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         int width = 500, height = 420;\r
  85         if(System.getProperty("os.name").startsWith("Mac"))\r
  86         {\r
  87           width = 570;\r
  88           height = 460;\r
  89         }\r
  90 \r
  91         Desktop.addInternalFrame(frame, "Preferences", width, height);\r
  92         frame.setMinimumSize(new Dimension(width, height));\r
  93 \r
  94         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  95         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  96         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  97 \r
  98         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  99         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 100         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 101 \r
 102         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
 103         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
 104         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
 105 \r
 106         for (int i = 0; i < 13; i++)\r
 107         {\r
 108             colour.addItem(ColourSchemeProperty.getColourName(i));\r
 109         }\r
 110 \r
 111         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 112 \r
 113         colour.setSelectedItem(string);\r
 114 \r
 115         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 116                                                      .getAvailableFontFamilyNames();\r
 117 \r
 118         for (int i = 0; i < fonts.length; i++)\r
 119         {\r
 120             fontNameCB.addItem(fonts[i]);\r
 121         }\r
 122 \r
 123         for (int i = 1; i < 31; i++)\r
 124         {\r
 125             fontSizeCB.addItem(i + "");\r
 126         }\r
 127 \r
 128         fontStyleCB.addItem("plain");\r
 129         fontStyleCB.addItem("bold");\r
 130         fontStyleCB.addItem("italic");\r
 131 \r
 132         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 133         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 134         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 135 \r
 136         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 137 \r
 138         wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 139 \r
 140         gapSymbolCB.addItem("-");\r
 141         gapSymbolCB.addItem(".");\r
 142 \r
 143         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 144 \r
 145         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 146         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 147          "http://www.jalview.org/examples/exampleFile.jar"));\r
 148 \r
 149         sortby.addItem("No sort");\r
 150         sortby.addItem("Id");\r
 151         sortby.addItem("Pairwise Identity");\r
 152         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 153 \r
 154         epsRendering.addItem("Prompt each time");\r
 155         epsRendering.addItem("Lineart");\r
 156         epsRendering.addItem("Text");\r
 157         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 158 \r
 159         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 160         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 161         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 162         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 163         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 164         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 165         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 166 \r
 167         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 168 \r
 169         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 170         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 171 \r
 172   /****************************************************\r
 173    * Set up Connections\r
 174    */\r
 175         nameLinks = new Vector();\r
 176         urlLinks = new Vector();\r
 177         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 178         {\r
 179           String link = sequenceURLLinks.elementAt(i).toString();\r
 180           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 181           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 182         }\r
 183 \r
 184         updateLinkData();\r
 185 \r
 186         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 187         proxyServerTB.setEnabled(useProxy.isSelected());\r
 188         proxyPortTB.setEnabled(useProxy.isSelected());\r
 189         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 190         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 191 \r
 192         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 193     try\r
 194     {\r
 195       jbInit();\r
 196     }\r
 197     catch (Exception ex)\r
 198     {\r
 199       ex.printStackTrace();\r
 200     }\r
 201 \r
 202   }\r
 203 \r
 204 \r
 205     /**\r
 206      * DOCUMENT ME!\r
 207      *\r
 208      * @param e DOCUMENT ME!\r
 209      */\r
 210     public void ok_actionPerformed(ActionEvent e)\r
 211     {\r
 212 \r
 213       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 214       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 215 \r
 216       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 217       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 218       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 219       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 220 \r
 221       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 222       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 223 \r
 224       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 225       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 226       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 227 \r
 228       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 229 \r
 230       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
 231 \r
 232       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 233       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 234 \r
 235       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 236 \r
 237       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 238         Cache.applicationProperties.remove("EPS_RENDERING");\r
 239       else\r
 240         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 241 \r
 242       if(defaultBrowser.getText().trim().length()<1)\r
 243         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 244       else\r
 245         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 246                                                 defaultBrowser.getText());\r
 247 \r
 248         jalview.util.BrowserLauncher.resetBrowser();\r
 249 \r
 250         if(nameLinks.size()>0)\r
 251         {\r
 252           StringBuffer links = new StringBuffer();\r
 253           sequenceURLLinks = new Vector();\r
 254           for (int i = 0; i < nameLinks.size(); i++)\r
 255           {\r
 256             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 257             links.append(sequenceURLLinks.elementAt(i).toString());\r
 258             links.append("|");\r
 259           }\r
 260           // remove last "|"\r
 261           links.setLength( links.length()-1 );\r
 262           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 263         }\r
 264         else\r
 265           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 266 \r
 267 \r
 268         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 269 \r
 270         if (proxyServerTB.getText().trim().length() < 1)\r
