src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 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 jalview.io.*;
  22
  23 import jalview.jbgui.*;
  24
  25 import jalview.schemes.*;
  26
  27 import java.awt.*;
  28 import java.awt.event.*;
  29
  30 import javax.swing.*;
  31
  32 import java.util.*;
  33
  34 import jalview.bin.Cache;
  35
  36
  37 /**
  38  * DOCUMENT ME!
  39  *
  40  * @author $author$
  41  * @version $Revision$
  42  */
  43 public class Preferences extends GPreferences
  44 {
  45     /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
  46     public static Vector sequenceURLLinks;
  47     static
  48     {
  49       String string = Cache.getDefault("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           sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
  59         }
  60       }
  61       catch (Exception ex)
  62       {
  63         System.out.println(ex + "\nError parsing sequence links");
  64       }
  65     }
  66     Vector nameLinks, urlLinks;
  67
  68     JInternalFrame frame;
  69
  70     DasSourceBrowser dasSource;
  71
  72
  73     /**
  74      * Creates a new Preferences object.
  75      */
  76     public Preferences()
  77     {
  78
  79         frame = new JInternalFrame();
  80         frame.setContentPane(this);
  81         dasSource = new DasSourceBrowser();
  82         dasPanel.add(dasSource, BorderLayout.CENTER);
  83
  84         int width = 500, height = 420;
  85         if(System.getProperty("os.name").startsWith("Mac"))
  86         {
  87           width = 570;
  88           height = 460;
  89         }
  90
  91         Desktop.addInternalFrame(frame, "Preferences", width, height);
  92         frame.setMinimumSize(new Dimension(width, height));
  93
  94         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
  95         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
  96         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
  97
  98         conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
  99         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 100         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 101
 102         conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 103         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 104         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 105
 106         for (int i = 0; i < 13; i++)
 107         {
 108             colour.addItem(ColourSchemeProperty.getColourName(i));
 109         }
 110
 111         String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 112
 113         colour.setSelectedItem(string);
 114
 115         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
 116                                                      .getAvailableFontFamilyNames();
 117
 118         for (int i = 0; i < fonts.length; i++)
 119         {
 120             fontNameCB.addItem(fonts[i]);
 121         }
 122
 123         for (int i = 1; i < 31; i++)
 124         {
 125             fontSizeCB.addItem(i + "");
 126         }
 127
 128         fontStyleCB.addItem("plain");
 129         fontStyleCB.addItem("bold");
 130         fontStyleCB.addItem("italic");
 131
 132         fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 133         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 134         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
 135
 136         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 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.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", "Prompt each time"));
 158
 159         blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
 160         clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
 161         fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
 162         msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
 163         pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
 164         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
 165         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 166
 167         modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
 168
 169         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 170         padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
 171
 172   /****************************************************
 173    * Set up Connections
 174    */
 175         nameLinks = new Vector();
 176         urlLinks = new Vector();
 177         for(int i=0; i<sequenceURLLinks.size(); i++)
 178         {
 179           String link = sequenceURLLinks.elementAt(i).toString();
 180           nameLinks.addElement(link.substring(0, link.indexOf("|")) );
 181           urlLinks.addElement(link.substring(link.indexOf("|")+1));
 182         }
 183
 184         updateLinkData();
 185
 186         useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
 187         proxyServerTB.setEnabled(useProxy.isSelected());
 188         proxyPortTB.setEnabled(useProxy.isSelected());
 189         proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
 190         proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 191
 192         defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
 193     try
 194     {
 195       jbInit();
 196     }
 197     catch (Exception ex)
 198     {
 199       ex.printStackTrace();
 200     }
 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", Boolean.toString(seqLimit.isSelected()));
 214       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
 215
 216       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
 217       Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
 218       Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
 219       Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
 220
 221       Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
 222       Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
 223
 224       Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
 225       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
 226       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
 227
 228       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
 229
 230       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
 231
 232       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
 233       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 234
 235       Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
 236
 237       if(epsRendering.getSelectedItem().equals("Prompt each time"))
 238         Cache.applicationProperties.remove("EPS_RENDERING");
 239       else
 240         Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
 241
 242       if(defaultBrowser.getText().trim().length()<1)
 243         Cache.applicationProperties.remove("DEFAULT_BROWSER");
 244       else
 245         Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 246                                                 defaultBrowser.getText());
 247
 248         jalview.util.BrowserLauncher.resetBrowser();
 249
 250         if(nameLinks.size()>0)
 251         {
 252           StringBuffer links = new StringBuffer();
 253           sequenceURLLinks = new Vector();
 254           for (int i = 0; i < nameLinks.size(); i++)
 255           {
 256             sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
 257             links.append(sequenceURLLinks.elementAt(i).toString());
 258             links.append("|");
 259           }
 260           // remove last "|"
 261           links.setLength( links.length()-1 );
 262           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
 263         }
 264         else
 265           Cache.applicationProperties.remove("SEQUENCE_LINKS");
 266
 267
 268         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
 269
 270         if (proxyServerTB.getText().trim().length() < 1)
 271           Cache.applicationProperties.remove("PROXY_SERVER");
 272         else
 273           Cache.applicationProperties.setProperty("PROXY_SERVER",
 274                                                   proxyServerTB.getText());
 275
 276         if (proxyPortTB.getText().trim().length() < 1)
 277           Cache.applicationProperties.remove("PROXY_PORT");
 278         else
 279           Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
 280
 281         if(useProxy.isSelected())
 282         {
 283           System.setProperty("http.proxyHost", proxyServerTB.getText());
 284           System.setProperty("http.proxyPort", proxyPortTB.getText());
 285         }
 286         else
 287         {
 288           System.setProperty("http.proxyHost","");
 289           System.setProperty("http.proxyPort","");
 290         }
 291
 292
 293         Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
 294         Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
 295         Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
 296         Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
 297         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
 298         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
 299         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
 300         Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
 301         jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 302
 303         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 304                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));
 305         Cache.applicationProperties.setProperty("PAD_GAPS",
 306                                                 Boolean.toString(padGaps.isSelected()));
 307
 308         dasSource.saveProperties(Cache.applicationProperties);
 309
 310         Cache.saveProperties();
 311         try
 312         {
 313             frame.setClosed(true);
 314         }
 315         catch (Exception ex)
 316         {
 317         }
 318     }
 319
 320     /**
 321      * DOCUMENT ME!
