src/jalview/gui/Preferences.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 jalview.io.*;\r
  22 \r
  23 import jalview.jbgui.*;\r
  24 \r
  25 import jalview.schemes.*;\r
  26 \r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 \r
  30 import javax.swing.*;\r
  31 \r
  32 import java.util.*;\r
  33 \r
  34 import jalview.bin.Cache;\r
  35 \r
  36 \r
  37 /**\r
  38  * DOCUMENT ME!\r
  39  *\r
  40  * @author $author$\r
  41  * @version $Revision$\r
  42  */\r
  43 public class Preferences extends GPreferences\r
  44 {\r
  45     /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
  46     public static Vector sequenceURLLinks;\r
  47     static\r
  48     {\r
  49       String string = Cache.getDefault("SEQUENCE_LINKS",\r
  50                                        "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\r
  51       sequenceURLLinks = new Vector();\r
  52 \r
  53       try\r
  54       {\r
  55         StringTokenizer st = new StringTokenizer(string, "|");\r
  56         while (st.hasMoreElements())\r
  57         {\r
  58           sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
  59         }\r
  60       }\r
  61       catch (Exception ex)\r
  62       {\r
  63         System.out.println(ex + "\nError parsing sequence links");\r
  64       }\r
  65     }\r
  66     Vector nameLinks, urlLinks;\r
  67 \r
  68     JInternalFrame frame;\r
  69 \r
  70     DasSourceBrowser dasSource;\r
  71 \r
  72 \r
  73     /**\r
  74      * Creates a new Preferences object.\r
  75      */\r
  76     public Preferences()\r
  77     {\r
  78 \r
  79         frame = new JInternalFrame();\r
  80         frame.setContentPane(this);\r
  81         dasSource = new DasSourceBrowser();\r
  82         dasPanel.add(dasSource, BorderLayout.CENTER);\r
  83 \r
  84         int width = 500, height = 420;\r
  85         if(System.getProperty("os.name").startsWith("Mac"))\r
  86         {\r
  87           width = 570;\r
  88           height = 460;\r
  89         }\r
  90 \r
  91         Desktop.addInternalFrame(frame, "Preferences", width, height);\r
  92         frame.setMinimumSize(new Dimension(width, height));\r
  93 \r
  94         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  95         rightAlign.setSelected(  Cache.getDefault("RIGHT_ALIGN_IDS", false));\r
  96         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  97         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  98 \r
  99         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 100         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 101         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 102 \r
 103         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
 104         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
 105         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
 106 \r
 107         for (int i = 0; i < 13; i++)\r
 108         {\r
 109             colour.addItem(ColourSchemeProperty.getColourName(i));\r
 110         }\r
 111 \r
 112         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 113 \r
 114         colour.setSelectedItem(string);\r
 115 \r
 116         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 117                                                      .getAvailableFontFamilyNames();\r
 118 \r
 119         for (int i = 0; i < fonts.length; i++)\r
 120         {\r
 121             fontNameCB.addItem(fonts[i]);\r
 122         }\r
 123 \r
 124         for (int i = 1; i < 31; i++)\r
 125         {\r
 126             fontSizeCB.addItem(i + "");\r
 127         }\r
 128 \r
 129         fontStyleCB.addItem("plain");\r
 130         fontStyleCB.addItem("bold");\r
 131         fontStyleCB.addItem("italic");\r
 132 \r
 133         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 134         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 135         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 136 \r
 137         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 138 \r
 139         idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
 140 \r
 141         wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 142 \r
 143         gapSymbolCB.addItem("-");\r
 144         gapSymbolCB.addItem(".");\r
 145 \r
 146         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 147 \r
 148         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 149         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 150          "http://www.jalview.org/examples/exampleFile.jar"));\r
 151 \r
 152         sortby.addItem("No sort");\r
 153         sortby.addItem("Id");\r
 154         sortby.addItem("Pairwise Identity");\r
 155         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 156 \r
 157         epsRendering.addItem("Prompt each time");\r
 158         epsRendering.addItem("Lineart");\r
 159         epsRendering.addItem("Text");\r
 160         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 161 \r
 162         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 163         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 164         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 165         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 166         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 167         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 168         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 169 \r
 170         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 171 \r
 172         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 173         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 174 \r
 175   /****************************************************\r
 176    * Set up Connections\r
