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         dbRef.setSelected(      Cache.getDefault("SHOW_DBREF", true));\r
  83         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  84         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  85         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  86 \r
  87         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  88         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  89         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  90 \r
  91         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  92         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  93         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  94 \r
  95         for (int i = 0; i < 13; i++)\r
  96         {\r
  97             colour.addItem(ColourSchemeProperty.getColourName(i));\r
  98         }\r
  99 \r
 100         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 101 \r
 102         colour.setSelectedItem(string);\r
 103 \r
 104         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 105                                                      .getAvailableFontFamilyNames();\r
 106 \r
 107         for (int i = 0; i < fonts.length; i++)\r
 108         {\r
 109             fontNameCB.addItem(fonts[i]);\r
 110         }\r
 111 \r
 112         for (int i = 1; i < 31; i++)\r
 113         {\r
 114             fontSizeCB.addItem(i + "");\r
 115         }\r
 116 \r
 117         fontStyleCB.addItem("plain");\r
 118         fontStyleCB.addItem("bold");\r
 119         fontStyleCB.addItem("italic");\r
 120 \r
 121         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 122         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 123         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 124 \r
 125         gapSymbolCB.addItem("-");\r
 126         gapSymbolCB.addItem(".");\r
 127 \r
 128         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 129 \r
 130         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 131         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 132          "http://www.jalview.org/examples/exampleFile.jar"));\r
 133 \r
 134         sortby.addItem("No sort");\r
 135         sortby.addItem("Id");\r
 136         sortby.addItem("Pairwise Identity");\r
 137         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 138 \r
 139         epsRendering.addItem("Prompt each time");\r
 140         epsRendering.addItem("Lineart");\r
 141         epsRendering.addItem("Text");\r
 142         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 143 \r
 144         blcdb.setSelected( Cache.getDefault("BLC_DBPREFIX", false) );\r
 145         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 146         clustaldb.setSelected( Cache.getDefault("CLUSTAL_DBPREFIX", false) );\r
 147         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 148         fastadb.setSelected( Cache.getDefault("FASTA_DBPREFIX", false) );\r
 149         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 150         msfdb.setSelected( Cache.getDefault("MSF_DBPREFIX", false) );\r
 151         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 152         pfamdb.setSelected( Cache.getDefault("PFAM_DBPREFIX", false) );\r
 153         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 154         pileupdb.setSelected( Cache.getDefault("PILEUP_DBPREFIX", false) );\r
 155         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 156         pirdb.setSelected( Cache.getDefault("PIR_DBPREFIX", false) );\r
 157         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 158 \r
 159   /****************************************************\r
 160    * Set up Connections\r
 161    */\r
 162         nameLinks = new Vector();\r
 163         urlLinks = new Vector();\r
 164         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 165         {\r
 166           String link = sequenceURLLinks.elementAt(i).toString();\r
 167           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 168           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 169         }\r
 170 \r
 171         updateLinkData();\r
 172 \r
 173         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 174         proxyServerTB.setEnabled(useProxy.isSelected());\r
 175         proxyPortTB.setEnabled(useProxy.isSelected());\r
 176         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 177         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 178 \r
 179         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 180     try\r
 181     {\r
 182       jbInit();\r
 183     }\r
 184     catch (Exception ex)\r
 185     {\r
 186       ex.printStackTrace();\r
 187     }\r
 188 \r
 189   }\r
 190 \r
 191 \r
 192     /**\r
 193      * DOCUMENT ME!\r
 194      *\r
 195      * @param e DOCUMENT ME!\r
 196      */\r
 197     public void ok_actionPerformed(ActionEvent e)\r
 198     {\r
 199 \r
 200       Cache.applicationProperties.setProperty("SHOW_DBREF", Boolean.toString(dbRef.isSelected()));\r
 201       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 202       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 203 \r
 204       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 205       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 206       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 207       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 208 \r
 209       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 210       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 211 \r
 212       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 213       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 214       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\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_DBPREFIX", Boolean.toString(blcdb.isSelected()) );\r
 278         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 279         Cache.applicationProperties.setProperty("CLUSTAL_DBPREFIX", Boolean.toString(clustaldb.isSelected()) );\r
 280         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 281         Cache.applicationProperties.setProperty("FASTA_DBPREFIX", Boolean.toString(fastadb.isSelected()) );\r
 282         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 283         Cache.applicationProperties.setProperty("MSF_DBPREFIX", Boolean.toString(msfdb.isSelected()) );\r
