src/jalview/bin/JalviewLite.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.bin;
  20
  21 import jalview.appletgui.AlignFrame;
  22
  23 import jalview.datamodel.*;
  24
  25 import jalview.io.*;
  26
  27 import java.applet.*;
  28
  29 import java.awt.*;
  30 import java.awt.event.*;
  31
  32
  33 /**
  34  * Jalview Applet. Runs in Java 1.18 runtime
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class JalviewLite extends Applet
  40 {
  41     static int lastFrameX = 200;
  42     static int lastFrameY = 200;
  43     boolean fileFound = true;
  44     String file = "No file";
  45     Button launcher = new Button("Start Jalview");
  46
  47     //The currentAlignFrame is static, it will change
  48     //if and when the user selects a new window
  49     static AlignFrame currentAlignFrame;
  50
  51     //This is the first frame to be displayed, and does not change
  52     AlignFrame initialAlignFrame;
  53
  54     boolean embedded = false;
  55
  56
  57     /**
  58      * init method for Jalview Applet
  59      */
  60     public void init()
  61     {
  62         int r = 255;
  63         int g = 255;
  64         int b = 255;
  65         String param = getParameter("RGB");
  66
  67         if (param != null)
  68         {
  69             try
  70             {
  71                 r = Integer.parseInt(param.substring(0, 2), 16);
  72                 g = Integer.parseInt(param.substring(2, 4), 16);
  73                 b = Integer.parseInt(param.substring(4, 6), 16);
  74             }
  75             catch (Exception ex)
  76             {
  77                 r = 255;
  78                 g = 255;
  79                 b = 255;
  80             }
  81         }
  82
  83         param = getParameter("label");
  84         if(param != null)
  85           launcher.setLabel(param);
  86
  87         this.setBackground(new Color(r, g, b));
  88
  89         file = getParameter("file");
  90
  91         if(file==null)
  92         {
  93           //Maybe the sequences are added as parameters
  94           StringBuffer data = new StringBuffer("PASTE");
  95           int i=1;
  96           while( (file=getParameter("sequence"+i))!=null)
  97           {
  98             data.append(file.toString()+"\n");
  99             i++;
 100           }
 101           if(data.length()>5)
 102             file = data.toString();
 103         }
 104
 105         final JalviewLite applet = this;
 106         if(getParameter("embedded")!=null
 107            && getParameter("embedded").equalsIgnoreCase("true"))
 108         {
 109           embedded = true;
 110           LoadingThread loader = new LoadingThread(file, applet);
 111           loader.start();
 112         }
 113         else if (file != null)
 114         {
 115             add(launcher);
 116
 117             launcher.addActionListener(new java.awt.event.ActionListener()
 118                 {
 119                     public void actionPerformed(ActionEvent e)
 120                     {
 121                         LoadingThread loader = new LoadingThread(file,
 122                             applet);
 123                         loader.start();
 124                       }
 125                 });
 126         }
 127         else
 128         {
 129             file = "NO FILE";
 130             fileFound = false;
 131         }
 132     }
 133
 134
 135     public static void main(String [] args)
 136     {
 137       if(args.length!=1)
 138       {
 139         System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
 140         System.exit(1);
 141       }
 142
 143       String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);
 144
 145       SequenceI[] sequences = null;
 146      try{
 147        sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
 148      }catch(java.io.IOException ex)
 149      {
 150        ex.printStackTrace();
 151      }
 152       if ( (sequences != null) && (sequences.length > 0))
 153       {
 154         AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
 155         af.statusBar.setText("Successfully loaded file " + args[0]);
 156       }
 157     }
 158
 159
 160     /**
 161      * Initialises and displays a new java.awt.Frame
 162      *
 163      * @param frame java.awt.Frame to be displayed
 164      * @param title title of new frame
 165      * @param width width if new frame
 166      * @param height height of new frame
 167      */
 168     public static void addFrame(final Frame frame, String title, int width,
 169         int height)
 170     {
 171         frame.setLocation(lastFrameX, lastFrameY);
 172         lastFrameX += 40;
 173         lastFrameY += 40;
 174         frame.setSize(width, height);
 175         frame.setTitle(title);
 176         frame.addWindowListener(new WindowAdapter()
 177             {
 178                 public void windowClosing(WindowEvent e)
 179                 {
 180                     if(currentAlignFrame == frame)
 181                     {
 182                       currentAlignFrame = null;
