2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.awt.event.*;
29 import jalview.jbgui.*;
30 import jalview.schemes.*;
38 public class Preferences extends GPreferences
41 * Holds name and link separated with | character. Sequence ID must be
42 * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
44 public static Vector sequenceURLLinks;
50 "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
51 sequenceURLLinks = new Vector();
55 StringTokenizer st = new StringTokenizer(string, "|");
56 while (st.hasMoreElements())
58 String name = st.nextToken();
59 String url = st.nextToken();
60 // check for '|' within a regex
61 int rxstart = url.indexOf("$SEQUENCE_ID$");
62 while (rxstart == -1 && url.indexOf("/=$") == -1)
64 url = url + "|" + st.nextToken();
66 sequenceURLLinks.addElement(name + "|" + url);
68 } catch (Exception ex)
70 System.out.println(ex + "\nError parsing sequence links");
74 Vector nameLinks, urlLinks;
78 DasSourceBrowser dasSource;
81 * Creates a new Preferences object.
86 frame = new JInternalFrame();
87 frame.setContentPane(this);
88 dasSource = new DasSourceBrowser();
89 dasPanel.add(dasSource, BorderLayout.CENTER);
91 int width = 500, height = 420;
92 if (new jalview.util.Platform().isAMac())
98 Desktop.addInternalFrame(frame, "Preferences", width, height);
99 frame.setMinimumSize(new Dimension(width, height));
101 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
102 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
103 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
104 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
106 conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
107 quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
108 identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
110 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
111 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
112 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
113 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
115 for (int i = 0; i < 13; i++)
117 colour.addItem(ColourSchemeProperty.getColourName(i));
120 String string = Cache.getDefault("DEFAULT_COLOUR", "None");
122 colour.setSelectedItem(string);
124 String[] fonts = java.awt.GraphicsEnvironment
125 .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
127 for (int i = 0; i < fonts.length; i++)
129 fontNameCB.addItem(fonts[i]);
132 for (int i = 1; i < 31; i++)
134 fontSizeCB.addItem(i + "");
137 fontStyleCB.addItem("plain");
138 fontStyleCB.addItem("bold");
139 fontStyleCB.addItem("italic");
141 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
142 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
143 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
146 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
148 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
150 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
152 gapSymbolCB.addItem("-");
153 gapSymbolCB.addItem(".");
155 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
158 .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
159 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
160 "http://www.jalview.org/examples/exampleFile_2_3.jar"));
162 sortby.addItem("No sort");
163 sortby.addItem("Id");
164 sortby.addItem("Pairwise Identity");
165 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
167 epsRendering.addItem("Prompt each time");
168 epsRendering.addItem("Lineart");
169 epsRendering.addItem("Text");
170 epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
171 "Prompt each time"));
173 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
174 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
175 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
176 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
177 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
178 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
179 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
181 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
183 autoCalculateConsCheck.setSelected(Cache.getDefault(
184 "AUTO_CALC_CONSENSUS", true));
185 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
187 /***************************************************************************
190 nameLinks = new Vector();
191 urlLinks = new Vector();
192 for (int i = 0; i < sequenceURLLinks.size(); i++)
194 String link = sequenceURLLinks.elementAt(i).toString();
195 nameLinks.addElement(link.substring(0, link.indexOf("|")));
196 urlLinks.addElement(link.substring(link.indexOf("|") + 1));
201 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
202 proxyServerTB.setEnabled(useProxy.isSelected());
203 proxyPortTB.setEnabled(useProxy.isSelected());
204 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
205 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
207 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
211 } catch (Exception ex)
213 ex.printStackTrace();
224 public void ok_actionPerformed(ActionEvent e)
227 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
228 .toString(seqLimit.isSelected()));
229 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
230 .toString(rightAlign.isSelected()));
231 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
232 .toString(fullScreen.isSelected()));
233 Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
234 .toString(openoverv.isSelected()));
235 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
236 .toString(annotations.isSelected()));
237 Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
238 .toString(conservation.isSelected()));
239 Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
240 .toString(quality.isSelected()));
241 Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
242 .toString(identity.isSelected()));
244 Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
245 .getSelectedItem().toString());
246 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
247 .getSelectedItem().toString());
249 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
250 .getSelectedItem().toString());
251 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
252 .getSelectedItem().toString());
253 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
254 .getSelectedItem().toString());
