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     DasSourceBrowser dasSource;\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         dasSource = new DasSourceBrowser();\r
  82         dasPanel.add(dasSource, BorderLayout.CENTER);\r
  83 \r
  84         Desktop.addInternalFrame(frame, "Preferences", 490, 405);\r
  85         frame.setMinimumSize(new Dimension(490,395));\r
  86 \r
  87         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  88         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  89         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  90 \r
  91         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  92         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  93         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  94 \r
  95         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  96         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  97         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  98 \r
  99         for (int i = 0; i < 13; i++)\r
 100         {\r
 101             colour.addItem(ColourSchemeProperty.getColourName(i));\r
 102         }\r
 103 \r
 104         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 105 \r
 106         colour.setSelectedItem(string);\r
 107 \r
 108         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 109                                                      .getAvailableFontFamilyNames();\r
 110 \r
 111         for (int i = 0; i < fonts.length; i++)\r
 112         {\r
 113             fontNameCB.addItem(fonts[i]);\r
 114         }\r
 115 \r
 116         for (int i = 1; i < 31; i++)\r
 117         {\r
 118             fontSizeCB.addItem(i + "");\r
 119         }\r
 120 \r
 121         fontStyleCB.addItem("plain");\r
 122         fontStyleCB.addItem("bold");\r
 123         fontStyleCB.addItem("italic");\r
 124 \r
 125         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 126         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 127         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 128 \r
 129         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 130 \r
 131         gapSymbolCB.addItem("-");\r
 132         gapSymbolCB.addItem(".");\r
 133 \r
 134         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 135 \r
 136         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 137         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 138          "http://www.jalview.org/examples/exampleFile.jar"));\r
 139 \r
 140         sortby.addItem("No sort");\r
 141         sortby.addItem("Id");\r
 142         sortby.addItem("Pairwise Identity");\r
 143         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 144 \r
 145         epsRendering.addItem("Prompt each time");\r
 146         epsRendering.addItem("Lineart");\r
 147         epsRendering.addItem("Text");\r
 148         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 149 \r
 150         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 151         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 152         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 153         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 154         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 155         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 156         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 157 \r
 158         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 159 \r
 160         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 161         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 162 \r
 163   /****************************************************\r
 164    * Set up Connections\r
 165    */\r
 166         nameLinks = new Vector();\r
 167         urlLinks = new Vector();\r
 168         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 169         {\r
 170           String link = sequenceURLLinks.elementAt(i).toString();\r
 171           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 172           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 173         }\r
 174 \r
 175         updateLinkData();\r
 176 \r
 177         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 178         proxyServerTB.setEnabled(useProxy.isSelected());\r
 179         proxyPortTB.setEnabled(useProxy.isSelected());\r
 180         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 181         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 182 \r
 183         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 184     try\r
 185     {\r
 186       jbInit();\r
 187     }\r
 188     catch (Exception ex)\r
 189     {\r
 190       ex.printStackTrace();\r
 191     }\r
 192 \r
 193   }\r
 194 \r
 195 \r
 196     /**\r
 197      * DOCUMENT ME!\r
 198      *\r
 199      * @param e DOCUMENT ME!\r
 200      */\r
 201     public void ok_actionPerformed(ActionEvent e)\r
 202     {\r
 203 \r
 204       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 205       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 206 \r
 207       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 208       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 209       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 210       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 211 \r
 212       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 213       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 214 \r
 215       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 216       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 217       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 218 \r
 219       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 220 \r
 221       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 222       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 223 \r
 224       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 225 \r
 226       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 227         Cache.applicationProperties.remove("EPS_RENDERING");\r
 228       else\r
 229         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 230 \r
 231       if(defaultBrowser.getText().trim().length()<1)\r
 232         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 233       else\r
 234         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 235                                                 defaultBrowser.getText());\r
 236 \r
 237         jalview.util.BrowserLauncher.resetBrowser();\r
 238 \r
 239         if(nameLinks.size()>0)\r
 240         {\r
 241           StringBuffer links = new StringBuffer();\r
 242           sequenceURLLinks = new Vector();\r
 243           for (int i = 0; i < nameLinks.size(); i++)\r
 244           {\r
 245             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 246             links.append(sequenceURLLinks.elementAt(i).toString());\r
 247             links.append("|");\r
 248           }\r
 249           // remove last "|"\r
 250           links.setLength( links.length()-1 );\r
 251           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 252         }\r
 253         else\r
 254           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 255 \r
 256 \r
 257         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 258 \r
 259         if (proxyServerTB.getText().trim().length() < 1)\r
