2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.jbgui;
\r
23 import javax.swing.*;
\r
24 import javax.swing.border.TitledBorder;
\r
25 import java.awt.event.*;
\r
26 import javax.swing.event.*;
\r
33 * @version $Revision$
\r
35 public class GPreferences extends JPanel
\r
37 JTabbedPane tabbedPane = new JTabbedPane();
\r
39 JButton ok = new JButton();
\r
40 JButton cancel = new JButton();
\r
41 JPanel okCancelPanel = new JPanel();
\r
42 BorderLayout borderLayout1 = new BorderLayout();
\r
43 protected JCheckBox quality = new JCheckBox();
\r
44 JPanel visualTab = new JPanel();
\r
45 protected JCheckBox fullScreen = new JCheckBox();
\r
46 protected JCheckBox conservation = new JCheckBox();
\r
47 protected JCheckBox identity = new JCheckBox();
\r
48 protected JCheckBox annotations = new JCheckBox();
\r
49 JLabel gapLabel = new JLabel();
\r
50 protected JComboBox colour = new JComboBox();
\r
51 JLabel colourLabel = new JLabel();
\r
52 JLabel fontLabel = new JLabel();
\r
53 protected JComboBox fontSizeCB = new JComboBox();
\r
54 protected JComboBox fontStyleCB = new JComboBox();
\r
55 protected JComboBox fontNameCB = new JComboBox();
\r
56 protected JComboBox gapSymbolCB = new JComboBox();
\r
57 protected JCheckBox startupCheckbox = new JCheckBox();
\r
58 protected JTextField startupFileTextfield = new JTextField();
\r
59 JPanel connectTab = new JPanel();
\r
60 JLabel serverLabel = new JLabel();
\r
61 protected JList linkURLList = new JList();
\r
62 protected JTextField proxyServerTB = new JTextField();
\r
63 protected JTextField proxyPortTB = new JTextField();
\r
64 JLabel portLabel = new JLabel();
\r
65 JLabel browserLabel = new JLabel();
\r
66 protected JTextField defaultBrowser = new JTextField();
\r
67 JButton newLink = new JButton();
\r
68 JButton editLink = new JButton();
\r
69 JButton deleteLink = new JButton();
\r
70 JScrollPane linkScrollPane = new JScrollPane();
\r
71 JPanel linkPanel = new JPanel();
\r
72 BorderLayout borderLayout2 = new BorderLayout();
\r
73 JPanel editLinkButtons = new JPanel();
\r
74 GridLayout gridLayout1 = new GridLayout();
\r
75 protected JList linkNameList = new JList();
\r
76 JPanel linkPanel2 = new JPanel();
\r
77 BorderLayout borderLayout3 = new BorderLayout();
\r
78 protected JCheckBox useProxy = new JCheckBox();
\r
79 JPanel jPanel1 = new JPanel();
\r
80 TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
\r
81 TitledBorder titledBorder2 = new TitledBorder("File Output");
\r
82 GridBagLayout gridBagLayout2 = new GridBagLayout();
\r
83 GridBagLayout gridBagLayout1 = new GridBagLayout();
\r
84 GridBagLayout gridBagLayout3 = new GridBagLayout();
\r
85 protected JComboBox sortby = new JComboBox();
\r
86 JLabel sortLabel = new JLabel();
\r
87 JPanel jPanel2 = new JPanel();
\r
88 GridLayout gridLayout2 = new GridLayout();
\r
89 JPanel jPanel3 = new JPanel();
\r
90 JPanel exportTab = new JPanel();
\r
91 JLabel epsLabel = new JLabel();
\r
92 protected JComboBox epsRendering = new JComboBox();
\r
93 JLabel jLabel1 = new JLabel();
\r
94 protected JCheckBox blcjv = new JCheckBox();
\r
95 protected JCheckBox pileupjv = new JCheckBox();
\r
96 protected JCheckBox clustaljv = new JCheckBox();
\r
97 protected JCheckBox msfjv = new JCheckBox();
\r
98 protected JCheckBox fastajv = new JCheckBox();
\r
99 protected JCheckBox pfamjv = new JCheckBox();
\r
100 FlowLayout flowLayout1 = new FlowLayout();
\r
101 protected JCheckBox pirjv = new JCheckBox();
\r
102 JPanel jPanel11 = new JPanel();
\r
103 Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
\r
104 protected JCheckBox seqLimit = new JCheckBox();
\r
105 GridLayout gridLayout3 = new GridLayout();
\r
107 * Creates a new GPreferences object.
