+ seqLimits.setText("Show Sequence Limits");\r
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));\r
+ seqLimits.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ seqLimit_actionPerformed(e);\r
+ }\r
+ });\r
+ epsFile.setText("EPS");\r
+ epsFile.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createEPS(null);\r
+ }\r
+ });\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Associated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadtreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleRight_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ sort.addMenuListener(new MenuListener()\r
+ {\r
+ public void menuSelected(MenuEvent e)\r
+ {\r
+ buildTreeMenu();\r
+ }\r
+\r
+ public void menuDeselected(MenuEvent e)\r
+ {\r
+ }\r
+\r
+ public void menuCanceled(MenuEvent e)\r
+ {\r
+ }\r
+ });\r
+ calculate.setText("Calculate Tree");\r
+\r
+ jMenu2.setText("Export Image");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
+ padGapsMenuitem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ vamsasStore.setVisible(false);\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasStore_actionPerformed(e);\r
+ }\r
+ });\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showTranslation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ featureSettings_actionPerformed(e);\r
+ }\r
+ });\r
+ fetchSequence.setText("Fetch Sequence(s)...");\r
+ fetchSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ fetchSequence_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ annotationColour.setText("By Annotation...");\r
+ annotationColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ annotationColour_actionPerformed(e);\r
+ }\r
+ });\r
+ associatedData.setText("Load Features / Annotations");\r
+ associatedData.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ associatedData_actionPerformed(e);\r
+ }\r
+ });\r
+ autoCalculate.setText("Autocalculate Consensus");\r
+ autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+ autoCalculate.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ autoCalculate_actionPerformed(e);\r
+ }\r
+ });\r
+ addSequenceMenu.setText("Add Sequences");\r
+ addFromFile.setText("From File");\r
+ addFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromFile_actionPerformed(e);\r
+ }\r
+ });\r
+ addFromText.setText("From Textbox");\r
+ addFromText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromText_actionPerformed(e);\r
+ }\r
+ });\r
+ addFromURL.setText("From URL");\r
+ addFromURL.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromURL_actionPerformed(e);\r
+ }\r
+ });\r
+ exportFeatures.setText("Export Features...");\r
+ exportFeatures.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ exportFeatures_actionPerformed(e);\r
+ }\r
+ });\r
+ exportAnnotations.setText("Export Annotations...");\r
+ exportAnnotations.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ exportAnnotations_actionPerformed(e);\r
+ }\r
+ });\r
+ statusPanel.setLayout(gridLayout1);\r
+ jMenu3.setText("Show");\r
+ showAllSeqs.setText("All Sequences");\r
+ showAllSeqs.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showAllSeqs_actionPerformed(e);\r
+ }\r
+ });\r
+ showAllColumns.setText("All Columns");\r
+ showAllColumns.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showAllColumns_actionPerformed(e);\r
+ }\r
+ });\r
+ hideMenu.setText("Hide");\r
+ hideSelSequences.setText("Selected Sequences");\r
+ hideSelSequences.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSelSequences_actionPerformed(e);\r
+ }\r
+ });\r
+ hideSelColumns.setText("Selected Columns");\r
+ hideSelColumns.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSelColumns_actionPerformed(e);\r
+ }\r
+ });\r
+ hiddenMarkers.setText("Show Hidden Markers");\r
+ hiddenMarkers.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hiddenMarkers_actionPerformed(e);\r
+ }\r
+ });\r
+ invertColSel.setText("Invert Column Selection");\r
+ invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_I,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
+ | java.awt.event.KeyEvent.ALT_MASK,\r
+ false));\r
+ invertColSel.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ invertColSel_actionPerformed(e);\r
+ }\r
+ });\r
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ JTabbedPane pane = (JTabbedPane) evt.getSource();\r
+ int sel = pane.getSelectedIndex();\r
+ tabSelectionChanged(sel);\r
+ }\r
+ });\r
+ tabbedPane.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ tabbedPane_mousePressed(e);\r
+ }\r
+ });\r
+ tabbedPane.addFocusListener(new FocusAdapter()\r
+ {\r
+ public void focusGained(FocusEvent e)\r
+ {\r
+ tabbedPane_focusGained(e);\r
+ }\r
+ });\r
+ save.setText("Save");\r
+ save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ save.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ save_actionPerformed(e);\r
+ }\r
+ });\r
+ reload.setEnabled(false);\r
+ reload.setText("Reload");\r
+ reload.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ reload_actionPerformed(e);\r
+ }\r
+ });\r
+ newView.setText("New View");\r
+ newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ newView.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ newView_actionPerformed(e);\r
+ }\r
+ });\r
+ tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
+ +\r
+ "<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed(e);\r
+ }\r
+ });\r
+ formatMenu.setText("Format");\r
+ selectMenu.setText("Select");\r
+ idRightAlign.setText("Right Align Sequence Id");\r
+ idRightAlign.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ idRightAlign_actionPerformed(e);\r
+ }\r
+ });\r
+ gatherViews.setEnabled(false);\r
+ gatherViews.setText("Gather Views");\r
+ gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_G, 0, false));\r
+ gatherViews.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ gatherViews_actionPerformed(e);\r
+ }\r
+ });\r
+ expandViews.setEnabled(false);\r
+ expandViews.setText("Expand Views");\r
+ expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_X, 0, false));\r
+ expandViews.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ expandViews_actionPerformed(e);\r
+ }\r
+ });\r
+ pageSetup.setText("Page Setup ...");\r
+ pageSetup.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pageSetup_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.add(addSequenceMenu);\r
+ fileMenu.add(reload);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(vamsasStore);\r
+ fileMenu.add(save);\r
+ fileMenu.add(saveAs);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(pageSetup);\r
+ fileMenu.add(printMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(jMenu2);\r
+ fileMenu.add(exportFeatures);\r
+ fileMenu.add(exportAnnotations);\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.add(associatedData);\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(pasteMenu);\r
+ editMenu.add(delete);\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
+ viewMenu.add(newView);\r
+ viewMenu.add(expandViews);\r
+ viewMenu.add(gatherViews);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(jMenu3);\r
+ viewMenu.add(hideMenu);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(showSeqFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.add(textColour);\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
+ colourMenu.add(annotationColour);\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(showTranslation);\r
+ calculateMenu.add(autoCalculate);\r
+ webServiceNoServices = new JMenuItem("<No Services>");\r
+ webService.add(webServiceNoServices);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ sort.add(sortByTreeMenu);\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
+ addSequenceMenu.add(addFromFile);\r
+ addSequenceMenu.add(addFromText);\r
+ addSequenceMenu.add(addFromURL);\r
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+ statusPanel.add(statusBar, null);\r
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
+ jMenu3.add(showAllColumns);\r
+ jMenu3.add(showAllSeqs);\r
+ hideMenu.add(hideSelColumns);\r
+ hideMenu.add(hideSelSequences);\r
+ formatMenu.add(font);\r
+ formatMenu.addSeparator();\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(idRightAlign);\r
+ formatMenu.add(hiddenMarkers);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(deleteGroups);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ public void addFromFile_actionPerformed(ActionEvent e)\r