src/jalview/gui/Preferences.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\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         rightAlign.setSelected(  Cache.getDefault("RIGHT_ALIGN_IDS", false));\r
  96         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
  97         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
  98 \r
  99         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 100         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 101         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 102 \r
 103         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
 104         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
 105         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
 106 \r
 107         for (int i = 0; i < 13; i++)\r
 108         {\r
 109             colour.addItem(ColourSchemeProperty.getColourName(i));\r
 110         }\r
 111 \r
 112         String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
 113 \r
 114         colour.setSelectedItem(string);\r
 115 \r
 116         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
 117                                                      .getAvailableFontFamilyNames();\r
 118 \r
 119         for (int i = 0; i < fonts.length; i++)\r
 120         {\r
 121             fontNameCB.addItem(fonts[i]);\r
 122         }\r
 123 \r
 124         for (int i = 1; i < 31; i++)\r
 125         {\r
 126             fontSizeCB.addItem(i + "");\r
 127         }\r
 128 \r
 129         fontStyleCB.addItem("plain");\r
 130         fontStyleCB.addItem("bold");\r
 131         fontStyleCB.addItem("italic");\r
 132 \r
 133         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
 134         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
 135         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
 136 \r
 137         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 138 \r
 139         wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 140 \r
 141         gapSymbolCB.addItem("-");\r
 142         gapSymbolCB.addItem(".");\r
 143 \r
 144         gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
 145 \r
 146         startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
 147         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
 148          "http://www.jalview.org/examples/exampleFile.jar"));\r
 149 \r
 150         sortby.addItem("No sort");\r
 151         sortby.addItem("Id");\r
 152         sortby.addItem("Pairwise Identity");\r
 153         sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
 154 \r
 155         epsRendering.addItem("Prompt each time");\r
 156         epsRendering.addItem("Lineart");\r
 157         epsRendering.addItem("Text");\r
 158         epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
 159 \r
 160         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
 161         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
 162         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
 163         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
 164         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
 165         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
 166         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 167 \r
 168         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
 169 \r
 170         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 171         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 172 \r
 173   /****************************************************\r
 174    * Set up Connections\r
 175    */\r
 176         nameLinks = new Vector();\r
 177         urlLinks = new Vector();\r
 178         for(int i=0; i<sequenceURLLinks.size(); i++)\r
 179         {\r
 180           String link = sequenceURLLinks.elementAt(i).toString();\r
 181           nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
 182           urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
 183         }\r
 184 \r
 185         updateLinkData();\r
 186 \r
 187         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
 188         proxyServerTB.setEnabled(useProxy.isSelected());\r
 189         proxyPortTB.setEnabled(useProxy.isSelected());\r
 190         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
 191         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
 192 \r
 193         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
 194     try\r
 195     {\r
 196       jbInit();\r
 197     }\r
 198     catch (Exception ex)\r
 199     {\r
 200       ex.printStackTrace();\r
 201     }\r
 202 \r
 203   }\r
 204 \r
 205 \r
 206     /**\r
 207      * DOCUMENT ME!\r
 208      *\r
 209      * @param e DOCUMENT ME!\r
 210      */\r
 211     public void ok_actionPerformed(ActionEvent e)\r
 212     {\r
 213 \r
 214       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
 215       Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected()));\r
 216       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 217 \r
 218       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
 219       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
 220       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
 221       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
 222 \r
 223       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
 224       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
 225 \r
 226       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
 227       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
 228       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 229 \r
 230       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 231 \r
 232       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
 233 \r
 234       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
 235       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 236 \r
 237       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
 238 \r
 239       if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
 240         Cache.applicationProperties.remove("EPS_RENDERING");\r
 241       else\r
 242         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
 243 \r
 244       if(defaultBrowser.getText().trim().length()<1)\r
 245         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
 246       else\r
 247         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
 248                                                 defaultBrowser.getText());\r
 249 \r
 250         jalview.util.BrowserLauncher.resetBrowser();\r
 251 \r
 252         if(nameLinks.size()>0)\r
 253         {\r
 254           StringBuffer links = new StringBuffer();\r
 255           sequenceURLLinks = new Vector();\r
 256           for (int i = 0; i < nameLinks.size(); i++)\r
 257           {\r
 258             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
 259             links.append(sequenceURLLinks.elementAt(i).toString());\r
 260             links.append("|");\r
 261           }\r
 262           // remove last "|"\r
 263           links.setLength( links.length()-1 );\r
 264           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
 265         }\r
 266         else\r
 267           Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
 268 \r
 269 \r
 270         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
 271 \r
 272         if (proxyServerTB.getText().trim().length() < 1)\r
 273           Cache.applicationProperties.remove("PROXY_SERVER");\r
