src/jalview/gui/Preferences.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\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
   9  *\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
  14  *\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
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import java.util.*;\r
  22 \r
  23 import java.awt.*;\r
  24 import java.awt.event.*;\r
  25 import javax.swing.*;\r
  26 \r
  27 import jalview.bin.*;\r
  28 import jalview.io.*;\r
  29 import jalview.jbgui.*;\r
  30 import jalview.schemes.*;\r
  31 \r
  32 /**\r
  33  * DOCUMENT ME!\r
  34  *\r
  35  * @author $author$\r
  36  * @version $Revision$\r
  37  */\r
  38 public class Preferences\r
  39     extends GPreferences\r
  40 {\r
  41   /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
  42   public static Vector sequenceURLLinks;\r
  43   static\r
  44   {\r
  45     String string = Cache.getDefault("SEQUENCE_LINKS",\r
  46                                      "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\r
  47     sequenceURLLinks = new Vector();\r
  48 \r
  49     try\r
  50     {\r
  51       StringTokenizer st = new StringTokenizer(string, "|");\r
  52       while (st.hasMoreElements())\r
  53       {\r
  54         sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
  55       }\r
  56     }\r
  57     catch (Exception ex)\r
  58     {\r
  59       System.out.println(ex + "\nError parsing sequence links");\r
  60     }\r
  61   }\r
  62 \r
  63   Vector nameLinks, urlLinks;\r
  64 \r
  65   JInternalFrame frame;\r
  66 \r
  67   DasSourceBrowser dasSource;\r
  68 \r
  69   /**\r
  70    * Creates a new Preferences object.\r
  71    */\r
  72   public Preferences()\r
  73   {\r
  74 \r
  75     frame = new JInternalFrame();\r
  76     frame.setContentPane(this);\r
  77     dasSource = new DasSourceBrowser();\r
  78     dasPanel.add(dasSource, BorderLayout.CENTER);\r
  79 \r
  80     int width = 500, height = 420;\r
  81     if (System.getProperty("os.name").startsWith("Mac"))\r
  82     {\r
  83       width = 570;\r
  84       height = 460;\r
  85     }\r
  86 \r
  87     Desktop.addInternalFrame(frame, "Preferences", width, height);\r
  88     frame.setMinimumSize(new Dimension(width, height));\r
  89 \r
  90     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));\r
  91     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));\r
  92     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));\r
  93     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  94 \r
  95     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  96     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  97     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  98 \r
  99     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
 100     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
 101     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
 102     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));\r
 103 \r
 104     for (int i = 0; i < 13; i++)\r
 105     {\r
 106       colour.addItem(ColourSchemeProperty.getColourName(i));\r
 107     }\r
 108 \r
 109     String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 110 \r
 111     colour.setSelectedItem(string);\r
 112 \r
 113     String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 114         .getAvailableFontFamilyNames();\r
 115 \r
 116     for (int i = 0; i < fonts.length; i++)\r
 117     {\r
 118       fontNameCB.addItem(fonts[i]);\r
 119     }\r
 120 \r
 121     for (int i = 1; i < 31; i++)\r
 122     {\r
 123       fontSizeCB.addItem(i + "");\r
 124     }\r
 125 \r
 126     fontStyleCB.addItem("plain");\r
 127     fontStyleCB.addItem("bold");\r
 128     fontStyleCB.addItem("italic");\r
 129 \r
 130     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 131     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 132     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));\r
 133 \r
 134     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 135 \r
 136     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
 137 \r
 138     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 139 \r
 140     gapSymbolCB.addItem("-");\r
 141     gapSymbolCB.addItem(".");\r
 142 \r
 143     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));\r
 144 \r
 145     startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));\r
 146     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 147                                                   "http://www.jalview.org/examples/exampleFile.jar"));\r
 148 \r
 149     sortby.addItem("No sort");\r
 150     sortby.addItem("Id");\r
 151     sortby.addItem("Pairwise Identity");\r
 152     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));\r
 153 \r
 154     epsRendering.addItem("Prompt each time");\r
 155     epsRendering.addItem("Lineart");\r
 156     epsRendering.addItem("Text");\r
 157     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",\r
 158                                                   "Prompt each time"));\r
 159 \r
 160     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));\r
 161     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
