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         Desktop.addInternalFrame(frame, "Preferences", 490, 405);\r
  85         frame.setMinimumSize(new Dimension(490,395));\r
  86 \r
  87         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
  88         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  89         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  90 \r
  91         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  92         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  93         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  94 \r
  95         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
  96         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
  97         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
  98 \r
  99         for (int i = 0; i < 13; i++)\r
 100         {\r
 101             colour.addItem(ColourSchemeProperty.getColourName(i));\r
 102         }\r
 103 \r
 104         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 105 \r
 106         colour.setSelectedItem(string);\r
 107 \r
 108         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 109                                                      .getAvailableFontFamilyNames();\r
 110 \r
 111         for (int i = 0; i < fonts.length; i++)\r
 112         {\r
 113             fontNameCB.addItem(fonts[i]);\r
 114         }\r
 115 \r
 116         for (int i = 1; i < 31; i++)\r
 117         {\r
 118             fontSizeCB.addItem(i + "");\r
 119         }\r
 120 \r
 121         fontStyleCB.addItem("plain");\r
 122         fontStyleCB.addItem("bold");\r
 123         fontStyleCB.addItem("italic");\r
 124 \r
 125         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 126         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 127         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 128 \r
 129         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 130 \r
 131         wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 132 \r
 133         gapSymbolCB.addItem("-");\r
 134         gapSymbolCB.addItem(".");\r
 135 \r
 136         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 137 \r
 138         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 139         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 140          "http://www.jalview.org/examples/exampleFile.jar"));\r
 141 \r
 142         sortby.addItem("No sort");\r
 143         sortby.addItem("Id");\r
 144         sortby.addItem("Pairwise Identity");\r
 145         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 146 \r
 147         epsRendering.addItem("Prompt each time");\r
 148         epsRendering.addItem("Lineart");\r
 149         epsRendering.addItem("Text");\r
 150         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 151 \r
 152         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 153         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 154         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 155         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 156         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 157         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 158         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 159 \r
 160         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 161 \r
 162         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 163         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 164 \r
 165   /****************************************************\r
 166    * Set up Connections\r
 167    */\r
 168         nameLinks = new Vector();\r
 169         urlLinks = new Vector();\r
 170         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 171         {\r
 172           String link = sequenceURLLinks.elementAt(i).toString();\r
 173           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 174           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 175         }\r
 176 \r
 177         updateLinkData();\r
 178 \r
 179         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 180         proxyServerTB.setEnabled(useProxy.isSelected());\r
 181         proxyPortTB.setEnabled(useProxy.isSelected());\r
 182         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 183         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 184 \r
 185         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 186     try\r
 187     {\r
 188       jbInit();\r
 189     }\r
 190     catch (Exception ex)\r
 191     {\r
 192       ex.printStackTrace();\r
 193     }\r
 194 \r
 195   }\r
 196 \r
 197 \r
 198     /**\r
 199      * DOCUMENT ME!\r
 200      *\r
 201      * @param e DOCUMENT ME!\r
 202      */\r
 203     public void ok_actionPerformed(ActionEvent e)\r
 204     {\r
 205 \r
 206       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 207       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 208 \r
 209       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 210       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 211       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 212       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 213 \r
 214       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 215       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 216 \r
 217       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 218       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 219       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 220 \r
 221       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 222 \r
 223       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
 224 \r
 225       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 226       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 227 \r
 228       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 229 \r
 230       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 231         Cache.applicationProperties.remove("EPS_RENDERING");\r
 232       else\r
 233         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 234 \r
 235       if(defaultBrowser.getText().trim().length()<1)\r
 236         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 237       else\r
 238         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 239                                                 defaultBrowser.getText());\r
 240 \r
 241         jalview.util.BrowserLauncher.resetBrowser();\r
 242 \r
 243         if(nameLinks.size()>0)\r
 244         {\r
 245           StringBuffer links = new StringBuffer();\r
 246           sequenceURLLinks = new Vector();\r
 247           for (int i = 0; i < nameLinks.size(); i++)\r
 248           {\r
 249             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 250             links.append(sequenceURLLinks.elementAt(i).toString());\r
 251             links.append("|");\r
 252           }\r
 253           // remove last "|"\r
 254           links.setLength( links.length()-1 );\r
 255           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 256         }\r
 257         else\r
 258           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 259 \r
 260 \r
 261         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 262 \r
 263         if (proxyServerTB.getText().trim().length() < 1)\r
 264           Cache.applicationProperties.remove("PROXY_SERVER");\r
 265         else\r
