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 $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ */
  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         String name=st.nextToken();
  55         String url= st.nextToken();
  56         // check for '|' within a regex
  57         int rxstart = url.indexOf("$SEQUENCE_ID$");
  58         while (rxstart==-1 && url.indexOf("/=$")==-1)
  59         {
  60           url = url + "|" + st.nextToken();
  61         }
  62         sequenceURLLinks.addElement(name + "|" + url);
  63       }
  64     }
  65     catch (Exception ex)
  66     {
  67       System.out.println(ex + "\nError parsing sequence links");
  68     }
  69   }
  70
  71   Vector nameLinks, urlLinks;
  72
  73   JInternalFrame frame;
  74
  75   DasSourceBrowser dasSource;
  76
  77   /**
  78    * Creates a new Preferences object.
  79    */
  80   public Preferences()
  81   {
  82
  83     frame = new JInternalFrame();
  84     frame.setContentPane(this);
  85     dasSource = new DasSourceBrowser();
  86     dasPanel.add(dasSource, BorderLayout.CENTER);
  87
  88     int width = 500, height = 420;
  89     if (new jalview.util.Platform().isAMac())
  90     {
  91       width = 570;
  92       height = 460;
  93     }
  94
  95     Desktop.addInternalFrame(frame, "Preferences", width, height);
  96     frame.setMinimumSize(new Dimension(width, height));
  97
  98     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
  99     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 100     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 101     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 102
 103     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 104     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 105     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 106
 107     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 108     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 109     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 110     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 111
 112     for (int i = 0; i < 13; i++)
 113     {
 114       colour.addItem(ColourSchemeProperty.getColourName(i));
 115     }
 116
 117     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 118
 119     colour.setSelectedItem(string);
 120
 121     String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
 122         .getAvailableFontFamilyNames();
 123
 124     for (int i = 0; i < fonts.length; i++)
 125     {
 126       fontNameCB.addItem(fonts[i]);
 127     }
 128
 129     for (int i = 1; i < 31; i++)
 130     {
 131       fontSizeCB.addItem(i + "");
 132     }
 133
 134     fontStyleCB.addItem("plain");
 135     fontStyleCB.addItem("bold");
 136     fontStyleCB.addItem("italic");
 137
 138     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 139     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 140     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 141
 142     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 143
 144     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 145
 146     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 147
 148     gapSymbolCB.addItem("-");
 149     gapSymbolCB.addItem(".");
 150
 151     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 152
 153     startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 154     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 155                                                   "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 156
 157     sortby.addItem("No sort");
 158     sortby.addItem("Id");
 159     sortby.addItem("Pairwise Identity");
 160     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 161
 162     epsRendering.addItem("Prompt each time");
 163     epsRendering.addItem("Lineart");
 164     epsRendering.addItem("Text");
 165     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 166                                                   "Prompt each time"));
 167
 168     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 169     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 170     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 171     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 172     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 173     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 174     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 175
 176     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 177
 178     autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 179     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 180
 181     /****************************************************
 182      * Set up Connections
 183      */
 184     nameLinks = new Vector();
 185     urlLinks = new Vector();
 186     for (int i = 0; i < sequenceURLLinks.size(); i++)
 187     {
 188       String link = sequenceURLLinks.elementAt(i).toString();
 189       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 190       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 191     }
 192
 193     updateLinkData();
 194
 195     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 196     proxyServerTB.setEnabled(useProxy.isSelected());
 197     proxyPortTB.setEnabled(useProxy.isSelected());
 198     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 199     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 200
 201     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 202     try
 203     {
 204       jbInit();
 205     }
 206     catch (Exception ex)
 207     {
 208       ex.printStackTrace();
 209     }
 210
 211   }
 212
 213   /**
 214    * DOCUMENT ME!
 215    *
 216    * @param e DOCUMENT ME!
 217    */
 218   public void ok_actionPerformed(ActionEvent e)
 219   {
 220
 221     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 222                                             Boolean.toString(seqLimit.
 223         isSelected()));
 224     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 225                                             Boolean.toString(rightAlign.
 226         isSelected()));
 227     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 228                                             Boolean.toString(fullScreen.
 229         isSelected()));
 230     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 231                                             Boolean.toString(openoverv.
 232         isSelected()));
 233     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 234                                             Boolean.
