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   /**
  48    * Holds name and link separated with | character. Sequence IDS and Sequences must be
  49    * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$
  50    * and separation character for first and second token specified after a pipe character at end |,|.
  51    * (TODO: proper escape for using | to separate ids or sequences
  52    */
  53
  54   public static Vector groupURLLinks;
  55   static
  56   {
  57     String string = Cache
  58             .getDefault(
  59                     "SEQUENCE_LINKS",
  60                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  61     sequenceURLLinks = new Vector();
  62
  63     try
  64     {
  65       StringTokenizer st = new StringTokenizer(string, "|");
  66       while (st.hasMoreElements())
  67       {
  68         String name = st.nextToken();
  69         String url = st.nextToken();
  70         // check for '|' within a regex
  71         int rxstart = url.indexOf("$SEQUENCE_ID$");
  72         while (rxstart == -1 && url.indexOf("/=$") == -1)
  73         {
  74           url = url + "|" + st.nextToken();
  75         }
  76         sequenceURLLinks.addElement(name + "|" + url);
  77       }
  78     } catch (Exception ex)
  79     {
  80       System.out.println(ex + "\nError parsing sequence links");
  81     }
  82     /**
  83      * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings
  84      */
  85
  86     groupURLLinks = new Vector();
  87     groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
  88     groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
  89
  90   }
  91
  92   Vector nameLinks, urlLinks;
  93
  94   JInternalFrame frame;
  95
  96   DasSourceBrowser dasSource;
  97
  98   /**
  99    * Creates a new Preferences object.
 100    */
 101   public Preferences()
 102   {
 103
 104     frame = new JInternalFrame();
 105     frame.setContentPane(this);
 106     dasSource = new DasSourceBrowser();
 107     dasPanel.add(dasSource, BorderLayout.CENTER);
 108
 109     int width = 500, height = 420;
 110     if (new jalview.util.Platform().isAMac())
 111     {
 112       width = 570;
 113       height = 460;
 114     }
 115
 116     Desktop.addInternalFrame(frame, "Preferences", width, height);
 117     frame.setMinimumSize(new Dimension(width, height));
 118
 119     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 120     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 121     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 122     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 123
 124     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 125     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 126     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 127
 128     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 129     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 130     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 131     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 132     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 133
 134     for (int i = 0; i < 13; i++)
 135     {
 136       colour.addItem(ColourSchemeProperty.getColourName(i));
 137     }
 138
 139     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 140
 141     colour.setSelectedItem(string);
 142
 143     String[] fonts = java.awt.GraphicsEnvironment
 144             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 145
 146     for (int i = 0; i < fonts.length; i++)
 147     {
 148       fontNameCB.addItem(fonts[i]);
 149     }
 150
 151     for (int i = 1; i < 31; i++)
 152     {
 153       fontSizeCB.addItem(i + "");
 154     }
 155
 156     fontStyleCB.addItem("plain");
 157     fontStyleCB.addItem("bold");
 158     fontStyleCB.addItem("italic");
 159
 160     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 161     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 162     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 163             + ""));
 164
 165     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 166
 167     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 168
 169     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 170
 171     gapSymbolCB.addItem("-");
 172     gapSymbolCB.addItem(".");
 173
 174     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 175
 176     startupCheckbox
 177             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 178     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 179             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 180
 181     sortby.addItem("No sort");
 182     sortby.addItem("Id");
 183     sortby.addItem("Pairwise Identity");
 184     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 185
 186     epsRendering.addItem("Prompt each time");
 187     epsRendering.addItem("Lineart");
 188     epsRendering.addItem("Text");
 189     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 190             "Prompt each time"));
 191
 192     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 193     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 194     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 195     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 196     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 197     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 198     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 199
 200     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 201
 202     autoCalculateConsCheck.setSelected(Cache.getDefault(
 203             "AUTO_CALC_CONSENSUS", true));
 204     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 205
 206     /***************************************************************************
 207      * Set up Connections
 208      */
 209     nameLinks = new Vector();
 210     urlLinks = new Vector();
 211     for (int i = 0; i < sequenceURLLinks.size(); i++)
 212     {
 213       String link = sequenceURLLinks.elementAt(i).toString();
 214       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 215       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 216     }
 217
 218     updateLinkData();
 219
 220     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 221     proxyServerTB.setEnabled(useProxy.isSelected());
 222     proxyPortTB.setEnabled(useProxy.isSelected());
 223     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 224     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 225
 226     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 227
 228     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 229     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
 230     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
 231
 232     try
 233     {
 234       jbInit();
 235     } catch (Exception ex)
 236     {
 237       ex.printStackTrace();
 238     }
 239
 240   }
 241
 242   /**
 243    * DOCUMENT ME!
