File GPreferences.java

Branches:

Statements:

814

Methods:

Classes:

LOC:

1,870

NCLOC:

1,395

Total complexity:

Complexity density:

0.1

Statements/Method:

11.97

Methods/Class:

22.67

Average method complexity:

1.22

Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage
GPreferences	81	799	76	885	0.00%
GPreferences.RadioButtonRenderer	1802	9	3	13	0.00%
GPreferences.RadioButtonEditor	1837	6	4	10	0.00%

Class GPreferences

Class GPreferences	Line # 81	Total Statements 799	Complexity 76	Uncovered Elements 885	TOTAL Coverage 0.00%
GPreferences() GPreferences()	281281	3.03	2.02	3.03	0.0 0.00%
stateChanged(ChangeEvent) : void stateChanged(ChangeEvent) : void	346346	5.05	4.04	9.09	0.0 0.00%
jbInit() : void jbInit() : void	297297	17.017	2.02	19.019	0.0 0.00%
initEditingTab() : JPanel initEditingTab() : JPanel	369369	16.016	1.01	16.016	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	470470	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	491491	1.01	1.01	1.01	0.0 0.00%
initOutputTab() : JPanel initOutputTab() : JPanel	398398	96.096	2.02	98.098	0.0 0.00%
mouseClicked(MouseEvent) : void mouseClicked(MouseEvent) : void	557557	2.02	2.02	4.04	0.0 0.00%
initConnectionsTab() : JPanel initConnectionsTab() : JPanel	539539	24.024	1.01	24.024	0.0 0.00%
initLinksTab() : JPanel initLinksTab() : JPanel	616616	37.037	1.01	37.037	0.0 0.00%
initLinkTabFilterPanel() : JPanel initLinkTabFilterPanel() : JPanel	677677	34.034	1.01	34.034	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	742742	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	752752	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	762762	1.01	1.01	1.01	0.0 0.00%
initLinkTabUrlButtons() : JPanel initLinkTabUrlButtons() : JPanel	726726	37.037	1.01	37.037	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	829829	1.01	1.01	1.01	0.0 0.00%
initConnTabProxyPanel() : JPanel initConnTabProxyPanel() : JPanel	806806	23.023	1.01	23.023	0.0 0.00%
initConnTabCheckboxes() : void initConnTabCheckboxes() : void	869869	12.012	1.01	12.012	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	904904	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	914914	1.01	1.01	1.01	0.0 0.00%
initOkCancelPanel() : JPanel initOkCancelPanel() : JPanel	898898	10.010	1.01	10.010	0.0 0.00%
mousePressed(MouseEvent) : void mousePressed(MouseEvent) : void	946946	1.01	1.01	1.01	0.0 0.00%
mousePressed(MouseEvent) : void mousePressed(MouseEvent) : void	961961	1.01	1.01	1.01	0.0 0.00%
initColoursTab() : JPanel initColoursTab() : JPanel	931931	40.040	1.01	40.040	0.0 0.00%
mousePressed(MouseEvent) : void mousePressed(MouseEvent) : void	10261026	1.01	1.01	1.01	0.0 0.00%
mousePressed(MouseEvent) : void mousePressed(MouseEvent) : void	10401040	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	10701070	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	11281128	1.01	1.01	1.01	0.0 0.00%
initOverviewTab() : JPanel initOverviewTab() : JPanel	10131013	78.078	1.01	78.078	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	11761176	4.04	1.01	4.04	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	12221222	1.01	1.01	1.01	0.0 0.00%
mouseClicked(MouseEvent) : void mouseClicked(MouseEvent) : void	12471247	4.04	3.03	8.08	0.0 0.00%
initStructureTab() : JPanel initStructureTab() : JPanel	11581158	82.082	2.02	84.084	0.0 0.00%
structureViewer_actionPerformed(String) : void structureViewer_actionPerformed(String) : void	13081308	0.00	1.01	0.00	-1.0 -1.0 -
openFileChooser() : String openFileChooser() : String	13181318	8.08	2.02	10.010	0.0 0.00%
validateStructure(FocusEvent) : boolean validateStructure(FocusEvent) : boolean	13421342	4.04	2.02	6.06	0.0 0.00%
validateStructure() : boolean validateStructure() : boolean	13521352	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	14571457	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	14651465	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	14731473	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	14871487	1.01	1.01	1.01	0.0 0.00%
mouseClicked(MouseEvent) : void mouseClicked(MouseEvent) : void	15581558	2.02	2.02	4.04	0.0 0.00%
initVisualTab() : JPanel initVisualTab() : JPanel	13621362	236.0236	2.02	238.0238	0.0 0.00%
autoIdWidth_actionPerformed() : void autoIdWidth_actionPerformed() : void	16861686	0.00	1.01	0.00	-1.0 -1.0 -
userIdWidth_actionPerformed() : void userIdWidth_actionPerformed() : void	16921692	0.00	1.01	0.00	-1.0 -1.0 -
maxColour_actionPerformed(JPanel) : void maxColour_actionPerformed(JPanel) : void	16981698	0.00	1.01	0.00	-1.0 -1.0 -
minColour_actionPerformed(JPanel) : void minColour_actionPerformed(JPanel) : void	17021702	0.00	1.01	0.00	-1.0 -1.0 -
gapColour_actionPerformed(JPanel) : void gapColour_actionPerformed(JPanel) : void	17061706	0.00	1.01	0.00	-1.0 -1.0 -
hiddenColour_actionPerformed(JPanel) : void hiddenColour_actionPerformed(JPanel) : void	17101710	0.00	1.01	0.00	-1.0 -1.0 -
showunconserved_actionPerformed(ActionEvent) : void showunconserved_actionPerformed(ActionEvent) : void	17141714	0.00	1.01	0.00	-1.0 -1.0 -
useLegacyGaps_actionPerformed(ActionEvent) : void useLegacyGaps_actionPerformed(ActionEvent) : void	17201720	0.00	1.01	0.00	-1.0 -1.0 -
resetOvDefaults_actionPerformed(ActionEvent) : void resetOvDefaults_actionPerformed(ActionEvent) : void	17241724	0.00	1.01	0.00	-1.0 -1.0 -
ok_actionPerformed(ActionEvent) : void ok_actionPerformed(ActionEvent) : void	17341734	0.00	1.01	0.00	-1.0 -1.0 -
cancel_actionPerformed(ActionEvent) : void cancel_actionPerformed(ActionEvent) : void	17441744	0.00	1.01	0.00	-1.0 -1.0 -
annotations_actionPerformed(ActionEvent) : void annotations_actionPerformed(ActionEvent) : void	17541754	0.00	1.01	0.00	-1.0 -1.0 -
startupFileTextfield_mouseClicked() : void startupFileTextfield_mouseClicked() : void	17611761	0.00	1.01	0.00	-1.0 -1.0 -
newLink_actionPerformed(ActionEvent) : void newLink_actionPerformed(ActionEvent) : void	17651765	0.00	1.01	0.00	-1.0 -1.0 -
editLink_actionPerformed(ActionEvent) : void editLink_actionPerformed(ActionEvent) : void	17701770	0.00	1.01	0.00	-1.0 -1.0 -
deleteLink_actionPerformed(ActionEvent) : void deleteLink_actionPerformed(ActionEvent) : void	17751775	0.00	1.01	0.00	-1.0 -1.0 -
defaultBrowser_mouseClicked(MouseEvent) : void defaultBrowser_mouseClicked(MouseEvent) : void	17801780	0.00	1.01	0.00	-1.0 -1.0 -
linkURLList_keyTyped(KeyEvent) : void linkURLList_keyTyped(KeyEvent) : void	17851785	0.00	1.01	0.00	-1.0 -1.0 -
useProxy_actionPerformed() : void useProxy_actionPerformed() : void	17901790	5.05	1.01	5.05	0.0 0.00%

Class GPreferences.RadioButtonRenderer

Class GPreferences.RadioButtonRenderer	Line # 1802	Total Statements 9	Complexity 3	Uncovered Elements 13	TOTAL Coverage 0.00%
RadioButtonRenderer() RadioButtonRenderer()	18051805	2.02	1.01	2.02	0.0 0.00%
getTableCellRendererComponent(JTable,Object,boolean,boolean,int,int) : Component getTableCellRendererComponent(JTable,Object,boolean,boolean,int,int) : Component	18111811	7.07	2.02	9.09	0.0 0.00%

Class GPreferences.RadioButtonEditor

Class GPreferences.RadioButtonEditor	Line # 1837	Total Statements 6	Complexity 4	Uncovered Elements 10	TOTAL Coverage 0.00%
actionPerformed(ActionEvent) : void actionPerformed(ActionEvent) : void	18471847	1.01	1.01	1.01	0.0 0.00%
RadioButtonEditor() RadioButtonEditor()	18421842	2.02	1.01	2.02	0.0 0.00%
getTableCellEditorComponent(JTable,Object,boolean,int,int) : Component getTableCellEditorComponent(JTable,Object,boolean,int,int) : Component	18551855	2.02	1.01	2.02	0.0 0.00%
getCellEditorValue() : Object getCellEditorValue() : Object	18631863	1.01	1.01	1.01	0.0 0.00%

Contributing tests

No tests hitting this source file were found.

