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, 395);\r
  80         frame.setMinimumSize(new Dimension(480,395));\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         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 154 \r
 155         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 156         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 157 \r
 158   /****************************************************\r
 159    * Set up Connections\r
 160    */\r
 161         nameLinks = new Vector();\r
 162         urlLinks = new Vector();\r
 163         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 164         {\r
 165           String link = sequenceURLLinks.elementAt(i).toString();\r
 166           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 167           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 168         }\r
 169 \r
 170         updateLinkData();\r
 171 \r
 172         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 173         proxyServerTB.setEnabled(useProxy.isSelected());\r
 174         proxyPortTB.setEnabled(useProxy.isSelected());\r
 175         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 176         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 177 \r
 178         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 179     try\r
 180     {\r
 181       jbInit();\r
 182     }\r
 183     catch (Exception ex)\r
 184     {\r
 185       ex.printStackTrace();\r
 186     }\r
 187 \r
 188   }\r
 189 \r
 190 \r
 191     /**\r
 192      * DOCUMENT ME!\r
 193      *\r
 194      * @param e DOCUMENT ME!\r
 195      */\r
 196     public void ok_actionPerformed(ActionEvent e)\r
 197     {\r
 198 \r
 199       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 200       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 201 \r
 202       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 203       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 204       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 205       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 206 \r
 207       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 208       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 209 \r
 210       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 211       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 212       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 213 \r
 214       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 215 \r
 216       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 217       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 218 \r
 219       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 220 \r
 221       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 222         Cache.applicationProperties.remove("EPS_RENDERING");\r
 223       else\r
 224         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 225 \r
 226       if(defaultBrowser.getText().trim().length()<1)\r
 227         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 228       else\r
 229         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 230                                                 defaultBrowser.getText());\r
 231 \r
 232         jalview.util.BrowserLauncher.resetBrowser();\r
 233 \r
 234         if(nameLinks.size()>0)\r
 235         {\r
 236           StringBuffer links = new StringBuffer();\r
 237           sequenceURLLinks = new Vector();\r
 238           for (int i = 0; i < nameLinks.size(); i++)\r
 239           {\r
 240             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 241             links.append(sequenceURLLinks.elementAt(i).toString());\r
 242             links.append("|");\r
 243           }\r
 244           // remove last "|"\r
 245           links.setLength( links.length()-1 );\r
 246           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 247         }\r
 248         else\r
 249           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 250 \r
 251 \r
 252         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 253 \r
 254         if (proxyServerTB.getText().trim().length() < 1)\r
 255           Cache.applicationProperties.remove("PROXY_SERVER");\r
 256         else\r
 257           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 258                                                   proxyServerTB.getText());\r
 259 \r
 260         if (proxyPortTB.getText().trim().length() < 1)\r
 261           Cache.applicationProperties.remove("PROXY_PORT");\r
 262         else\r
 263           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 264 \r
 265         if(useProxy.isSelected())\r
 266         {\r
 267           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 268           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 269         }\r
 270         else\r
 271         {\r
 272           System.setProperty("http.proxyHost","");\r
 273           System.setProperty("http.proxyPort","");\r
 274         }\r
 275 \r
 276 \r
 277         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 278         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 279         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 280         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 281         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 282         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 283         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 284         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 285         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 286 \r
 287         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 288                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 289         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 290                                                 Boolean.toString(padGaps.isSelected()));\r