 235                                             toString(annotations.isSelected()));
 236     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 237                                             Boolean.
 238                                             toString(conservation.isSelected()));
 239     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 240                                             Boolean.toString(quality.isSelected()));
 241     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 242                                             Boolean.toString(identity.
 243         isSelected()));
 244
 245     Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
 246                                             colour.getSelectedItem().toString());
 247     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 248                                             gapSymbolCB.getSelectedItem().
 249                                             toString());
 250
 251     Cache.applicationProperties.setProperty("FONT_NAME",
 252                                             fontNameCB.getSelectedItem().
 253                                             toString());
 254     Cache.applicationProperties.setProperty("FONT_STYLE",
 255                                             fontStyleCB.getSelectedItem().
 256                                             toString());
 257     Cache.applicationProperties.setProperty("FONT_SIZE",
 258                                             fontSizeCB.getSelectedItem().
 259                                             toString());
 260
 261     Cache.applicationProperties.setProperty("ID_ITALICS",
 262                                             Boolean.toString(idItalics.
 263         isSelected()));
 264
 265     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 266                                             Boolean.toString(smoothFont.
 267         isSelected()));
 268
 269     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 270                                             Boolean.toString(wrap.isSelected()));
 271
 272     Cache.applicationProperties.setProperty("STARTUP_FILE",
 273                                             startupFileTextfield.getText());
 274     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 275                                             Boolean.
 276                                             toString(startupCheckbox.isSelected()));
 277
 278     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 279                                             sortby.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",
 288                                               epsRendering.getSelectedItem().
 289                                               toString());
 290     }
 291
 292     if (defaultBrowser.getText().trim().length() < 1)
 293     {
 294       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 295     }
 296     else
 297     {
 298       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 299                                               defaultBrowser.getText());
 300     }
 301
 302     jalview.util.BrowserLauncher.resetBrowser();
 303
 304     if (nameLinks.size() > 0)
 305     {
 306       StringBuffer links = new StringBuffer();
 307       sequenceURLLinks = new Vector();
 308       for (int i = 0; i < nameLinks.size(); i++)
 309       {
 310         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
 311                                     urlLinks.elementAt(i));
 312         links.append(sequenceURLLinks.elementAt(i).toString());
 313         links.append("|");
 314       }
 315       // remove last "|"
 316       links.setLength(links.length() - 1);
 317       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
 318     }
 319     else
 320     {
 321       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 322     }
 323
 324     Cache.applicationProperties.setProperty("USE_PROXY",
 325                                             Boolean.toString(useProxy.
 326         isSelected()));
 327
 328     if (proxyServerTB.getText().trim().length() < 1)
 329     {
 330       Cache.applicationProperties.remove("PROXY_SERVER");
 331     }
 332     else
 333     {
 334       Cache.applicationProperties.setProperty("PROXY_SERVER",
 335                                               proxyServerTB.getText());
 336     }
 337
 338     if (proxyPortTB.getText().trim().length() < 1)
 339     {
 340       Cache.applicationProperties.remove("PROXY_PORT");
 341     }
 342     else
 343     {
 344       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.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
 358     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 359                                             Boolean.toString(blcjv.isSelected()));
 360     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 361                                             Boolean.
 362                                             toString(clustaljv.isSelected()));
 363     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 364                                             Boolean.toString(fastajv.isSelected()));
 365     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 366                                             Boolean.toString(msfjv.isSelected()));
 367     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 368                                             Boolean.toString(pfamjv.isSelected()));
 369     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 370                                             Boolean.toString(pileupjv.
 371         isSelected()));
 372     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 373                                             Boolean.toString(pirjv.isSelected()));
 374     Cache.applicationProperties.setProperty("PIR_MODELLER",
 375                                             Boolean.toString(modellerOutput.
 376         isSelected()));
 377     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 378
 379     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 380                                             Boolean.toString(
 381         autoCalculateConsCheck.isSelected()));
 382     Cache.applicationProperties.setProperty("PAD_GAPS",
 383                                             Boolean.toString(padGaps.isSelected()));
 384
 385     dasSource.saveProperties(Cache.applicationProperties);
 386
 387     Cache.saveProperties();
 388     try
 389     {
 390       frame.setClosed(true);
 391     }
 392     catch (Exception ex)
 393     {
 394     }
 395   }
 396
 397   /**
 398    * DOCUMENT ME!
