+
+ useLegacyGap = new JCheckBox(
+ MessageManager.getString("label.ov_legacy_gap"));
+ useLegacyGap.setFont(LABEL_FONT);
+ useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+ useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+ gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
+ MessageManager.getString("label.ov_show_hide_default"));
+ showHiddenAtStart.setFont(LABEL_FONT);
+ showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
+ JLabel hiddenLabel = new JLabel(
+ MessageManager.getString("label.hidden_colour"));
+ hiddenLabel.setFont(LABEL_FONT);
+ hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+ useLegacyGap.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useLegacyGaps_actionPerformed(e);
+ }
+ });
+
+ overviewPanel.setLayout(new GridBagLayout());
+ GridBagConstraints c1 = new GridBagConstraints();
+
+ c1.fill = GridBagConstraints.HORIZONTAL;
+ c1.gridx = 0;
+ c1.gridy = 0;
+ c1.weightx = 1;
+ c1.ipady = 20;
+ c1.anchor = GridBagConstraints.FIRST_LINE_START;
+ overviewPanel.add(useLegacyGap, c1);
+
+ GridBagConstraints c2 = new GridBagConstraints();
+ c2.fill = GridBagConstraints.HORIZONTAL;
+ c2.gridx = 1;
+ c2.gridy = 0;
+ c2.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(gapLabel, c2);
+
+ GridBagConstraints c3 = new GridBagConstraints();
+ c3.fill = GridBagConstraints.HORIZONTAL;
+ c3.gridx = 2;
+ c3.gridy = 0;
+ c3.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(gapColour, c3);
+
+ GridBagConstraints c4 = new GridBagConstraints();
+ c4.fill = GridBagConstraints.HORIZONTAL;
+ c4.gridx = 0;
+ c4.gridy = 1;
+ c4.weightx = 1;
+ overviewPanel.add(showHiddenAtStart, c4);
+
+ GridBagConstraints c5 = new GridBagConstraints();
+ c5.fill = GridBagConstraints.HORIZONTAL;
+ c5.gridx = 1;
+ c5.gridy = 1;
+ c5.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(hiddenLabel, c5);
+
+ GridBagConstraints c6 = new GridBagConstraints();
+ c6.fill = GridBagConstraints.HORIZONTAL;
+ c6.gridx = 2;
+ c6.gridy = 1;
+ c6.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(hiddenColour, c6);
+
+ JButton resetButton = new JButton(
+ MessageManager.getString("label.reset_to_defaults"));
+
+ resetButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetOvDefaults_actionPerformed(e);
+ }
+ });
+
+ GridBagConstraints c7 = new GridBagConstraints();
+ c7.fill = GridBagConstraints.NONE;
+ c7.gridx = 0;
+ c7.gridy = 2;
+ c7.insets = new Insets(10, 0, 0, 0);
+ c7.anchor = GridBagConstraints.WEST;
+ overviewPanel.add(resetButton, c7);
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ overviewPanel.add(spacePanel,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 0, 0));
+
+ return overviewPanel;
+ }
+
+ /**
+ * Initialises the Structure tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initStructureTab()
+ {
+ structureTab = new JPanel();
+
+ structureTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.structure_options")));
+ structureTab.setLayout(null);
+ final int width = 400;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 15;
+
+ structFromPdb.setFont(LABEL_FONT);
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
+ structFromPdb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
+ }
+ });
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ useRnaView.setFont(LABEL_FONT);
+ useRnaView.setText(MessageManager.getString("label.use_rnaview"));
+ useRnaView.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(useRnaView);
+
+ ypos += lineSpacing;
+ addSecondaryStructure.setFont(LABEL_FONT);
+ addSecondaryStructure
+ .setText(MessageManager.getString("label.autoadd_secstr"));
+ addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addSecondaryStructure);
+
+ ypos += lineSpacing;
+ addTempFactor.setFont(LABEL_FONT);
+ addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
+ addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addTempFactor);
+
+ ypos += lineSpacing;
+ JLabel viewerLabel = new JLabel();
+ viewerLabel.setFont(LABEL_FONT);
+ viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
+ viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
+ structureTab.add(viewerLabel);
+
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
+
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
+ }
+ });
+ structureTab.add(structViewer);
+
+ // BH 2019.07.12
+ ypos += lineSpacing;
+ JLabel dimLabel = new JLabel();
+ dimLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ dimLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ dimLabel.setText(
+ MessageManager.getString("label.structure_dimensions"));
+ dimLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(dimLabel);
+
+ structureDimensions.setFont(LABEL_FONT);
+ structureDimensions.setBounds(new Rectangle(160, ypos, 120, height));
+ structureTab.add(structureDimensions);
+
+ ypos += lineSpacing;
+ JLabel pathLabel = new JLabel();
+ pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ pathLabel.setText(MessageManager.getString("label.chimera_path"));
+ pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(pathLabel);
+
+ chimeraPath.setFont(LABEL_FONT);
+ chimeraPath.setText("");
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ chimeraPath.setToolTipText(tooltip);
+ chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ chimeraPath.setText(chosen);
+ }
+ }
+ }
+ });
+ structureTab.add(chimeraPath);
+
+ ypos += lineSpacing;
+ nwMapping.setFont(LABEL_FONT);
+ nwMapping.setText(MessageManager.getString("label.nw_mapping"));
+ siftsMapping.setFont(LABEL_FONT);
+ siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
+ mappingMethod.add(nwMapping);
+ mappingMethod.add(siftsMapping);
+ JPanel mappingPanel = new JPanel();
+ mappingPanel.setFont(LABEL_FONT);
+ TitledBorder mmTitledBorder = new TitledBorder(
+ MessageManager.getString("label.mapping_method"));
+ mmTitledBorder.setTitleFont(LABEL_FONT);
+ mappingPanel.setBorder(mmTitledBorder);
+ mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
+ // GridLayout mappingLayout = new GridLayout();
+ mappingPanel.setLayout(new GridLayout());
+ mappingPanel.add(nwMapping);
+ mappingPanel.add(siftsMapping);
+ structureTab.add(mappingPanel);
+
+ ypos += lineSpacing;
+ ypos += lineSpacing;
+ FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
+ PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
+ docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
+ structureTab.add(docFieldPref);
+
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
+ pathLabel.setVisible(false);
+ chimeraPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }