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 = new Vector();\r
  49     static { sequenceURLLinks.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");}\r
  50     Vector nameLinks, urlLinks;\r
  51 \r
  52     JInternalFrame frame;\r
  53 \r
  54 \r
  55     /**\r
  56      * Creates a new Preferences object.\r
  57      */\r
  58     public Preferences()\r
  59     {\r
  60 \r
  61         frame = new JInternalFrame();\r
  62         frame.setContentPane(this);\r
  63         Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
  64         frame.setMinimumSize(new Dimension(480,390));\r
  65 \r
  66         fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
  67         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  68         annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
  69         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  70 \r
  71         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  72         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  73 \r
  74         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  75         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  76         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  77 \r
  78         for (int i = 0; i < 12; i++)\r
  79         {\r
  80             colour.addItem(ColourSchemeProperty.getColourName(i));\r
  81         }\r
  82 \r
  83         String string = Cache.getProperty("DEFAULT_COLOUR");\r
  84 \r
  85         if (string != null)\r
  86         {\r
  87             colour.setSelectedItem(string);\r
  88         }\r
  89         else\r
  90         {\r
  91             colour.setSelectedIndex(11);\r
  92         }\r
  93 \r
  94         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
  95                                                      .getAvailableFontFamilyNames();\r
  96 \r
  97         for (int i = 0; i < fonts.length; i++)\r
  98         {\r
  99             fontNameCB.addItem(fonts[i]);\r
 100         }\r
 101 \r
 102         for (int i = 1; i < 31; i++)\r
 103         {\r
 104             fontSizeCB.addItem(i + "");\r
 105         }\r
 106 \r
 107         fontStyleCB.addItem("plain");\r
 108         fontStyleCB.addItem("bold");\r
 109         fontStyleCB.addItem("italic");\r
 110 \r
 111         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 112         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 113         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 114 \r
 115         gapSymbolCB.addItem("-");\r
 116         gapSymbolCB.addItem(".");\r
 117 \r
 118         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 119 \r
 120         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 121         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 122          "http://www.jalview.org/examples/exampleFile.jar"));\r
 123 \r
 124   /****************************************************\r
 125    * Set up Connections\r
 126    */\r
 127 \r
 128       string = Cache.getDefault("SEQUENCE_LINKS",\r
 129                             "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
 130       sequenceURLLinks = new Vector();\r
 131 \r
 132         try{\r
 133           StringTokenizer st = new StringTokenizer(string, "|");\r
 134           while (st.hasMoreElements())\r
 135           {\r
 136             sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
 137           }\r
 138         }catch(Exception ex)\r
 139         {System.out.println(ex+"\nError parsing sequence links");}\r
 140 \r
 141         nameLinks = new Vector();\r
 142         urlLinks = new Vector();\r
 143         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 144         {\r
 145           String link = sequenceURLLinks.elementAt(i).toString();\r
 146           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 147           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 148         }\r
 149 \r
 150         updateLinkData();\r
 151 \r
 152         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 153         proxyServerTB.setEnabled(useProxy.isSelected());\r
 154         proxyPortTB.setEnabled(useProxy.isSelected());\r
 155         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 156         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 157 \r
 158         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 159     try\r
 160     {\r
 161       jbInit();\r
 162     }\r
 163     catch (Exception ex)\r
 164     {\r
 165       ex.printStackTrace();\r
 166     }\r
 167 \r
 168   }\r
 169 \r
 170 \r
 171     /**\r
 172      * DOCUMENT ME!\r
 173      *\r
 174      * @param e DOCUMENT ME!\r
 175      */\r
 176     public void ok_actionPerformed(ActionEvent e)\r
 177     {\r
 178 \r
 179       Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
 180       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 181 \r
 182       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 183       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 184       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 185       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 186 \r
 187       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 188       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 189 \r
 190       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 191       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 192       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 193 \r
 194       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 195       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 196 \r
 197       if(defaultBrowser.getText().trim().length()<1)\r
 198         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 199       else\r
 200       {\r
 201         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 202                                                 defaultBrowser.getText());\r
 203         jalview.util.BrowserLauncher.resetBrowser();\r
 204       }\r
 205 \r
 206         if(nameLinks.size()>0)\r
 207         {\r
 208           StringBuffer links = new StringBuffer();\r
 209           sequenceURLLinks = new Vector();\r
 210           for (int i = 0; i < nameLinks.size(); i++)\r
 211           {\r
 212             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 213             links.append(sequenceURLLinks.elementAt(i).toString());\r
 214             links.append("|");\r
 215           }\r
 216           // remove last "|"\r
 217           links.setLength( links.length()-1 );\r
 218           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 219         }\r
 220         else\r
 221           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 222 \r
