src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27
  28 import jalview.bin.*;
  29 import jalview.io.*;
  30 import jalview.jbgui.*;
  31 import jalview.schemes.*;
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class Preferences extends GPreferences
  40 {
  41
  42   /**
  43    * Holds name and link separated with | character. Sequence ID must be
  44    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  45    */
  46   public static Vector sequenceURLLinks;
  47   static
  48   {
  49     String string = Cache
  50             .getDefault(
  51                     "SEQUENCE_LINKS",
  52                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  53     sequenceURLLinks = new Vector();
  54
  55     try
  56     {
  57       StringTokenizer st = new StringTokenizer(string, "|");
  58       while (st.hasMoreElements())
  59       {
  60         String name = st.nextToken();
  61         String url = st.nextToken();
  62         // check for '|' within a regex
  63         int rxstart = url.indexOf("$SEQUENCE_ID$");
  64         while (rxstart == -1 && url.indexOf("/=$") == -1)
  65         {
  66           url = url + "|" + st.nextToken();
  67         }
  68         sequenceURLLinks.addElement(name + "|" + url);
  69       }
  70     } catch (Exception ex)
  71     {
  72       System.out.println(ex + "\nError parsing sequence links");
  73     }
  74   }
  75
  76   Vector nameLinks, urlLinks;
  77
  78   JInternalFrame frame;
  79
  80   DasSourceBrowser dasSource;
  81
  82   /**
  83    * Creates a new Preferences object.
  84    */
  85   public Preferences()
  86   {
  87
  88     frame = new JInternalFrame();
  89     frame.setContentPane(this);
  90     dasSource = new DasSourceBrowser();
  91     dasPanel.add(dasSource, BorderLayout.CENTER);
  92
  93     int width = 500, height = 420;
  94     if (new jalview.util.Platform().isAMac())
  95     {
  96       width = 570;
  97       height = 460;
  98     }
  99
 100     Desktop.addInternalFrame(frame, "Preferences", width, height);
 101     frame.setMinimumSize(new Dimension(width, height));
 102
 103     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 104     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 105     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 106     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 107
 108     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 109     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 110     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 111
 112     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 113     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 114     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 115     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 116     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 117
 118     for (int i = 0; i < 13; i++)
 119     {
 120       colour.addItem(ColourSchemeProperty.getColourName(i));
 121     }
 122
 123     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 124
 125     colour.setSelectedItem(string);
 126
 127     String[] fonts = java.awt.GraphicsEnvironment
 128             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 129
 130     for (int i = 0; i < fonts.length; i++)
 131     {
 132       fontNameCB.addItem(fonts[i]);
 133     }
 134
 135     for (int i = 1; i < 31; i++)
 136     {
 137       fontSizeCB.addItem(i + "");
 138     }
 139
 140     fontStyleCB.addItem("plain");
 141     fontStyleCB.addItem("bold");
 142     fontStyleCB.addItem("italic");
 143
 144     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 145     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 146     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 147             + ""));
 148
 149     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 150
 151     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 152
 153     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 154
 155     gapSymbolCB.addItem("-");
 156     gapSymbolCB.addItem(".");
 157
 158     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 159
 160     startupCheckbox
 161             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 162     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 163             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 164
 165     sortby.addItem("No sort");
 166     sortby.addItem("Id");
 167     sortby.addItem("Pairwise Identity");
 168     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 169
 170     epsRendering.addItem("Prompt each time");
 171     epsRendering.addItem("Lineart");
 172     epsRendering.addItem("Text");
 173     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 174             "Prompt each time"));
 175
 176     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 177     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 178     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 179     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 180     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 181     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 182     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 183
 184     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 185
 186     autoCalculateConsCheck.setSelected(Cache.getDefault(
 187             "AUTO_CALC_CONSENSUS", true));
 188     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 189
 190     /***************************************************************************
 191      * Set up Connections
 192      */
 193     nameLinks = new Vector();
 194     urlLinks = new Vector();
 195     for (int i = 0; i < sequenceURLLinks.size(); i++)
 196     {
 197       String link = sequenceURLLinks.elementAt(i).toString();
 198       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 199       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 200     }
 201
 202     updateLinkData();
 203
 204     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 205     proxyServerTB.setEnabled(useProxy.isSelected());
 206     proxyPortTB.setEnabled(useProxy.isSelected());
 207     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 208     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 209
 210     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 211
 212     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 213     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
 214     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
 215
 216     try
 217     {
 218       jbInit();
 219     } catch (Exception ex)
 220     {
 221       ex.printStackTrace();
 222     }
 223
 224   }
 225
 226   /**
 227    * DOCUMENT ME!
