- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
- wrap.setHorizontalAlignment(SwingConstants.TRAILING);
- wrap.setHorizontalTextPosition(SwingConstants.LEADING);
- wrap.setText(MessageManager.getString("label.wrap_alignment"));
- rightAlign.setFont(JvSwingUtils.getLabelFont());
- rightAlign.setForeground(Color.black);
- rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
- rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
- rightAlign.setText(MessageManager.getString("label.right_align_ids"));
- idItalics.setFont(JvSwingUtils.getLabelFont());
- idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
- idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager
- .getString("label.sequence_name_italics"));
- openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand(MessageManager
- .getString("label.open_overview"));
- openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
- openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText(MessageManager.getString(("label.open_overview")));
- jPanel2.add(fullScreen);
- jPanel2.add(openoverv);
- jPanel2.add(seqLimit);
- jPanel2.add(rightAlign);
- jPanel2.add(fontLabel);
- jPanel2.add(showUnconserved);
- jPanel2.add(idItalics);
- jPanel2.add(smoothFont);
- jPanel2.add(gapLabel);
- jPanel2.add(wrap);
- jPanel2.add(sortLabel);
- jPanel2.add(startupCheckbox);
- visualTab.add(annotations);
- visualTab.add(startupFileTextfield);
- visualTab.add(sortby);
- visualTab.add(gapSymbolCB);
- visualTab.add(fontNameCB);
- visualTab.add(fontSizeCB);
- visualTab.add(fontStyleCB);
+ /**
+ * Initialises the Visual tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initVisualTab()
+ {
+ JPanel visualTab = new JPanel();
+ visualTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_alignment")));
+ visualTab.setLayout(null);
+ fullScreen.setFont(verdana11);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
+ quality.setEnabled(false);
+ quality.setFont(verdana11);
+ quality.setHorizontalAlignment(SwingConstants.RIGHT);
+ quality.setHorizontalTextPosition(SwingConstants.LEFT);
+ quality.setSelected(true);
+ quality.setText(MessageManager.getString("label.quality"));
+ conservation.setEnabled(false);
+ conservation.setFont(verdana11);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText(MessageManager.getString("label.conservation"));
+ identity.setEnabled(false);
+ identity.setFont(verdana11);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText(MessageManager.getString("label.consensus"));
+ JLabel showGroupbits = new JLabel();
+ showGroupbits.setFont(verdana11);
+ showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupbits.setText(MessageManager.getString("action.show_group")
+ + ":");
+ JLabel showConsensbits = new JLabel();
+ showConsensbits.setFont(verdana11);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits.setText(MessageManager.getString("label.consensus")
+ + ":");
+ showConsensHistogram.setEnabled(false);
+ showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensHistogram.setSelected(true);
+ showConsensHistogram.setText(MessageManager
+ .getString("label.histogram"));
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(verdana11);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
+ showGroupConsensus.setEnabled(false);
+ showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConsensus.setSelected(true);
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
+ showGroupConservation.setEnabled(false);
+ showGroupConservation.setFont(verdana11);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation.setText(MessageManager
+ .getString("label.conservation"));
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(verdana11);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText(MessageManager
+ .getString("label.non_positional_features"));
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip.setText(MessageManager
+ .getString("label.database_references"));
+ annotations.setFont(verdana11);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEADING);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showUnconserved.setFont(verdana11);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved.setText(MessageManager
+ .getString("action.show_unconserved"));
+ showUnconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showunconserved_actionPerformed(e);
+ }
+ });
+
+ // TODO these are not yet added to / action from Preferences
+ // JCheckBox shareSelections = new JCheckBox();
+ // shareSelections.setFont(verdana11);
+ // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ // shareSelections.setSelected(true);
+ // shareSelections.setText(MessageManager
+ // .getString("label.share_selection_across_views"));
+ // JCheckBox followHighlight = new JCheckBox();
+ // followHighlight.setFont(verdana11);
+ // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // followHighlight.setSelected(true);
+ // followHighlight.setText(MessageManager
+ // .getString("label.scroll_highlighted_regions"));
+
+ seqLimit.setFont(verdana11);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
+ smoothFont.setFont(verdana11);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ JLabel gapLabel = new JLabel();
+ gapLabel.setFont(verdana11);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(verdana11);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText(MessageManager.getString("label.font"));
+ fontSizeCB.setFont(verdana11);
+ fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
+ fontStyleCB.setFont(verdana11);
+ fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
+ fontNameCB.setFont(verdana11);
+ fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
+ gapSymbolCB.setFont(verdana11);
+ gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
+
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(verdana11);
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+ startupCheckbox.setSelected(true);
+ startupFileTextfield.setFont(verdana11);
+ startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
+ startupFileTextfield.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ startupFileTextfield_mouseClicked();
+ }
+ }
+ });
+
+ sortby.setFont(verdana11);
+ sortby.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel sortLabel = new JLabel();
+ sortLabel.setFont(verdana11);
+ sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortLabel.setText(MessageManager.getString("label.sort_by"));
+ sortAnnBy.setFont(verdana11);
+ sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
+ JLabel sortAnnLabel = new JLabel();
+ sortAnnLabel.setFont(verdana11);
+ sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
+ sortAutocalc.setFont(verdana11);
+ sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
+ JPanel annsettingsPanel = new JPanel();