 291         Cache.saveProperties();\r
 292         try\r
 293         {\r
 294             frame.setClosed(true);\r
 295         }\r
 296         catch (Exception ex)\r
 297         {\r
 298         }\r
 299     }\r
 300 \r
 301     /**\r
 302      * DOCUMENT ME!\r
 303      */\r
 304     public void startupFileTextfield_mouseClicked()\r
 305     {\r
 306         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 307                     "LAST_DIRECTORY"),\r
 308                 new String[]\r
 309                 {\r
 310                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 311                     "jar"\r
 312                 },\r
 313                 new String[]\r
 314                 {\r
 315                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 316                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 317         chooser.setFileView(new JalviewFileView());\r
 318         chooser.setDialogTitle("Select startup file");\r
 319 \r
 320         int value = chooser.showOpenDialog(this);\r
 321 \r
 322         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 323         {\r
 324             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 325                 chooser.getSelectedFormat());\r
 326             startupFileTextfield.setText(chooser.getSelectedFile()\r
 327                                                 .getAbsolutePath());\r
 328         }\r
 329     }\r
 330 \r
 331     /**\r
 332      * DOCUMENT ME!\r
 333      *\r
 334      * @param e DOCUMENT ME!\r
 335      */\r
 336     public void cancel_actionPerformed(ActionEvent e)\r
 337     {\r
 338         try\r
 339         {\r
 340             frame.setClosed(true);\r
 341         }\r
 342         catch (Exception ex)\r
 343         {\r
 344         }\r
 345     }\r
 346 \r
 347     /**\r
 348      * DOCUMENT ME!\r
 349      *\r
 350      * @param e DOCUMENT ME!\r
 351      */\r
 352     public void annotations_actionPerformed(ActionEvent e)\r
 353     {\r
 354         conservation.setEnabled(annotations.isSelected());\r
 355         quality.setEnabled(annotations.isSelected());\r
 356         identity.setEnabled(annotations.isSelected());\r
 357     }\r
 358 \r
 359 \r
 360     public void newLink_actionPerformed(ActionEvent e) {\r
 361 \r
 362       GSequenceLink link = new GSequenceLink();\r
 363       boolean valid = false;\r
 364       while( !valid )\r
 365       {\r
 366         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 367                                                   "New sequence URL link",\r
 368                                                   JOptionPane.OK_CANCEL_OPTION\r
 369                                                   ,-1, null)\r
 370             == JOptionPane.OK_OPTION)\r
 371         {\r
 372           if (link.checkValid())\r
 373           {\r
 374             nameLinks.addElement(link.getName());\r
 375             urlLinks.addElement(link.getURL());\r
 376             updateLinkData();\r
 377             valid = true;\r
 378           }\r
 379         }\r
 380         else\r
 381           break;\r
 382       }\r
 383     }\r
 384 \r
 385     public void editLink_actionPerformed(ActionEvent e) {\r
 386       GSequenceLink link = new GSequenceLink();\r
 387 \r
 388       int index = linkNameList.getSelectedIndex();\r
 389       if(index==-1)\r
 390       {\r
 391         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 392             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 393         return;\r
 394       }\r
 395 \r
 396       link.setName( nameLinks.elementAt(index).toString() );\r
 397       link.setURL( urlLinks.elementAt(index).toString() );\r
 398 \r
 399       boolean valid = false;\r
 400       while (!valid)\r
 401       {\r
 402 \r
 403         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 404                                                   "New sequence URL link",\r
 405                                                   JOptionPane.OK_CANCEL_OPTION\r
 406                                                   ,-1, null)\r
 407             == JOptionPane.OK_OPTION)\r
 408         {\r
 409           if (link.checkValid())\r
 410           {\r
 411             nameLinks.setElementAt(link.getName(), index);\r
 412             urlLinks.setElementAt(link.getURL(), index);\r
 413             updateLinkData();\r
 414             valid = true;\r
 415           }\r
 416         }\r
 417 \r
 418         else\r
 419           break;\r
 420       }\r
 421     }\r
 422 \r
 423     public void deleteLink_actionPerformed(ActionEvent e) {\r
 424       int index = linkNameList.getSelectedIndex();\r
 425       if(index==-1)\r
 426       {\r
 427         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 428             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 429         return;\r
 430       }\r
 431       nameLinks.removeElementAt(index);\r
 432       urlLinks.removeElementAt(index);\r
 433       updateLinkData();\r
 434     }\r
 435 \r
 436     void updateLinkData()\r
 437     {\r
 438       linkNameList.setListData(nameLinks);\r
 439       linkURLList.setListData(urlLinks);\r
 440     }\r
 441 \r
 442     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 443     {\r
 444       JFileChooser chooser = new JFileChooser(".");\r
 445       chooser.setDialogTitle("Select default web browser");\r
 446 \r
 447       int value = chooser.showOpenDialog(this);\r
 448 \r
 449       if (value == JFileChooser.APPROVE_OPTION)\r
 450       {\r
 451         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 452       }\r
 453 \r
 454   }\r
 455 \r
 456   private void jbInit()\r
 457       throws Exception\r
 458   {\r
 459   }\r
 460 }\r