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