Source view

* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

* Copyright (C) $$Year-Rel$$ The Jalview Authors

* This file is part of Jalview.

* Jalview is free software: you can redistribute it and/or

* modify it under the terms of the GNU General Public License

* as published by the Free Software Foundation, either version 3

* of the License, or (at your option) any later version.

* Jalview is distributed in the hope that it will be useful, but

* WITHOUT ANY WARRANTY; without even the implied warranty

* of MERCHANTABILITY or FITNESS FOR A PARTICULAR

* PURPOSE. See the GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with Jalview. If not, see <http://www.gnu.org/licenses/>.

* The Jalview Authors are detailed in the 'AUTHORS' file.

package jalview.jbgui;

import jalview.bin.Jalview;

import jalview.fts.core.FTSDataColumnPreferences;

import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;

import jalview.fts.service.pdb.PDBFTSRestClient;

import jalview.gui.JvSwingUtils;

import jalview.gui.StructureViewer.ViewerType;

import jalview.util.MessageManager;

import java.awt.BorderLayout;

import java.awt.Color;

import java.awt.Component;

import java.awt.Dimension;

import java.awt.FlowLayout;

import java.awt.Font;

import java.awt.GridBagConstraints;

import java.awt.GridBagLayout;

import java.awt.GridLayout;

import java.awt.Insets;

import java.awt.Rectangle;

import java.awt.event.ActionEvent;

import java.awt.event.ActionListener;

import java.awt.event.FocusEvent;

import java.awt.event.KeyEvent;

import java.awt.event.MouseAdapter;

import java.awt.event.MouseEvent;

import javax.swing.AbstractCellEditor;

import javax.swing.BorderFactory;

import javax.swing.ButtonGroup;

import javax.swing.DefaultListCellRenderer;

import javax.swing.JButton;

import javax.swing.JCheckBox;

import javax.swing.JComboBox;

import javax.swing.JFileChooser;

import javax.swing.JLabel;

import javax.swing.JPanel;

import javax.swing.JRadioButton;

import javax.swing.JScrollPane;

import javax.swing.JTabbedPane;

import javax.swing.JTable;

import javax.swing.JTextField;

import javax.swing.ListSelectionModel;

import javax.swing.SwingConstants;

import javax.swing.border.Border;

import javax.swing.border.EmptyBorder;

import javax.swing.border.EtchedBorder;

import javax.swing.border.TitledBorder;

import javax.swing.event.ChangeEvent;

import javax.swing.event.ChangeListener;

import javax.swing.table.TableCellEditor;

import javax.swing.table.TableCellRenderer;

/**

* Base class for the Preferences panel.

* @author $author$

* @version $Revision$

public class GPreferences extends JPanel

{

private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();

private static final Font LABEL_FONT_ITALIC = JvSwingUtils

.getLabelFont(false, true);

* Visual tab components

protected JCheckBox fullScreen = new JCheckBox();

protected JCheckBox openoverv = new JCheckBox();

protected JCheckBox seqLimit = new JCheckBox();

protected JCheckBox rightAlign = new JCheckBox();

protected JComboBox<String> fontSizeCB = new JComboBox<>();

100

101

protected JComboBox<String> fontStyleCB = new JComboBox<>();

102

103

protected JComboBox<String> fontNameCB = new JComboBox<>();

104

105

protected JCheckBox showOccupancy = new JCheckBox();

106

107

protected JCheckBox showUnconserved = new JCheckBox();

108

109

protected JCheckBox idItalics = new JCheckBox();

110

111

protected JCheckBox smoothFont = new JCheckBox();

112

113

protected JCheckBox scaleProteinToCdna = new JCheckBox();

114

115

protected JComboBox<String> gapSymbolCB = new JComboBox<>();

116

117

protected JCheckBox wrap = new JCheckBox();

118

119

protected JComboBox<String> sortby = new JComboBox<>();

120

121

protected JComboBox<String> sortAnnBy = new JComboBox<>();

122

123

protected JComboBox<String> sortAutocalc = new JComboBox<>();

124

125

protected JCheckBox startupCheckbox = new JCheckBox();

126

127

protected JTextField startupFileTextfield = new JTextField();

128

129

// below are in the 'second column'

130

protected JCheckBox annotations = new JCheckBox();

131

132

protected JCheckBox quality = new JCheckBox();

133

134

protected JCheckBox conservation = new JCheckBox();

135

136

protected JCheckBox identity = new JCheckBox();

137

138

protected JCheckBox showGroupConsensus = new JCheckBox();

139

140

protected JCheckBox showGroupConservation = new JCheckBox();

141

142

protected JCheckBox showConsensHistogram = new JCheckBox();

143

144

protected JCheckBox showConsensLogo = new JCheckBox();

145

146

protected JCheckBox showDbRefTooltip = new JCheckBox();

147

148

protected JCheckBox showNpTooltip = new JCheckBox();

149

150

151

* Structure tab and components

152

153

protected JPanel structureTab;

154

155

protected JCheckBox structFromPdb = new JCheckBox();

156

157

protected JCheckBox useRnaView = new JCheckBox();

158

159

protected JCheckBox addSecondaryStructure = new JCheckBox();

160

161

protected JCheckBox addTempFactor = new JCheckBox();

162

163

protected JComboBox<String> structViewer = new JComboBox<>();

164

165

protected JTextField chimeraPath = new JTextField();

166

167

protected ButtonGroup mappingMethod = new ButtonGroup();

168

169

protected JRadioButton siftsMapping = new JRadioButton();

170

171

protected JRadioButton nwMapping = new JRadioButton();

172

173

174

* Colours tab components

175

176

protected JPanel minColour = new JPanel();

177

178

protected JPanel maxColour = new JPanel();

179

180

protected JComboBox<String> protColour = new JComboBox<>();

181

182

protected JComboBox<String> nucColour = new JComboBox<>();

183

184

185

* Overview tab components

186

187

protected JPanel gapColour = new JPanel();

188

189

protected JPanel hiddenColour = new JPanel();

190

191

protected JCheckBox useLegacyGap;

192

193

protected JCheckBox showHiddenAtStart;

194

195

protected JLabel gapLabel;

196

197

198

* Connections tab components

199

200

protected JTable linkUrlTable = new JTable();

201

202

protected JButton editLink = new JButton();

203

204

protected JButton deleteLink = new JButton();

205

206

protected JTextField filterTB = new JTextField();

207

208

protected JButton doReset = new JButton();

209

210

protected JButton userOnly = new JButton();

211

212

protected JLabel portLabel = new JLabel();

213

214

protected JLabel serverLabel = new JLabel();

215

216

protected JTextField proxyServerTB = new JTextField();

217

218

protected JTextField proxyPortTB = new JTextField();

219

220

protected JTextField defaultBrowser = new JTextField();

221

222

protected JCheckBox useProxy = new JCheckBox();

223

224

protected JCheckBox usagestats = new JCheckBox();

225

226

protected JCheckBox questionnaire = new JCheckBox();

227

228

protected JCheckBox versioncheck = new JCheckBox();

229

230

231

* Output tab components

232

233

protected JComboBox<Object> epsRendering = new JComboBox<>();

234

235

protected JComboBox<Object> htmlRendering = new JComboBox<>();

236

237

protected JComboBox<Object> svgRendering = new JComboBox<>();

238

239

protected JLabel userIdWidthlabel = new JLabel();

240

241

protected JCheckBox autoIdWidth = new JCheckBox();

242

243

protected JTextField userIdWidth = new JTextField();

244

245

protected JCheckBox blcjv = new JCheckBox();

246

247

protected JCheckBox pileupjv = new JCheckBox();

248

249

protected JCheckBox clustaljv = new JCheckBox();

250

251

protected JCheckBox msfjv = new JCheckBox();

252

253

protected JCheckBox fastajv = new JCheckBox();

254

255

protected JCheckBox pfamjv = new JCheckBox();

256

257

protected JCheckBox pirjv = new JCheckBox();

258

259

protected JCheckBox modellerOutput = new JCheckBox();

260

261

protected JCheckBox embbedBioJSON = new JCheckBox();

262

263

264

* Editing tab components

265

266

protected JCheckBox autoCalculateConsCheck = new JCheckBox();

267

268

protected JCheckBox padGaps = new JCheckBox();

269

270

protected JCheckBox sortByTree = new JCheckBox();

* Web Services tab

protected JPanel wsTab = new JPanel();

277

278

/**

279

* Creates a new GPreferences object.

280

281

public GPreferences()

{

try

{

jbInit();

} catch (Exception ex)

287

{

288

ex.printStackTrace();

}

}

/**

* Construct the panel and its tabbed sub-panels.

