+ /**
+ * Action on choosing a structure viewer from combobox options.
+ *
+ * @param selectedItem
+ */
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ }
+
+ /**
+ * Show a dialog for the user to choose a file. Returns the chosen path, or
+ * null on Cancel.
+ *
+ * @return
+ */
+ protected String openFileChooser()
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+
+ // chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ /**
+ * Validate the structure tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateStructure(FocusEvent e)
+ {
+ if (!validateStructure())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
+ * 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(LABEL_FONT);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
+ quality.setEnabled(false);
+ quality.setFont(LABEL_FONT);
+ quality.setHorizontalAlignment(SwingConstants.RIGHT);
+ quality.setHorizontalTextPosition(SwingConstants.LEFT);
+ quality.setSelected(true);
+ quality.setText(MessageManager.getString("label.quality"));
+ conservation.setEnabled(false);
+ conservation.setFont(LABEL_FONT);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText(MessageManager.getString("label.conservation"));
+ identity.setEnabled(false);
+ identity.setFont(LABEL_FONT);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText(MessageManager.getString("label.consensus"));
+ showOccupancy.setFont(LABEL_FONT);
+ showOccupancy.setEnabled(false);
+ showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
+ showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
+ showOccupancy.setSelected(true);
+ showOccupancy.setText(MessageManager.getString("label.occupancy"));
+
+ JLabel showGroupbits = new JLabel();
+ showGroupbits.setFont(LABEL_FONT);
+ showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupbits
+ .setText(MessageManager.getString("action.show_group") + ":");
+ JLabel showConsensbits = new JLabel();
+ showConsensbits.setFont(LABEL_FONT);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits
+ .setText(MessageManager.getString("label.consensus") + ":");
+ showConsensHistogram.setEnabled(false);
+ showConsensHistogram.setFont(LABEL_FONT);
+ showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensHistogram.setSelected(true);
+ showConsensHistogram
+ .setText(MessageManager.getString("label.histogram"));
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(LABEL_FONT);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
+ showGroupConsensus.setEnabled(false);
+ showGroupConsensus.setFont(LABEL_FONT);
+ showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConsensus.setSelected(true);
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
+ showGroupConservation.setEnabled(false);
+ showGroupConservation.setFont(LABEL_FONT);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation
+ .setText(MessageManager.getString("label.conservation"));
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(LABEL_FONT);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText(
+ MessageManager.getString("label.non_positional_features"));
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(LABEL_FONT);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip
+ .setText(MessageManager.getString("label.database_references"));
+ annotations.setFont(LABEL_FONT);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ // annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ identity.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showUnconserved.setFont(LABEL_FONT);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved
+ .setText(MessageManager.getString("action.show_unconserved"));
+ showUnconserved.addActionListener(new ActionListener()
+ {
+ @Override
+ 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(LABEL_FONT);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
+ smoothFont.setFont(LABEL_FONT);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ scaleProteinToCdna.setFont(LABEL_FONT);
+ scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
+ scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
+ scaleProteinToCdna.setText(
+ MessageManager.getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(
+ MessageManager.getString("label.scale_protein_to_cdna_tip"));
+ JLabel gapLabel = new JLabel();
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(LABEL_FONT);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText(MessageManager.getString("label.font"));
+ fontSizeCB.setFont(LABEL_FONT);
+ fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
+ fontStyleCB.setFont(LABEL_FONT);
+ fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
+ fontNameCB.setFont(LABEL_FONT);
+ fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
+ gapSymbolCB.setFont(LABEL_FONT);
+ gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
+
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(LABEL_FONT);