 223 \r
 224         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 225 \r
 226         if (proxyServerTB.getText().trim().length() < 1)\r
 227           Cache.applicationProperties.remove("PROXY_SERVER");\r
 228         else\r
 229           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 230                                                   proxyServerTB.getText());\r
 231 \r
 232         if (proxyPortTB.getText().trim().length() < 1)\r
 233           Cache.applicationProperties.remove("PROXY_PORT");\r
 234         else\r
 235           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 236 \r
 237         if(useProxy.isSelected())\r
 238         {\r
 239           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 240           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 241         }\r
 242         else\r
 243         {\r
 244           System.setProperty("http.proxyHost","");\r
 245           System.setProperty("http.proxyPort","");\r
 246         }\r
 247 \r
 248 \r
 249 \r
 250         Cache.saveProperties();\r
 251         try\r
 252         {\r
 253             frame.setClosed(true);\r
 254         }\r
 255         catch (Exception ex)\r
 256         {\r
 257         }\r
 258     }\r
 259 \r
 260     /**\r
 261      * DOCUMENT ME!\r
 262      */\r
 263     public void startupFileTextfield_mouseClicked()\r
 264     {\r
 265         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 266                     "LAST_DIRECTORY"),\r
 267                 new String[]\r
 268                 {\r
 269                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 270                     "jar"\r
 271                 },\r
 272                 new String[]\r
 273                 {\r
 274                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 275                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 276         chooser.setFileView(new JalviewFileView());\r
 277         chooser.setDialogTitle("Select startup file");\r
 278 \r
 279         int value = chooser.showOpenDialog(this);\r
 280 \r
 281         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 282         {\r
 283             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 284                 chooser.getSelectedFormat());\r
 285             startupFileTextfield.setText(chooser.getSelectedFile()\r
 286                                                 .getAbsolutePath());\r
 287         }\r
 288     }\r
 289 \r
 290     /**\r
 291      * DOCUMENT ME!\r
 292      *\r
 293      * @param e DOCUMENT ME!\r
 294      */\r
 295     public void cancel_actionPerformed(ActionEvent e)\r
 296     {\r
 297         try\r
 298         {\r
 299             frame.setClosed(true);\r
 300         }\r
 301         catch (Exception ex)\r
 302         {\r
 303         }\r
 304     }\r
 305 \r
 306     /**\r
 307      * DOCUMENT ME!\r
 308      *\r
 309      * @param e DOCUMENT ME!\r
 310      */\r
 311     public void annotations_actionPerformed(ActionEvent e)\r
 312     {\r
 313         conservation.setEnabled(annotations.isSelected());\r
 314         quality.setEnabled(annotations.isSelected());\r
 315         identity.setEnabled(annotations.isSelected());\r
 316     }\r
 317 \r
 318 \r
 319     public void newLink_actionPerformed(ActionEvent e) {\r
 320 \r
 321       GSequenceLink link = new GSequenceLink();\r
 322       boolean valid = false;\r
 323       while( !valid )\r
 324       {\r
 325         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 326                                                   "New sequence URL link",\r
 327                                                   JOptionPane.OK_CANCEL_OPTION\r
 328                                                   ,-1, null)\r
 329             == JOptionPane.OK_OPTION)\r
 330         {\r
 331           if (link.checkValid())\r
 332           {\r
 333             nameLinks.addElement(link.getName());\r
 334             urlLinks.addElement(link.getURL());\r
 335             updateLinkData();\r
 336             valid = true;\r
 337           }\r
 338         }\r
 339         else\r
 340           break;\r
 341       }\r
 342     }\r
 343 \r
 344     public void editLink_actionPerformed(ActionEvent e) {\r
 345       GSequenceLink link = new GSequenceLink();\r
 346 \r
 347       int index = linkNameList.getSelectedIndex();\r
 348       if(index==-1)\r
 349       {\r
 350         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 351             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 352         return;\r
 353       }\r
 354 \r
 355       link.setName( nameLinks.elementAt(index).toString() );\r
 356       link.setURL( urlLinks.elementAt(index).toString() );\r
 357 \r
 358       boolean valid = false;\r
 359       while (!valid)\r
 360       {\r
 361 \r
 362         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 363                                                   "New sequence URL link",\r
 364                                                   JOptionPane.OK_CANCEL_OPTION\r
 365                                                   ,-1, null)\r
 366             == JOptionPane.OK_OPTION)\r
 367         {\r
 368           if (link.checkValid())\r
 369           {\r
 370             nameLinks.setElementAt(link.getName(), index);\r
 371             urlLinks.setElementAt(link.getURL(), index);\r
 372             updateLinkData();\r
 373             valid = true;\r
 374           }\r
 375         }\r
 376 \r
 377         else\r
 378           break;\r
 379       }\r
 380     }\r
 381 \r
 382     public void deleteLink_actionPerformed(ActionEvent e) {\r
 383       int index = linkNameList.getSelectedIndex();\r
 384       if(index==-1)\r
 385       {\r
 386         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 387             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 388         return;\r
 389       }\r
 390       nameLinks.removeElementAt(index);\r
 391       urlLinks.removeElementAt(index);\r
 392       updateLinkData();\r
 393     }\r
 394 \r
 395     void updateLinkData()\r
 396     {\r
 397       linkNameList.setListData(nameLinks);\r
 398       linkURLList.setListData(urlLinks);\r
 399     }\r
 400 \r
 401     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 402     {\r
 403       JFileChooser chooser = new JFileChooser(".");\r
 404       chooser.setDialogTitle("Select default web browser");\r
 405 \r
 406       int value = chooser.showOpenDialog(this);\r
 407 \r
 408       if (value == JFileChooser.APPROVE_OPTION)\r
 409       {\r
 410         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 411       }\r
 412 \r
 413   }\r
 414 \r
 415   private void jbInit()\r
 416       throws Exception\r
 417   {\r
 418   }\r
 419 }\r