 228    *
 229    * @param e
 230    *                DOCUMENT ME!
 231    */
 232   public void ok_actionPerformed(ActionEvent e)
 233   {
 234
 235     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 236             .toString(seqLimit.isSelected()));
 237     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 238             .toString(rightAlign.isSelected()));
 239     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 240             .toString(fullScreen.isSelected()));
 241     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 242             .toString(openoverv.isSelected()));
 243     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 244             .toString(annotations.isSelected()));
 245     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 246             .toString(conservation.isSelected()));
 247     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 248             .toString(quality.isSelected()));
 249     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 250             .toString(identity.isSelected()));
 251
 252     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 253             .getSelectedItem().toString());
 254     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 255             .getSelectedItem().toString());
 256
 257     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 258             .getSelectedItem().toString());
 259     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 260             .getSelectedItem().toString());
 261     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 262             .getSelectedItem().toString());
 263
 264     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 265             .toString(idItalics.isSelected()));
 266     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 267     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 268             .toString(smoothFont.isSelected()));
 269
 270     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 271             .toString(wrap.isSelected()));
 272
 273     Cache.applicationProperties.setProperty("STARTUP_FILE",
 274             startupFileTextfield.getText());
 275     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 276             .toString(startupCheckbox.isSelected()));
 277
 278     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 279             .getSelectedItem().toString());
 280
 281     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 282     {
 283       Cache.applicationProperties.remove("EPS_RENDERING");
 284     }
 285     else
 286     {
 287       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 288               .getSelectedItem().toString());
 289     }
 290
 291     if (defaultBrowser.getText().trim().length() < 1)
 292     {
 293       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 294     }
 295     else
 296     {
 297       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 298               defaultBrowser.getText());
 299     }
 300
 301     jalview.util.BrowserLauncher.resetBrowser();
 302
 303     if (nameLinks.size() > 0)
 304     {
 305       StringBuffer links = new StringBuffer();
 306       sequenceURLLinks = new Vector();
 307       for (int i = 0; i < nameLinks.size(); i++)
 308       {
 309         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 310                 + urlLinks.elementAt(i));
 311         links.append(sequenceURLLinks.elementAt(i).toString());
 312         links.append("|");
 313       }
 314       // remove last "|"
 315       links.setLength(links.length() - 1);
 316       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 317               .toString());
 318     }
 319     else
 320     {
 321       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 322     }
 323
 324     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 325             .toString(useProxy.isSelected()));
 326
 327     if (proxyServerTB.getText().trim().length() < 1)
 328     {
 329       Cache.applicationProperties.remove("PROXY_SERVER");
 330     }
 331     else
 332     {
 333       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 334               .getText());
 335     }
 336
 337     if (proxyPortTB.getText().trim().length() < 1)
 338     {
 339       Cache.applicationProperties.remove("PROXY_PORT");
 340     }
 341     else
 342     {
 343       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 344               .getText());
 345     }
 346
 347     if (useProxy.isSelected())
 348     {
 349       System.setProperty("http.proxyHost", proxyServerTB.getText());
 350       System.setProperty("http.proxyPort", proxyPortTB.getText());
 351     }
 352     else
 353     {
 354       System.setProperty("http.proxyHost", "");
 355       System.setProperty("http.proxyPort", "");
 356     }
 357     Cache.setProperty("VERSION_CHECK", Boolean
 358             .toString(versioncheck.isSelected()));
 359     if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) {
 360       // default is false - we only set this if the user has actively agreed
 361       Cache.setProperty("USAGESTATS",Boolean
 362             .toString(usagestats.isSelected()));
 363     }
 364     if (!questionnaire.isSelected())
 365     {
 366       Cache.setProperty("NOQUESTIONNAIRES", "true");
 367     } else {
 368       // special - made easy to edit a property file to disable questionnaires by just adding the given line
 369       Cache.removeProperty("NOQUESTIONNAIRES");
 370     }
 371     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 372             .toString(blcjv.isSelected()));
 373     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 374             .toString(clustaljv.isSelected()));
 375     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 376             .toString(fastajv.isSelected()));
 377     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 378             .toString(msfjv.isSelected()));
 379     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 380             .toString(pfamjv.isSelected()));
 381     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 382             .toString(pileupjv.isSelected()));
 383     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 384             .toString(pirjv.isSelected()));
 385     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 386             .toString(modellerOutput.isSelected()));
 387     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 388
 389     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 390             .toString(autoCalculateConsCheck.isSelected()));
 391     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 392             .toString(padGaps.isSelected()));
 393
 394     dasSource.saveProperties(Cache.applicationProperties);
 395
 396     Cache.saveProperties();
 397     try
 398     {
 399       frame.setClosed(true);
 400     } catch (Exception ex)
 401     {
 402     }
 403   }
 404
 405   /**
 406    * DOCUMENT ME!