 162     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));\r
 163     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));\r
 164     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));\r
 165     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));\r
 166     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));\r
 167 \r
 168     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));\r
 169 \r
 170     autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 171     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));\r
 172 \r
 173     /****************************************************\r
 174      * Set up Connections\r
 175      */\r
 176     nameLinks = new Vector();\r
 177     urlLinks = new Vector();\r
 178     for (int i = 0; i < sequenceURLLinks.size(); i++)\r
 179     {\r
 180       String link = sequenceURLLinks.elementAt(i).toString();\r
 181       nameLinks.addElement(link.substring(0, link.indexOf("|")));\r
 182       urlLinks.addElement(link.substring(link.indexOf("|") + 1));\r
 183     }\r
 184 \r
 185     updateLinkData();\r
 186 \r
 187     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));\r
 188     proxyServerTB.setEnabled(useProxy.isSelected());\r
 189     proxyPortTB.setEnabled(useProxy.isSelected());\r
 190     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));\r
 191     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 192 \r
 193     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));\r
 194     try\r
 195     {\r
 196       jbInit();\r
 197     }\r
 198     catch (Exception ex)\r
 199     {\r
 200       ex.printStackTrace();\r
 201     }\r
 202 \r
 203   }\r
 204 \r
 205   /**\r
 206    * DOCUMENT ME!\r
 207    *\r
 208    * @param e DOCUMENT ME!\r
 209    */\r
 210   public void ok_actionPerformed(ActionEvent e)\r
 211   {\r
 212 \r
 213     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",\r
 214                                             Boolean.toString(seqLimit.\r
 215         isSelected()));\r
 216     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",\r
 217                                             Boolean.toString(rightAlign.\r
 218         isSelected()));\r
 219     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",\r
 220                                             Boolean.toString(fullScreen.\r
 221         isSelected()));\r
 222     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",\r
 223                                             Boolean.toString(openoverv.\r
 224         isSelected()));\r
 225     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",\r
 226                                             Boolean.\r
 227                                             toString(annotations.isSelected()));\r
 228     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",\r
 229                                             Boolean.\r
 230                                             toString(conservation.isSelected()));\r
 231     Cache.applicationProperties.setProperty("SHOW_QUALITY",\r
 232                                             Boolean.toString(quality.isSelected()));\r
 233     Cache.applicationProperties.setProperty("SHOW_IDENTITY",\r
 234                                             Boolean.toString(identity.\r
 235         isSelected()));\r
 236 \r
 237     Cache.applicationProperties.setProperty("DEFAULT_COLOUR",\r
 238                                             colour.getSelectedItem().toString());\r
 239     Cache.applicationProperties.setProperty("GAP_SYMBOL",\r
 240                                             gapSymbolCB.getSelectedItem().\r
 241                                             toString());\r
 242 \r
 243     Cache.applicationProperties.setProperty("FONT_NAME",\r
 244                                             fontNameCB.getSelectedItem().\r
 245                                             toString());\r
 246     Cache.applicationProperties.setProperty("FONT_STYLE",\r
 247                                             fontStyleCB.getSelectedItem().\r
 248                                             toString());\r
 249     Cache.applicationProperties.setProperty("FONT_SIZE",\r
 250                                             fontSizeCB.getSelectedItem().\r
 251                                             toString());\r
 252 \r
 253     Cache.applicationProperties.setProperty("ID_ITALICS",\r
 254                                             Boolean.toString(idItalics.\r
 255         isSelected()));\r
 256 \r
 257     Cache.applicationProperties.setProperty("ANTI_ALIAS",\r
 258                                             Boolean.toString(smoothFont.\r
 259         isSelected()));\r
 260 \r
 261     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",\r
 262                                             Boolean.toString(wrap.isSelected()));\r
 263 \r
 264     Cache.applicationProperties.setProperty("STARTUP_FILE",\r
 265                                             startupFileTextfield.getText());\r
 266     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",\r
 267                                             Boolean.\r
 268                                             toString(startupCheckbox.isSelected()));\r
 269 \r