\r
109 public GPreferences()
\r
115 catch (Exception ex)
\r
117 ex.printStackTrace();
\r
124 * @throws Exception DOCUMENT ME!
\r
126 private void jbInit() throws Exception
\r
128 this.setLayout(borderLayout1);
\r
130 ok.addActionListener(new ActionListener()
\r
132 public void actionPerformed(ActionEvent e)
\r
134 ok_actionPerformed(e);
\r
137 cancel.setText("Cancel");
\r
138 cancel.addActionListener(new ActionListener()
\r
140 public void actionPerformed(ActionEvent e)
\r
142 cancel_actionPerformed(e);
\r
145 quality.setEnabled(false);
\r
146 quality.setFont(verdana11);
\r
147 quality.setHorizontalAlignment(SwingConstants.RIGHT);
\r
148 quality.setHorizontalTextPosition(SwingConstants.LEFT);
\r
149 quality.setSelected(true);
\r
150 quality.setText("Quality");
\r
151 visualTab.setBorder(new TitledBorder("Open new alignment"));
\r
152 visualTab.setLayout(null);
\r
153 fullScreen.setFont(verdana11);
\r
154 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
\r
155 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
\r
156 fullScreen.setMargin(new Insets(2, 2, 2, 0));
\r
157 fullScreen.setText("Maximise Window");
\r
158 conservation.setEnabled(false);
\r
159 conservation.setFont(verdana11);
\r
160 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
\r
161 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
\r
162 conservation.setSelected(true);
\r
163 conservation.setText("Conservation");
\r
164 identity.setEnabled(false);
\r
165 identity.setFont(verdana11);
\r
166 identity.setHorizontalAlignment(SwingConstants.RIGHT);
\r
167 identity.setHorizontalTextPosition(SwingConstants.LEFT);
\r
168 identity.setSelected(true);
\r
169 identity.setText("Consensus");
\r
170 annotations.setFont(verdana11);
\r
171 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
\r
172 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
\r
173 annotations.setMargin(new Insets(2, 4, 2, 0));
\r
174 annotations.setSelected(true);
\r
175 annotations.setText("Show Annotations");
\r
176 annotations.addActionListener(new ActionListener()
\r
178 public void actionPerformed(ActionEvent e)
\r
180 annotations_actionPerformed(e);
\r
183 gapLabel.setFont(verdana11);
\r
184 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
185 gapLabel.setText("Gap Symbol ");
\r
186 colour.setFont(verdana11);
\r
187 colour.setBounds(new Rectangle(170, 170, 155, 21));
\r
188 colourLabel.setFont(verdana11);
\r
189 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
190 colourLabel.setText("Colour ");
\r
191 fontLabel.setFont(verdana11);
\r
192 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
193 fontLabel.setText("Font ");
\r
194 fontSizeCB.setFont(verdana11);
\r
195 fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));
\r
196 fontStyleCB.setFont(verdana11);
\r
197 fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));
\r
198 fontNameCB.setFont(verdana11);
\r
199 fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));
\r
200 gapSymbolCB.setFont(verdana11);
\r
201 gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21));
\r
202 startupCheckbox.setText("Open file");
\r
203 startupCheckbox.setFont(verdana11);
\r
204 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
\r
205 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
\r
206 startupCheckbox.setSelected(true);
\r
207 startupFileTextfield.setFont(verdana11);
\r
208 startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));
\r
209 startupFileTextfield.addMouseListener(new MouseAdapter()
\r
211 public void mouseClicked(MouseEvent e)
\r
213 if (e.getClickCount() > 1)
\r
215 startupFileTextfield_mouseClicked();
\r
220 connectTab.setLayout(gridBagLayout3);
\r
221 serverLabel.setText("Address");
\r
222 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
223 serverLabel.setFont(verdana11);
\r
224 proxyServerTB.setFont(verdana11);
\r
225 proxyPortTB.setFont(verdana11);
\r
226 portLabel.setFont(verdana11);
\r
227 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
228 portLabel.setText("Port");
\r
229 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
\r
230 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
\r
231 browserLabel.setText("Default Browser (Unix)");
\r
232 defaultBrowser.setFont(verdana11);
\r
233 defaultBrowser.setText("");
\r
234 newLink.setText("New");
