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