+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
+ protected void documentation_actionPerformed()
+ {
+ alignPanel.av.applet.openJalviewHelpUrl();
+ }
+
+ protected void about_actionPerformed()
+ {
+
+ class AboutPanel extends Canvas
+ {
+ String version;
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
+ {
+ this.version = version;
+ this.builddate = builddate;
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ FontMetrics fm = g.getFontMetrics();
+ int fh = fm.getHeight();
+ int y = 5, x = 7;
+ g.setColor(Color.black);
+ // TODO: update this text for each release or centrally store it for
+ // lite and application
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));
+ g.drawString(MessageManager.formatMessage(
+ "label.jalviewLite_release", new String[]
+ { version }), x, y += fh);
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));
+ g.drawString(MessageManager.formatMessage(
+ "label.jaview_build_date", new String[]
+ { builddate }), x, y += fh);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
+ x, y += fh * 1.5);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
+ g.drawString(
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_authors"),
+ x, y += fh);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
+ x, y += fh);
+ }
+ }
+
+ Frame frame = new Frame();
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
+
+ }
+
+ public void showURL(String url, String target)
+ {
+ if (viewport.applet == null)
+ {
+ System.out.println("Not running as applet - no browser available.");
+ }
+ else
+ {
+ viewport.applet.showURL(url, target);
+ }
+ }
+
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ MenuBar alignFrameMenuBar = new MenuBar();
+
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
+
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
+
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features").concat("..."));
+
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations").concat("..."));
+
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
+
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
+
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
+
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
+
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
+
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
+
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
+
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
+
+ MenuItem remove2LeftMenuItem = new MenuItem();
+
+ MenuItem remove2RightMenuItem = new MenuItem();
+
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+
+ MenuItem sortIDMenuItem = new MenuItem();
+
+ MenuItem sortLengthMenuItem = new MenuItem();
+
+ MenuItem sortGroupMenuItem = new MenuItem();
+
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+ MenuItem PCAMenuItem = new MenuItem();
+
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
+
+ MenuItem neighbourTreeMenuItem = new MenuItem();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ public Label statusBar = new Label();
+
+ Menu outputTextboxMenu = new Menu();
+
+ MenuItem clustalColour = new MenuItem();
+
+ MenuItem zappoColour = new MenuItem();
+
+ MenuItem taylorColour = new MenuItem();
+
+ MenuItem hydrophobicityColour = new MenuItem();
+
+ MenuItem helixColour = new MenuItem();
+
+ MenuItem strandColour = new MenuItem();
+
+ MenuItem turnColour = new MenuItem();
+
+ MenuItem buriedColour = new MenuItem();