 271           Cache.applicationProperties.remove("PROXY_SERVER");\r
 272         else\r
 273           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 274                                                   proxyServerTB.getText());\r
 275 \r
 276         if (proxyPortTB.getText().trim().length() < 1)\r
 277           Cache.applicationProperties.remove("PROXY_PORT");\r
 278         else\r
 279           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 280 \r
 281         if(useProxy.isSelected())\r
 282         {\r
 283           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 284           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 285         }\r
 286         else\r
 287         {\r
 288           System.setProperty("http.proxyHost","");\r
 289           System.setProperty("http.proxyPort","");\r
 290         }\r
 291 \r
 292 \r
 293         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 294         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 295         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 296         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 297         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 298         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 299         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 300         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 301         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 302 \r
 303         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 304                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 305         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 306                                                 Boolean.toString(padGaps.isSelected()));\r
 307 \r
 308         dasSource.saveProperties(Cache.applicationProperties);\r
 309 \r
 310         Cache.saveProperties();\r
 311         try\r
 312         {\r
 313             frame.setClosed(true);\r
 314         }\r
 315         catch (Exception ex)\r
 316         {\r
 317         }\r
 318     }\r
 319 \r
 320     /**\r
 321      * DOCUMENT ME!\r
 322      */\r
 323     public void startupFileTextfield_mouseClicked()\r
 324     {\r
 325         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 326                     "LAST_DIRECTORY"),\r
 327                 new String[]\r
 328                 {\r
 329                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 330                     "jar"\r
 331                 },\r
 332                 new String[]\r
 333                 {\r
 334                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 335                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 336         chooser.setFileView(new JalviewFileView());\r
 337         chooser.setDialogTitle("Select startup file");\r
 338 \r
 339         int value = chooser.showOpenDialog(this);\r
 340 \r
 341         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 342         {\r
 343             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 344                 chooser.getSelectedFormat());\r
 345             startupFileTextfield.setText(chooser.getSelectedFile()\r
 346                                                 .getAbsolutePath());\r
 347         }\r
 348     }\r
 349 \r
 350     /**\r
 351      * DOCUMENT ME!\r
 352      *\r
 353      * @param e DOCUMENT ME!\r
 354      */\r
 355     public void cancel_actionPerformed(ActionEvent e)\r
 356     {\r
 357         try\r
 358         {\r
 359             frame.setClosed(true);\r
 360         }\r
 361         catch (Exception ex)\r
 362         {\r
 363         }\r
 364     }\r
 365 \r
 366     /**\r
 367      * DOCUMENT ME!\r
 368      *\r
 369      * @param e DOCUMENT ME!\r
 370      */\r
 371     public void annotations_actionPerformed(ActionEvent e)\r
 372     {\r
 373         conservation.setEnabled(annotations.isSelected());\r
 374         quality.setEnabled(annotations.isSelected());\r
 375         identity.setEnabled(annotations.isSelected());\r
 376     }\r
 377 \r
 378 \r
 379     public void newLink_actionPerformed(ActionEvent e) {\r
 380 \r
 381       GSequenceLink link = new GSequenceLink();\r
 382       boolean valid = false;\r
 383       while( !valid )\r
 384       {\r
 385         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 386                                                   "New sequence URL link",\r
 387                                                   JOptionPane.OK_CANCEL_OPTION\r
 388                                                   ,-1, null)\r
 389             == JOptionPane.OK_OPTION)\r
 390         {\r
 391           if (link.checkValid())\r
 392           {\r
 393             nameLinks.addElement(link.getName());\r
 394             urlLinks.addElement(link.getURL());\r
 395             updateLinkData();\r
 396             valid = true;\r
 397           }\r
 398         }\r
 399         else\r
 400           break;\r
 401       }\r
 402     }\r
 403 \r
 404     public void editLink_actionPerformed(ActionEvent e) {\r
 405       GSequenceLink link = new GSequenceLink();\r
 406 \r
 407       int index = linkNameList.getSelectedIndex();\r
 408       if(index==-1)\r
 409       {\r
 410         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 411             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 412         return;\r
 413       }\r
 414 \r
 415       link.setName( nameLinks.elementAt(index).toString() );\r
 416       link.setURL( urlLinks.elementAt(index).toString() );\r
 417 \r
 418       boolean valid = false;\r
 419       while (!valid)\r
 420       {\r
 421 \r
 422         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 423                                                   "New sequence URL link",\r
 424                                                   JOptionPane.OK_CANCEL_OPTION\r
 425                                                   ,-1, null)\r
 426             == JOptionPane.OK_OPTION)\r
 427         {\r
 428           if (link.checkValid())\r
 429           {\r
 430             nameLinks.setElementAt(link.getName(), index);\r
 431             urlLinks.setElementAt(link.getURL(), index);\r
 432             updateLinkData();\r
 433             valid = true;\r
 434           }\r
 435         }\r
 436 \r
 437         else\r
 438           break;\r
 439       }\r
 440     }\r
 441 \r
 442     public void deleteLink_actionPerformed(ActionEvent e) {\r
 443       int index = linkNameList.getSelectedIndex();\r
 444       if(index==-1)\r
 445       {\r
 446         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 447             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 448         return;\r
 449       }\r
 450       nameLinks.removeElementAt(index);\r
 451       urlLinks.removeElementAt(index);\r
 452       updateLinkData();\r
 453     }\r
 454 \r
 455     void updateLinkData()\r
 456     {\r
 457       linkNameList.setListData(nameLinks);\r
 458       linkURLList.setListData(urlLinks);\r
 459     }\r
 460 \r
 461     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 462     {\r
 463       JFileChooser chooser = new JFileChooser(".");\r
 464       chooser.setDialogTitle("Select default web browser");\r
 465 \r
 466       int value = chooser.showOpenDialog(this);\r
 467 \r
 468       if (value == JFileChooser.APPROVE_OPTION)\r
 469       {\r
 470         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 471       }\r
 472 \r
 473   }\r
 474 \r
 475   private void jbInit()\r
 476       throws Exception\r
 477   {\r
 478   }\r
 479 }\r