* @throws Exception

private void jbInit() throws Exception

298

{

299

final JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();

300

this.setLayout(new BorderLayout());

301

JPanel okCancelPanel = initOkCancelPanel();

302

this.add(tabbedPane, BorderLayout.CENTER);

303

this.add(okCancelPanel, BorderLayout.SOUTH);

304

305

tabbedPane.add(initVisualTab(),

306

MessageManager.getString("label.visual"));

307

308

tabbedPane.add(initColoursTab(),

309

MessageManager.getString("label.colours"));

310

311

tabbedPane.add(initOverviewTab(),

312

MessageManager.getString("label.overview"));

313

314

tabbedPane.add(initStructureTab(),

315

MessageManager.getString("label.structure"));

316

317

tabbedPane.add(initConnectionsTab(),

318

MessageManager.getString("label.connections"));

319

320

tabbedPane.add(initLinksTab(),

321

MessageManager.getString("label.urllinks"));

322

323

tabbedPane.add(initOutputTab(),

324

MessageManager.getString("label.output"));

325

326

tabbedPane.add(initEditingTab(),

327

MessageManager.getString("label.editing"));

328

329

330

* See WsPreferences for the real work of configuring this tab.

if (!Jalview.isJS())

{

wsTab.setLayout(new BorderLayout());

335

tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));

}

* Handler to validate a tab before leaving it - currently only for

340

* Structure.

341

342

tabbedPane.addChangeListener(new ChangeListener()

343

{

344

private Component lastTab;

345

346

@Override

347

public void stateChanged(ChangeEvent e)

348

{

349

if (lastTab == structureTab

350

&& tabbedPane.getSelectedComponent() != structureTab)

351

{

352

if (!validateStructure())

353

{

354

tabbedPane.setSelectedComponent(structureTab);

return;

}

}

lastTab = tabbedPane.getSelectedComponent();

}

});

}

/**

* Initialises the Editing tabbed panel.

* @return

private JPanel initEditingTab()

370

{

371

JPanel editingTab = new JPanel();

372

editingTab.setLayout(null);

373

autoCalculateConsCheck.setFont(LABEL_FONT);

374

autoCalculateConsCheck.setText(

375

MessageManager.getString("label.autocalculate_consensus"));

376

autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));

377

padGaps.setFont(LABEL_FONT);

378

padGaps.setText(

379

MessageManager.getString("label.pad_gaps_when_editing"));

380

padGaps.setBounds(new Rectangle(22, 94, 168, 23));

381

sortByTree.setFont(LABEL_FONT);

382

sortByTree

383

.setText(MessageManager.getString("label.sort_with_new_tree"));

384

sortByTree.setToolTipText(MessageManager.getString(

385

"label.any_trees_calculated_or_loaded_alignment_automatically_sort"));

386

sortByTree.setBounds(new Rectangle(22, 136, 168, 23));

387

editingTab.add(autoCalculateConsCheck);

388

editingTab.add(padGaps);

389

editingTab.add(sortByTree);

return editingTab;

}

/**

* Initialises the Output tab

* @return

private JPanel initOutputTab()

399

{

400

JPanel outputTab = new JPanel();

401

outputTab.setLayout(null);

402

403

JLabel epsLabel = new JLabel(

404

MessageManager.formatMessage("label.rendering_style", "EPS"));

405

epsLabel.setFont(LABEL_FONT);

406

epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);

407

epsLabel.setBounds(new Rectangle(9, 31, 160, 24));

408

epsRendering.setFont(LABEL_FONT);

409

epsRendering.setBounds(new Rectangle(174, 34, 187, 21));

410

JLabel htmlLabel = new JLabel(

411

MessageManager.formatMessage("label.rendering_style", "HTML"));

412

htmlLabel.setFont(LABEL_FONT);

413

htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);

414

htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));

415

htmlRendering.setFont(LABEL_FONT);

416

htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));

417

JLabel svgLabel = new JLabel(

418

MessageManager.formatMessage("label.rendering_style", "SVG"));

419

svgLabel.setFont(LABEL_FONT);

420

svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);

421

svgLabel.setBounds(new Rectangle(9, 79, 160, 24));

422

svgRendering.setFont(LABEL_FONT);

423

svgRendering.setBounds(new Rectangle(174, 82, 187, 21));

424

425

JLabel jLabel1 = new JLabel();

426

jLabel1.setFont(LABEL_FONT);

427

jLabel1.setHorizontalAlignment(SwingConstants.CENTER);

428

jLabel1.setText(MessageManager.getString("label.append_start_end"));

429

jLabel1.setFont(LABEL_FONT);

430

431

fastajv.setFont(LABEL_FONT);

432

fastajv.setHorizontalAlignment(SwingConstants.LEFT);

433

clustaljv.setText(MessageManager.getString("label.clustal") + " ");

434

blcjv.setText(MessageManager.getString("label.blc") + " ");

435

fastajv.setText(MessageManager.getString("label.fasta") + " ");

436

msfjv.setText(MessageManager.getString("label.msf") + " ");

437

pfamjv.setText(MessageManager.getString("label.pfam") + " ");

438

pileupjv.setText(MessageManager.getString("label.pileup") + " ");

439

msfjv.setFont(LABEL_FONT);

440

msfjv.setHorizontalAlignment(SwingConstants.LEFT);

441

pirjv.setText(MessageManager.getString("label.pir") + " ");

442

JPanel jPanel11 = new JPanel();

443

jPanel11.setFont(LABEL_FONT);

444

TitledBorder titledBorder2 = new TitledBorder(

445

MessageManager.getString("label.file_output"));

446

jPanel11.setBorder(titledBorder2);

447

jPanel11.setBounds(new Rectangle(30, 120, 196, 182));

448

GridLayout gridLayout3 = new GridLayout();

449

jPanel11.setLayout(gridLayout3);

450

gridLayout3.setRows(8);

451

blcjv.setFont(LABEL_FONT);

452

blcjv.setHorizontalAlignment(SwingConstants.LEFT);

453

clustaljv.setFont(LABEL_FONT);

454

clustaljv.setHorizontalAlignment(SwingConstants.LEFT);

455

pfamjv.setFont(LABEL_FONT);

456

pfamjv.setHorizontalAlignment(SwingConstants.LEFT);

457

pileupjv.setFont(LABEL_FONT);

458

pileupjv.setHorizontalAlignment(SwingConstants.LEFT);

459

pirjv.setFont(LABEL_FONT);

460

pirjv.setHorizontalAlignment(SwingConstants.LEFT);

461

autoIdWidth.setFont(LABEL_FONT);

462

autoIdWidth.setText(

463

MessageManager.getString("label.automatically_set_id_width"));

464

autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager

465

.getString("label.adjusts_width_generated_eps_png")));

466

autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));

467

autoIdWidth.addActionListener(new ActionListener()

{

@Override

public void actionPerformed(ActionEvent e)

472

{

473

autoIdWidth_actionPerformed();

474

}

475

});

476

userIdWidthlabel.setFont(LABEL_FONT);

477

userIdWidthlabel.setText(

478

MessageManager.getString("label.figure_id_column_width"));

479

userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager

480

.getString("label.manually_specify_width_left_column")));

481

userIdWidthlabel.setToolTipText(

482

JvSwingUtils.wrapTooltip(true, MessageManager.getString(

483

"label.manually_specify_width_left_column")));

484

userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));

485

userIdWidth.setFont(JvSwingUtils.getTextAreaFont());

486

userIdWidth.setText("");

487

userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));

488

userIdWidth.addActionListener(new ActionListener()

{

@Override

public void actionPerformed(ActionEvent e)

493

{

494

userIdWidth_actionPerformed();

495

}

496

});

497

modellerOutput.setFont(LABEL_FONT);

498

modellerOutput

499

.setText(MessageManager.getString("label.use_modeller_output"));

500

modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));

501

embbedBioJSON.setFont(LABEL_FONT);

502

embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));

503

embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));

504

505

jPanel11.add(jLabel1);

506

jPanel11.add(blcjv);

507

jPanel11.add(clustaljv);

508

jPanel11.add(fastajv);

509

jPanel11.add(msfjv);

510

jPanel11.add(pfamjv);

511

jPanel11.add(pileupjv);

512

jPanel11.add(pirjv);

513

outputTab.add(autoIdWidth);

514

outputTab.add(userIdWidth);

515

outputTab.add(userIdWidthlabel);

516

outputTab.add(modellerOutput);

if (!Jalview.isJS())

{

* JalviewJS doesn't support Lineart option or SVG output

521

522

outputTab.add(embbedBioJSON);

523

outputTab.add(epsLabel);

524

outputTab.add(epsRendering);

525

outputTab.add(htmlLabel);

526

outputTab.add(htmlRendering);

527

outputTab.add(svgLabel);

528

outputTab.add(svgRendering);

529

}

530

outputTab.add(jPanel11);

return outputTab;

}

/**

* Initialises the Connections tabbed panel.