\r
235 newLink.addActionListener(new java.awt.event.ActionListener() {
\r
236 public void actionPerformed(ActionEvent e) {
\r
237 newLink_actionPerformed(e);
\r
240 editLink.setText("Edit");
\r
241 editLink.addActionListener(new java.awt.event.ActionListener() {
\r
242 public void actionPerformed(ActionEvent e) {
\r
243 editLink_actionPerformed(e);
\r
246 deleteLink.setText("Delete");
\r
247 deleteLink.addActionListener(new java.awt.event.ActionListener() {
\r
248 public void actionPerformed(ActionEvent e) {
\r
249 deleteLink_actionPerformed(e);
\r
253 linkURLList.addListSelectionListener(new ListSelectionListener()
\r
255 public void valueChanged(ListSelectionEvent e)
\r
257 int index = linkURLList.getSelectedIndex();
\r
258 linkNameList.setSelectedIndex(index);
\r
262 linkNameList.addListSelectionListener(new ListSelectionListener()
\r
264 public void valueChanged(ListSelectionEvent e)
\r
266 int index = linkNameList.getSelectedIndex();
\r
267 linkURLList.setSelectedIndex(index);
\r
271 linkScrollPane.setBorder(null);
\r
272 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
\r
273 linkPanel.setLayout(borderLayout2);
\r
274 editLinkButtons.setLayout(gridLayout1);
\r
275 gridLayout1.setRows(3);
\r
276 linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
\r
277 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
\r
278 linkPanel2.setLayout(borderLayout3);
\r
279 linkURLList.setFont(verdana11);
\r
280 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
\r
282 defaultBrowser.addMouseListener(new MouseAdapter()
\r
284 public void mouseClicked(MouseEvent e)
\r
286 if (e.getClickCount() > 1)
\r
288 defaultBrowser_mouseClicked(e);
\r
292 useProxy.setFont(verdana11);
\r
293 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
\r
294 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
\r
295 useProxy.setText("Use a proxy server");
\r
296 useProxy.addActionListener(new ActionListener()
\r
298 public void actionPerformed(ActionEvent e)
\r
300 useProxy_actionPerformed();
\r
303 jPanel1.setBorder(titledBorder1);
\r
304 jPanel1.setLayout(gridBagLayout1);
\r
305 sortby.setFont(verdana11);
\r
306 sortby.setBounds(new Rectangle(170, 200, 155, 21));
\r
307 sortLabel.setFont(verdana11);
\r
308 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
309 sortLabel.setText("Sort by ");
\r
310 jPanel2.setBounds(new Rectangle(7, 17, 158, 242));
\r
311 jPanel2.setLayout(gridLayout2);
\r
312 gridLayout2.setRows(8);
\r
313 jPanel3.setBounds(new Rectangle(168, 47, 274, 26));
\r
314 exportTab.setLayout(null);
\r
315 epsLabel.setFont(verdana11);
\r
316 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
\r
317 epsLabel.setText("EPS Rendering Style");
\r
318 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
\r
319 epsRendering.setFont(verdana11);
\r
320 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
\r
321 jLabel1.setFont(verdana11);
\r
322 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
\r
323 jLabel1.setText("Append /start-end (/15-380)");
\r
324 jLabel1.setFont(verdana11);
\r
325 fastajv.setFont(verdana11);
\r
326 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
\r
327 clustaljv.setText("Clustal ");
\r
328 blcjv.setText("BLC ");
\r
329 fastajv.setText("Fasta ");
\r
330 msfjv.setText("MSF ");
\r
331 pfamjv.setText("PFAM ");
\r
332 pileupjv.setText("Pileup ");
\r
333 msfjv.setFont(verdana11);
\r
334 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
335 pirjv.setText("PIR ");
\r
336 jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
337 jPanel11.setBorder(titledBorder2);
\r
338 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
\r
339 jPanel11.setLayout(gridLayout3);
\r
340 blcjv.setFont(verdana11);
\r
341 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
342 clustaljv.setFont(verdana11);
\r
343 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
\r
344 pfamjv.setFont(verdana11);
\r
345 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
346 pileupjv.setFont(verdana11);
\r
347 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
348 pirjv.setFont(verdana11);
\r
349 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
350 seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
351 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
\r