 266           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 267                                                   proxyServerTB.getText());\r
 268 \r
 269         if (proxyPortTB.getText().trim().length() < 1)\r
 270           Cache.applicationProperties.remove("PROXY_PORT");\r
 271         else\r
 272           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 273 \r
 274         if(useProxy.isSelected())\r
 275         {\r
 276           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 277           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 278         }\r
 279         else\r
 280         {\r
 281           System.setProperty("http.proxyHost","");\r
 282           System.setProperty("http.proxyPort","");\r
 283         }\r
 284 \r
 285 \r
 286         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 287         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 288         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 289         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 290         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 291         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 292         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 293         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 294         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 295 \r
 296         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 297                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 298         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 299                                                 Boolean.toString(padGaps.isSelected()));\r
 300 \r
 301         dasSource.saveProperties(Cache.applicationProperties);\r
 302 \r
 303         Cache.saveProperties();\r
 304         try\r
 305         {\r
 306             frame.setClosed(true);\r
 307         }\r
 308         catch (Exception ex)\r
 309         {\r
 310         }\r
 311     }\r
 312 \r
 313     /**\r
 314      * DOCUMENT ME!\r
 315      */\r
 316     public void startupFileTextfield_mouseClicked()\r
 317     {\r
 318         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 319                     "LAST_DIRECTORY"),\r
 320                 new String[]\r
 321                 {\r
 322                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 323                     "jar"\r
 324                 },\r
 325                 new String[]\r
 326                 {\r
 327                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 328                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 329         chooser.setFileView(new JalviewFileView());\r
 330         chooser.setDialogTitle("Select startup file");\r
 331 \r
 332         int value = chooser.showOpenDialog(this);\r
 333 \r
 334         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 335         {\r
 336             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 337                 chooser.getSelectedFormat());\r
 338             startupFileTextfield.setText(chooser.getSelectedFile()\r
 339                                                 .getAbsolutePath());\r
 340         }\r
 341     }\r
 342 \r
 343     /**\r
 344      * DOCUMENT ME!\r
 345      *\r
 346      * @param e DOCUMENT ME!\r
 347      */\r
 348     public void cancel_actionPerformed(ActionEvent e)\r
 349     {\r
 350         try\r
 351         {\r
 352             frame.setClosed(true);\r
 353         }\r
 354         catch (Exception ex)\r
 355         {\r
 356         }\r
 357     }\r
 358 \r
 359     /**\r
 360      * DOCUMENT ME!\r
 361      *\r
 362      * @param e DOCUMENT ME!\r
 363      */\r
 364     public void annotations_actionPerformed(ActionEvent e)\r
 365     {\r
 366         conservation.setEnabled(annotations.isSelected());\r
 367         quality.setEnabled(annotations.isSelected());\r
 368         identity.setEnabled(annotations.isSelected());\r
 369     }\r
 370 \r
 371 \r
 372     public void newLink_actionPerformed(ActionEvent e) {\r
 373 \r
 374       GSequenceLink link = new GSequenceLink();\r
 375       boolean valid = false;\r
 376       while( !valid )\r
 377       {\r
 378         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 379                                                   "New sequence URL link",\r
 380                                                   JOptionPane.OK_CANCEL_OPTION\r
 381                                                   ,-1, null)\r
 382             == JOptionPane.OK_OPTION)\r
 383         {\r
 384           if (link.checkValid())\r
 385           {\r
 386             nameLinks.addElement(link.getName());\r
 387             urlLinks.addElement(link.getURL());\r
 388             updateLinkData();\r
 389             valid = true;\r
 390           }\r
 391         }\r
 392         else\r
 393           break;\r
 394       }\r
 395     }\r
 396 \r
 397     public void editLink_actionPerformed(ActionEvent e) {\r
 398       GSequenceLink link = new GSequenceLink();\r
 399 \r
 400       int index = linkNameList.getSelectedIndex();\r
 401       if(index==-1)\r
 402       {\r
 403         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 404             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 405         return;\r
 406       }\r
 407 \r
 408       link.setName( nameLinks.elementAt(index).toString() );\r
 409       link.setURL( urlLinks.elementAt(index).toString() );\r
 410 \r
 411       boolean valid = false;\r
 412       while (!valid)\r
 413       {\r
 414 \r
 415         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 416                                                   "New sequence URL link",\r
 417                                                   JOptionPane.OK_CANCEL_OPTION\r
 418                                                   ,-1, null)\r
 419             == JOptionPane.OK_OPTION)\r
 420         {\r
 421           if (link.checkValid())\r
 422           {\r
 423             nameLinks.setElementAt(link.getName(), index);\r
 424             urlLinks.setElementAt(link.getURL(), index);\r
 425             updateLinkData();\r
 426             valid = true;\r
 427           }\r
 428         }\r
 429 \r
 430         else\r
 431           break;\r
 432       }\r
 433     }\r
 434 \r
 435     public void deleteLink_actionPerformed(ActionEvent e) {\r
 436       int index = linkNameList.getSelectedIndex();\r
 437       if(index==-1)\r
 438       {\r
 439         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 440             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 441         return;\r
 442       }\r
 443       nameLinks.removeElementAt(index);\r
 444       urlLinks.removeElementAt(index);\r
 445       updateLinkData();\r
 446     }\r
 447 \r
 448     void updateLinkData()\r
 449     {\r
 450       linkNameList.setListData(nameLinks);\r
 451       linkURLList.setListData(urlLinks);\r
 452     }\r
 453 \r
 454     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 455     {\r
 456       JFileChooser chooser = new JFileChooser(".");\r
 457       chooser.setDialogTitle("Select default web browser");\r
 458 \r
 459       int value = chooser.showOpenDialog(this);\r
 460 \r
 461       if (value == JFileChooser.APPROVE_OPTION)\r
 462       {\r
 463         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 464       }\r
 465 \r
 466   }\r
 467 \r
 468   private void jbInit()\r
 469       throws Exception\r
 470   {\r
 471   }\r
 472 }\r