* @return

private JPanel initConnectionsTab()

540

{

541

JPanel connectTab = new JPanel();

542

connectTab.setLayout(new GridBagLayout());

543

544

// Label for browser text box

545

JLabel browserLabel = new JLabel();

546

browserLabel.setFont(LABEL_FONT);

547

browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);

548

browserLabel.setText(

549

MessageManager.getString("label.default_browser_unix"));

550

defaultBrowser.setFont(LABEL_FONT);

551

defaultBrowser.setText("");

552

final String tooltip = JvSwingUtils.wrapTooltip(true,

553

MessageManager.getString("label.double_click_to_browse"));

554

defaultBrowser.setToolTipText(tooltip);

555

defaultBrowser.addMouseListener(new MouseAdapter()

556

{

557

@Override

558

public void mouseClicked(MouseEvent e)

559

{

560

if (e.getClickCount() > 1)

561

{

562

defaultBrowser_mouseClicked(e);

}

}

});

JPanel proxyPanel = initConnTabProxyPanel();

568

initConnTabCheckboxes();

569

570

// Add default Browser text box

571

connectTab.add(browserLabel,

572

new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,

573

GridBagConstraints.WEST, GridBagConstraints.NONE,

574

new Insets(10, 0, 5, 5), 5, 1));

575

defaultBrowser.setFont(LABEL_FONT);

576

defaultBrowser.setText("");

577

578

connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,

579

0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,

580

new Insets(10, 0, 5, 10), 30, 1));

581

582

// Add proxy server panel

583

connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,

584

GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,

585

new Insets(10, 0, 5, 12), 4, 10));

586

587

// Add usage stats, version check and questionnaire checkboxes

588

connectTab.add(usagestats,

589

new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,

590

GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,

591

new Insets(0, 2, 5, 5), 70, 1));

592

connectTab.add(questionnaire,

593

new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,

594

GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,

595

new Insets(0, 2, 5, 10), 70, 1));

596

connectTab.add(versioncheck,

597

new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,

598

GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,

599

new Insets(0, 2, 5, 5), 70, 1));

600

601

// Add padding so the panel doesn't look ridiculous

602

JPanel spacePanel = new JPanel();

603

connectTab.add(spacePanel,

604

new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,

605

GridBagConstraints.WEST, GridBagConstraints.BOTH,

606

new Insets(0, 0, 0, 5), 70, 1));

return connectTab;

}

/**

* Initialises the Links tabbed panel.

* @return

private JPanel initLinksTab()

617

{

618

JPanel linkTab = new JPanel();

619

linkTab.setLayout(new GridBagLayout());

620

621

// Set up table for Url links

622

linkUrlTable.setFillsViewportHeight(true);

623

linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);

624

linkUrlTable.setAutoCreateRowSorter(true);

625

linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);

626

627

// adjust row height so radio buttons actually fit

628

// don't do this in the renderer, it causes the awt thread to activate

629

// constantly

630

JRadioButton temp = new JRadioButton();

631

linkUrlTable.setRowHeight(temp.getMinimumSize().height);

632

633

// Table in scrollpane so that the table is given a scrollbar

634

JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);

635

linkScrollPane.setBorder(null);

636

637

// Panel for links functionality

638

JPanel linkPanel = new JPanel(new GridBagLayout());

639

linkPanel.setBorder(new TitledBorder(

640

MessageManager.getString("label.url_linkfrom_sequence_id")));

641

642

// Put the Url links panel together

643

644

// Buttons go at top right, resizing only resizes the blank space vertically

645

JPanel buttonPanel = initLinkTabUrlButtons();

646

GridBagConstraints linkConstraints1 = new GridBagConstraints();

647

linkConstraints1.insets = new Insets(0, 0, 5, 0);

648

linkConstraints1.gridx = 0;

649

linkConstraints1.gridy = 0;

650

linkConstraints1.weightx = 1.0;

651

linkConstraints1.fill = GridBagConstraints.HORIZONTAL;

652

linkTab.add(buttonPanel, linkConstraints1);

653

654

// Links table goes at top left, resizing resizes the table

655

GridBagConstraints linkConstraints2 = new GridBagConstraints();

656

linkConstraints2.insets = new Insets(0, 0, 5, 5);

657

linkConstraints2.gridx = 0;

658

linkConstraints2.gridy = 1;

659

linkConstraints2.weightx = 1.0;

660

linkConstraints2.weighty = 1.0;

661

linkConstraints2.fill = GridBagConstraints.BOTH;

662

linkTab.add(linkScrollPane, linkConstraints2);

663

664

// Filter box and buttons goes at bottom left, resizing resizes the text box

665

JPanel filterPanel = initLinkTabFilterPanel();

666

GridBagConstraints linkConstraints3 = new GridBagConstraints();

667

linkConstraints3.insets = new Insets(0, 0, 0, 5);

668

linkConstraints3.gridx = 0;

669

linkConstraints3.gridy = 2;

670

linkConstraints3.weightx = 1.0;

671

linkConstraints3.fill = GridBagConstraints.HORIZONTAL;

672

linkTab.add(filterPanel, linkConstraints3);

return linkTab;

}

private JPanel initLinkTabFilterPanel()

678

{

679

// Filter textbox and reset button

680

JLabel filterLabel = new JLabel(

681

MessageManager.getString("label.filter"));

682

filterLabel.setFont(LABEL_FONT);

683

filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);

684

filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);

685

686

filterTB.setFont(LABEL_FONT);

687

filterTB.setText("");

688

689

doReset.setText(MessageManager.getString("action.showall"));

690

userOnly.setText(MessageManager.getString("action.customfilter"));

691

692

// Panel for filter functionality

693

JPanel filterPanel = new JPanel(new GridBagLayout());

694

filterPanel.setBorder(new TitledBorder("Filter"));

695

GridBagConstraints gbc = new GridBagConstraints();

696

gbc.gridx = 0;

697

gbc.gridy = 0;

698

gbc.fill = GridBagConstraints.NONE;

699

gbc.anchor = GridBagConstraints.WEST;

700

701

filterPanel.add(filterLabel, gbc);

702

703

GridBagConstraints gbc1 = new GridBagConstraints();

704

gbc1.gridx = 1;

705

gbc1.gridwidth = 2;

706

gbc1.fill = GridBagConstraints.HORIZONTAL;

707

gbc1.anchor = GridBagConstraints.WEST;

708

gbc1.weightx = 1.0;

709

filterPanel.add(filterTB, gbc1);

710

711

GridBagConstraints gbc2 = new GridBagConstraints();

712

gbc2.gridx = 3;

713

gbc2.fill = GridBagConstraints.NONE;

714

gbc2.anchor = GridBagConstraints.WEST;

715

filterPanel.add(doReset, gbc2);

716

717

GridBagConstraints gbc3 = new GridBagConstraints();

718

gbc3.gridx = 4;

719

gbc3.fill = GridBagConstraints.NONE;

720

gbc3.anchor = GridBagConstraints.WEST;

721

filterPanel.add(userOnly, gbc3);

return filterPanel;

}

private JPanel initLinkTabUrlButtons()

727

{

728

// Buttons for new / edit / delete Url links

729

JButton newLink = new JButton();

730

newLink.setText(MessageManager.getString("action.new"));

731

732

editLink.setText(MessageManager.getString("action.edit"));

733

734

deleteLink.setText(MessageManager.getString("action.delete"));

735

736

// no current selection, so initially disable delete/edit buttons

737

editLink.setEnabled(false);

738

deleteLink.setEnabled(false);

739

740

newLink.addActionListener(new java.awt.event.ActionListener()

741

{

742

@Override

743

public void actionPerformed(ActionEvent e)

744

{

745

newLink_actionPerformed(e);

}

});

editLink.setText(MessageManager.getString("action.edit"));

750

editLink.addActionListener(new java.awt.event.ActionListener()

751

{

752

@Override

753

public void actionPerformed(ActionEvent e)

754

{

755

editLink_actionPerformed(e);

}

});

deleteLink.setText(MessageManager.getString("action.delete"));

760

deleteLink.addActionListener(new java.awt.event.ActionListener()

761

{

762

@Override

763

public void actionPerformed(ActionEvent e)

764

{

765

deleteLink_actionPerformed(e);

}

});

JPanel buttonPanel = new JPanel(new GridBagLayout());

770

buttonPanel.setBorder(new TitledBorder("Edit links"));

771

GridBagConstraints gbc = new GridBagConstraints();

772

gbc.gridx = 0;

773

gbc.gridy = 0;

774

gbc.fill = GridBagConstraints.NONE;

775

buttonPanel.add(newLink, gbc);

776

777

GridBagConstraints gbc1 = new GridBagConstraints();

778

gbc1.gridx = 1;

779

gbc1.gridy = 0;

780

gbc1.fill = GridBagConstraints.NONE;

781

buttonPanel.add(editLink, gbc1);

782

783

GridBagConstraints gbc2 = new GridBagConstraints();

784

gbc2.gridx = 2;

785

gbc2.gridy = 0;

786

gbc2.fill = GridBagConstraints.NONE;

787

buttonPanel.add(deleteLink, gbc2);

788

789

GridBagConstraints gbc3 = new GridBagConstraints();

790

gbc3.gridx = 3;

791

gbc3.gridy = 0;

792

gbc3.fill = GridBagConstraints.HORIZONTAL;

793

gbc3.weightx = 1.0;

794

JPanel spacePanel = new JPanel();

795

spacePanel.setBorder(null);

796

buttonPanel.add(spacePanel, gbc3);

return buttonPanel;

}

/**

* Initialises the proxy server panel in the Connections tab

803

804

* @return the proxy server panel

805

806

private JPanel initConnTabProxyPanel()

807

{

808

// Label for server text box

809

serverLabel.setText(MessageManager.getString("label.address"));

810

serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);

811

serverLabel.setFont(LABEL_FONT);

812

813

// Proxy server and port text boxes

814

proxyServerTB.setFont(LABEL_FONT);