 244    *
 245    * @param e
 246    *                DOCUMENT ME!
 247    */
 248   public void ok_actionPerformed(ActionEvent e)
 249   {
 250
 251     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 252             .toString(seqLimit.isSelected()));
 253     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 254             .toString(rightAlign.isSelected()));
 255     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 256             .toString(fullScreen.isSelected()));
 257     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 258             .toString(openoverv.isSelected()));
 259     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 260             .toString(annotations.isSelected()));
 261     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 262             .toString(conservation.isSelected()));
 263     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 264             .toString(quality.isSelected()));
 265     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 266             .toString(identity.isSelected()));
 267
 268     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 269             .getSelectedItem().toString());
 270     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 271             .getSelectedItem().toString());
 272
 273     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 274             .getSelectedItem().toString());
 275     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 276             .getSelectedItem().toString());
 277     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 278             .getSelectedItem().toString());
 279
 280     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 281             .toString(idItalics.isSelected()));
 282     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 283     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 284             .toString(smoothFont.isSelected()));
 285
 286     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 287             .toString(wrap.isSelected()));
 288
 289     Cache.applicationProperties.setProperty("STARTUP_FILE",
 290             startupFileTextfield.getText());
 291     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 292             .toString(startupCheckbox.isSelected()));
 293
 294     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 295             .getSelectedItem().toString());
 296
 297     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 298     {
 299       Cache.applicationProperties.remove("EPS_RENDERING");
 300     }
 301     else
 302     {
 303       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 304               .getSelectedItem().toString());
 305     }
 306
 307     if (defaultBrowser.getText().trim().length() < 1)
 308     {
 309       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 310     }
 311     else
 312     {
 313       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 314               defaultBrowser.getText());
 315     }
 316
 317     jalview.util.BrowserLauncher.resetBrowser();
 318
 319     if (nameLinks.size() > 0)
 320     {
 321       StringBuffer links = new StringBuffer();
 322       sequenceURLLinks = new Vector();
 323       for (int i = 0; i < nameLinks.size(); i++)
 324       {
 325         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 326                 + urlLinks.elementAt(i));
 327         links.append(sequenceURLLinks.elementAt(i).toString());
 328         links.append("|");
 329       }
 330       // remove last "|"
 331       links.setLength(links.length() - 1);
 332       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 333               .toString());
 334     }
 335     else
 336     {
 337       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 338     }
 339
 340     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 341             .toString(useProxy.isSelected()));
 342
 343     if (proxyServerTB.getText().trim().length() < 1)
 344     {
 345       Cache.applicationProperties.remove("PROXY_SERVER");
 346     }
 347     else
 348     {
 349       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 350               .getText());
 351     }
 352
 353     if (proxyPortTB.getText().trim().length() < 1)
 354     {
 355       Cache.applicationProperties.remove("PROXY_PORT");
 356     }
 357     else
 358     {
 359       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 360               .getText());
 361     }
 362
 363     if (useProxy.isSelected())
 364     {
 365       System.setProperty("http.proxyHost", proxyServerTB.getText());
 366       System.setProperty("http.proxyPort", proxyPortTB.getText());
 367     }
 368     else
 369     {
 370       System.setProperty("http.proxyHost", "");
 371       System.setProperty("http.proxyPort", "");
 372     }
 373     Cache.setProperty("VERSION_CHECK", Boolean
 374             .toString(versioncheck.isSelected()));
 375     if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) {
 376       // default is false - we only set this if the user has actively agreed
 377       Cache.setProperty("USAGESTATS",Boolean
 378             .toString(usagestats.isSelected()));
 379     }
 380     if (!questionnaire.isSelected())
 381     {
 382       Cache.setProperty("NOQUESTIONNAIRES", "true");
 383     } else {
 384       // special - made easy to edit a property file to disable questionnaires by just adding the given line
 385       Cache.removeProperty("NOQUESTIONNAIRES");
 386     }
 387     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 388             .toString(blcjv.isSelected()));
 389     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 390             .toString(clustaljv.isSelected()));
 391     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 392             .toString(fastajv.isSelected()));
 393     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 394             .toString(msfjv.isSelected()));
 395     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 396             .toString(pfamjv.isSelected()));
 397     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 398             .toString(pileupjv.isSelected()));
 399     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 400             .toString(pirjv.isSelected()));
 401     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 402             .toString(modellerOutput.isSelected()));
 403     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 404
 405     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 406             .toString(autoCalculateConsCheck.isSelected()));
 407     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 408             .toString(padGaps.isSelected()));
 409
 410     dasSource.saveProperties(Cache.applicationProperties);
 411
 412     Cache.saveProperties();
 413     try
 414     {
 415       frame.setClosed(true);
 416     } catch (Exception ex)
 417     {
 418     }
 419   }
 420
 421   /**
 422    * DOCUMENT ME!
