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     try
 212     {
 213       jbInit();
 214     } catch (Exception ex)
 215     {
 216       ex.printStackTrace();
 217     }
 218
 219   }
 220
 221   /**
 222    * DOCUMENT ME!
 223    *
 224    * @param e
 225    *                DOCUMENT ME!
 226    */
 227   public void ok_actionPerformed(ActionEvent e)
 228   {
 229
 230     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 231             .toString(seqLimit.isSelected()));
 232     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 233             .toString(rightAlign.isSelected()));
 234     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 235             .toString(fullScreen.isSelected()));
 236     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 237             .toString(openoverv.isSelected()));
 238     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 239             .toString(annotations.isSelected()));
 240     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 241             .toString(conservation.isSelected()));
 242     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 243             .toString(quality.isSelected()));
 244     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 245             .toString(identity.isSelected()));
 246
 247     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 248             .getSelectedItem().toString());
 249     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 250             .getSelectedItem().toString());
 251
 252     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 253             .getSelectedItem().toString());
 254     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 255             .getSelectedItem().toString());
 256     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 257             .getSelectedItem().toString());
 258
 259     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 260             .toString(idItalics.isSelected()));
 261     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 262     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 263             .toString(smoothFont.isSelected()));
 264
 265     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 266             .toString(wrap.isSelected()));
 267
 268     Cache.applicationProperties.setProperty("STARTUP_FILE",
 269             startupFileTextfield.getText());
 270     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 271             .toString(startupCheckbox.isSelected()));
 272
 273     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 274             .getSelectedItem().toString());
 275
 276     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 277     {
 278       Cache.applicationProperties.remove("EPS_RENDERING");
 279     }
 280     else
 281     {
 282       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 283               .getSelectedItem().toString());
 284     }
 285
 286     if (defaultBrowser.getText().trim().length() < 1)
 287     {
 288       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 289     }
 290     else
 291     {
 292       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 293               defaultBrowser.getText());
 294     }
 295
 296     jalview.util.BrowserLauncher.resetBrowser();
 297
 298     if (nameLinks.size() > 0)
 299     {
 300       StringBuffer links = new StringBuffer();
 301       sequenceURLLinks = new Vector();
 302       for (int i = 0; i < nameLinks.size(); i++)
 303       {
 304         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 305                 + urlLinks.elementAt(i));
 306         links.append(sequenceURLLinks.elementAt(i).toString());
 307         links.append("|");
 308       }
 309       // remove last "|"
 310       links.setLength(links.length() - 1);
 311       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 312               .toString());
 313     }
 314     else
 315     {
 316       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 317     }
 318
 319     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 320             .toString(useProxy.isSelected()));
 321
 322     if (proxyServerTB.getText().trim().length() < 1)
 323     {
 324       Cache.applicationProperties.remove("PROXY_SERVER");
 325     }
 326     else
 327     {
 328       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 329               .getText());
 330     }
 331
 332     if (proxyPortTB.getText().trim().length() < 1)
 333     {
 334       Cache.applicationProperties.remove("PROXY_PORT");
 335     }
 336     else
 337     {
 338       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 339               .getText());
 340     }
 341
 342     if (useProxy.isSelected())
 343     {
 344       System.setProperty("http.proxyHost", proxyServerTB.getText());
 345       System.setProperty("http.proxyPort", proxyPortTB.getText());
 346     }
 347     else
 348     {
 349       System.setProperty("http.proxyHost", "");
 350       System.setProperty("http.proxyPort", "");
 351     }
 352
 353     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 354             .toString(blcjv.isSelected()));
 355     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 356             .toString(clustaljv.isSelected()));
 357     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 358             .toString(fastajv.isSelected()));
 359     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 360             .toString(msfjv.isSelected()));
 361     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 362             .toString(pfamjv.isSelected()));
 363     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 364             .toString(pileupjv.isSelected()));
 365     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 366             .toString(pirjv.isSelected()));
 367     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 368             .toString(modellerOutput.isSelected()));
 369     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 370
 371     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 372             .toString(autoCalculateConsCheck.isSelected()));
 373     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 374             .toString(padGaps.isSelected()));
 375
 376     dasSource.saveProperties(Cache.applicationProperties);
 377
 378     Cache.saveProperties();
 379     try
 380     {
 381       frame.setClosed(true);
 382     } catch (Exception ex)
 383     {
 384     }
 385   }
 386
 387   /**
 388    * DOCUMENT ME!