 183                     }
 184                     lastFrameX -=40;
 185                     lastFrameY -=40;
 186                     frame.setMenuBar(null);
 187                     frame.dispose();
 188                 }
 189                 public void windowActivated(WindowEvent e)
 190                 {
 191                   if(frame instanceof AlignFrame)
 192                     currentAlignFrame = (AlignFrame)frame;
 193                 }
 194
 195             });
 196         frame.setVisible(true);
 197     }
 198
 199     public String getSelectedSequences()
 200     {
 201       StringBuffer result = new StringBuffer("");
 202
 203       if(initialAlignFrame.viewport.getSelectionGroup()!=null)
 204       {
 205         SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
 206             getSequencesInOrder(
 207                 initialAlignFrame.viewport.getAlignment());
 208
 209         for (int i = 0; i < seqs.length; i++)
 210           result.append(seqs[i].getName() + "¬");
 211       }
 212
 213       return result.toString();
 214     }
 215
 216     public String getAlignment(String format)
 217     {
 218       return getAlignment(format, "true");
 219     }
 220
 221     public String getAlignment(String format, String suffix)
 222     {
 223       try
 224       {
 225         boolean seqlimits = suffix.equalsIgnoreCase("true");
 226
 227         String reply = new AppletFormatAdapter().formatSequences(format,
 228             currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
 229         return reply;
 230       }
 231       catch (Exception ex)
 232       {
 233         ex.printStackTrace();
 234         return "Error retrieving alignment in " + format + " format. ";
 235       }
 236     }
 237
 238     /**
 239      * This paints the background surrounding the "Launch Jalview button"
 240      * <br>
 241      * <br>If file given in parameter not found, displays error message
 242      *
 243      * @param g graphics context
 244      */
 245     public void paint(Graphics g)
 246     {
 247         if (!fileFound)
 248         {
 249             g.setColor(new Color(200, 200, 200));
 250             g.setColor(Color.cyan);
 251             g.fillRect(0, 0, getSize().width, getSize().height);
 252             g.setColor(Color.red);
 253             g.drawString("Jalview can't open file", 5, 15);
 254             g.drawString("\"" + file + "\"", 5, 30);
 255         }
 256         else if(embedded)
 257         {
 258           g.setColor(Color.black);
 259           g.setFont(new Font("Arial", Font.BOLD, 24));
 260           g.drawString("Jalview Applet", 50, this.size().height/2 -30);
 261           g.drawString("Loading Data...", 50, this.size().height/2);
 262         }
 263
 264
 265     }
 266
 267     class LoadingThread extends Thread
 268     {
 269         String file;
 270         String protocol;
 271         String format;
 272         JalviewLite applet;
 273
 274         public LoadingThread(String _file,
 275                              JalviewLite _applet)
 276         {
 277             file = _file;
 278             if(file.startsWith("PASTE"))
 279             {
 280               file = file.substring(5);
 281               protocol = AppletFormatAdapter.PASTE;
 282             }
 283             else if(inArchive(file))
 284               protocol = AppletFormatAdapter.CLASSLOADER;
 285             else
 286             {
 287               file = addProtocol(file);
 288               protocol = AppletFormatAdapter.URL;
 289             }
 290             format = new jalview.io.IdentifyFile().Identify(file, protocol);
 291             applet = _applet;
 292         }
 293
 294         public void run()
 295         {
 296             SequenceI[] sequences = null;
 297             try{
 298               sequences = new AppletFormatAdapter().readFile(file, protocol,
 299                   format);
 300             }catch(java.io.IOException ex)
 301             {
 302               ex.printStackTrace();
 303             }
 304             if ((sequences != null) && (sequences.length > 0))
 305             {
 306               currentAlignFrame = new AlignFrame(new Alignment(sequences),
 307                                                  applet,
 308                                                  file,
 309                                                  embedded);
 310
 311               if(protocol==jalview.io.AppletFormatAdapter.PASTE)
 312                 currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 313
 314               initialAlignFrame = currentAlignFrame;
 315
 316               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 317
 318
 319                 String treeFile = applet.getParameter("tree");
 320                 if(treeFile==null)
 321                   treeFile = applet.getParameter("treeFile");
 322
 323                 if (treeFile != null)
 324                 {
 325                   try
 326                   {
 327                     if(inArchive(treeFile))