 270     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",\r
 271                                             sortby.getSelectedItem().toString());\r
 272 \r
 273     if (epsRendering.getSelectedItem().equals("Prompt each time"))\r
 274     {\r
 275       Cache.applicationProperties.remove("EPS_RENDERING");\r
 276     }\r
 277     else\r
 278     {\r
 279       Cache.applicationProperties.setProperty("EPS_RENDERING",\r
 280                                               epsRendering.getSelectedItem().\r
 281                                               toString());\r
 282     }\r
 283 \r
 284     if (defaultBrowser.getText().trim().length() < 1)\r
 285     {\r
 286       Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 287     }\r
 288     else\r
 289     {\r
 290       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 291                                               defaultBrowser.getText());\r
 292     }\r
 293 \r
 294     jalview.util.BrowserLauncher.resetBrowser();\r
 295 \r
 296     if (nameLinks.size() > 0)\r
 297     {\r
 298       StringBuffer links = new StringBuffer();\r
 299       sequenceURLLinks = new Vector();\r
 300       for (int i = 0; i < nameLinks.size(); i++)\r
 301       {\r
 302         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +\r
 303                                     urlLinks.elementAt(i));\r
 304         links.append(sequenceURLLinks.elementAt(i).toString());\r
 305         links.append("|");\r
 306       }\r
 307       // remove last "|"\r
 308       links.setLength(links.length() - 1);\r
 309       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 310     }\r
 311     else\r
 312     {\r
 313       Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 314     }\r
 315 \r
 316     Cache.applicationProperties.setProperty("USE_PROXY",\r
 317                                             Boolean.toString(useProxy.\r
 318         isSelected()));\r
 319 \r
 320     if (proxyServerTB.getText().trim().length() < 1)\r
 321     {\r
 322       Cache.applicationProperties.remove("PROXY_SERVER");\r
 323     }\r
 324     else\r
 325     {\r
 326       Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 327                                               proxyServerTB.getText());\r
 328     }\r
 329 \r
 330     if (proxyPortTB.getText().trim().length() < 1)\r
 331     {\r
 332       Cache.applicationProperties.remove("PROXY_PORT");\r
 333     }\r
 334     else\r
 335     {\r
 336       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 337     }\r
 338 \r
 339     if (useProxy.isSelected())\r
 340     {\r
 341       System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 342       System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 343     }\r
 344     else\r
 345     {\r
 346       System.setProperty("http.proxyHost", "");\r
 347       System.setProperty("http.proxyPort", "");\r
 348     }\r
 349 \r
 350     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",\r
 351                                             Boolean.toString(blcjv.isSelected()));\r
 352     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",\r
 353                                             Boolean.\r
 354                                             toString(clustaljv.isSelected()));\r
 355     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",\r
 356                                             Boolean.toString(fastajv.isSelected()));\r
 357     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",\r
 358                                             Boolean.toString(msfjv.isSelected()));\r
 359     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",\r
 360                                             Boolean.toString(pfamjv.isSelected()));\r
 361     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",\r
 362                                             Boolean.toString(pileupjv.\r
 363         isSelected()));\r
 364     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",\r
 365                                             Boolean.toString(pirjv.isSelected()));\r
 366     Cache.applicationProperties.setProperty("PIR_MODELLER",\r
 367                                             Boolean.toString(modellerOutput.\r
 368         isSelected()));\r
 369     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 370 \r
 371     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 372                                             Boolean.toString(\r
 373         autoCalculateConsCheck.isSelected()));\r
 374     Cache.applicationProperties.setProperty("PAD_GAPS",\r
 375                                             Boolean.toString(padGaps.isSelected()));\r
 376 \r
 377     dasSource.saveProperties(Cache.applicationProperties);\r
 378 \r
 379     Cache.saveProperties();\r
 380     try\r
 381     {\r
 382       frame.setClosed(true);\r
 383     }\r
 384     catch (Exception ex)\r
 385     {\r
 386     }\r
 387   }\r
 388 \r
 389   /**\r
 390    * DOCUMENT ME!\r
 391    */\r
 392   public void startupFileTextfield_mouseClicked()\r
 393   {\r
 394     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 395         getProperty(\r
 396             "LAST_DIRECTORY"),\r
 397         new String[]\r
 398         {\r
