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