352 seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);
\r
353 seqLimit.setText("Full Sequence Id");
\r
354 gridLayout3.setRows(8);
\r
355 jPanel2.add(fullScreen);
\r
356 jPanel2.add(annotations);
\r
357 jPanel2.add(seqLimit);
\r
358 jPanel2.add(fontLabel);
\r
359 jPanel2.add(gapLabel);
\r
360 jPanel2.add(colourLabel);
\r
361 jPanel2.add(sortLabel);
\r
362 jPanel2.add(startupCheckbox);
\r
363 visualTab.add(gapSymbolCB);
\r
364 visualTab.add(colour);
\r
365 visualTab.add(jPanel3);
\r
366 jPanel3.add(conservation);
\r
367 jPanel3.add(identity);
\r
368 jPanel3.add(quality);
\r
369 visualTab.add(sortby);
\r
370 visualTab.add(startupFileTextfield);
\r
371 visualTab.add(fontNameCB);
\r
372 visualTab.add(fontSizeCB);
\r
373 visualTab.add(fontStyleCB);
\r
374 visualTab.add(jPanel2);
\r
375 linkPanel.add(editLinkButtons, BorderLayout.EAST);
\r
376 editLinkButtons.add(newLink, null);
\r
377 editLinkButtons.add(editLink, null);
\r
378 editLinkButtons.add(deleteLink, null);
\r
379 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
\r
380 linkScrollPane.getViewport().add(linkPanel2, null);
\r
381 linkPanel2.add(linkURLList, BorderLayout.CENTER);
\r
382 linkPanel2.add(linkNameList, BorderLayout.WEST);
\r
383 okCancelPanel.add(ok);
\r
384 okCancelPanel.add(cancel);
\r
385 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
387 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
\r
388 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
\r
389 , GridBagConstraints.WEST, GridBagConstraints.NONE,
\r
390 new Insets(0, 2, 4, 0), 5, 0));
\r
391 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
\r
392 , GridBagConstraints.WEST,
\r
393 GridBagConstraints.NONE,
\r
394 new Insets(0, 0, 4, 0), 11, 6));
\r
395 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
\r
396 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
\r
397 new Insets(16, 0, 0, 12), 359, -17));
\r
398 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
\r
399 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
\r
400 new Insets(21, 0, 35, 12), 4, 6));
\r
401 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
\r
402 , GridBagConstraints.WEST, GridBagConstraints.NONE,
\r
403 new Insets(16, 0, 0, 0), 5, 1));
\r
404 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
\r
405 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
\r
406 new Insets(0, 2, 4, 2), 54, 1));
\r
407 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
\r
408 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
\r
409 new Insets(0, 2, 4, 0), 263, 1));
\r
410 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
\r
411 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
\r
412 new Insets(15, 0, 0, 15), 307, 1));
\r
415 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
\r
416 , GridBagConstraints.WEST,
\r
417 GridBagConstraints.NONE,
\r
418 new Insets(0, 2, 5, 185), 2,
\r
420 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
\r
421 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
\r
422 gapSymbolCB.setRenderer(dlcr);
\r
424 tabbedPane.add(visualTab, "Visual");
\r
425 tabbedPane.add(connectTab,"Connections");
\r
426 tabbedPane.add(exportTab, "Output");
\r
427 jPanel11.add(jLabel1);
\r
428 jPanel11.add(blcjv);
\r
429 jPanel11.add(clustaljv);
\r
430 jPanel11.add(fastajv);
\r
431 jPanel11.add(msfjv);
\r
432 jPanel11.add(pfamjv);
\r
433 jPanel11.add(pileupjv);
\r
434 jPanel11.add(pirjv);
\r
435 exportTab.add(epsLabel);
\r
436 exportTab.add(epsRendering);
\r
437 exportTab.add(jPanel11);
\r
443 * @param e DOCUMENT ME!
\r
445 public void ok_actionPerformed(ActionEvent e)
\r
452 * @param e DOCUMENT ME!
\r
454 public void cancel_actionPerformed(ActionEvent e)
\r
461 * @param e DOCUMENT ME!
\r
463 public void annotations_actionPerformed(ActionEvent e)
\r
471 public void startupFileTextfield_mouseClicked()
\r
476 public void newLink_actionPerformed(ActionEvent e) {
\r
480 public void editLink_actionPerformed(ActionEvent e) {
\r
484 public void deleteLink_actionPerformed(ActionEvent e) {
\r
488 public void defaultBrowser_mouseClicked(MouseEvent e)
\r
493 public void linkURLList_keyTyped(KeyEvent e)
\r
498 public void useProxy_actionPerformed()
\r
500 proxyServerTB.setEnabled(useProxy.isSelected());
\r
501 proxyPortTB.setEnabled(useProxy.isSelected());
\r