 399         "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 400         "jar"\r
 401     },\r
 402         new String[]\r
 403         {\r
 404         "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 405     }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 406     chooser.setFileView(new JalviewFileView());\r
 407     chooser.setDialogTitle("Select startup file");\r
 408 \r
 409     int value = chooser.showOpenDialog(this);\r
 410 \r
 411     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 412     {\r
 413       jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 414           chooser.getSelectedFormat());\r
 415       startupFileTextfield.setText(chooser.getSelectedFile()\r
 416                                    .getAbsolutePath());\r
 417     }\r
 418   }\r
 419 \r
 420   /**\r
 421    * DOCUMENT ME!\r
 422    *\r
 423    * @param e DOCUMENT ME!\r
 424    */\r
 425   public void cancel_actionPerformed(ActionEvent e)\r
 426   {\r
 427     try\r
 428     {\r
 429       frame.setClosed(true);\r
 430     }\r
 431     catch (Exception ex)\r
 432     {\r
 433     }\r
 434   }\r
 435 \r
 436   /**\r
 437    * DOCUMENT ME!\r
 438    *\r
 439    * @param e DOCUMENT ME!\r
 440    */\r
 441   public void annotations_actionPerformed(ActionEvent e)\r
 442   {\r
 443     conservation.setEnabled(annotations.isSelected());\r
 444     quality.setEnabled(annotations.isSelected());\r
 445     identity.setEnabled(annotations.isSelected());\r
 446   }\r
 447 \r
 448   public void newLink_actionPerformed(ActionEvent e)\r
 449   {\r
 450 \r
 451     GSequenceLink link = new GSequenceLink();\r
 452     boolean valid = false;\r
 453     while (!valid)\r
 454     {\r
 455       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 456                                                 "New sequence URL link",\r
 457                                                 JOptionPane.OK_CANCEL_OPTION\r
 458                                                 , -1, null)\r
 459           == JOptionPane.OK_OPTION)\r
 460       {\r
 461         if (link.checkValid())\r
 462         {\r
 463           nameLinks.addElement(link.getName());\r
 464           urlLinks.addElement(link.getURL());\r
 465           updateLinkData();\r
 466           valid = true;\r
 467         }\r
 468       }\r
 469       else\r
 470       {\r
 471         break;\r
 472       }\r
 473     }\r
 474   }\r
 475 \r
 476   public void editLink_actionPerformed(ActionEvent e)\r
 477   {\r
 478     GSequenceLink link = new GSequenceLink();\r
 479 \r
 480     int index = linkNameList.getSelectedIndex();\r
 481     if (index == -1)\r
 482     {\r
 483       JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 484                                             "No link selected!"\r
 485                                             , "No link selected",\r
 486                                             JOptionPane.WARNING_MESSAGE);\r
 487       return;\r
 488     }\r
 489 \r
 490     link.setName(nameLinks.elementAt(index).toString());\r
 491     link.setURL(urlLinks.elementAt(index).toString());\r
 492 \r
 493     boolean valid = false;\r
 494     while (!valid)\r
 495     {\r
 496 \r
 497       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 498                                                 "New sequence URL link",\r
 499                                                 JOptionPane.OK_CANCEL_OPTION\r
 500                                                 , -1, null)\r
 501           == JOptionPane.OK_OPTION)\r
 502       {\r
 503         if (link.checkValid())\r
 504         {\r
 505           nameLinks.setElementAt(link.getName(), index);\r
 506           urlLinks.setElementAt(link.getURL(), index);\r
 507           updateLinkData();\r
 508           valid = true;\r
 509         }\r
 510       }\r
 511 \r
 512       else\r
 513       {\r
 514         break;\r
 515       }\r
 516     }\r
 517   }\r
 518 \r
 519   public void deleteLink_actionPerformed(ActionEvent e)\r
 520   {\r
 521     int index = linkNameList.getSelectedIndex();\r
 522     if (index == -1)\r
 523     {\r
 524       JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 525                                             "No link selected!"\r
 526                                             , "No link selected",\r
 527                                             JOptionPane.WARNING_MESSAGE);\r
 528       return;\r
 529     }\r
 530     nameLinks.removeElementAt(index);\r
 531     urlLinks.removeElementAt(index);\r
 532     updateLinkData();\r
 533   }\r
 534 \r
 535   void updateLinkData()\r
 536   {\r
 537     linkNameList.setListData(nameLinks);\r
 538     linkURLList.setListData(urlLinks);\r
 539   }\r
 540 \r
 541   public void defaultBrowser_mouseClicked(MouseEvent e)\r
 542   {\r
 543     JFileChooser chooser = new JFileChooser(".");\r
 544     chooser.setDialogTitle("Select default web browser");\r
 545 \r
 546     int value = chooser.showOpenDialog(this);\r
 547 \r
 548     if (value == JFileChooser.APPROVE_OPTION)\r
 549     {\r
 550       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 551     }\r
 552 \r
 553   }\r
 554 \r
 555   private void jbInit()\r
 556       throws Exception\r
 557   {\r
 558   }\r
 559 }\r