 177    */\r
 178         nameLinks = new Vector();\r
 179         urlLinks = new Vector();\r
 180         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 181         {\r
 182           String link = sequenceURLLinks.elementAt(i).toString();\r
 183           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 184           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 185         }\r
 186 \r
 187         updateLinkData();\r
 188 \r
 189         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 190         proxyServerTB.setEnabled(useProxy.isSelected());\r
 191         proxyPortTB.setEnabled(useProxy.isSelected());\r
 192         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 193         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 194 \r
 195         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 196     try\r
 197     {\r
 198       jbInit();\r
 199     }\r
 200     catch (Exception ex)\r
 201     {\r
 202       ex.printStackTrace();\r
 203     }\r
 204 \r
 205   }\r
 206 \r
 207 \r
 208     /**\r
 209      * DOCUMENT ME!\r
 210      *\r
 211      * @param e DOCUMENT ME!\r
 212      */\r
 213     public void ok_actionPerformed(ActionEvent e)\r
 214     {\r
 215 \r
 216       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 217       Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected()));\r
 218       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 219 \r
 220       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 221       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 222       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 223       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 224 \r
 225       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 226       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 227 \r
 228       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 229       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 230       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 231 \r
 232       Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected()));\r
 233 \r
 234       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 235 \r
 236       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
 237 \r
 238       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 239       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 240 \r
 241       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 242 \r
 243       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 244         Cache.applicationProperties.remove("EPS_RENDERING");\r
 245       else\r
 246         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 247 \r
 248       if(defaultBrowser.getText().trim().length()<1)\r
 249         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 250       else\r
 251         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 252                                                 defaultBrowser.getText());\r
 253 \r
 254         jalview.util.BrowserLauncher.resetBrowser();\r
 255 \r
 256         if(nameLinks.size()>0)\r
 257         {\r
 258           StringBuffer links = new StringBuffer();\r
 259           sequenceURLLinks = new Vector();\r
 260           for (int i = 0; i < nameLinks.size(); i++)\r
 261           {\r
 262             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 263             links.append(sequenceURLLinks.elementAt(i).toString());\r
 264             links.append("|");\r
 265           }\r
 266           // remove last "|"\r
 267           links.setLength( links.length()-1 );\r
 268           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 269         }\r
 270         else\r
 271           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 272 \r
 273 \r
 274         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 275 \r
 276         if (proxyServerTB.getText().trim().length() < 1)\r
 277           Cache.applicationProperties.remove("PROXY_SERVER");\r
 278         else\r
 279           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 280                                                   proxyServerTB.getText());\r
 281 \r
 282         if (proxyPortTB.getText().trim().length() < 1)\r
 283           Cache.applicationProperties.remove("PROXY_PORT");\r
 284         else\r
 285           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 286 \r
 287         if(useProxy.isSelected())\r
 288         {\r
 289           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 290           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 291         }\r
 292         else\r
 293         {\r
 294           System.setProperty("http.proxyHost","");\r
 295           System.setProperty("http.proxyPort","");\r
 296         }\r
 297 \r
 298 \r
 299         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 300         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 301         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 302         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 303         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 304         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 305         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 306         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 307         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 308 \r
 309         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 310                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 311         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 312                                                 Boolean.toString(padGaps.isSelected()));\r
 313 \r
 314         dasSource.saveProperties(Cache.applicationProperties);\r
