src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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 import javax.swing.*;
  26
  27 import jalview.bin.*;
  28 import jalview.io.*;
  29 import jalview.jbgui.*;
  30 import jalview.schemes.*;
  31
  32 /**
  33  * DOCUMENT ME!
  34  *
  35  * @author $author$
  36  * @version $Revision$
  37  */
  38 public class Preferences
  39     extends GPreferences
  40 {
  41   /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
  42   public static Vector sequenceURLLinks;
  43   static
  44   {
  45     String string = Cache.getDefault("SEQUENCE_LINKS",
  46                                      "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  47     sequenceURLLinks = new Vector();
  48
  49     try
  50     {
  51       StringTokenizer st = new StringTokenizer(string, "|");
  52       while (st.hasMoreElements())
  53       {
  54         sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
  55       }
  56     }
  57     catch (Exception ex)
  58     {
  59       System.out.println(ex + "\nError parsing sequence links");
  60     }
  61   }
  62
  63   Vector nameLinks, urlLinks;
  64
  65   JInternalFrame frame;
  66
  67   DasSourceBrowser dasSource;
  68
  69   /**
  70    * Creates a new Preferences object.
  71    */
  72   public Preferences()
  73   {
  74
  75     frame = new JInternalFrame();
  76     frame.setContentPane(this);
  77     dasSource = new DasSourceBrowser();
  78     dasPanel.add(dasSource, BorderLayout.CENTER);
  79
  80     int width = 500, height = 420;
  81     if (new jalview.util.Platform().isAMac())
  82     {
  83       width = 570;
  84       height = 460;
  85     }
  86
  87     Desktop.addInternalFrame(frame, "Preferences", width, height);
  88     frame.setMinimumSize(new Dimension(width, height));
  89
  90     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
  91     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
  92     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
  93     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
  94
  95     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
  96     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
  97     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
  98
  99     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 100     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 101     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 102     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 103
 104     for (int i = 0; i < 13; i++)
 105     {
 106       colour.addItem(ColourSchemeProperty.getColourName(i));
 107     }
 108
 109     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 110
 111     colour.setSelectedItem(string);
 112
 113     String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
 114         .getAvailableFontFamilyNames();
 115
 116     for (int i = 0; i < fonts.length; i++)
 117     {
 118       fontNameCB.addItem(fonts[i]);
 119     }
 120
 121     for (int i = 1; i < 31; i++)
 122     {
 123       fontSizeCB.addItem(i + "");
 124     }
 125
 126     fontStyleCB.addItem("plain");
 127     fontStyleCB.addItem("bold");
 128     fontStyleCB.addItem("italic");
 129
 130     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 131     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 132     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 133
 134     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 135
 136     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 137
 138     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 139
 140     gapSymbolCB.addItem("-");
 141     gapSymbolCB.addItem(".");
 142
 143     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 144
 145     startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 146     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 147                                                   "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 148
 149     sortby.addItem("No sort");
 150     sortby.addItem("Id");
 151     sortby.addItem("Pairwise Identity");
 152     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 153
 154     epsRendering.addItem("Prompt each time");
 155     epsRendering.addItem("Lineart");
 156     epsRendering.addItem("Text");
 157     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 158                                                   "Prompt each time"));
 159
 160     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 161     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 162     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 163     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 164     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 165     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 166     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 167
 168     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 169
 170     autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 171     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 172
 173     /****************************************************
 174      * Set up Connections
 175      */
 176     nameLinks = new Vector();
 177     urlLinks = new Vector();
 178     for (int i = 0; i < sequenceURLLinks.size(); i++)
 179     {
 180       String link = sequenceURLLinks.elementAt(i).toString();
 181       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 182       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 183     }
 184
 185     updateLinkData();
 186
 187     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 188     proxyServerTB.setEnabled(useProxy.isSelected());
 189     proxyPortTB.setEnabled(useProxy.isSelected());
 190     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 191     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 192
 193     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 194     try
 195     {
 196       jbInit();
 197     }
 198     catch (Exception ex)
 199     {
 200       ex.printStackTrace();
 201     }
 202
 203   }
 204
 205   /**
 206    * DOCUMENT ME!
 207    *
 208    * @param e DOCUMENT ME!
 209    */
 210   public void ok_actionPerformed(ActionEvent e)
 211   {
 212
 213     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 214                                             Boolean.toString(seqLimit.
 215         isSelected()));
 216     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 217                                             Boolean.toString(rightAlign.
 218         isSelected()));
 219     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 220                                             Boolean.toString(fullScreen.
 221         isSelected()));
 222     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 223                                             Boolean.toString(openoverv.
 224         isSelected()));
 225     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 226                                             Boolean.
 227                                             toString(annotations.isSelected()));
 228     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 229                                             Boolean.