 407    */
 408   public void startupFileTextfield_mouseClicked()
 409   {
 410     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 411             .getProperty("LAST_DIRECTORY"), new String[]
 412     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 413             new String[]
 414             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 415             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 416     chooser.setFileView(new JalviewFileView());
 417     chooser.setDialogTitle("Select startup file");
 418
 419     int value = chooser.showOpenDialog(this);
 420
 421     if (value == JalviewFileChooser.APPROVE_OPTION)
 422     {
 423       jalview.bin.Cache.applicationProperties.setProperty(
 424               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 425       startupFileTextfield.setText(chooser.getSelectedFile()
 426               .getAbsolutePath());
 427     }
 428   }
 429
 430   /**
 431    * DOCUMENT ME!
 432    *
 433    * @param e
 434    *                DOCUMENT ME!
 435    */
 436   public void cancel_actionPerformed(ActionEvent e)
 437   {
 438     try
 439     {
 440       frame.setClosed(true);
 441     } catch (Exception ex)
 442     {
 443     }
 444   }
 445
 446   /**
 447    * DOCUMENT ME!
 448    *
 449    * @param e
 450    *                DOCUMENT ME!
 451    */
 452   public void annotations_actionPerformed(ActionEvent e)
 453   {
 454     conservation.setEnabled(annotations.isSelected());
 455     quality.setEnabled(annotations.isSelected());
 456     identity.setEnabled(annotations.isSelected());
 457   }
 458
 459   public void newLink_actionPerformed(ActionEvent e)
 460   {
 461
 462     GSequenceLink link = new GSequenceLink();
 463     boolean valid = false;
 464     while (!valid)
 465     {
 466       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 467               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 468               null) == JOptionPane.OK_OPTION)
 469       {
 470         if (link.checkValid())
 471         {
 472           nameLinks.addElement(link.getName());
 473           urlLinks.addElement(link.getURL());
 474           updateLinkData();
 475           valid = true;
 476         }
 477       }
 478       else
 479       {
 480         break;
 481       }
 482     }
 483   }
 484
 485   public void editLink_actionPerformed(ActionEvent e)
 486   {
 487     GSequenceLink link = new GSequenceLink();
 488
 489     int index = linkNameList.getSelectedIndex();
 490     if (index == -1)
 491     {
 492       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 493               "No link selected!", "No link selected",
 494               JOptionPane.WARNING_MESSAGE);
 495       return;
 496     }
 497
 498     link.setName(nameLinks.elementAt(index).toString());
 499     link.setURL(urlLinks.elementAt(index).toString());
 500
 501     boolean valid = false;
 502     while (!valid)
 503     {
 504
 505       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 506               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 507               null) == JOptionPane.OK_OPTION)
 508       {
 509         if (link.checkValid())
 510         {
 511           nameLinks.setElementAt(link.getName(), index);
 512           urlLinks.setElementAt(link.getURL(), index);
 513           updateLinkData();
 514           valid = true;
 515         }
 516       }
 517
 518       else
 519       {
 520         break;
 521       }
 522     }
 523   }
 524
 525   public void deleteLink_actionPerformed(ActionEvent e)
 526   {
 527     int index = linkNameList.getSelectedIndex();
 528     if (index == -1)
 529     {
 530       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 531               "No link selected!", "No link selected",
 532               JOptionPane.WARNING_MESSAGE);
 533       return;
 534     }
 535     nameLinks.removeElementAt(index);
 536     urlLinks.removeElementAt(index);
 537     updateLinkData();
 538   }
 539
 540   void updateLinkData()
 541   {
 542     linkNameList.setListData(nameLinks);
 543     linkURLList.setListData(urlLinks);
 544   }
 545
 546   public void defaultBrowser_mouseClicked(MouseEvent e)
 547   {
 548     JFileChooser chooser = new JFileChooser(".");
 549     chooser.setDialogTitle("Select default web browser");
 550
 551     int value = chooser.showOpenDialog(this);
 552
 553     if (value == JFileChooser.APPROVE_OPTION)
 554     {
 555       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 556     }
 557
 558   }
 559   /* (non-Javadoc)
 560    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 561    */
 562   protected void showunconserved_actionPerformed(ActionEvent e)
 563   {
 564     // TODO Auto-generated method stub
 565     super.showunconserved_actionPerformed(e);
 566   }
 567
 568   private void jbInit() throws Exception
 569   {
 570   }
 571 }