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.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/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\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 \r
  71     /**\r
  72      * Creates a new Preferences object.\r
  73      */\r
  74     public Preferences()\r
  75     {\r
  76 \r
  77         frame = new JInternalFrame();\r
  78         frame.setContentPane(this);\r
  79         Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
  80         frame.setMinimumSize(new Dimension(480,390));\r
  81 \r
  82         dbRef.setSelected(      Cache.getDefault("SHOW_DBREF", true));\r
  83         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  84         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  85         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  86 \r
  87         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  88         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  89         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  90 \r
  91         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  92         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  93         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  94 \r
  95         for (int i = 0; i < 13; i++)\r
  96         {\r
  97             colour.addItem(ColourSchemeProperty.getColourName(i));\r
  98         }\r
  99 \r
 100         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 101 \r
 102         colour.setSelectedItem(string);\r
 103 \r
 104         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 105                                                      .getAvailableFontFamilyNames();\r
 106 \r
 107         for (int i = 0; i < fonts.length; i++)\r
 108         {\r
 109             fontNameCB.addItem(fonts[i]);\r
 110         }\r
 111 \r
 112         for (int i = 1; i < 31; i++)\r
 113         {\r
 114             fontSizeCB.addItem(i + "");\r
 115         }\r
 116 \r
 117         fontStyleCB.addItem("plain");\r
 118         fontStyleCB.addItem("bold");\r
 119         fontStyleCB.addItem("italic");\r
 120 \r
 121         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 122         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 123         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 124 \r
 125         gapSymbolCB.addItem("-");\r
 126         gapSymbolCB.addItem(".");\r
 127 \r
 128         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 129 \r
 130         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 131         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 132          "http://www.jalview.org/examples/exampleFile.jar"));\r
 133 \r
 134         sortby.addItem("No sort");\r
 135         sortby.addItem("Id");\r
 136         sortby.addItem("Pairwise Identity");\r
 137         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 138 \r
 139         epsRendering.addItem("Prompt each time");\r
 140         epsRendering.addItem("Lineart");\r
 141         epsRendering.addItem("Text");\r
 142         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 143 \r
 144         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 145         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 146         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 147         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 148         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 149         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 150         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 151 \r
 152   /****************************************************\r
 153    * Set up Connections\r
 154    */\r
 155         nameLinks = new Vector();\r
 156         urlLinks = new Vector();\r
 157         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 158         {\r
 159           String link = sequenceURLLinks.elementAt(i).toString();\r
 160           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 161           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 162         }\r
 163 \r
 164         updateLinkData();\r
 165 \r
 166         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 167         proxyServerTB.setEnabled(useProxy.isSelected());\r
 168         proxyPortTB.setEnabled(useProxy.isSelected());\r
 169         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 170         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 171 \r
 172         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 173     try\r
 174     {\r
 175       jbInit();\r
 176     }\r
 177     catch (Exception ex)\r
 178     {\r
 179       ex.printStackTrace();\r
 180     }\r
 181 \r
 182   }\r
 183 \r
 184 \r
 185     /**\r
 186      * DOCUMENT ME!\r
 187      *\r
 188      * @param e DOCUMENT ME!\r
 189      */\r
 190     public void ok_actionPerformed(ActionEvent e)\r
 191     {\r
 192 \r
 193       Cache.applicationProperties.setProperty("SHOW_DBREF", Boolean.toString(dbRef.isSelected()));\r
 194       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 195       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 196 \r
 197       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 198       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 199       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 200       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 201 \r
 202       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 203       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 204 \r
 205       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 206       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 207       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 208 \r
 209       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 210       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 211 \r
 212       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 213 \r
 214       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 215         Cache.applicationProperties.remove("EPS_RENDERING");\r
 216       else\r
 217         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 218 \r
 219       if(defaultBrowser.getText().trim().length()<1)\r
 220         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 221       else\r
 222         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 223                                                 defaultBrowser.getText());\r
 224 \r
 225         jalview.util.BrowserLauncher.resetBrowser();\r
 226 \r
 227         if(nameLinks.size()>0)\r
 228         {\r
 229           StringBuffer links = new StringBuffer();\r
 230           sequenceURLLinks = new Vector();\r
 231           for (int i = 0; i < nameLinks.size(); i++)\r
 232           {\r
 233             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 234             links.append(sequenceURLLinks.elementAt(i).toString());\r
 235             links.append("|");\r