 230                                             toString(conservation.isSelected()));
 231     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 232                                             Boolean.toString(quality.isSelected()));
 233     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 234                                             Boolean.toString(identity.
 235         isSelected()));
 236
 237     Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
 238                                             colour.getSelectedItem().toString());
 239     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 240                                             gapSymbolCB.getSelectedItem().
 241                                             toString());
 242
 243     Cache.applicationProperties.setProperty("FONT_NAME",
 244                                             fontNameCB.getSelectedItem().
 245                                             toString());
 246     Cache.applicationProperties.setProperty("FONT_STYLE",
 247                                             fontStyleCB.getSelectedItem().
 248                                             toString());
 249     Cache.applicationProperties.setProperty("FONT_SIZE",
 250                                             fontSizeCB.getSelectedItem().
 251                                             toString());
 252
 253     Cache.applicationProperties.setProperty("ID_ITALICS",
 254                                             Boolean.toString(idItalics.
 255         isSelected()));
 256
 257     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 258                                             Boolean.toString(smoothFont.
 259         isSelected()));
 260
 261     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 262                                             Boolean.toString(wrap.isSelected()));
 263
 264     Cache.applicationProperties.setProperty("STARTUP_FILE",
 265                                             startupFileTextfield.getText());
 266     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 267                                             Boolean.
 268                                             toString(startupCheckbox.isSelected()));
 269
 270     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 271                                             sortby.getSelectedItem().toString());
 272
 273     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 274     {
 275       Cache.applicationProperties.remove("EPS_RENDERING");
 276     }
 277     else
 278     {
 279       Cache.applicationProperties.setProperty("EPS_RENDERING",
 280                                               epsRendering.getSelectedItem().
 281                                               toString());
 282     }
 283
 284     if (defaultBrowser.getText().trim().length() < 1)
 285     {
 286       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 287     }
 288     else
 289     {
 290       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 291                                               defaultBrowser.getText());
 292     }
 293
 294     jalview.util.BrowserLauncher.resetBrowser();
 295
 296     if (nameLinks.size() > 0)
 297     {
 298       StringBuffer links = new StringBuffer();
 299       sequenceURLLinks = new Vector();
 300       for (int i = 0; i < nameLinks.size(); i++)
 301       {
 302         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
 303                                     urlLinks.elementAt(i));
 304         links.append(sequenceURLLinks.elementAt(i).toString());
 305         links.append("|");
 306       }
 307       // remove last "|"
 308       links.setLength(links.length() - 1);
 309       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
 310     }
 311     else
 312     {
 313       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 314     }
 315
 316     Cache.applicationProperties.setProperty("USE_PROXY",
 317                                             Boolean.toString(useProxy.
 318         isSelected()));
 319
 320     if (proxyServerTB.getText().trim().length() < 1)
 321     {
 322       Cache.applicationProperties.remove("PROXY_SERVER");
 323     }
 324     else
 325     {
 326       Cache.applicationProperties.setProperty("PROXY_SERVER",
 327                                               proxyServerTB.getText());
 328     }
 329
 330     if (proxyPortTB.getText().trim().length() < 1)
 331     {
 332       Cache.applicationProperties.remove("PROXY_PORT");
 333     }
 334     else
 335     {
 336       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
 337     }
 338
 339     if (useProxy.isSelected())
 340     {
 341       System.setProperty("http.proxyHost", proxyServerTB.getText());
 342       System.setProperty("http.proxyPort", proxyPortTB.getText());
 343     }
 344     else
 345     {
 346       System.setProperty("http.proxyHost", "");
 347       System.setProperty("http.proxyPort", "");
 348     }
 349
 350     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 351                                             Boolean.toString(blcjv.isSelected()));
 352     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 353                                             Boolean.
 354                                             toString(clustaljv.isSelected()));
 355     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 356                                             Boolean.toString(fastajv.isSelected()));
 357     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 358                                             Boolean.toString(msfjv.isSelected()));
 359     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 360                                             Boolean.toString(pfamjv.isSelected()));
 361     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 362                                             Boolean.toString(pileupjv.
 363         isSelected()));
 364     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 365                                             Boolean.toString(pirjv.isSelected()));
 366     Cache.applicationProperties.setProperty("PIR_MODELLER",
 367                                             Boolean.toString(modellerOutput.
 368         isSelected()));
 369     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 370
 371     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 372                                             Boolean.toString(
 373         autoCalculateConsCheck.isSelected()));
 374     Cache.applicationProperties.setProperty("PAD_GAPS",
 375                                             Boolean.toString(padGaps.isSelected()));
 376
 377     dasSource.saveProperties(Cache.applicationProperties);
 378
 379     Cache.saveProperties();
 380     try
 381     {
 382       frame.setClosed(true);
 383     }
 384     catch (Exception ex)
 385     {
 386     }
 387   }
 388
 389   /**
 390    * DOCUMENT ME!