815

proxyPortTB.setFont(LABEL_FONT);

816

817

// Label for Port text box

818

portLabel.setFont(LABEL_FONT);

819

portLabel.setHorizontalAlignment(SwingConstants.RIGHT);

820

portLabel.setText(MessageManager.getString("label.port"));

821

822

// Use proxy server checkbox

823

useProxy.setFont(LABEL_FONT);

824

useProxy.setHorizontalAlignment(SwingConstants.RIGHT);

825

useProxy.setHorizontalTextPosition(SwingConstants.LEADING);

826

useProxy.setText(MessageManager.getString("label.use_proxy_server"));

827

useProxy.addActionListener(new ActionListener()

828

{

829

@Override

830

public void actionPerformed(ActionEvent e)

831

{

832

useProxy_actionPerformed();

}

});

// Make proxy server panel

837

JPanel proxyPanel = new JPanel();

838

TitledBorder titledBorder1 = new TitledBorder(

839

MessageManager.getString("label.proxy_server"));

840

proxyPanel.setBorder(titledBorder1);

841

proxyPanel.setLayout(new GridBagLayout());

842

proxyPanel.add(serverLabel,

843

new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,

844

GridBagConstraints.WEST, GridBagConstraints.NONE,

845

new Insets(0, 2, 2, 0), 5, 0));

846

proxyPanel.add(portLabel,

847

new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,

848

GridBagConstraints.WEST, GridBagConstraints.NONE,

849

new Insets(0, 0, 2, 0), 11, 0));

850

proxyPanel.add(useProxy,

851

new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,

852

GridBagConstraints.WEST, GridBagConstraints.NONE,

853

new Insets(0, 2, 5, 185), 2, -4));

854

proxyPanel.add(proxyPortTB,

855

new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,

856

GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,

857

new Insets(0, 2, 2, 2), 54, 1));

858

proxyPanel.add(proxyServerTB,

859

new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,

860

GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,

861

new Insets(0, 2, 2, 0), 263, 1));

return proxyPanel;

}

/**

* Initialises the checkboxes in the Connections tab

868

869

private void initConnTabCheckboxes()

870

{

871

// Usage stats checkbox label

872

usagestats.setText(

873

MessageManager.getString("label.send_usage_statistics"));

874

usagestats.setFont(LABEL_FONT);

875

usagestats.setHorizontalAlignment(SwingConstants.RIGHT);

876

usagestats.setHorizontalTextPosition(SwingConstants.LEADING);

877

878

// Questionnaire checkbox label

879

questionnaire.setText(

880

MessageManager.getString("label.check_for_questionnaires"));

881

questionnaire.setFont(LABEL_FONT);

882

questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);

883

questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);

884

885

// Check for latest version checkbox label

886

versioncheck.setText(

887

MessageManager.getString("label.check_for_latest_version"));

888

versioncheck.setFont(LABEL_FONT);

889

versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);

890

versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);

}

/**

* Initialises the parent panel which contains the tabbed sections.

* @return

private JPanel initOkCancelPanel()

899

{

900

JButton ok = new JButton();

901

ok.setText(MessageManager.getString("action.ok"));

902

ok.addActionListener(new ActionListener()

903

{

904

@Override

905

public void actionPerformed(ActionEvent e)

906

{

907

ok_actionPerformed(e);

908

}

909

});

910

JButton cancel = new JButton();

911

cancel.setText(MessageManager.getString("action.cancel"));

912

cancel.addActionListener(new ActionListener()

913

{

914

@Override

915

public void actionPerformed(ActionEvent e)

916

{

917

cancel_actionPerformed(e);

918

}

919

});

920

JPanel okCancelPanel = new JPanel();

921

okCancelPanel.add(ok);

922

okCancelPanel.add(cancel);

923

return okCancelPanel;

}

/**

* Initialises the Colours tabbed panel.

* @return

private JPanel initColoursTab()

932

{

933

JPanel coloursTab = new JPanel();

934

coloursTab.setBorder(new TitledBorder(

935

MessageManager.getString("action.open_new_alignment")));

936

coloursTab.setLayout(new FlowLayout());

937

JLabel mincolourLabel = new JLabel();

938

mincolourLabel.setFont(LABEL_FONT);

939

mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);

940

mincolourLabel.setText(MessageManager.getString("label.min_colour"));

941

minColour.setFont(LABEL_FONT);

942

minColour.setBorder(BorderFactory.createEtchedBorder());

943

minColour.setPreferredSize(new Dimension(40, 20));

944

minColour.addMouseListener(new MouseAdapter()

945

{

946

@Override

947

public void mousePressed(MouseEvent e)

948

{

949

minColour_actionPerformed(minColour);

950

}

951

});

952

JLabel maxcolourLabel = new JLabel();

953

maxcolourLabel.setFont(LABEL_FONT);

954

maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);

955

maxcolourLabel.setText(MessageManager.getString("label.max_colour"));

956

maxColour.setFont(LABEL_FONT);

957

maxColour.setBorder(BorderFactory.createEtchedBorder());

958

maxColour.setPreferredSize(new Dimension(40, 20));

959

maxColour.addMouseListener(new MouseAdapter()

960

{

961

@Override

962

public void mousePressed(MouseEvent e)

963

{

964

maxColour_actionPerformed(maxColour);

}

});

protColour.setFont(LABEL_FONT);

969

protColour.setBounds(new Rectangle(172, 225, 155, 21));

970

JLabel protColourLabel = new JLabel();

971

protColourLabel.setFont(LABEL_FONT);

972

protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);

973

protColourLabel.setText(

974

MessageManager.getString("label.prot_alignment_colour") + " ");

975

JvSwingUtils.addtoLayout(coloursTab,

976

MessageManager

977

.getString("label.default_colour_scheme_for_alignment"),

978

protColourLabel, protColour);

979

980

nucColour.setFont(LABEL_FONT);

981

nucColour.setBounds(new Rectangle(172, 240, 155, 21));

982

JLabel nucColourLabel = new JLabel();

983

nucColourLabel.setFont(LABEL_FONT);

984

nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);

985

nucColourLabel.setText(

986

MessageManager.getString("label.nuc_alignment_colour") + " ");

987

JvSwingUtils.addtoLayout(coloursTab,

988

MessageManager

989

.getString("label.default_colour_scheme_for_alignment"),

990

nucColourLabel, nucColour);

991

992

JPanel annotationShding = new JPanel();

993

annotationShding.setBorder(new TitledBorder(

994

MessageManager.getString("label.annotation_shading_default")));

995

annotationShding.setLayout(new GridLayout(1, 2));

996

JvSwingUtils.addtoLayout(annotationShding,

997

MessageManager.getString(

998

"label.default_minimum_colour_annotation_shading"),

999

mincolourLabel, minColour);

1000

JvSwingUtils.addtoLayout(annotationShding,

1001

MessageManager.getString(

1002

"label.default_maximum_colour_annotation_shading"),

1003

maxcolourLabel, maxColour);

1004

coloursTab.add(annotationShding); // , FlowLayout.LEFT);

return coloursTab;

}

/**

* Initialises the Overview tabbed panel.

* @return

private JPanel initOverviewTab()

1014

{

1015

JPanel overviewPanel = new JPanel();

1016

overviewPanel.setBorder(new TitledBorder(

1017

MessageManager.getString("label.overview_settings")));

1018

1019

gapColour.setFont(LABEL_FONT);

1020

// fixing the border colours stops apparent colour bleed from the panel

1021

gapColour.setBorder(

1022

BorderFactory.createEtchedBorder(Color.white, Color.lightGray));

1023

gapColour.setPreferredSize(new Dimension(40, 20));

1024

gapColour.addMouseListener(new MouseAdapter()

1025

{

1026

@Override

1027

public void mousePressed(MouseEvent e)

1028

{

1029

gapColour_actionPerformed(gapColour);

}

});

hiddenColour.setFont(LABEL_FONT);

1034

// fixing the border colours stops apparent colour bleed from the panel

1035

hiddenColour.setBorder(

1036

BorderFactory.createEtchedBorder(Color.white, Color.lightGray));

1037

hiddenColour.setPreferredSize(new Dimension(40, 20));

1038

hiddenColour.addMouseListener(new MouseAdapter()

1039

{

1040

@Override

1041

public void mousePressed(MouseEvent e)

1042

{

1043

hiddenColour_actionPerformed(hiddenColour);

}

});

useLegacyGap = new JCheckBox(

1048

MessageManager.getString("label.ov_legacy_gap"));

1049

useLegacyGap.setFont(LABEL_FONT);

1050

useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);

1051

useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);

1052

gapLabel = new JLabel(

1053

MessageManager.getString("label.gap_colour"));

1054

gapLabel.setFont(LABEL_FONT);

1055

gapLabel.setHorizontalAlignment(SwingConstants.LEFT);

1056

gapLabel.setVerticalTextPosition(SwingConstants.TOP);

1057

showHiddenAtStart = new JCheckBox(

1058

MessageManager.getString("label.ov_show_hide_default"));

1059

showHiddenAtStart.setFont(LABEL_FONT);

1060

showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);

1061

showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);

1062

JLabel hiddenLabel = new JLabel(

1063

MessageManager.getString("label.hidden_colour"));