 274         else\r
 275           Cache.applicationProperties.setProperty("PROXY_SERVER",\r
 276                                                   proxyServerTB.getText());\r
 277 \r
 278         if (proxyPortTB.getText().trim().length() < 1)\r
 279           Cache.applicationProperties.remove("PROXY_PORT");\r
 280         else\r
 281           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
 282 \r
 283         if(useProxy.isSelected())\r
 284         {\r
 285           System.setProperty("http.proxyHost", proxyServerTB.getText());\r
 286           System.setProperty("http.proxyPort", proxyPortTB.getText());\r
 287         }\r
 288         else\r
 289         {\r
 290           System.setProperty("http.proxyHost","");\r
 291           System.setProperty("http.proxyPort","");\r
 292         }\r
 293 \r
 294 \r
 295         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
 296         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
 297         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
 298         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
 299         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
 300         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
 301         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
 302         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
 303         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 304 \r
 305         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
 306                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
 307         Cache.applicationProperties.setProperty("PAD_GAPS",\r
 308                                                 Boolean.toString(padGaps.isSelected()));\r
 309 \r
 310         dasSource.saveProperties(Cache.applicationProperties);\r
 311 \r
 312         Cache.saveProperties();\r
 313         try\r
 314         {\r
 315             frame.setClosed(true);\r
 316         }\r
 317         catch (Exception ex)\r
 318         {\r
 319         }\r
 320     }\r
 321 \r
 322     /**\r
 323      * DOCUMENT ME!\r
 324      */\r
 325     public void startupFileTextfield_mouseClicked()\r
 326     {\r
 327         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 328                     "LAST_DIRECTORY"),\r
 329                 new String[]\r
 330                 {\r
 331                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 332                     "jar"\r
 333                 },\r
 334                 new String[]\r
 335                 {\r
 336                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 337                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 338         chooser.setFileView(new JalviewFileView());\r
 339         chooser.setDialogTitle("Select startup file");\r
 340 \r
 341         int value = chooser.showOpenDialog(this);\r
 342 \r
 343         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 344         {\r
 345             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
 346                 chooser.getSelectedFormat());\r
 347             startupFileTextfield.setText(chooser.getSelectedFile()\r
 348                                                 .getAbsolutePath());\r
 349         }\r
 350     }\r
 351 \r
 352     /**\r
 353      * DOCUMENT ME!\r
 354      *\r
 355      * @param e DOCUMENT ME!\r
 356      */\r
 357     public void cancel_actionPerformed(ActionEvent e)\r
 358     {\r
 359         try\r
 360         {\r
 361             frame.setClosed(true);\r
 362         }\r
 363         catch (Exception ex)\r
 364         {\r
 365         }\r
 366     }\r
 367 \r
 368     /**\r
 369      * DOCUMENT ME!\r
 370      *\r
 371      * @param e DOCUMENT ME!\r
 372      */\r
 373     public void annotations_actionPerformed(ActionEvent e)\r
 374     {\r
 375         conservation.setEnabled(annotations.isSelected());\r
 376         quality.setEnabled(annotations.isSelected());\r
 377         identity.setEnabled(annotations.isSelected());\r
 378     }\r
 379 \r
 380 \r
 381     public void newLink_actionPerformed(ActionEvent e) {\r
 382 \r
 383       GSequenceLink link = new GSequenceLink();\r
 384       boolean valid = false;\r
 385       while( !valid )\r
 386       {\r
 387         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 388                                                   "New sequence URL link",\r
 389                                                   JOptionPane.OK_CANCEL_OPTION\r
 390                                                   ,-1, null)\r
 391             == JOptionPane.OK_OPTION)\r
 392         {\r
 393           if (link.checkValid())\r
 394           {\r
 395             nameLinks.addElement(link.getName());\r
 396             urlLinks.addElement(link.getURL());\r
 397             updateLinkData();\r
 398             valid = true;\r
 399           }\r
 400         }\r
 401         else\r
 402           break;\r
 403       }\r
 404     }\r
 405 \r
 406     public void editLink_actionPerformed(ActionEvent e) {\r
 407       GSequenceLink link = new GSequenceLink();\r
 408 \r
 409       int index = linkNameList.getSelectedIndex();\r
 410       if(index==-1)\r
 411       {\r
 412         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 413             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 414         return;\r
 415       }\r
 416 \r
 417       link.setName( nameLinks.elementAt(index).toString() );\r
 418       link.setURL( urlLinks.elementAt(index).toString() );\r
 419 \r
 420       boolean valid = false;\r
 421       while (!valid)\r
 422       {\r
 423 \r
 424         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
 425                                                   "New sequence URL link",\r
 426                                                   JOptionPane.OK_CANCEL_OPTION\r
 427                                                   ,-1, null)\r
 428             == JOptionPane.OK_OPTION)\r
 429         {\r
 430           if (link.checkValid())\r
 431           {\r
 432             nameLinks.setElementAt(link.getName(), index);\r
 433             urlLinks.setElementAt(link.getURL(), index);\r
 434             updateLinkData();\r
 435             valid = true;\r
 436           }\r
 437         }\r
 438 \r
 439         else\r
 440           break;\r
 441       }\r
 442     }\r
 443 \r
 444     public void deleteLink_actionPerformed(ActionEvent e) {\r
 445       int index = linkNameList.getSelectedIndex();\r
 446       if(index==-1)\r
 447       {\r
 448         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
 449             ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
 450         return;\r
 451       }\r
 452       nameLinks.removeElementAt(index);\r
 453       urlLinks.removeElementAt(index);\r
 454       updateLinkData();\r
 455     }\r
 456 \r
 457     void updateLinkData()\r
 458     {\r
 459       linkNameList.setListData(nameLinks);\r
 460       linkURLList.setListData(urlLinks);\r
 461     }\r
 462 \r
 463     public void defaultBrowser_mouseClicked(MouseEvent e)\r
 464     {\r
 465       JFileChooser chooser = new JFileChooser(".");\r
 466       chooser.setDialogTitle("Select default web browser");\r
 467 \r
 468       int value = chooser.showOpenDialog(this);\r
 469 \r
 470       if (value == JFileChooser.APPROVE_OPTION)\r
 471       {\r
 472         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
 473       }\r
 474 \r
 475   }\r
 476 \r
 477   private void jbInit()\r
 478       throws Exception\r
 479   {\r
 480   }\r
 481 }\r