 391    */
 392   public void startupFileTextfield_mouseClicked()
 393   {
 394     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 395         getProperty(
 396             "LAST_DIRECTORY"),
 397         new String[]
 398         {
 399         "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 400         "jar"
 401     },
 402         new String[]
 403         {
 404         "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
 405     }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 406     chooser.setFileView(new JalviewFileView());
 407     chooser.setDialogTitle("Select startup file");
 408
 409     int value = chooser.showOpenDialog(this);
 410
 411     if (value == JalviewFileChooser.APPROVE_OPTION)
 412     {
 413       jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 414           chooser.getSelectedFormat());
 415       startupFileTextfield.setText(chooser.getSelectedFile()
 416                                    .getAbsolutePath());
 417     }
 418   }
 419
 420   /**
 421    * DOCUMENT ME!
 422    *
 423    * @param e DOCUMENT ME!
 424    */
 425   public void cancel_actionPerformed(ActionEvent e)
 426   {
 427     try
 428     {
 429       frame.setClosed(true);
 430     }
 431     catch (Exception ex)
 432     {
 433     }
 434   }
 435
 436   /**
 437    * DOCUMENT ME!
 438    *
 439    * @param e DOCUMENT ME!
 440    */
 441   public void annotations_actionPerformed(ActionEvent e)
 442   {
 443     conservation.setEnabled(annotations.isSelected());
 444     quality.setEnabled(annotations.isSelected());
 445     identity.setEnabled(annotations.isSelected());
 446   }
 447
 448   public void newLink_actionPerformed(ActionEvent e)
 449   {
 450
 451     GSequenceLink link = new GSequenceLink();
 452     boolean valid = false;
 453     while (!valid)
 454     {
 455       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 456                                                 "New sequence URL link",
 457                                                 JOptionPane.OK_CANCEL_OPTION
 458                                                 , -1, null)
 459           == JOptionPane.OK_OPTION)
 460       {
 461         if (link.checkValid())
 462         {
 463           nameLinks.addElement(link.getName());
 464           urlLinks.addElement(link.getURL());
 465           updateLinkData();
 466           valid = true;
 467         }
 468       }
 469       else
 470       {
 471         break;
 472       }
 473     }
 474   }
 475
 476   public void editLink_actionPerformed(ActionEvent e)
 477   {
 478     GSequenceLink link = new GSequenceLink();
 479
 480     int index = linkNameList.getSelectedIndex();
 481     if (index == -1)
 482     {
 483       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 484                                             "No link selected!"
 485                                             , "No link selected",
 486                                             JOptionPane.WARNING_MESSAGE);
 487       return;
 488     }
 489
 490     link.setName(nameLinks.elementAt(index).toString());
 491     link.setURL(urlLinks.elementAt(index).toString());
 492
 493     boolean valid = false;
 494     while (!valid)
 495     {
 496
 497       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 498                                                 "New sequence URL link",
 499                                                 JOptionPane.OK_CANCEL_OPTION
 500                                                 , -1, null)
 501           == JOptionPane.OK_OPTION)
 502       {
 503         if (link.checkValid())
 504         {
 505           nameLinks.setElementAt(link.getName(), index);
 506           urlLinks.setElementAt(link.getURL(), index);
 507           updateLinkData();
 508           valid = true;
 509         }
 510       }
 511
 512       else
 513       {
 514         break;
 515       }
 516     }
 517   }
 518
 519   public void deleteLink_actionPerformed(ActionEvent e)
 520   {
 521     int index = linkNameList.getSelectedIndex();
 522     if (index == -1)
 523     {
 524       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 525                                             "No link selected!"
 526                                             , "No link selected",
 527                                             JOptionPane.WARNING_MESSAGE);
 528       return;
 529     }
 530     nameLinks.removeElementAt(index);
 531     urlLinks.removeElementAt(index);
 532     updateLinkData();
 533   }
 534
 535   void updateLinkData()
 536   {
 537     linkNameList.setListData(nameLinks);
 538     linkURLList.setListData(urlLinks);
 539   }
 540
 541   public void defaultBrowser_mouseClicked(MouseEvent e)
 542   {
 543     JFileChooser chooser = new JFileChooser(".");
 544     chooser.setDialogTitle("Select default web browser");
 545
 546     int value = chooser.showOpenDialog(this);
 547
 548     if (value == JFileChooser.APPROVE_OPTION)
 549     {
 550       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 551     }
 552
 553   }
 554
 555   private void jbInit()
 556       throws Exception
 557   {
 558   }
 559 }