1064

hiddenLabel.setFont(LABEL_FONT);

1065

hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);

1066

hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);

1067

1068

useLegacyGap.addActionListener(new ActionListener()

1069

{

1070

@Override

1071

public void actionPerformed(ActionEvent e)

1072

{

1073

useLegacyGaps_actionPerformed(e);

}

});

overviewPanel.setLayout(new GridBagLayout());

1078

GridBagConstraints c1 = new GridBagConstraints();

1079

1080

c1.fill = GridBagConstraints.HORIZONTAL;

c1.gridx = 0;

c1.gridy = 0;

c1.weightx = 1;

c1.ipady = 20;

c1.anchor = GridBagConstraints.FIRST_LINE_START;

1086

overviewPanel.add(useLegacyGap, c1);

1087

1088

GridBagConstraints c2 = new GridBagConstraints();

1089

c2.fill = GridBagConstraints.HORIZONTAL;

1090

c2.gridx = 1;

1091

c2.gridy = 0;

1092

c2.insets = new Insets(0, 15, 0, 10);

1093

overviewPanel.add(gapLabel, c2);

1094

1095

GridBagConstraints c3 = new GridBagConstraints();

1096

c3.fill = GridBagConstraints.HORIZONTAL;

1097

c3.gridx = 2;

1098

c3.gridy = 0;

1099

c3.insets = new Insets(0, 0, 0, 15);

1100

overviewPanel.add(gapColour, c3);

1101

1102

GridBagConstraints c4 = new GridBagConstraints();

1103

c4.fill = GridBagConstraints.HORIZONTAL;

c4.gridx = 0;

c4.gridy = 1;

c4.weightx = 1;

overviewPanel.add(showHiddenAtStart, c4);

1108

1109

GridBagConstraints c5 = new GridBagConstraints();

1110

c5.fill = GridBagConstraints.HORIZONTAL;

1111

c5.gridx = 1;

1112

c5.gridy = 1;

1113

c5.insets = new Insets(0, 15, 0, 10);

1114

overviewPanel.add(hiddenLabel, c5);

1115

1116

GridBagConstraints c6 = new GridBagConstraints();

1117

c6.fill = GridBagConstraints.HORIZONTAL;

1118

c6.gridx = 2;

1119

c6.gridy = 1;

1120

c6.insets = new Insets(0, 0, 0, 15);

1121

overviewPanel.add(hiddenColour, c6);

1122

1123

JButton resetButton = new JButton(

1124

MessageManager.getString("label.reset_to_defaults"));

1125

1126

resetButton.addActionListener(new ActionListener()

1127

{

1128

@Override

1129

public void actionPerformed(ActionEvent e)

1130

{

1131

resetOvDefaults_actionPerformed(e);

}

});

GridBagConstraints c7 = new GridBagConstraints();

1136

c7.fill = GridBagConstraints.NONE;

1137

c7.gridx = 0;

1138

c7.gridy = 2;

1139

c7.insets = new Insets(10, 0, 0, 0);

1140

c7.anchor = GridBagConstraints.WEST;

1141

overviewPanel.add(resetButton, c7);

1142

1143

// Add padding so the panel doesn't look ridiculous

1144

JPanel spacePanel = new JPanel();

1145

overviewPanel.add(spacePanel,

1146

new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,

1147

GridBagConstraints.WEST, GridBagConstraints.BOTH,

1148

new Insets(0, 0, 0, 5), 0, 0));

1149

1150

return overviewPanel;

}

/**

* Initialises the Structure tabbed panel.

* @return

private JPanel initStructureTab()

1159

{

1160

structureTab = new JPanel();

1161

1162

structureTab.setBorder(new TitledBorder(

1163

MessageManager.getString("label.structure_options")));

1164

structureTab.setLayout(null);

1165

final int width = 400;

1166

final int height = 22;

1167

final int lineSpacing = 25;

1168

int ypos = 15;

1169

1170

structFromPdb.setFont(LABEL_FONT);

1171

structFromPdb

1172

.setText(MessageManager.getString("label.struct_from_pdb"));

1173

structFromPdb.setBounds(new Rectangle(5, ypos, width, height));

1174

structFromPdb.addActionListener(new ActionListener()

1175

{

1176

@Override

1177

public void actionPerformed(ActionEvent e)

1178

{

1179

boolean selected = structFromPdb.isSelected();

1180

// enable other options only when the first is checked

1181

useRnaView.setEnabled(selected);

1182

addSecondaryStructure.setEnabled(selected);

1183

addTempFactor.setEnabled(selected);

1184

}

1185

});

1186

structureTab.add(structFromPdb);

1187

1188

// indent checkboxes that are conditional on the first one

1189

ypos += lineSpacing;

1190

useRnaView.setFont(LABEL_FONT);

1191

useRnaView.setText(MessageManager.getString("label.use_rnaview"));

1192

useRnaView.setBounds(new Rectangle(25, ypos, width, height));

1193

structureTab.add(useRnaView);

1194

1195

ypos += lineSpacing;

1196

addSecondaryStructure.setFont(LABEL_FONT);

1197

addSecondaryStructure

1198

.setText(MessageManager.getString("label.autoadd_secstr"));

1199

addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));

1200

structureTab.add(addSecondaryStructure);

1201

1202

ypos += lineSpacing;

1203

addTempFactor.setFont(LABEL_FONT);

1204

addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));

1205

addTempFactor.setBounds(new Rectangle(25, ypos, width, height));

1206

structureTab.add(addTempFactor);

1207

1208

ypos += lineSpacing;

1209

JLabel viewerLabel = new JLabel();

1210

viewerLabel.setFont(LABEL_FONT);

1211

viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);

1212

viewerLabel.setText(MessageManager.getString("label.structure_viewer"));

1213

viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));

1214

structureTab.add(viewerLabel);

1215

1216

structViewer.setFont(LABEL_FONT);

1217

structViewer.setBounds(new Rectangle(160, ypos, 120, height));

1218

structViewer.addItem(ViewerType.JMOL.name());

1219

structViewer.addItem(ViewerType.CHIMERA.name());

1220

structViewer.addActionListener(new ActionListener()

1221

{

1222

@Override

1223

public void actionPerformed(ActionEvent e)

1224

{

1225

structureViewer_actionPerformed(

1226

(String) structViewer.getSelectedItem());

1227

}

1228

});

1229

structureTab.add(structViewer);

1230

1231

ypos += lineSpacing;

1232

JLabel pathLabel = new JLabel();

1233

pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));

1234

pathLabel.setHorizontalAlignment(SwingConstants.LEFT);

1235

pathLabel.setText(MessageManager.getString("label.chimera_path"));

1236

pathLabel.setBounds(new Rectangle(10, ypos, 140, height));

1237

structureTab.add(pathLabel);

1238

1239

chimeraPath.setFont(LABEL_FONT);

1240

chimeraPath.setText("");

1241

final String tooltip = JvSwingUtils.wrapTooltip(true,

1242

MessageManager.getString("label.chimera_path_tip"));

1243

chimeraPath.setToolTipText(tooltip);

1244

chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));

1245

chimeraPath.addMouseListener(new MouseAdapter()

1246

{

1247

@Override

1248

public void mouseClicked(MouseEvent e)

1249

{

1250

if (e.getClickCount() == 2)

1251

{

1252

String chosen = openFileChooser();

1253

if (chosen != null)

1254

{

1255

chimeraPath.setText(chosen);

}

}

}

});

structureTab.add(chimeraPath);

1261

1262

ypos += lineSpacing;

1263

nwMapping.setFont(LABEL_FONT);

1264

nwMapping.setText(MessageManager.getString("label.nw_mapping"));

1265

siftsMapping.setFont(LABEL_FONT);

1266

siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));

1267

mappingMethod.add(nwMapping);

1268

mappingMethod.add(siftsMapping);

1269

JPanel mappingPanel = new JPanel();

1270

mappingPanel.setFont(LABEL_FONT);

1271

TitledBorder mmTitledBorder = new TitledBorder(

1272

MessageManager.getString("label.mapping_method"));

1273

mmTitledBorder.setTitleFont(LABEL_FONT);

1274

mappingPanel.setBorder(mmTitledBorder);

1275

mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));

1276

// GridLayout mappingLayout = new GridLayout();

1277

mappingPanel.setLayout(new GridLayout());

1278

mappingPanel.add(nwMapping);

1279

mappingPanel.add(siftsMapping);

1280

structureTab.add(mappingPanel);

ypos += lineSpacing;

ypos += lineSpacing;

FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(

1285

PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());

1286

docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));

1287

structureTab.add(docFieldPref);

1288

1289

1290

* hide Chimera options in JalviewJS

if (Jalview.isJS())

{

pathLabel.setVisible(false);

1295

chimeraPath.setVisible(false);

1296

viewerLabel.setVisible(false);

1297

structViewer.setVisible(false);

}

return structureTab;

}

/**

* Action on choosing a structure viewer from combobox options.

