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