 423    */
 424   public void startupFileTextfield_mouseClicked()
 425   {
 426     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 427             .getProperty("LAST_DIRECTORY"), new String[]
 428     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 429             new String[]
 430             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 431             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 432     chooser.setFileView(new JalviewFileView());
 433     chooser.setDialogTitle("Select startup file");
 434
 435     int value = chooser.showOpenDialog(this);
 436
 437     if (value == JalviewFileChooser.APPROVE_OPTION)
 438     {
 439       jalview.bin.Cache.applicationProperties.setProperty(
 440               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 441       startupFileTextfield.setText(chooser.getSelectedFile()
 442               .getAbsolutePath());
 443     }
 444   }
 445
 446   /**
 447    * DOCUMENT ME!
 448    *
 449    * @param e
 450    *                DOCUMENT ME!
 451    */
 452   public void cancel_actionPerformed(ActionEvent e)
 453   {
 454     try
 455     {
 456       frame.setClosed(true);
 457     } catch (Exception ex)
 458     {
 459     }
 460   }
 461
 462   /**
 463    * DOCUMENT ME!
 464    *
 465    * @param e
 466    *                DOCUMENT ME!
 467    */
 468   public void annotations_actionPerformed(ActionEvent e)
 469   {
 470     conservation.setEnabled(annotations.isSelected());
 471     quality.setEnabled(annotations.isSelected());
 472     identity.setEnabled(annotations.isSelected());
 473   }
 474
 475   public void newLink_actionPerformed(ActionEvent e)
 476   {
 477
 478     GSequenceLink link = new GSequenceLink();
 479     boolean valid = false;
 480     while (!valid)
 481     {
 482       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 483               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 484               null) == JOptionPane.OK_OPTION)
 485       {
 486         if (link.checkValid())
 487         {
 488           nameLinks.addElement(link.getName());
 489           urlLinks.addElement(link.getURL());
 490           updateLinkData();
 491           valid = true;
 492         }
 493       }
 494       else
 495       {
 496         break;
 497       }
 498     }
 499   }
 500
 501   public void editLink_actionPerformed(ActionEvent e)
 502   {
 503     GSequenceLink link = new GSequenceLink();
 504
 505     int index = linkNameList.getSelectedIndex();
 506     if (index == -1)
 507     {
 508       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 509               "No link selected!", "No link selected",
 510               JOptionPane.WARNING_MESSAGE);
 511       return;
 512     }
 513
 514     link.setName(nameLinks.elementAt(index).toString());
 515     link.setURL(urlLinks.elementAt(index).toString());
 516
 517     boolean valid = false;
 518     while (!valid)
 519     {
 520
 521       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 522               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 523               null) == JOptionPane.OK_OPTION)
 524       {
 525         if (link.checkValid())
 526         {
 527           nameLinks.setElementAt(link.getName(), index);
 528           urlLinks.setElementAt(link.getURL(), index);
 529           updateLinkData();
 530           valid = true;
 531         }
 532       }
 533
 534       else
 535       {
 536         break;
 537       }
 538     }
 539   }
 540
 541   public void deleteLink_actionPerformed(ActionEvent e)
 542   {
 543     int index = linkNameList.getSelectedIndex();
 544     if (index == -1)
 545     {
 546       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 547               "No link selected!", "No link selected",
 548               JOptionPane.WARNING_MESSAGE);
 549       return;
 550     }
 551     nameLinks.removeElementAt(index);
 552     urlLinks.removeElementAt(index);
 553     updateLinkData();
 554   }
 555
 556   void updateLinkData()
 557   {
 558     linkNameList.setListData(nameLinks);
 559     linkURLList.setListData(urlLinks);
 560   }
 561
 562   public void defaultBrowser_mouseClicked(MouseEvent e)
 563   {
 564     JFileChooser chooser = new JFileChooser(".");
 565     chooser.setDialogTitle("Select default web browser");
 566
 567     int value = chooser.showOpenDialog(this);
 568
 569     if (value == JFileChooser.APPROVE_OPTION)
 570     {
 571       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 572     }
 573
 574   }
 575   /* (non-Javadoc)
 576    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 577    */
 578   protected void showunconserved_actionPerformed(ActionEvent e)
 579   {
 580     // TODO Auto-generated method stub
 581     super.showunconserved_actionPerformed(e);
 582   }
 583
 584   private void jbInit() throws Exception
 585   {
 586   }
 587 }