src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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 extends GPreferences
  39 {
  40   /**
  41    * Holds name and link separated with | character. Sequence ID must be
  42    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  43    */
  44   public static Vector sequenceURLLinks;
  45   static
  46   {
  47     String string = Cache
  48             .getDefault(
  49                     "SEQUENCE_LINKS",
  50                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  51     sequenceURLLinks = new Vector();
  52
  53     try
  54     {
  55       StringTokenizer st = new StringTokenizer(string, "|");
  56       while (st.hasMoreElements())
  57       {
  58         String name = st.nextToken();
  59         String url = st.nextToken();
  60         // check for '|' within a regex
  61         int rxstart = url.indexOf("$SEQUENCE_ID$");
  62         while (rxstart == -1 && url.indexOf("/=$") == -1)
  63         {
  64           url = url + "|" + st.nextToken();
  65         }
  66         sequenceURLLinks.addElement(name + "|" + url);
  67       }
  68     } catch (Exception ex)
  69     {
  70       System.out.println(ex + "\nError parsing sequence links");
  71     }
  72   }
  73
  74   Vector nameLinks, urlLinks;
  75
  76   JInternalFrame frame;
  77
  78   DasSourceBrowser dasSource;
  79
  80   /**
  81    * Creates a new Preferences object.
  82    */
  83   public Preferences()
  84   {
  85
  86     frame = new JInternalFrame();
  87     frame.setContentPane(this);
  88     dasSource = new DasSourceBrowser();
  89     dasPanel.add(dasSource, BorderLayout.CENTER);
  90
  91     int width = 500, height = 420;
  92     if (new jalview.util.Platform().isAMac())
  93     {
  94       width = 570;
  95       height = 460;
  96     }
  97
  98     Desktop.addInternalFrame(frame, "Preferences", width, height);
  99     frame.setMinimumSize(new Dimension(width, height));
 100
 101     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 102     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 103     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 104     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 105
 106     conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 107     quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 108     identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 109
 110     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 111     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 112     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 113     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 114
 115     for (int i = 0; i < 13; i++)
 116     {
 117       colour.addItem(ColourSchemeProperty.getColourName(i));
 118     }
 119
 120     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 121
 122     colour.setSelectedItem(string);
 123
 124     String[] fonts = java.awt.GraphicsEnvironment
 125             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 126
 127     for (int i = 0; i < fonts.length; i++)
 128     {
 129       fontNameCB.addItem(fonts[i]);
 130     }
 131
 132     for (int i = 1; i < 31; i++)
 133     {
 134       fontSizeCB.addItem(i + "");
 135     }
 136
 137     fontStyleCB.addItem("plain");
 138     fontStyleCB.addItem("bold");
 139     fontStyleCB.addItem("italic");
 140
 141     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 142     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 143     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 144             + ""));
 145
 146     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 147
 148     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 149
 150     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 151
 152     gapSymbolCB.addItem("-");
 153     gapSymbolCB.addItem(".");
 154
 155     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 156
 157     startupCheckbox
 158             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 159     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 160             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 161
 162     sortby.addItem("No sort");
 163     sortby.addItem("Id");
 164     sortby.addItem("Pairwise Identity");
 165     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 166
 167     epsRendering.addItem("Prompt each time");
 168     epsRendering.addItem("Lineart");
 169     epsRendering.addItem("Text");
 170     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 171             "Prompt each time"));
 172
 173     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 174     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 175     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 176     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 177     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 178     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 179     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 180
 181     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 182
 183     autoCalculateConsCheck.setSelected(Cache.getDefault(
 184             "AUTO_CALC_CONSENSUS", true));
 185     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 186
 187     /***************************************************************************
 188      * Set up Connections
 189      */
 190     nameLinks = new Vector();
 191     urlLinks = new Vector();
 192     for (int i = 0; i < sequenceURLLinks.size(); i++)
 193     {
 194       String link = sequenceURLLinks.elementAt(i).toString();
 195       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 196       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 197     }
 198
 199     updateLinkData();
 200
 201     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 202     proxyServerTB.setEnabled(useProxy.isSelected());
 203     proxyPortTB.setEnabled(useProxy.isSelected());
 204     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 205     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 206
 207     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 208     try
 209     {
 210       jbInit();
 211     } catch (Exception ex)
 212     {
 213       ex.printStackTrace();
 214     }
 215
 216   }
 217
 218   /**
 219    * DOCUMENT ME!