 389    */
 390   public void startupFileTextfield_mouseClicked()
 391   {
 392     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 393             .getProperty("LAST_DIRECTORY"), new String[]
 394     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 395             new String[]
 396             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 397             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 398     chooser.setFileView(new JalviewFileView());
 399     chooser.setDialogTitle("Select startup file");
 400
 401     int value = chooser.showOpenDialog(this);
 402
 403     if (value == JalviewFileChooser.APPROVE_OPTION)
 404     {
 405       jalview.bin.Cache.applicationProperties.setProperty(
 406               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 407       startupFileTextfield.setText(chooser.getSelectedFile()
 408               .getAbsolutePath());
 409     }
 410   }
 411
 412   /**
 413    * DOCUMENT ME!
 414    *
 415    * @param e
 416    *                DOCUMENT ME!
 417    */
 418   public void cancel_actionPerformed(ActionEvent e)
 419   {
 420     try
 421     {
 422       frame.setClosed(true);
 423     } catch (Exception ex)
 424     {
 425     }
 426   }
 427
 428   /**
 429    * DOCUMENT ME!
 430    *
 431    * @param e
 432    *                DOCUMENT ME!
 433    */
 434   public void annotations_actionPerformed(ActionEvent e)
 435   {
 436     conservation.setEnabled(annotations.isSelected());
 437     quality.setEnabled(annotations.isSelected());
 438     identity.setEnabled(annotations.isSelected());
 439   }
 440
 441   public void newLink_actionPerformed(ActionEvent e)
 442   {
 443
 444     GSequenceLink link = new GSequenceLink();
 445     boolean valid = false;
 446     while (!valid)
 447     {
 448       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 449               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 450               null) == JOptionPane.OK_OPTION)
 451       {
 452         if (link.checkValid())
 453         {
 454           nameLinks.addElement(link.getName());
 455           urlLinks.addElement(link.getURL());
 456           updateLinkData();
 457           valid = true;
 458         }
 459       }
 460       else
 461       {
 462         break;
 463       }
 464     }
 465   }
 466
 467   public void editLink_actionPerformed(ActionEvent e)
 468   {
 469     GSequenceLink link = new GSequenceLink();
 470
 471     int index = linkNameList.getSelectedIndex();
 472     if (index == -1)
 473     {
 474       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 475               "No link selected!", "No link selected",
 476               JOptionPane.WARNING_MESSAGE);
 477       return;
 478     }
 479
 480     link.setName(nameLinks.elementAt(index).toString());
 481     link.setURL(urlLinks.elementAt(index).toString());
 482
 483     boolean valid = false;
 484     while (!valid)
 485     {
 486
 487       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 488               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 489               null) == JOptionPane.OK_OPTION)
 490       {
 491         if (link.checkValid())
 492         {
 493           nameLinks.setElementAt(link.getName(), index);
 494           urlLinks.setElementAt(link.getURL(), index);
 495           updateLinkData();
 496           valid = true;
 497         }
 498       }
 499
 500       else
 501       {
 502         break;
 503       }
 504     }
 505   }
 506
 507   public void deleteLink_actionPerformed(ActionEvent e)
 508   {
 509     int index = linkNameList.getSelectedIndex();
 510     if (index == -1)
 511     {
 512       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 513               "No link selected!", "No link selected",
 514               JOptionPane.WARNING_MESSAGE);
 515       return;
 516     }
 517     nameLinks.removeElementAt(index);
 518     urlLinks.removeElementAt(index);
 519     updateLinkData();
 520   }
 521
 522   void updateLinkData()
 523   {
 524     linkNameList.setListData(nameLinks);
 525     linkURLList.setListData(urlLinks);
 526   }
 527
 528   public void defaultBrowser_mouseClicked(MouseEvent e)
 529   {
 530     JFileChooser chooser = new JFileChooser(".");
 531     chooser.setDialogTitle("Select default web browser");
 532
 533     int value = chooser.showOpenDialog(this);
 534
 535     if (value == JFileChooser.APPROVE_OPTION)
 536     {
 537       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 538     }
 539
 540   }
 541   /* (non-Javadoc)
 542    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 543    */
 544   protected void showunconserved_actionPerformed(ActionEvent e)
 545   {
 546     // TODO Auto-generated method stub
 547     super.showunconserved_actionPerformed(e);
 548   }
 549
 550   private void jbInit() throws Exception
 551   {
 552   }
 553 }