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