src/jalview/gui/Preferences.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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.bin.*;\r
  22 \r
  23 import jalview.io.*;\r
  24 \r
  25 import jalview.jbgui.*;\r
  26 \r
  27 import jalview.schemes.*;\r
  28 \r
  29 import java.awt.*;\r
  30 import java.awt.event.*;\r
  31 \r
  32 import javax.swing.*;\r
  33 \r
  34 import java.util.*;\r
  35 \r
  36 import jalview.bin.Cache;\r
  37 \r
  38 \r
  39 /**\r
  40  * DOCUMENT ME!\r
  41  *\r
  42  * @author $author$\r
  43  * @version $Revision$\r
  44  */\r
  45 public class Preferences extends GPreferences\r
  46 {\r
  47     /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
  48     public static Vector sequenceURLLinks;\r
  49     static\r
  50     {\r
  51       String string = Cache.getDefault("SEQUENCE_LINKS",\r
  52                                        "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
  53       sequenceURLLinks = new Vector();\r
  54 \r
  55       try\r
  56       {\r
  57         StringTokenizer st = new StringTokenizer(string, "|");\r
  58         while (st.hasMoreElements())\r
  59         {\r
  60           sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
  61         }\r
  62       }\r
  63       catch (Exception ex)\r
  64       {\r
  65         System.out.println(ex + "\nError parsing sequence links");\r
  66       }\r
  67     }\r
  68     Vector nameLinks, urlLinks;\r
  69 \r
  70     JInternalFrame frame;\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         Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
  82         frame.setMinimumSize(new Dimension(480,390));\r
  83 \r
  84         fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
  85         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  86         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  87 \r
  88         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  89         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  90         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  91 \r
  92         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  93         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  94         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  95 \r
  96         for (int i = 0; i < 13; i++)\r
  97         {\r
  98             colour.addItem(ColourSchemeProperty.getColourName(i));\r
  99         }\r
 100 \r
 101         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 102 \r
 103         colour.setSelectedItem(string);\r
 104 \r
 105         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 106                                                      .getAvailableFontFamilyNames();\r
 107 \r
 108         for (int i = 0; i < fonts.length; i++)\r
 109         {\r
 110             fontNameCB.addItem(fonts[i]);\r
 111         }\r
 112 \r
 113         for (int i = 1; i < 31; i++)\r
 114         {\r
 115             fontSizeCB.addItem(i + "");\r
 116         }\r
 117 \r
 118         fontStyleCB.addItem("plain");\r
 119         fontStyleCB.addItem("bold");\r
 120         fontStyleCB.addItem("italic");\r
 121 \r
 122         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 123         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 124         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 125 \r
 126         gapSymbolCB.addItem("-");\r
 127         gapSymbolCB.addItem(".");\r
 128 \r
 129         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 130 \r
 131         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 132         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 133          "http://www.jalview.org/examples/exampleFile.jar"));\r
 134 \r
 135         sortby.addItem("No sort");\r
 136         sortby.addItem("Id");\r
 137         sortby.addItem("Pairwise Identity");\r
 138         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 139 \r
 140         epsRendering.addItem("Prompt each time");\r
 141         epsRendering.addItem("Lineart");\r
 142         epsRendering.addItem("Text");\r
 143         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 144 \r
 145   /****************************************************\r
 146    * Set up Connections\r
 147    */\r
 148         nameLinks = new Vector();\r
 149         urlLinks = new Vector();\r
 150         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 151         {\r
 152           String link = sequenceURLLinks.elementAt(i).toString();\r
 153           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 154           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 155         }\r
 156 \r
 157         updateLinkData();\r
 158 \r
 159         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 160         proxyServerTB.setEnabled(useProxy.isSelected());\r
 161         proxyPortTB.setEnabled(useProxy.isSelected());\r
 162         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 163         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 164 \r
 165         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 166     try\r
 167     {\r
 168       jbInit();\r
 169     }\r
 170     catch (Exception ex)\r
 171     {\r
 172       ex.printStackTrace();\r
 173     }\r
 174 \r
 175   }\r
 176 \r
 177 \r
 178     /**\r
 179      * DOCUMENT ME!\r
 180      *\r
 181      * @param e DOCUMENT ME!\r
 182      */\r
 183     public void ok_actionPerformed(ActionEvent e)\r
 184     {\r
 185 \r
 186       Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
 187       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 188 \r
 189       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 190       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 191       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 192       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 193 \r
 194       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 195       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 196 \r
 197       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 198       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 199       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 200 \r
 201       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 202       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 203 \r
 204       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 205 \r
 206       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 207         Cache.applicationProperties.remove("EPS_RENDERING");\r
 208       else\r
 209         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 210 \r
 211       if(defaultBrowser.getText().trim().length()<1)\r
 212         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 213       else\r
 214         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 215                                                 defaultBrowser.getText());\r
 216 \r
 217         jalview.util.BrowserLauncher.resetBrowser();\r
 218 \r
 219         if(nameLinks.size()>0)\r
 220         {\r
 221           StringBuffer links = new StringBuffer();\r
 222           sequenceURLLinks = new Vector();\r
 223           for (int i = 0; i < nameLinks.size(); i++)\r
