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