 260           Cache.applicationProperties.remove("PROXY_SERVER");\r
 261         else\r
 262           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 263                                                   proxyServerTB.getText());\r
 264 \r
 265         if (proxyPortTB.getText().trim().length() < 1)\r
 266           Cache.applicationProperties.remove("PROXY_PORT");\r
 267         else\r
 268           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 269 \r
 270         if(useProxy.isSelected())\r
 271         {\r
 272           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 273           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 274         }\r
 275         else\r
 276         {\r
 277           System.setProperty("http.proxyHost","");\r
 278           System.setProperty("http.proxyPort","");\r
 279         }\r
 280 \r
 281 \r
 282         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 283         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 284         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 285         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 286         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 287         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 288         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 289         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 290         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 291 \r
 292         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 293                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 294         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 295                                                 Boolean.toString(padGaps.isSelected()));\r
 296 \r
 297         dasSource.saveProperties(Cache.applicationProperties);\r
 298 \r
 299         Cache.saveProperties();\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     public void startupFileTextfield_mouseClicked()\r
 313     {\r
 314         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 315                     "LAST_DIRECTORY"),\r
 316                 new String[]\r
 317                 {\r
 318                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 319                     "jar"\r
 320                 },\r
 321                 new String[]\r
 322                 {\r
 323                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 324                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 325         chooser.setFileView(new JalviewFileView());\r
 326         chooser.setDialogTitle("Select startup file");\r
 327 \r
 328         int value = chooser.showOpenDialog(this);\r
 329 \r
 330         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 331         {\r
 332             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 333                 chooser.getSelectedFormat());\r
 334             startupFileTextfield.setText(chooser.getSelectedFile()\r
 335                                                 .getAbsolutePath());\r
 336         }\r
 337     }\r
 338 \r
 339     /**\r
 340      * DOCUMENT ME!\r
 341      *\r
 342      * @param e DOCUMENT ME!\r
 343      */\r
 344     public void cancel_actionPerformed(ActionEvent e)\r
 345     {\r
 346         try\r
 347         {\r
 348             frame.setClosed(true);\r
 349         }\r
 350         catch (Exception ex)\r
 351         {\r
 352         }\r
 353     }\r
 354 \r
 355     /**\r
 356      * DOCUMENT ME!\r
 357      *\r
 358      * @param e DOCUMENT ME!\r
 359      */\r
 360     public void annotations_actionPerformed(ActionEvent e)\r
 361     {\r
 362         conservation.setEnabled(annotations.isSelected());\r
 363         quality.setEnabled(annotations.isSelected());\r
 364         identity.setEnabled(annotations.isSelected());\r
 365     }\r
 366 \r
 367 \r
 368     public void newLink_actionPerformed(ActionEvent e) {\r
 369 \r
 370       GSequenceLink link = new GSequenceLink();\r
 371       boolean valid = false;\r
 372       while( !valid )\r
 373       {\r
 374         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 375                                                   "New sequence URL link",\r
 376                                                   JOptionPane.OK_CANCEL_OPTION\r
 377                                                   ,-1, null)\r
 378             == JOptionPane.OK_OPTION)\r
 379         {\r
 380           if (link.checkValid())\r
 381           {\r
 382             nameLinks.addElement(link.getName());\r
 383             urlLinks.addElement(link.getURL());\r
 384             updateLinkData();\r
 385             valid = true;\r
 386           }\r
 387         }\r
 388         else\r
 389           break;\r
 390       }\r
 391     }\r
 392 \r
 393     public void editLink_actionPerformed(ActionEvent e) {\r
 394       GSequenceLink link = new GSequenceLink();\r
 395 \r
 396       int index = linkNameList.getSelectedIndex();\r
 397       if(index==-1)\r
 398       {\r
 399         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 400             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 401         return;\r
 402       }\r
 403 \r
 404       link.setName( nameLinks.elementAt(index).toString() );\r
 405       link.setURL( urlLinks.elementAt(index).toString() );\r
 406 \r
 407       boolean valid = false;\r
 408       while (!valid)\r
 409       {\r
 410 \r
 411         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 412                                                   "New sequence URL link",\r
 413                                                   JOptionPane.OK_CANCEL_OPTION\r
 414                                                   ,-1, null)\r
 415             == JOptionPane.OK_OPTION)\r
 416         {\r
 417           if (link.checkValid())\r
 418           {\r
 419             nameLinks.setElementAt(link.getName(), index);\r
 420             urlLinks.setElementAt(link.getURL(), index);\r
 421             updateLinkData();\r
 422             valid = true;\r
 423           }\r
 424         }\r
 425 \r
 426         else\r
 427           break;\r
 428       }\r
 429     }\r
 430 \r
 431     public void deleteLink_actionPerformed(ActionEvent e) {\r
 432       int index = linkNameList.getSelectedIndex();\r
 433       if(index==-1)\r
 434       {\r
 435         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 436             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 437         return;\r
 438       }\r
 439       nameLinks.removeElementAt(index);\r
 440       urlLinks.removeElementAt(index);\r
 441       updateLinkData();\r
 442     }\r
 443 \r
 444     void updateLinkData()\r
 445     {\r
 446       linkNameList.setListData(nameLinks);\r
 447       linkURLList.setListData(urlLinks);\r
 448     }\r
 449 \r
 450     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 451     {\r
 452       JFileChooser chooser = new JFileChooser(".");\r
 453       chooser.setDialogTitle("Select default web browser");\r
 454 \r
 455       int value = chooser.showOpenDialog(this);\r
 456 \r
 457       if (value == JFileChooser.APPROVE_OPTION)\r
 458       {\r
 459         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 460       }\r
 461 \r
 462   }\r
 463 \r
 464   private void jbInit()\r
 465       throws Exception\r
 466   {\r
 467   }\r
 468 }\r