 224           {\r
 225             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 226             links.append(sequenceURLLinks.elementAt(i).toString());\r
 227             links.append("|");\r
 228           }\r
 229           // remove last "|"\r
 230           links.setLength( links.length()-1 );\r
 231           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 232         }\r
 233         else\r
 234           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 235 \r
 236 \r
 237         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 238 \r
 239         if (proxyServerTB.getText().trim().length() < 1)\r
 240           Cache.applicationProperties.remove("PROXY_SERVER");\r
 241         else\r
 242           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 243                                                   proxyServerTB.getText());\r
 244 \r
 245         if (proxyPortTB.getText().trim().length() < 1)\r
 246           Cache.applicationProperties.remove("PROXY_PORT");\r
 247         else\r
 248           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 249 \r
 250         if(useProxy.isSelected())\r
 251         {\r
 252           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 253           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 254         }\r
 255         else\r
 256         {\r
 257           System.setProperty("http.proxyHost","");\r
 258           System.setProperty("http.proxyPort","");\r
 259         }\r
 260 \r
 261 \r
 262 \r
 263         Cache.saveProperties();\r
 264         try\r
 265         {\r
 266             frame.setClosed(true);\r
 267         }\r
 268         catch (Exception ex)\r
 269         {\r
 270         }\r
 271     }\r
 272 \r
 273     /**\r
 274      * DOCUMENT ME!\r
 275      */\r
 276     public void startupFileTextfield_mouseClicked()\r
 277     {\r
 278         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 279                     "LAST_DIRECTORY"),\r
 280                 new String[]\r
 281                 {\r
 282                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 283                     "jar"\r
 284                 },\r
 285                 new String[]\r
 286                 {\r
 287                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 288                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 289         chooser.setFileView(new JalviewFileView());\r
 290         chooser.setDialogTitle("Select startup file");\r
 291 \r
 292         int value = chooser.showOpenDialog(this);\r
 293 \r
 294         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 295         {\r
 296             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 297                 chooser.getSelectedFormat());\r
 298             startupFileTextfield.setText(chooser.getSelectedFile()\r
 299                                                 .getAbsolutePath());\r
 300         }\r
 301     }\r
 302 \r
 303     /**\r
 304      * DOCUMENT ME!\r
 305      *\r
 306      * @param e DOCUMENT ME!\r
 307      */\r
 308     public void cancel_actionPerformed(ActionEvent e)\r
 309     {\r
 310         try\r
 311         {\r
 312             frame.setClosed(true);\r
 313         }\r
 314         catch (Exception ex)\r
 315         {\r
 316         }\r
 317     }\r
 318 \r
 319     /**\r
 320      * DOCUMENT ME!\r
 321      *\r
 322      * @param e DOCUMENT ME!\r
 323      */\r
 324     public void annotations_actionPerformed(ActionEvent e)\r
 325     {\r
 326         conservation.setEnabled(annotations.isSelected());\r
 327         quality.setEnabled(annotations.isSelected());\r
 328         identity.setEnabled(annotations.isSelected());\r
 329     }\r
 330 \r
 331 \r
 332     public void newLink_actionPerformed(ActionEvent e) {\r
 333 \r
 334       GSequenceLink link = new GSequenceLink();\r
 335       boolean valid = false;\r
 336       while( !valid )\r
 337       {\r
 338         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 339                                                   "New sequence URL link",\r
 340                                                   JOptionPane.OK_CANCEL_OPTION\r
 341                                                   ,-1, null)\r
 342             == JOptionPane.OK_OPTION)\r
 343         {\r
 344           if (link.checkValid())\r
 345           {\r
 346             nameLinks.addElement(link.getName());\r
 347             urlLinks.addElement(link.getURL());\r
 348             updateLinkData();\r
 349             valid = true;\r
 350           }\r
 351         }\r
 352         else\r
 353           break;\r
 354       }\r
 355     }\r
 356 \r
 357     public void editLink_actionPerformed(ActionEvent e) {\r
 358       GSequenceLink link = new GSequenceLink();\r
 359 \r
 360       int index = linkNameList.getSelectedIndex();\r
 361       if(index==-1)\r
 362       {\r
 363         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 364             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 365         return;\r
 366       }\r
 367 \r
 368       link.setName( nameLinks.elementAt(index).toString() );\r
 369       link.setURL( urlLinks.elementAt(index).toString() );\r
 370 \r
 371       boolean valid = false;\r
 372       while (!valid)\r
 373       {\r
 374 \r
 375         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 376                                                   "New sequence URL link",\r
 377                                                   JOptionPane.OK_CANCEL_OPTION\r
 378                                                   ,-1, null)\r
 379             == JOptionPane.OK_OPTION)\r
 380         {\r
 381           if (link.checkValid())\r
 382           {\r
 383             nameLinks.setElementAt(link.getName(), index);\r
 384             urlLinks.setElementAt(link.getURL(), index);\r
 385             updateLinkData();\r
 386             valid = true;\r
 387           }\r
 388         }\r
 389 \r
 390         else\r
 391           break;\r
 392       }\r
 393     }\r
 394 \r
 395     public void deleteLink_actionPerformed(ActionEvent e) {\r
 396       int index = linkNameList.getSelectedIndex();\r
 397       if(index==-1)\r
 398       {\r
 399         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 400             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 401         return;\r
 402       }\r
 403       nameLinks.removeElementAt(index);\r
 404       urlLinks.removeElementAt(index);\r
 405       updateLinkData();\r
 406     }\r
 407 \r
 408     void updateLinkData()\r
 409     {\r
 410       linkNameList.setListData(nameLinks);\r
 411       linkURLList.setListData(urlLinks);\r
 412     }\r
 413 \r
 414     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 415     {\r
 416       JFileChooser chooser = new JFileChooser(".");\r
 417       chooser.setDialogTitle("Select default web browser");\r
 418 \r
 419       int value = chooser.showOpenDialog(this);\r
 420 \r
 421       if (value == JFileChooser.APPROVE_OPTION)\r
 422       {\r
 423         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 424       }\r
 425 \r
 426   }\r
 427 \r
 428   private void jbInit()\r
 429       throws Exception\r
 430   {\r
 431   }\r
 432 }\r