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