+ void NewTreePanel(String type, String pwType, String title)
+ {
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ SequenceI current;
+ int Width = viewport.getAlignment().getWidth();
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+
+ if (current.getLength() < Width)
+ {
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());
+ }
+ }
+ alignPanel.paintAlignment(true);
+
+ }
+
+ if ((viewport.getSelectionGroup() != null && viewport
+ .getSelectionGroup().getSize() > 1)
+ || (viewport.getAlignment().getHeight() > 1))
+ {
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
+
+ addTreeMenuItem(tp, title);
+
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+ }
+ }
+
+ void loadTree_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
+ cap.setTreeImport();
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.paste_newick_file"), 400, 300);
+ }
+
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)
+ {
+ TreePanel tp = new TreePanel(alignPanel, treeFile,
+ MessageManager.getString("label.load_tree_from_file"), tree);
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+ addTreeMenuItem(tp, treeFile);
+ }
+
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
+ {
+ final MenuItem item = new MenuItem(title);
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ sortByTree(treePanel, title); // treePanel.getTitle());
+ }
+ });
+
+ treePanel.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
+ @Override
+ public void windowClosing(WindowEvent e)
+ {
+ sortByTreeMenu.remove(item);
+ };
+ });
+ }
+
+ 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();
+
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ MenuItem RNAInteractionColour = new MenuItem();
+
+ MenuItem RNAHelixColour = new MenuItem();
+
+ MenuItem userDefinedColour = new MenuItem();
+
+ MenuItem PIDColour = new MenuItem();
+
+ MenuItem BLOSUM62Colour = new MenuItem();
+
+ MenuItem tcoffeeColour = new MenuItem();
+
+ MenuItem njTreeBlosumMenuItem = new MenuItem();
+
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
+
+ MenuItem overviewMenuItem = new MenuItem();
+
+ MenuItem undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ MenuItem findMenuItem = new MenuItem();
+
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+ MenuItem nucleotideColour = new MenuItem();
+
+ MenuItem deleteGroups = new MenuItem();
+
+ MenuItem grpsFromSelection = new MenuItem();
+
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
+ MenuItem delete = new MenuItem();
+
+ MenuItem copy = new MenuItem();
+
+ MenuItem cut = new MenuItem();
+
+ Menu pasteMenu = new Menu();
+
+ MenuItem pasteNew = new MenuItem();
+
+ MenuItem pasteThis = new MenuItem();
+
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+ MenuItem font = new MenuItem();
+
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();