1305

1306

* @param selectedItem

1307

1308

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()

1319

{

1320

String choice = null;

1321

JFileChooser chooser = new JFileChooser();

1322

1323

// chooser.setFileView(new JalviewFileView());

1324

chooser.setDialogTitle(

1325

MessageManager.getString("label.open_local_file"));

1326

chooser.setToolTipText(MessageManager.getString("action.open"));

1327

1328

int value = chooser.showOpenDialog(this);

1329

1330

if (value == JFileChooser.APPROVE_OPTION)

1331

{

1332

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)

1343

{

1344

if (!validateStructure())

1345

{

1346

e.getComponent().requestFocusInWindow();

return false;

}

return true;

}

protected boolean validateStructure()

{

return false;

}

/**

* Initialises the Visual tabbed panel.

* @return

private JPanel initVisualTab()

1363

{

1364

JPanel visualTab = new JPanel();

1365

visualTab.setBorder(new TitledBorder(

1366

MessageManager.getString("action.open_new_alignment")));

1367

visualTab.setLayout(null);

1368

fullScreen.setFont(LABEL_FONT);

1369

fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);

1370

fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);

1371

fullScreen.setText(MessageManager.getString("label.maximize_window"));

1372

quality.setEnabled(false);

1373

quality.setFont(LABEL_FONT);

1374

quality.setHorizontalAlignment(SwingConstants.RIGHT);

1375

quality.setHorizontalTextPosition(SwingConstants.LEFT);

1376

quality.setSelected(true);

1377

quality.setText(MessageManager.getString("label.quality"));

1378

conservation.setEnabled(false);

1379

conservation.setFont(LABEL_FONT);

1380

conservation.setHorizontalAlignment(SwingConstants.RIGHT);

1381

conservation.setHorizontalTextPosition(SwingConstants.LEFT);

1382

conservation.setSelected(true);

1383

conservation.setText(MessageManager.getString("label.conservation"));

1384

identity.setEnabled(false);

1385

identity.setFont(LABEL_FONT);

1386

identity.setHorizontalAlignment(SwingConstants.RIGHT);

1387

identity.setHorizontalTextPosition(SwingConstants.LEFT);

1388

identity.setSelected(true);

1389

identity.setText(MessageManager.getString("label.consensus"));

1390

showOccupancy.setFont(LABEL_FONT);

1391

showOccupancy.setEnabled(false);

1392

showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);

1393

showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);

1394

showOccupancy.setSelected(true);

1395

showOccupancy.setText(MessageManager.getString("label.occupancy"));

1396

1397

JLabel showGroupbits = new JLabel();

1398

showGroupbits.setFont(LABEL_FONT);

1399

showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);

1400

showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);

1401

showGroupbits

1402

.setText(MessageManager.getString("action.show_group") + ":");

1403

JLabel showConsensbits = new JLabel();

1404

showConsensbits.setFont(LABEL_FONT);

1405

showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);

1406

showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);

1407

showConsensbits

1408

.setText(MessageManager.getString("label.consensus") + ":");

1409

showConsensHistogram.setEnabled(false);

1410

showConsensHistogram.setFont(LABEL_FONT);

1411

showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);

1412

showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);

1413

showConsensHistogram.setSelected(true);

1414

showConsensHistogram

1415

.setText(MessageManager.getString("label.histogram"));

1416

showConsensLogo.setEnabled(false);

1417

showConsensLogo.setFont(LABEL_FONT);

1418

showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);

1419

showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);

1420

showConsensLogo.setSelected(true);

1421

showConsensLogo.setText(MessageManager.getString("label.logo"));

1422

showGroupConsensus.setEnabled(false);

1423

showGroupConsensus.setFont(LABEL_FONT);

1424

showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);

1425

showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);

1426

showGroupConsensus.setSelected(true);

1427

showGroupConsensus.setText(MessageManager.getString("label.consensus"));

1428

showGroupConservation.setEnabled(false);

1429

showGroupConservation.setFont(LABEL_FONT);

1430

showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);

1431

showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);

1432

showGroupConservation.setSelected(true);

1433

showGroupConservation

1434

.setText(MessageManager.getString("label.conservation"));

1435

showNpTooltip.setEnabled(true);

1436

showNpTooltip.setFont(LABEL_FONT);

1437

showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);

1438

showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);

1439

showNpTooltip.setSelected(true);

1440

showNpTooltip.setText(

1441

MessageManager.getString("label.non_positional_features"));

1442

showDbRefTooltip.setEnabled(true);

1443

showDbRefTooltip.setFont(LABEL_FONT);

1444

showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);

1445

showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);

1446

showDbRefTooltip.setSelected(true);

1447

showDbRefTooltip

1448

.setText(MessageManager.getString("label.database_references"));

1449

annotations.setFont(LABEL_FONT);

1450

annotations.setHorizontalAlignment(SwingConstants.RIGHT);

1451

annotations.setHorizontalTextPosition(SwingConstants.LEFT);

1452

annotations.setSelected(true);

1453

annotations.setText(MessageManager.getString("label.show_annotations"));

1454

// annotations.setBounds(new Rectangle(169, 12, 200, 23));

1455

annotations.addActionListener(new ActionListener()

1456

{

1457

@Override

1458

public void actionPerformed(ActionEvent e)

1459

{

1460

annotations_actionPerformed(e);

1461

}

1462

});

1463

identity.addActionListener(new ActionListener()

1464

{

1465

@Override

1466

public void actionPerformed(ActionEvent e)

1467

{

1468

annotations_actionPerformed(e);

1469

}

1470

});

1471

showGroupConsensus.addActionListener(new ActionListener()

1472

{

1473

@Override

1474

public void actionPerformed(ActionEvent e)

1475

{

1476

annotations_actionPerformed(e);

1477

}

1478

});

1479

showUnconserved.setFont(LABEL_FONT);

1480

showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);

1481

showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);

1482

showUnconserved.setSelected(true);

1483

showUnconserved

1484

.setText(MessageManager.getString("action.show_unconserved"));

1485

showUnconserved.addActionListener(new ActionListener()

1486

{

1487

@Override

1488

public void actionPerformed(ActionEvent e)

1489

{

1490

showunconserved_actionPerformed(e);

}

});

// TODO these are not yet added to / action from Preferences

1495

// JCheckBox shareSelections = new JCheckBox();

1496

// shareSelections.setFont(verdana11);

1497

// shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);

1498

// shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);

1499

// shareSelections.setSelected(true);

1500

// shareSelections.setText(MessageManager

1501

// .getString("label.share_selection_across_views"));

1502

// JCheckBox followHighlight = new JCheckBox();

1503

// followHighlight.setFont(verdana11);

1504

// followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);

1505

// followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);

1506

// // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));

1507

// followHighlight.setSelected(true);

1508

// followHighlight.setText(MessageManager

1509

// .getString("label.scroll_highlighted_regions"));

1510

1511

seqLimit.setFont(LABEL_FONT);

1512

seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);

1513

seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);

1514

seqLimit.setText(MessageManager.getString("label.full_sequence_id"));

1515

smoothFont.setFont(LABEL_FONT);

1516

smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);

1517

smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);

1518

smoothFont.setText(MessageManager.getString("label.smooth_font"));

1519

scaleProteinToCdna.setFont(LABEL_FONT);

1520

scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);

1521

scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);

1522

scaleProteinToCdna.setText(

1523

MessageManager.getString("label.scale_protein_to_cdna"));

1524

scaleProteinToCdna.setToolTipText(

1525

MessageManager.getString("label.scale_protein_to_cdna_tip"));

1526

JLabel gapLabel = new JLabel();

1527

gapLabel.setFont(LABEL_FONT);

1528

gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);

1529

gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");

1530

JLabel fontLabel = new JLabel();

1531

fontLabel.setFont(LABEL_FONT);

1532

fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);

1533

fontLabel.setText(MessageManager.getString("label.font"));

1534

fontSizeCB.setFont(LABEL_FONT);

1535

fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));

1536

fontStyleCB.setFont(LABEL_FONT);

1537

fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));

1538

fontNameCB.setFont(LABEL_FONT);

1539

fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));

1540

gapSymbolCB.setFont(LABEL_FONT);

1541

gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));

1542

DefaultListCellRenderer dlcr = new DefaultListCellRenderer();

1543

dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);

1544

gapSymbolCB.setRenderer(dlcr);

1545

1546

startupCheckbox.setText(MessageManager.getString("action.open_file"));

1547

startupCheckbox.setFont(LABEL_FONT);

1548

startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);

1549

startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);

1550

startupCheckbox.setSelected(true);

1551

startupFileTextfield.setFont(LABEL_FONT);

1552

startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));

1553

final String tooltip = JvSwingUtils.wrapTooltip(true,

1554

MessageManager.getString("label.double_click_to_browse"));

1555

startupFileTextfield.setToolTipText(tooltip);

1556

startupFileTextfield.addMouseListener(new MouseAdapter()

1557

{

1558

@Override

1559

public void mouseClicked(MouseEvent e)

1560

{

1561

if (e.getClickCount() > 1)

1562

{

1563

startupFileTextfield_mouseClicked();

}

}

});

sortby.setFont(LABEL_FONT);

1569

sortby.setBounds(new Rectangle(172, 260, 155, 21));

1570

JLabel sortLabel = new JLabel();

1571

sortLabel.setFont(LABEL_FONT);

1572

sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);