 328                       protocol = AppletFormatAdapter.CLASSLOADER;
 329                     else
 330                     {
 331                       protocol = AppletFormatAdapter.URL;
 332                       treeFile = addProtocol(treeFile);
 333                     }
 334
 335                     jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol);
 336
 337                     fin.parse();
 338
 339                     if (fin.getTree() != null)
 340                     {
 341                       currentAlignFrame.loadTree(fin, treeFile);
 342                     }
 343                   }
 344                   catch (Exception ex)
 345                   {
 346                     ex.printStackTrace();
 347                   }
 348               }
 349
 350               String param = getParameter("features");
 351               if (param != null)
 352               {
 353                 if( !inArchive(param) )
 354                   param = addProtocol( param );
 355
 356                 currentAlignFrame.parseFeaturesFile(param, protocol);
 357               }
 358
 359               param = getParameter("showFeatureSettings");
 360               if(param !=null && param.equalsIgnoreCase("true"))
 361               {
 362                 currentAlignFrame.viewport.showSequenceFeatures(true);
 363                 currentAlignFrame.featureSettings_actionPerformed();
 364               }
 365
 366              param = getParameter("annotations");
 367              if (param != null)
 368              {
 369                if( !inArchive(param) )
 370                   param = addProtocol( param );
 371
 372                new AnnotationFile().readAnnotationFile(
 373                    currentAlignFrame.viewport.getAlignment(),
 374                    param);
 375
 376                currentAlignFrame.alignPanel.fontChanged();
 377                currentAlignFrame.alignPanel.setScrollValues(0,0);
 378
 379              }
 380
 381              param = getParameter("jnetfile");
 382              if (param != null)
 383              {
 384                try
 385                {
 386                  if (inArchive(param))
 387                    protocol = AppletFormatAdapter.CLASSLOADER;
 388                  else
 389                  {
 390                    protocol = AppletFormatAdapter.URL;
 391                    param = addProtocol(param);
 392                  }
 393
 394                  jalview.io.JPredFile predictions = new jalview.io.JPredFile(
 395                      param, protocol);
 396                  new JnetAnnotationMaker().add_annotation(predictions,
 397                      currentAlignFrame.viewport.getAlignment(),
 398                      0,false); // do not add sequence profile from concise output
 399                  currentAlignFrame.alignPanel.fontChanged();
 400                  currentAlignFrame.alignPanel.setScrollValues(0, 0);
 401                } catch (Exception ex) {
 402                  ex.printStackTrace();
 403                }
 404              }
 405
 406
 407                 String pdbfile = applet.getParameter("PDBFILE");
 408                 if(pdbfile!=null)
 409                 {
 410                   if( inArchive(pdbfile) )
 411                     protocol = AppletFormatAdapter.CLASSLOADER;
 412                   else
 413                   {
 414                     protocol = AppletFormatAdapter.URL;
 415                     pdbfile = addProtocol(pdbfile);
 416                   }
 417
 418                   String sequence = applet.getParameter("PDBSEQ");
 419
 420                   if(sequence!=null)
 421                   {
 422                     new MCview.AppletPDBViewer(pdbfile, protocol,
 423                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
 424                                                currentAlignFrame.getSeqcanvas());
 425                   }
 426
 427                 }
 428             }
 429             else
 430             {
 431                 fileFound = false;
 432                 remove(launcher);
 433                 repaint();
 434             }
 435         }
 436
 437         /**
 438          * Discovers whether the given file is in the Applet Archive
 439          * @param file String
 440          * @return boolean
 441          */
 442         boolean inArchive(String file)
 443         {
 444           //This might throw a security exception in certain browsers
 445           //Netscape Communicator for instance.
 446           try{
 447             return (getClass().getResourceAsStream("/" + file) != null);
 448           }catch(Exception ex)
 449           {
 450             System.out.println("Exception checking resources: "+file+" "+ex);
 451             return false;
 452           }
 453         }
 454
 455         String addProtocol(String file)
 456         {
 457           if (file.indexOf("://") == -1)
 458              file = getCodeBase() + file;
 459
 460           return file;
 461         }
 462
 463     }
 464 }