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