actionPerformed(e); + } + }); + 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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 Sequence 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("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortPairwiseMenuItem_actionPerformed(e); + } + }); + sortIDMenuItem.setText("by ID"); + sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortIDMenuItem_actionPerformed(e); + } + }); + sortGroupMenuItem.setText("by 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); + } + }); + 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.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( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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.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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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); + } + }); + showSeqFeatures.setText("Show Sequence Features"); + showSeqFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + showSeqFeatures_actionPerformed(actionEvent); + } + }); + nucleotideColour.setText("Nucleotide"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideColour_actionPerformed(e); + } + }); + 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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(null); + } + }); + 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); + } + }); + + seqLimits.setText("Show Sequence Limits"); + seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true)); + seqLimits.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + seqLimit_actionPerformed(e); + } + }); + epsFile.setText("EPS"); + epsFile.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createEPS(null); + } + }); + LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); + LoadtreeMenuItem.setText("Load Associated Tree"); + LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + LoadtreeMenuItem_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("By Tree Order"); + sort.setText("Sort"); + calculate.setText("Calculate Tree"); + + jMenu2.setText("Export"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + vamsasStore.setVisible(false); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + vamsasStore_actionPerformed(e); + } + }); + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(e); + } + }); + + /* tabbedPane.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent ece) + { + + tabSelected(); + } + });*/ + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); + } + }); + fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchSequence_actionPerformed(e); + } + }); + smoothFont.setText("Smooth Fonts"); + smoothFont.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + smoothFont_actionPerformed(e); + } + }); + smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false)); + annotationColour.setText("By Annotation..."); + annotationColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(e); + } + }); + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + associatedData_actionPerformed(e); + } + }); + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); + addSequenceMenu.setText("Add Sequences"); + addFromFile.setText("From File"); + addFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromFile_actionPerformed(e); + } + }); + addFromText.setText("From Textbox"); + addFromText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromText_actionPerformed(e); + } + }); + addFromURL.setText("From URL"); + addFromURL.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromURL_actionPerformed(e); + } + }); + exportFeatures.setText("Export Features..."); + exportFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportFeatures_actionPerformed(e); + } + }); + exportAnnotations.setText("Export Annotations..."); + exportAnnotations.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportAnnotations_actionPerformed(e); + } + }); + statusPanel.setLayout(gridLayout1); + jMenu3.setText("Show"); + showAllSeqs.setText("All Sequences"); + showAllSeqs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllSeqs_actionPerformed(e); + } + }); + showAllColumns.setText("All Columns"); + showAllColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllColumns_actionPerformed(e); + } + }); + jMenu4.setText("Hide"); + hideSelSequences.setText("Selected Sequences"); + hideSelSequences.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelSequences_actionPerformed(e); + } + }); + hideSelColumns.setText("Selected Columns"); + hideSelColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelColumns_actionPerformed(e); + } + }); + hiddenMarkers.setText("Hidden Markers"); + hiddenMarkers.setState(true); + hiddenMarkers.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hiddenMarkers_actionPerformed(e); + } + }); + invertColSel.setText("Invert Column Selection"); + invertColSel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertColSel_actionPerformed(e); + } + }); + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(addSequenceMenu); + fileMenu.add(fetchSequence); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); + fileMenu.add(saveAlignmentMenu); + fileMenu.add(jMenu2); + fileMenu.add(outputTextboxMenu); + fileMenu.add(printMenuItem); + fileMenu.addSeparator(); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); + fileMenu.add(LoadtreeMenuItem); + fileMenu.add(associatedData); + 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(invertColSel); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + editMenu.addSeparator(); + editMenu.add(padGapsMenuitem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.add(smoothFont); + viewMenu.addSeparator(); + viewMenu.add(jMenu3); + viewMenu.add(jMenu4); + viewMenu.add(hiddenMarkers); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(seqLimits); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + 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); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.addSeparator(); + calculateMenu.add(showTranslation); + calculateMenu.add(autoCalculate); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices);jMenu1.add(pasteNew); + jMenu1.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + jMenu2.add(htmlMenuItem); + jMenu2.add(epsFile); + jMenu2.add(createPNG); + addSequenceMenu.add(addFromFile); + addSequenceMenu.add(addFromText); + addSequenceMenu.add(addFromURL); + this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); + statusPanel.add(statusBar, null); + jMenu3.add(showAllColumns); + jMenu3.add(showAllSeqs); + jMenu4.add(hideSelColumns); + jMenu4.add(hideSelSequences); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + } + + public void addFromFile_actionPerformed(ActionEvent e) + { + + } + + public void addFromText_actionPerformed(ActionEvent e) + { + + } + + public void addFromURL_actionPerformed(ActionEvent e) + { + + } + + public void exportFeatures_actionPerformed(ActionEvent e) + { + + } + + public void exportAnnotations_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 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 showSeqFeatures_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) + { + } + + public void createPNG(java.io.File f) + { + } + + protected void font_actionPerformed(ActionEvent e) + { + } + + protected void seqLimit_actionPerformed(ActionEvent e) + { + } + + public void seqDBRef_actionPerformed(ActionEvent e) + { + + } + + + public void createEPS(java.io.File f) + { + } + + 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 saveAlignmentMenu_actionPerformed(ActionEvent e) + { + } + + protected void padGapsMenuitem_actionPerformed(ActionEvent e) + { + } + + + public void vamsasStore_actionPerformed(ActionEvent e) + { + + } + + public void vamsasLoad_actionPerformed(ActionEvent e) + { + + } + + public void showTranslation_actionPerformed(ActionEvent e) + { + + } + + public void featureSettings_actionPerformed(ActionEvent e) + { + + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + + } + + public void smoothFont_actionPerformed(ActionEvent e) + { + + } + + public void annotationColour_actionPerformed(ActionEvent e) + { + + } + + + public void associatedData_actionPerformed(ActionEvent e) + { + + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + + } + + public void showAllSeqs_actionPerformed(ActionEvent e) + { + + } + + public void showAllColumns_actionPerformed(ActionEvent e) + { + + } + + public void hideSelSequences_actionPerformed(ActionEvent e) + { + + } + + public void hideSelColumns_actionPerformed(ActionEvent e) + { + + } + + public void hiddenMarkers_actionPerformed(ActionEvent e) + { + + } + + public void findPdbId_actionPerformed(ActionEvent e) + { + + } + + public void enterPdbId_actionPerformed(ActionEvent e) + { + + } + + public void pdbFile_actionPerformed(ActionEvent e) + { + + } + + public void invertColSel_actionPerformed(ActionEvent e) + { + + } +}