 220    *
 221    * @param e
 222    *                DOCUMENT ME!
 223    */
 224   public void ok_actionPerformed(ActionEvent e)
 225   {
 226
 227     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 228             .toString(seqLimit.isSelected()));
 229     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 230             .toString(rightAlign.isSelected()));
 231     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 232             .toString(fullScreen.isSelected()));
 233     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 234             .toString(openoverv.isSelected()));
 235     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 236             .toString(annotations.isSelected()));
 237     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 238             .toString(conservation.isSelected()));
 239     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 240             .toString(quality.isSelected()));
 241     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 242             .toString(identity.isSelected()));
 243
 244     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 245             .getSelectedItem().toString());
 246     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 247             .getSelectedItem().toString());
 248
 249     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 250             .getSelectedItem().toString());
 251     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 252             .getSelectedItem().toString());
 253     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 254             .getSelectedItem().toString());
 255
 256     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 257             .toString(idItalics.isSelected()));
 258
 259     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 260             .toString(smoothFont.isSelected()));
 261
 262     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 263             .toString(wrap.isSelected()));
 264
 265     Cache.applicationProperties.setProperty("STARTUP_FILE",
 266             startupFileTextfield.getText());
 267     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 268             .toString(startupCheckbox.isSelected()));
 269
 270     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 271             .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", epsRendering
 280               .getSelectedItem().toString());
 281     }
 282
 283     if (defaultBrowser.getText().trim().length() < 1)
 284     {
 285       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 286     }
 287     else
 288     {
 289       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 290               defaultBrowser.getText());
 291     }
 292
 293     jalview.util.BrowserLauncher.resetBrowser();
 294
 295     if (nameLinks.size() > 0)
 296     {
 297       StringBuffer links = new StringBuffer();
 298       sequenceURLLinks = new Vector();
 299       for (int i = 0; i < nameLinks.size(); i++)
 300       {
 301         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 302                 + urlLinks.elementAt(i));
 303         links.append(sequenceURLLinks.elementAt(i).toString());
 304         links.append("|");
 305       }
 306       // remove last "|"
 307       links.setLength(links.length() - 1);
 308       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 309               .toString());
 310     }
 311     else
 312     {
 313       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 314     }
 315
 316     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 317             .toString(useProxy.isSelected()));
 318
 319     if (proxyServerTB.getText().trim().length() < 1)
 320     {
 321       Cache.applicationProperties.remove("PROXY_SERVER");
 322     }
 323     else
 324     {
 325       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 326               .getText());
 327     }
 328
 329     if (proxyPortTB.getText().trim().length() < 1)
 330     {
 331       Cache.applicationProperties.remove("PROXY_PORT");
 332     }
 333     else
 334     {
 335       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 336               .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", Boolean
 351             .toString(blcjv.isSelected()));
 352     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 353             .toString(clustaljv.isSelected()));
 354     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 355             .toString(fastajv.isSelected()));
 356     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 357             .toString(msfjv.isSelected()));
 358     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 359             .toString(pfamjv.isSelected()));
 360     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 361             .toString(pileupjv.isSelected()));
 362     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 363             .toString(pirjv.isSelected()));
 364     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 365             .toString(modellerOutput.isSelected()));
 366     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 367
 368     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 369             .toString(autoCalculateConsCheck.isSelected()));
 370     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 371             .toString(padGaps.isSelected()));
 372
 373     dasSource.saveProperties(Cache.applicationProperties);
 374
 375     Cache.saveProperties();
 376     try
 377     {
 378       frame.setClosed(true);
 379     } catch (Exception ex)
 380     {
 381     }
 382   }
 383
 384   /**
 385    * DOCUMENT ME!