 322      */
 323     public void startupFileTextfield_mouseClicked()
 324     {
 325         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 326                     "LAST_DIRECTORY"),
 327                 new String[]
 328                 {
 329                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 330                     "jar"
 331                 },
 332                 new String[]
 333                 {
 334                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
 335                 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 336         chooser.setFileView(new JalviewFileView());
 337         chooser.setDialogTitle("Select startup file");
 338
 339         int value = chooser.showOpenDialog(this);
 340
 341         if (value == JalviewFileChooser.APPROVE_OPTION)
 342         {
 343             jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 344                 chooser.getSelectedFormat());
 345             startupFileTextfield.setText(chooser.getSelectedFile()
 346                                                 .getAbsolutePath());
 347         }
 348     }
 349
 350     /**
 351      * DOCUMENT ME!
 352      *
 353      * @param e DOCUMENT ME!
 354      */
 355     public void cancel_actionPerformed(ActionEvent e)
 356     {
 357         try
 358         {
 359             frame.setClosed(true);
 360         }
 361         catch (Exception ex)
 362         {
 363         }
 364     }
 365
 366     /**
 367      * DOCUMENT ME!
 368      *
 369      * @param e DOCUMENT ME!
 370      */
 371     public void annotations_actionPerformed(ActionEvent e)
 372     {
 373         conservation.setEnabled(annotations.isSelected());
 374         quality.setEnabled(annotations.isSelected());
 375         identity.setEnabled(annotations.isSelected());
 376     }
 377
 378
 379     public void newLink_actionPerformed(ActionEvent e) {
 380
 381       GSequenceLink link = new GSequenceLink();
 382       boolean valid = false;
 383       while( !valid )
 384       {
 385         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 386                                                   "New sequence URL link",
 387                                                   JOptionPane.OK_CANCEL_OPTION
 388                                                   ,-1, null)
 389             == JOptionPane.OK_OPTION)
 390         {
 391           if (link.checkValid())
 392           {
 393             nameLinks.addElement(link.getName());
 394             urlLinks.addElement(link.getURL());
 395             updateLinkData();
 396             valid = true;
 397           }
 398         }
 399         else
 400           break;
 401       }
 402     }
 403
 404     public void editLink_actionPerformed(ActionEvent e) {
 405       GSequenceLink link = new GSequenceLink();
 406
 407       int index = linkNameList.getSelectedIndex();
 408       if(index==-1)
 409       {
 410         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
 411             ,"No link selected", JOptionPane.WARNING_MESSAGE);
 412         return;
 413       }
 414
 415       link.setName( nameLinks.elementAt(index).toString() );
 416       link.setURL( urlLinks.elementAt(index).toString() );
 417
 418       boolean valid = false;
 419       while (!valid)
 420       {
 421
 422         if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 423                                                   "New sequence URL link",
 424                                                   JOptionPane.OK_CANCEL_OPTION
 425                                                   ,-1, null)
 426             == JOptionPane.OK_OPTION)
 427         {
 428           if (link.checkValid())
 429           {
 430             nameLinks.setElementAt(link.getName(), index);
 431             urlLinks.setElementAt(link.getURL(), index);
 432             updateLinkData();
 433             valid = true;
 434           }
 435         }
 436
 437         else
 438           break;
 439       }
 440     }
 441
 442     public void deleteLink_actionPerformed(ActionEvent e) {
 443       int index = linkNameList.getSelectedIndex();
 444       if(index==-1)
 445       {
 446         JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
 447             ,"No link selected", JOptionPane.WARNING_MESSAGE);
 448         return;
 449       }
 450       nameLinks.removeElementAt(index);
 451       urlLinks.removeElementAt(index);
 452       updateLinkData();
 453     }
 454
 455     void updateLinkData()
 456     {
 457       linkNameList.setListData(nameLinks);
 458       linkURLList.setListData(urlLinks);
 459     }
 460
 461     public void defaultBrowser_mouseClicked(MouseEvent e)
 462     {
 463       JFileChooser chooser = new JFileChooser(".");
 464       chooser.setDialogTitle("Select default web browser");
 465
 466       int value = chooser.showOpenDialog(this);
 467
 468       if (value == JFileChooser.APPROVE_OPTION)
 469       {
 470         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 471       }
 472
 473   }
 474
 475   private void jbInit()
 476       throws Exception
 477   {
 478   }
 479 }