 315 \r
 316         Cache.saveProperties();\r
 317         try\r
 318         {\r
 319             frame.setClosed(true);\r
 320         }\r
 321         catch (Exception ex)\r
 322         {\r
 323         }\r
 324     }\r
 325 \r
 326     /**\r
 327      * DOCUMENT ME!\r
 328      */\r
 329     public void startupFileTextfield_mouseClicked()\r
 330     {\r
 331         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 332                     "LAST_DIRECTORY"),\r
 333                 new String[]\r
 334                 {\r
 335                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 336                     "jar"\r
 337                 },\r
 338                 new String[]\r
 339                 {\r
 340                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 341                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 342         chooser.setFileView(new JalviewFileView());\r
 343         chooser.setDialogTitle("Select startup file");\r
 344 \r
 345         int value = chooser.showOpenDialog(this);\r
 346 \r
 347         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 348         {\r
 349             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 350                 chooser.getSelectedFormat());\r
 351             startupFileTextfield.setText(chooser.getSelectedFile()\r
 352                                                 .getAbsolutePath());\r
 353         }\r
 354     }\r
 355 \r
 356     /**\r
 357      * DOCUMENT ME!\r
 358      *\r
 359      * @param e DOCUMENT ME!\r
 360      */\r
 361     public void cancel_actionPerformed(ActionEvent e)\r
 362     {\r
 363         try\r
 364         {\r
 365             frame.setClosed(true);\r
 366         }\r
 367         catch (Exception ex)\r
 368         {\r
 369         }\r
 370     }\r
 371 \r
 372     /**\r
 373      * DOCUMENT ME!\r
 374      *\r
 375      * @param e DOCUMENT ME!\r
 376      */\r
 377     public void annotations_actionPerformed(ActionEvent e)\r
 378     {\r
 379         conservation.setEnabled(annotations.isSelected());\r
 380         quality.setEnabled(annotations.isSelected());\r
 381         identity.setEnabled(annotations.isSelected());\r
 382     }\r
 383 \r
 384 \r
 385     public void newLink_actionPerformed(ActionEvent e) {\r
 386 \r
 387       GSequenceLink link = new GSequenceLink();\r
 388       boolean valid = false;\r
 389       while( !valid )\r
 390       {\r
 391         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 392                                                   "New sequence URL link",\r
 393                                                   JOptionPane.OK_CANCEL_OPTION\r
 394                                                   ,-1, null)\r
 395             == JOptionPane.OK_OPTION)\r
 396         {\r
 397           if (link.checkValid())\r
 398           {\r
 399             nameLinks.addElement(link.getName());\r
 400             urlLinks.addElement(link.getURL());\r
 401             updateLinkData();\r
 402             valid = true;\r
 403           }\r
 404         }\r
 405         else\r
 406           break;\r
 407       }\r
 408     }\r
 409 \r
 410     public void editLink_actionPerformed(ActionEvent e) {\r
 411       GSequenceLink link = new GSequenceLink();\r
 412 \r
 413       int index = linkNameList.getSelectedIndex();\r
 414       if(index==-1)\r
 415       {\r
 416         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 417             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 418         return;\r
 419       }\r
 420 \r
 421       link.setName( nameLinks.elementAt(index).toString() );\r
 422       link.setURL( urlLinks.elementAt(index).toString() );\r
 423 \r
 424       boolean valid = false;\r
 425       while (!valid)\r
 426       {\r
 427 \r
 428         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 429                                                   "New sequence URL link",\r
 430                                                   JOptionPane.OK_CANCEL_OPTION\r
 431                                                   ,-1, null)\r
 432             == JOptionPane.OK_OPTION)\r
 433         {\r
 434           if (link.checkValid())\r
 435           {\r
 436             nameLinks.setElementAt(link.getName(), index);\r
 437             urlLinks.setElementAt(link.getURL(), index);\r
 438             updateLinkData();\r
 439             valid = true;\r
 440           }\r
 441         }\r
 442 \r
 443         else\r
 444           break;\r
 445       }\r
 446     }\r
 447 \r
 448     public void deleteLink_actionPerformed(ActionEvent e) {\r
 449       int index = linkNameList.getSelectedIndex();\r
 450       if(index==-1)\r
 451       {\r
 452         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 453             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 454         return;\r
 455       }\r
 456       nameLinks.removeElementAt(index);\r
 457       urlLinks.removeElementAt(index);\r
 458       updateLinkData();\r
 459     }\r
 460 \r
 461     void updateLinkData()\r
 462     {\r
 463       linkNameList.setListData(nameLinks);\r
 464       linkURLList.setListData(urlLinks);\r
 465     }\r
 466 \r
 467     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 468     {\r
 469       JFileChooser chooser = new JFileChooser(".");\r
 470       chooser.setDialogTitle("Select default web browser");\r
 471 \r
 472       int value = chooser.showOpenDialog(this);\r
 473 \r
 474       if (value == JFileChooser.APPROVE_OPTION)\r
 475       {\r
 476         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 477       }\r
 478 \r
 479   }\r
 480 \r
 481   private void jbInit()\r
 482       throws Exception\r
 483   {\r
 484   }\r
 485 }\r