 236           }\r
 237           // remove last "|"\r
 238           links.setLength( links.length()-1 );\r
 239           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 240         }\r
 241         else\r
 242           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 243 \r
 244 \r
 245         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 246 \r
 247         if (proxyServerTB.getText().trim().length() < 1)\r
 248           Cache.applicationProperties.remove("PROXY_SERVER");\r
 249         else\r
 250           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 251                                                   proxyServerTB.getText());\r
 252 \r
 253         if (proxyPortTB.getText().trim().length() < 1)\r
 254           Cache.applicationProperties.remove("PROXY_PORT");\r
 255         else\r
 256           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 257 \r
 258         if(useProxy.isSelected())\r
 259         {\r
 260           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 261           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 262         }\r
 263         else\r
 264         {\r
 265           System.setProperty("http.proxyHost","");\r
 266           System.setProperty("http.proxyPort","");\r
 267         }\r
 268 \r
 269 \r
 270         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 271         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 272         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 273         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 274         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 275         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 276         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 277 \r
 278 \r
 279         Cache.saveProperties();\r
 280         try\r
 281         {\r
 282             frame.setClosed(true);\r
 283         }\r
 284         catch (Exception ex)\r
 285         {\r
 286         }\r
 287     }\r
 288 \r
 289     /**\r
 290      * DOCUMENT ME!\r
 291      */\r
 292     public void startupFileTextfield_mouseClicked()\r
 293     {\r
 294         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 295                     "LAST_DIRECTORY"),\r
 296                 new String[]\r
 297                 {\r
 298                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 299                     "jar"\r
 300                 },\r
 301                 new String[]\r
 302                 {\r
 303                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 304                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 305         chooser.setFileView(new JalviewFileView());\r
 306         chooser.setDialogTitle("Select startup file");\r
 307 \r
 308         int value = chooser.showOpenDialog(this);\r
 309 \r
 310         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 311         {\r
 312             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 313                 chooser.getSelectedFormat());\r
 314             startupFileTextfield.setText(chooser.getSelectedFile()\r
 315                                                 .getAbsolutePath());\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 cancel_actionPerformed(ActionEvent e)\r
 325     {\r
 326         try\r
 327         {\r
 328             frame.setClosed(true);\r
 329         }\r
 330         catch (Exception ex)\r
 331         {\r
 332         }\r
 333     }\r
 334 \r
 335     /**\r
 336      * DOCUMENT ME!\r
 337      *\r
 338      * @param e DOCUMENT ME!\r
 339      */\r
 340     public void annotations_actionPerformed(ActionEvent e)\r
 341     {\r
 342         conservation.setEnabled(annotations.isSelected());\r
 343         quality.setEnabled(annotations.isSelected());\r
 344         identity.setEnabled(annotations.isSelected());\r
 345     }\r
 346 \r
 347 \r
 348     public void newLink_actionPerformed(ActionEvent e) {\r
 349 \r
 350       GSequenceLink link = new GSequenceLink();\r
 351       boolean valid = false;\r
 352       while( !valid )\r
 353       {\r
 354         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 355                                                   "New sequence URL link",\r
 356                                                   JOptionPane.OK_CANCEL_OPTION\r
 357                                                   ,-1, null)\r
 358             == JOptionPane.OK_OPTION)\r
 359         {\r
 360           if (link.checkValid())\r
 361           {\r
 362             nameLinks.addElement(link.getName());\r
 363             urlLinks.addElement(link.getURL());\r
 364             updateLinkData();\r
 365             valid = true;\r
 366           }\r
 367         }\r
 368         else\r
 369           break;\r
 370       }\r
 371     }\r
 372 \r
 373     public void editLink_actionPerformed(ActionEvent e) {\r
 374       GSequenceLink link = new GSequenceLink();\r
 375 \r
 376       int index = linkNameList.getSelectedIndex();\r
 377       if(index==-1)\r
 378       {\r
 379         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 380             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 381         return;\r
 382       }\r
 383 \r
 384       link.setName( nameLinks.elementAt(index).toString() );\r
 385       link.setURL( urlLinks.elementAt(index).toString() );\r
 386 \r
 387       boolean valid = false;\r
 388       while (!valid)\r
 389       {\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.setElementAt(link.getName(), index);\r
 400             urlLinks.setElementAt(link.getURL(), index);\r
 401             updateLinkData();\r
 402             valid = true;\r
 403           }\r
 404         }\r
 405 \r
 406         else\r
 407           break;\r
 408       }\r
 409     }\r
 410 \r
 411     public void deleteLink_actionPerformed(ActionEvent e) {\r
 412       int index = linkNameList.getSelectedIndex();\r
 413       if(index==-1)\r
 414       {\r
 415         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 416             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 417         return;\r
 418       }\r
 419       nameLinks.removeElementAt(index);\r
 420       urlLinks.removeElementAt(index);\r
 421       updateLinkData();\r
 422     }\r
 423 \r
 424     void updateLinkData()\r
 425     {\r
 426       linkNameList.setListData(nameLinks);\r
 427       linkURLList.setListData(urlLinks);\r
 428     }\r
 429 \r
 430     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 431     {\r
 432       JFileChooser chooser = new JFileChooser(".");\r
 433       chooser.setDialogTitle("Select default web browser");\r
 434 \r
 435       int value = chooser.showOpenDialog(this);\r
 436 \r
 437       if (value == JFileChooser.APPROVE_OPTION)\r
 438       {\r
 439         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 440       }\r
 441 \r
 442   }\r
 443 \r
 444   private void jbInit()\r
 445       throws Exception\r
 446   {\r
 447   }\r
 448 }\r