 399    */
 400   public void startupFileTextfield_mouseClicked()
 401   {
 402     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 403         getProperty(
 404             "LAST_DIRECTORY"),
 405         new String[]
 406         {
 407         "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 408         "jar"
 409     },
 410         new String[]
 411         {
 412         "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
 413     }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 414     chooser.setFileView(new JalviewFileView());
 415     chooser.setDialogTitle("Select startup file");
 416
 417     int value = chooser.showOpenDialog(this);
 418
 419     if (value == JalviewFileChooser.APPROVE_OPTION)
 420     {
 421       jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 422           chooser.getSelectedFormat());
 423       startupFileTextfield.setText(chooser.getSelectedFile()
 424                                    .getAbsolutePath());
 425     }
 426   }
 427
 428   /**
 429    * DOCUMENT ME!
 430    *
 431    * @param e DOCUMENT ME!
 432    */
 433   public void cancel_actionPerformed(ActionEvent e)
 434   {
 435     try
 436     {
 437       frame.setClosed(true);
 438     }
 439     catch (Exception ex)
 440     {
 441     }
 442   }
 443
 444   /**
 445    * DOCUMENT ME!
 446    *
 447    * @param e DOCUMENT ME!
 448    */
 449   public void annotations_actionPerformed(ActionEvent e)
 450   {
 451     conservation.setEnabled(annotations.isSelected());
 452     quality.setEnabled(annotations.isSelected());
 453     identity.setEnabled(annotations.isSelected());
 454   }
 455
 456   public void newLink_actionPerformed(ActionEvent e)
 457   {
 458
 459     GSequenceLink link = new GSequenceLink();
 460     boolean valid = false;
 461     while (!valid)
 462     {
 463       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 464                                                 "New sequence URL link",
 465                                                 JOptionPane.OK_CANCEL_OPTION
 466                                                 , -1, null)
 467           == JOptionPane.OK_OPTION)
 468       {
 469         if (link.checkValid())
 470         {
 471           nameLinks.addElement(link.getName());
 472           urlLinks.addElement(link.getURL());
 473           updateLinkData();
 474           valid = true;
 475         }
 476       }
 477       else
 478       {
 479         break;
 480       }
 481     }
 482   }
 483
 484   public void editLink_actionPerformed(ActionEvent e)
 485   {
 486     GSequenceLink link = new GSequenceLink();
 487
 488     int index = linkNameList.getSelectedIndex();
 489     if (index == -1)
 490     {
 491       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 492                                             "No link selected!"
 493                                             , "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",
 507                                                 JOptionPane.OK_CANCEL_OPTION
 508                                                 , -1, null)
 509           == JOptionPane.OK_OPTION)
 510       {
 511         if (link.checkValid())
 512         {
 513           nameLinks.setElementAt(link.getName(), index);
 514           urlLinks.setElementAt(link.getURL(), index);
 515           updateLinkData();
 516           valid = true;
 517         }
 518       }
 519
 520       else
 521       {
 522         break;
 523       }
 524     }
 525   }
 526
 527   public void deleteLink_actionPerformed(ActionEvent e)
 528   {
 529     int index = linkNameList.getSelectedIndex();
 530     if (index == -1)
 531     {
 532       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 533                                             "No link selected!"
 534                                             , "No link selected",
 535                                             JOptionPane.WARNING_MESSAGE);
 536       return;
 537     }
 538     nameLinks.removeElementAt(index);
 539     urlLinks.removeElementAt(index);
 540     updateLinkData();
 541   }
 542
 543   void updateLinkData()
 544   {
 545     linkNameList.setListData(nameLinks);
 546     linkURLList.setListData(urlLinks);
 547   }
 548
 549   public void defaultBrowser_mouseClicked(MouseEvent e)
 550   {
 551     JFileChooser chooser = new JFileChooser(".");
 552     chooser.setDialogTitle("Select default web browser");
 553
 554     int value = chooser.showOpenDialog(this);
 555
 556     if (value == JFileChooser.APPROVE_OPTION)
 557     {
 558       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 559     }
 560
 561   }
 562
 563   private void jbInit()
 564       throws Exception
 565   {
 566   }
 567 }