 284         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 285         Cache.applicationProperties.setProperty("PFAM_DBPREFIX", Boolean.toString(pfamdb.isSelected()) );\r
 286         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 287         Cache.applicationProperties.setProperty("PILEUP_DBPREFIX", Boolean.toString(pileupdb.isSelected()) );\r
 288         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 289         Cache.applicationProperties.setProperty("PIR_DBPREFIX", Boolean.toString(pirdb.isSelected()) );\r
 290         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 291 \r
 292 \r
 293         Cache.saveProperties();\r
 294         try\r
 295         {\r
 296             frame.setClosed(true);\r
 297         }\r
 298         catch (Exception ex)\r
 299         {\r
 300         }\r
 301     }\r
 302 \r
 303     /**\r
 304      * DOCUMENT ME!\r
 305      */\r
 306     public void startupFileTextfield_mouseClicked()\r
 307     {\r
 308         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 309                     "LAST_DIRECTORY"),\r
 310                 new String[]\r
 311                 {\r
 312                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 313                     "jar"\r
 314                 },\r
 315                 new String[]\r
 316                 {\r
 317                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 318                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 319         chooser.setFileView(new JalviewFileView());\r
 320         chooser.setDialogTitle("Select startup file");\r
 321 \r
 322         int value = chooser.showOpenDialog(this);\r
 323 \r
 324         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 325         {\r
 326             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 327                 chooser.getSelectedFormat());\r
 328             startupFileTextfield.setText(chooser.getSelectedFile()\r
 329                                                 .getAbsolutePath());\r
 330         }\r
 331     }\r
 332 \r
 333     /**\r
 334      * DOCUMENT ME!\r
 335      *\r
 336      * @param e DOCUMENT ME!\r
 337      */\r
 338     public void cancel_actionPerformed(ActionEvent e)\r
 339     {\r
 340         try\r
 341         {\r
 342             frame.setClosed(true);\r
 343         }\r
 344         catch (Exception ex)\r
 345         {\r
 346         }\r
 347     }\r
 348 \r
 349     /**\r
 350      * DOCUMENT ME!\r
 351      *\r
 352      * @param e DOCUMENT ME!\r
 353      */\r
 354     public void annotations_actionPerformed(ActionEvent e)\r
 355     {\r
 356         conservation.setEnabled(annotations.isSelected());\r
 357         quality.setEnabled(annotations.isSelected());\r
 358         identity.setEnabled(annotations.isSelected());\r
 359     }\r
 360 \r
 361 \r
 362     public void newLink_actionPerformed(ActionEvent e) {\r
 363 \r
 364       GSequenceLink link = new GSequenceLink();\r
 365       boolean valid = false;\r
 366       while( !valid )\r
 367       {\r
 368         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 369                                                   "New sequence URL link",\r
 370                                                   JOptionPane.OK_CANCEL_OPTION\r
 371                                                   ,-1, null)\r
 372             == JOptionPane.OK_OPTION)\r
 373         {\r
 374           if (link.checkValid())\r
 375           {\r
 376             nameLinks.addElement(link.getName());\r
 377             urlLinks.addElement(link.getURL());\r
 378             updateLinkData();\r
 379             valid = true;\r
 380           }\r
 381         }\r
 382         else\r
 383           break;\r
 384       }\r
 385     }\r
 386 \r
 387     public void editLink_actionPerformed(ActionEvent e) {\r
 388       GSequenceLink link = new GSequenceLink();\r
 389 \r
 390       int index = linkNameList.getSelectedIndex();\r
 391       if(index==-1)\r
 392       {\r
 393         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 394             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 395         return;\r
 396       }\r
 397 \r
 398       link.setName( nameLinks.elementAt(index).toString() );\r
 399       link.setURL( urlLinks.elementAt(index).toString() );\r
 400 \r
 401       boolean valid = false;\r
 402       while (!valid)\r
 403       {\r
 404 \r
 405         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 406                                                   "New sequence URL link",\r
 407                                                   JOptionPane.OK_CANCEL_OPTION\r
 408                                                   ,-1, null)\r
 409             == JOptionPane.OK_OPTION)\r
 410         {\r
 411           if (link.checkValid())\r
 412           {\r
 413             nameLinks.setElementAt(link.getName(), index);\r
 414             urlLinks.setElementAt(link.getURL(), index);\r
 415             updateLinkData();\r
 416             valid = true;\r
 417           }\r
 418         }\r
 419 \r
 420         else\r
 421           break;\r
 422       }\r
 423     }\r
 424 \r
 425     public void deleteLink_actionPerformed(ActionEvent e) {\r
 426       int index = linkNameList.getSelectedIndex();\r
 427       if(index==-1)\r
 428       {\r
 429         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 430             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 431         return;\r
 432       }\r
 433       nameLinks.removeElementAt(index);\r
 434       urlLinks.removeElementAt(index);\r
 435       updateLinkData();\r
 436     }\r
 437 \r
 438     void updateLinkData()\r
 439     {\r
 440       linkNameList.setListData(nameLinks);\r
 441       linkURLList.setListData(urlLinks);\r
 442     }\r
 443 \r
 444     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 445     {\r
 446       JFileChooser chooser = new JFileChooser(".");\r
 447       chooser.setDialogTitle("Select default web browser");\r
 448 \r
 449       int value = chooser.showOpenDialog(this);\r
 450 \r
 451       if (value == JFileChooser.APPROVE_OPTION)\r
 452       {\r
 453         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 454       }\r
 455 \r
 456   }\r
 457 \r
 458   private void jbInit()\r
 459       throws Exception\r
 460   {\r
 461   }\r
 462 }\r