 386    */
 387   public void startupFileTextfield_mouseClicked()
 388   {
 389     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 390             .getProperty("LAST_DIRECTORY"), new String[]
 391     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 392             new String[]
 393             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 394             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 395     chooser.setFileView(new JalviewFileView());
 396     chooser.setDialogTitle("Select startup file");
 397
 398     int value = chooser.showOpenDialog(this);
 399
 400     if (value == JalviewFileChooser.APPROVE_OPTION)
 401     {
 402       jalview.bin.Cache.applicationProperties.setProperty(
 403               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 404       startupFileTextfield.setText(chooser.getSelectedFile()
 405               .getAbsolutePath());
 406     }
 407   }
 408
 409   /**
 410    * DOCUMENT ME!
 411    *
 412    * @param e
 413    *                DOCUMENT ME!
 414    */
 415   public void cancel_actionPerformed(ActionEvent e)
 416   {
 417     try
 418     {
 419       frame.setClosed(true);
 420     } catch (Exception ex)
 421     {
 422     }
 423   }
 424
 425   /**
 426    * DOCUMENT ME!
 427    *
 428    * @param e
 429    *                DOCUMENT ME!
 430    */
 431   public void annotations_actionPerformed(ActionEvent e)
 432   {
 433     conservation.setEnabled(annotations.isSelected());
 434     quality.setEnabled(annotations.isSelected());
 435     identity.setEnabled(annotations.isSelected());
 436   }
 437
 438   public void newLink_actionPerformed(ActionEvent e)
 439   {
 440
 441     GSequenceLink link = new GSequenceLink();
 442     boolean valid = false;
 443     while (!valid)
 444     {
 445       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 446               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 447               null) == JOptionPane.OK_OPTION)
 448       {
 449         if (link.checkValid())
 450         {
 451           nameLinks.addElement(link.getName());
 452           urlLinks.addElement(link.getURL());
 453           updateLinkData();
 454           valid = true;
 455         }
 456       }
 457       else
 458       {
 459         break;
 460       }
 461     }
 462   }
 463
 464   public void editLink_actionPerformed(ActionEvent e)
 465   {
 466     GSequenceLink link = new GSequenceLink();
 467
 468     int index = linkNameList.getSelectedIndex();
 469     if (index == -1)
 470     {
 471       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 472               "No link selected!", "No link selected",
 473               JOptionPane.WARNING_MESSAGE);
 474       return;
 475     }
 476
 477     link.setName(nameLinks.elementAt(index).toString());
 478     link.setURL(urlLinks.elementAt(index).toString());
 479
 480     boolean valid = false;
 481     while (!valid)
 482     {
 483
 484       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 485               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 486               null) == JOptionPane.OK_OPTION)
 487       {
 488         if (link.checkValid())
 489         {
 490           nameLinks.setElementAt(link.getName(), index);
 491           urlLinks.setElementAt(link.getURL(), index);
 492           updateLinkData();
 493           valid = true;
 494         }
 495       }
 496
 497       else
 498       {
 499         break;
 500       }
 501     }
 502   }
 503
 504   public void deleteLink_actionPerformed(ActionEvent e)
 505   {
 506     int index = linkNameList.getSelectedIndex();
 507     if (index == -1)
 508     {
 509       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 510               "No link selected!", "No link selected",
 511               JOptionPane.WARNING_MESSAGE);
 512       return;
 513     }
 514     nameLinks.removeElementAt(index);
 515     urlLinks.removeElementAt(index);
 516     updateLinkData();
 517   }
 518
 519   void updateLinkData()
 520   {
 521     linkNameList.setListData(nameLinks);
 522     linkURLList.setListData(urlLinks);
 523   }
 524
 525   public void defaultBrowser_mouseClicked(MouseEvent e)
 526   {
 527     JFileChooser chooser = new JFileChooser(".");
 528     chooser.setDialogTitle("Select default web browser");
 529
 530     int value = chooser.showOpenDialog(this);
 531
 532     if (value == JFileChooser.APPROVE_OPTION)
 533     {
 534       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 535     }
 536
 537   }
 538
 539   private void jbInit() throws Exception
 540   {
 541   }
 542 }