256 Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
257 .toString(idItalics.isSelected()));
259 Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
260 .toString(smoothFont.isSelected()));
262 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
263 .toString(wrap.isSelected()));
265 Cache.applicationProperties.setProperty("STARTUP_FILE",
266 startupFileTextfield.getText());
267 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
268 .toString(startupCheckbox.isSelected()));
270 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
271 .getSelectedItem().toString());
273 if (epsRendering.getSelectedItem().equals("Prompt each time"))
275 Cache.applicationProperties.remove("EPS_RENDERING");
279 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
280 .getSelectedItem().toString());
283 if (defaultBrowser.getText().trim().length() < 1)
285 Cache.applicationProperties.remove("DEFAULT_BROWSER");
289 Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
290 defaultBrowser.getText());
293 jalview.util.BrowserLauncher.resetBrowser();
295 if (nameLinks.size() > 0)
297 StringBuffer links = new StringBuffer();
298 sequenceURLLinks = new Vector();
299 for (int i = 0; i < nameLinks.size(); i++)
301 sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
302 + urlLinks.elementAt(i));
303 links.append(sequenceURLLinks.elementAt(i).toString());
307 links.setLength(links.length() - 1);
308 Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
313 Cache.applicationProperties.remove("SEQUENCE_LINKS");
316 Cache.applicationProperties.setProperty("USE_PROXY", Boolean
317 .toString(useProxy.isSelected()));
319 if (proxyServerTB.getText().trim().length() < 1)
321 Cache.applicationProperties.remove("PROXY_SERVER");
325 Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
329 if (proxyPortTB.getText().trim().length() < 1)
331 Cache.applicationProperties.remove("PROXY_PORT");
335 Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
339 if (useProxy.isSelected())
341 System.setProperty("http.proxyHost", proxyServerTB.getText());
342 System.setProperty("http.proxyPort", proxyPortTB.getText());
346 System.setProperty("http.proxyHost", "");
347 System.setProperty("http.proxyPort", "");
350 Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
351 .toString(blcjv.isSelected()));
352 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
353 .toString(clustaljv.isSelected()));
354 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
355 .toString(fastajv.isSelected()));
356 Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
357 .toString(msfjv.isSelected()));
358 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
359 .toString(pfamjv.isSelected()));
360 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
361 .toString(pileupjv.isSelected()));
362 Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
363 .toString(pirjv.isSelected()));
364 Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
365 .toString(modellerOutput.isSelected()));
366 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
368 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
369 .toString(autoCalculateConsCheck.isSelected()));
370 Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
371 .toString(padGaps.isSelected()));
373 dasSource.saveProperties(Cache.applicationProperties);
375 Cache.saveProperties();
378 frame.setClosed(true);
379 } catch (Exception ex)
387 public void startupFileTextfield_mouseClicked()
389 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
390 .getProperty("LAST_DIRECTORY"), new String[]
391 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
393 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
394 jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
395 chooser.setFileView(new JalviewFileView());
396 chooser.setDialogTitle("Select startup file");
398 int value = chooser.showOpenDialog(this);
400 if (value == JalviewFileChooser.APPROVE_OPTION)
402 jalview.bin.Cache.applicationProperties.setProperty(
403 "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
404 startupFileTextfield.setText(chooser.getSelectedFile()
415 public void cancel_actionPerformed(ActionEvent e)
419 frame.setClosed(true);
420 } catch (Exception ex)
431 public void annotations_actionPerformed(ActionEvent e)
433 conservation.setEnabled(annotations.isSelected());
434 quality.setEnabled(annotations.isSelected());
435 identity.setEnabled(annotations.isSelected());
438 public void newLink_actionPerformed(ActionEvent e)
441 GSequenceLink link = new GSequenceLink();
442 boolean valid = false;
445 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
446 "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
447 null) == JOptionPane.OK_OPTION)
449 if (link.checkValid())
451 nameLinks.addElement(link.getName());
452 urlLinks.addElement(link.getURL());
464 public void editLink_actionPerformed(ActionEvent e)
466 GSequenceLink link = new GSequenceLink();
468 int index = linkNameList.getSelectedIndex();
471 JOptionPane.showInternalMessageDialog(Desktop.desktop,
472 "No link selected!", "No link selected",
473 JOptionPane.WARNING_MESSAGE);
477 link.setName(nameLinks.elementAt(index).toString());
478 link.setURL(urlLinks.elementAt(index).toString());
480 boolean valid = false;
484 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
485 "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
486 null) == JOptionPane.OK_OPTION)
488 if (link.checkValid())
490 nameLinks.setElementAt(link.getName(), index);
491 urlLinks.setElementAt(link.getURL(), index);
504 public void deleteLink_actionPerformed(ActionEvent e)
506 int index = linkNameList.getSelectedIndex();
509 JOptionPane.showInternalMessageDialog(Desktop.desktop,
510 "No link selected!", "No link selected",
511 JOptionPane.WARNING_MESSAGE);
514 nameLinks.removeElementAt(index);
515 urlLinks.removeElementAt(index);
519 void updateLinkData()
521 linkNameList.setListData(nameLinks);
522 linkURLList.setListData(urlLinks);
525 public void defaultBrowser_mouseClicked(MouseEvent e)
527 JFileChooser chooser = new JFileChooser(".");
528 chooser.setDialogTitle("Select default web browser");
530 int value = chooser.showOpenDialog(this);
532 if (value == JFileChooser.APPROVE_OPTION)
534 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
539 private void jbInit() throws Exception