1573

sortLabel.setText(MessageManager.getString("label.sort_by"));

1574

sortAnnBy.setFont(LABEL_FONT);

1575

sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));

1576

JLabel sortAnnLabel = new JLabel();

1577

sortAnnLabel.setFont(LABEL_FONT);

1578

sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);

1579

sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));

1580

sortAutocalc.setFont(LABEL_FONT);

1581

sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));

1582

1583

JPanel annsettingsPanel = new JPanel();

1584

annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));

1585

annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));

1586

annsettingsPanel.setBorder(new EtchedBorder());

1587

visualTab.add(annsettingsPanel);

1588

Border jb = new EmptyBorder(1, 1, 4, 5);

1589

annotations.setBorder(jb);

1590

showOccupancy.setBorder(jb);

1591

quality.setBorder(jb);

1592

conservation.setBorder(jb);

1593

identity.setBorder(jb);

1594

showConsensbits.setBorder(jb);

1595

showGroupbits.setBorder(jb);

1596

showGroupConsensus.setBorder(jb);

1597

showGroupConservation.setBorder(jb);

1598

showConsensHistogram.setBorder(jb);

1599

showConsensLogo.setBorder(jb);

1600

1601

JPanel autoAnnotSettings = new JPanel();

1602

annsettingsPanel.add(autoAnnotSettings);

1603

autoAnnotSettings.setLayout(new GridLayout(0, 2));

1604

autoAnnotSettings.add(annotations);

1605

autoAnnotSettings.add(quality);

1606

// second row of autoannotation box

1607

autoAnnotSettings = new JPanel();

1608

annsettingsPanel.add(autoAnnotSettings);

1609

1610

autoAnnotSettings.setLayout(new GridLayout(0, 3));

1611

autoAnnotSettings.add(conservation);

1612

autoAnnotSettings.add(identity);

1613

autoAnnotSettings.add(showOccupancy);

1614

autoAnnotSettings.add(showGroupbits);

1615

autoAnnotSettings.add(showGroupConservation);

1616

autoAnnotSettings.add(showGroupConsensus);

1617

autoAnnotSettings.add(showConsensbits);

1618

autoAnnotSettings.add(showConsensHistogram);

1619

autoAnnotSettings.add(showConsensLogo);

1620

1621

JPanel tooltipSettings = new JPanel();

1622

tooltipSettings.setBorder(new TitledBorder(

1623

MessageManager.getString("label.sequence_id_tooltip")));

1624

tooltipSettings.setBounds(173, 140, 220, 62);

1625

tooltipSettings.setLayout(new GridLayout(2, 1));

1626

tooltipSettings.add(showDbRefTooltip);

1627

tooltipSettings.add(showNpTooltip);

1628

visualTab.add(tooltipSettings);

1629

1630

wrap.setFont(LABEL_FONT);

1631

wrap.setHorizontalAlignment(SwingConstants.TRAILING);

1632

wrap.setHorizontalTextPosition(SwingConstants.LEADING);

1633

wrap.setText(MessageManager.getString("label.wrap_alignment"));

1634

rightAlign.setFont(LABEL_FONT);

1635

rightAlign.setForeground(Color.black);

1636

rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);

1637

rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);

1638

rightAlign.setText(MessageManager.getString("label.right_align_ids"));

1639

idItalics.setFont(LABEL_FONT_ITALIC);

1640

idItalics.setHorizontalAlignment(SwingConstants.RIGHT);

1641

idItalics.setHorizontalTextPosition(SwingConstants.LEADING);

1642

idItalics.setText(

1643

MessageManager.getString("label.sequence_name_italics"));

1644

openoverv.setFont(LABEL_FONT);

1645

openoverv.setActionCommand(

1646

MessageManager.getString("label.open_overview"));

1647

openoverv.setHorizontalAlignment(SwingConstants.RIGHT);

1648

openoverv.setHorizontalTextPosition(SwingConstants.LEFT);

1649

openoverv.setText(MessageManager.getString("label.open_overview"));

1650

JPanel jPanel2 = new JPanel();

1651

jPanel2.setBounds(new Rectangle(7, 17, 158, 310));

1652

jPanel2.setLayout(new GridLayout(14, 1));

1653

jPanel2.add(fullScreen);

1654

jPanel2.add(openoverv);

1655

jPanel2.add(seqLimit);

1656

jPanel2.add(rightAlign);

1657

jPanel2.add(fontLabel);

1658

jPanel2.add(showUnconserved);

1659

jPanel2.add(idItalics);

1660

jPanel2.add(smoothFont);

1661

jPanel2.add(scaleProteinToCdna);

1662

jPanel2.add(gapLabel);

1663

jPanel2.add(wrap);

1664

jPanel2.add(sortLabel);

1665

jPanel2.add(sortAnnLabel);

1666

jPanel2.add(startupCheckbox);

1667

visualTab.add(jPanel2);

1668

visualTab.add(startupFileTextfield);

1669

visualTab.add(sortby);

1670

visualTab.add(sortAnnBy);

1671

visualTab.add(sortAutocalc);

1672

visualTab.add(gapSymbolCB);

1673

visualTab.add(fontNameCB);

1674

visualTab.add(fontSizeCB);

1675

visualTab.add(fontStyleCB);

if (Jalview.isJS())

{

startupCheckbox.setVisible(false);

1680

startupFileTextfield.setVisible(false);

}

return visualTab;

}

protected void autoIdWidth_actionPerformed()

1687

{

1688

// TODO Auto-generated method stub

}

protected void userIdWidth_actionPerformed()

1693

{

1694

// TODO Auto-generated method stub

}

protected void maxColour_actionPerformed(JPanel panel)

{

}

protected void minColour_actionPerformed(JPanel panel)

{

}

protected void gapColour_actionPerformed(JPanel panel)

{

}

protected void hiddenColour_actionPerformed(JPanel panel)

{

}

protected void showunconserved_actionPerformed(ActionEvent e)

1715

{

1716

// TODO Auto-generated method stub

}

protected void useLegacyGaps_actionPerformed(ActionEvent e)

{

}

protected void resetOvDefaults_actionPerformed(ActionEvent e)

{

}

/**

* DOCUMENT ME!

* @param e

* DOCUMENT ME!

public void ok_actionPerformed(ActionEvent e)

{

}

/**

* DOCUMENT ME!

* @param e

* DOCUMENT ME!

public void cancel_actionPerformed(ActionEvent e)

{

}

/**

* DOCUMENT ME!

* @param e

* DOCUMENT ME!

public void annotations_actionPerformed(ActionEvent e)

{

}

/**

* DOCUMENT ME!

public void startupFileTextfield_mouseClicked()

{

}

public void newLink_actionPerformed(ActionEvent e)

{

}

public void editLink_actionPerformed(ActionEvent e)

{

}

public void deleteLink_actionPerformed(ActionEvent e)

{

}

public void defaultBrowser_mouseClicked(MouseEvent e)

{

}

public void linkURLList_keyTyped(KeyEvent e)

{

}

public void useProxy_actionPerformed()

1791

{

1792

boolean enabled = useProxy.isSelected();

1793

portLabel.setEnabled(enabled);

1794

serverLabel.setEnabled(enabled);

1795

proxyServerTB.setEnabled(enabled);

1796

proxyPortTB.setEnabled(enabled);

}

/**

* Customer renderer for JTable: supports column of radio buttons

1801

1802

public class RadioButtonRenderer extends JRadioButton

1803

implements TableCellRenderer

1804

{

1805

public RadioButtonRenderer()

1806

{

1807

setHorizontalAlignment(CENTER);

1808

setToolTipText(MessageManager.getString("label.urltooltip"));

}

@Override

public Component getTableCellRendererComponent(JTable table,

1813

Object value, boolean isSelected, boolean hasFocus, int row,

1814

int column)

1815

{

1816

setSelected((boolean) value);

1817

1818

// set colours to match rest of table

1819

if (isSelected)

1820

{

1821

setBackground(table.getSelectionBackground());

1822

setForeground(table.getSelectionForeground());

}

else

{

setBackground(table.getBackground());

1827

setForeground(table.getForeground());

}

return this;

}

}

/**

* Customer cell editor for JTable: supports column of radio buttons in

1835

* conjunction with renderer

1836

1837

public class RadioButtonEditor extends AbstractCellEditor

1838

implements TableCellEditor

1839

{

1840

private JRadioButton button = new JRadioButton();

1841

1842

public RadioButtonEditor()

1843

{

1844

button.setHorizontalAlignment(SwingConstants.CENTER);

1845

this.button.addActionListener(new ActionListener()

1846

{

1847

@Override

1848

public void actionPerformed(ActionEvent e)

1849

{

1850

fireEditingStopped();

}

});

}

@Override

public Component getTableCellEditorComponent(JTable table, Object value,

1857

boolean isSelected, int row, int column)

1858

{

1859

button.setSelected((boolean) value);

return button;

}

@Override

public Object getCellEditorValue()

1865

{

1866

return button.isSelected();

}

}

}

jalviewX

File GPreferences.java

Coverage histogram

Code metrics

Classes

Class GPreferences

Class GPreferences.RadioButtonRenderer

Class GPreferences.RadioButtonEditor

Contributing tests

Source view