+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+ if (undoname!=null)\r
+ {\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ return true;\r
+ }\r
+\r
+ protected void documentation_actionPerformed()\r
+ {\r
+ alignPanel.av.applet.openJalviewHelpUrl();\r
+ }\r
+\r
+ protected void about_actionPerformed()\r
+ {\r
+\r
+ class AboutPanel extends Canvas\r
+ {\r
+ String version;\r
+\r
+ String builddate;\r
+\r
+ public AboutPanel(String version, String builddate)\r
+ {\r
+ this.version = version;\r
+ this.builddate = builddate;\r
+ }\r
+\r
+ @Override\r
+ public void paint(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int fh = fm.getHeight();\r
+ int y = 5, x = 7;\r
+ g.setColor(Color.black);\r
+ // TODO: update this text for each release or centrally store it for\r
+ // lite and application\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
+ g.drawString("JalviewLite - Release " + version, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
+ g.drawString("Build date: " + builddate, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ g.drawString(\r
+ "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+ x, y += fh * 1.5);\r
+ g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+ g.drawString(\r
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
+ x, y += fh);\r
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);\r
+ g.drawString(\r
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
+ x, y += fh);\r
+ }\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
+ .getBuildDate()));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
+\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (viewport.applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ viewport.applet.showURL(url, target);\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////////////////////////////////////////\r
+ // JBuilder Graphics here\r
+\r
+ MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+ Menu fileMenu = new Menu("File");\r
+\r
+ MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+\r
+ MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+ Menu editMenu = new Menu("Edit");\r
+\r
+ Menu viewMenu = new Menu("View");\r
+\r
+ Menu colourMenu = new Menu("Colour");\r
+\r
+ Menu calculateMenu = new Menu("Calculate");\r
+\r
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+ MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+ MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+ MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+ MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+ MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+ MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+ MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+ MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+ MenuItem PCAMenuItem = new MenuItem();\r
+\r
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+ MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public Label statusBar = new Label();\r
+\r
+ Menu outputTextboxMenu = new Menu();\r
+\r
+ MenuItem clustalColour = new MenuItem();\r
+\r
+ MenuItem zappoColour = new MenuItem();\r
+\r
+ MenuItem taylorColour = new MenuItem();\r
+\r
+ MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+ MenuItem helixColour = new MenuItem();\r
+\r
+ MenuItem strandColour = new MenuItem();\r
+\r
+ MenuItem turnColour = new MenuItem();\r
+\r
+ MenuItem buriedColour = new MenuItem();\r
+\r
+ MenuItem purinePyrimidineColour = new MenuItem();\r
+ MenuItem RNAHelixColour = new MenuItem();\r
+\r
+ MenuItem userDefinedColour = new MenuItem();\r
+\r
+ MenuItem PIDColour = new MenuItem();\r
+\r
+ MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
+ MenuItem tcoffeeColour = new MenuItem();\r
+\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+\r
+ MenuItem undoMenuItem = new MenuItem();\r
+\r
+ MenuItem redoMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem findMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+ MenuItem nucleotideColour = new MenuItem();\r