src/jalview/bin/JalviewLite.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.bin;\r
  20 \r
  21 import jalview.appletgui.AlignFrame;\r
  22 \r
  23 import jalview.datamodel.*;\r
  24 \r
  25 import jalview.io.*;\r
  26 \r
  27 import java.applet.*;\r
  28 \r
  29 import java.awt.*;\r
  30 import java.awt.event.*;\r
  31 import jalview.appletgui.FeatureSettings;\r
  32 \r
  33 \r
  34 /**\r
  35  * Jalview Applet. Runs in Java 1.18 runtime\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class JalviewLite extends Applet\r
  41 {\r
  42 \r
  43   ///////////////////////////////////////////\r
  44   //The following public methods maybe called\r
  45   //externally, eg via javascript in HTML page\r
  46 \r
  47   public String getSelectedSequences()\r
  48     {\r
  49       StringBuffer result = new StringBuffer("");\r
  50 \r
  51       if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
  52       {\r
  53         SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
  54             getSequencesInOrder(\r
  55                 initialAlignFrame.viewport.getAlignment());\r
  56 \r
  57         for (int i = 0; i < seqs.length; i++)\r
  58           result.append(seqs[i].getName() + "¬");\r
  59       }\r
  60 \r
  61       return result.toString();\r
  62     }\r
  63 \r
  64     public String getAlignment(String format)\r
  65     {\r
  66       return getAlignment(format, "true");\r
  67     }\r
  68 \r
  69     public String getAlignment(String format, String suffix)\r
  70     {\r
  71       try\r
  72       {\r
  73         boolean seqlimits = suffix.equalsIgnoreCase("true");\r
  74 \r
  75         String reply = new AppletFormatAdapter().formatSequences(format,\r
  76             currentAlignFrame.viewport.getAlignment(), seqlimits);\r
  77         return reply;\r
  78       }\r
  79       catch (Exception ex)\r
  80       {\r
  81         ex.printStackTrace();\r
  82         return "Error retrieving alignment in " + format + " format. ";\r
  83       }\r
  84     }\r
  85 \r
  86     public void loadAnnotation(String annotation)\r
  87     {\r
  88       if (new AnnotationFile().readAnnotationFile(\r
  89           currentAlignFrame.getAlignViewport().getAlignment(), annotation,\r
  90           AppletFormatAdapter.PASTE))\r
  91       {\r
  92         currentAlignFrame.alignPanel.fontChanged();\r
  93         currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
  94       }\r
  95       else\r
  96       {\r
  97         currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
  98       }\r
  99     }\r
 100 \r
 101     public String getFeatures(String format)\r
 102     {\r
 103       return currentAlignFrame.outputFeatures(false, format);\r
 104     }\r
 105 \r
 106     public String getAnnotation()\r
 107     {\r
 108       return currentAlignFrame.outputAnnotations(false);\r
 109     }\r
 110 \r
 111     public void loadAlignment(String text, String title)\r
 112     {\r
 113         Alignment al = null;\r
 114         String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
 115         try{\r
 116           al = new AppletFormatAdapter().readFile(text,\r
 117                                                   AppletFormatAdapter.PASTE,\r
 118                                                   format);\r
 119           if (al.getHeight() > 0)\r
 120             new AlignFrame(al, this, title, false);\r
 121         }catch(java.io.IOException ex)\r
 122         {\r
 123           ex.printStackTrace();\r
 124         }\r
 125    }\r
 126 \r
 127     ////////////////////////////////////////////////\r
 128     ////////////////////////////////////////////////\r
 129 \r
 130 \r
 131 \r
 132     static int lastFrameX = 200;\r
 133     static int lastFrameY = 200;\r
 134     boolean fileFound = true;\r
 135     String file = "No file";\r
 136     Button launcher = new Button("Start Jalview");\r
 137 \r
 138     //The currentAlignFrame is static, it will change\r
 139     //if and when the user selects a new window\r
 140     public static AlignFrame currentAlignFrame;\r
 141 \r
 142     //This is the first frame to be displayed, and does not change\r
 143     AlignFrame initialAlignFrame;\r
 144 \r
 145     boolean embedded = false;\r
 146 \r
 147 \r
 148     /**\r
 149      * init method for Jalview Applet\r
 150      */\r
 151     public void init()\r
 152     {\r
 153         int r = 255;\r
 154         int g = 255;\r
 155         int b = 255;\r
 156         String param = getParameter("RGB");\r
 157 \r
 158         if (param != null)\r
 159         {\r
 160             try\r
 161             {\r
 162                 r = Integer.parseInt(param.substring(0, 2), 16);\r
 163                 g = Integer.parseInt(param.substring(2, 4), 16);\r
 164                 b = Integer.parseInt(param.substring(4, 6), 16);\r
 165             }\r
 166             catch (Exception ex)\r
 167             {\r
 168                 r = 255;\r
 169                 g = 255;\r
 170                 b = 255;\r
 171             }\r
 172         }\r
 173 \r
 174         param = getParameter("label");\r
 175         if(param != null)\r
 176           launcher.setLabel(param);\r
 177 \r
 178         this.setBackground(new Color(r, g, b));\r
 179 \r
 180         file = getParameter("file");\r
 181 \r
 182         if(file==null)\r
 183         {\r
 184           //Maybe the sequences are added as parameters\r
 185           StringBuffer data = new StringBuffer("PASTE");\r
 186           int i=1;\r
 187           while( (file=getParameter("sequence"+i))!=null)\r
 188           {\r
 189             data.append(file.toString()+"\n");\r
 190             i++;\r
 191           }\r
 192           if(data.length()>5)\r
 193             file = data.toString();\r
 194         }\r
 195 \r
 196         final JalviewLite applet = this;\r
 197         if(getParameter("embedded")!=null\r
 198            && getParameter("embedded").equalsIgnoreCase("true"))\r
 199         {\r
 200           embedded = true;\r
 201           LoadingThread loader = new LoadingThread(file, applet);\r
 202           loader.start();\r
 203         }\r
 204         else if (file != null)\r
 205         {\r
 206             add(launcher);\r
 207 \r
 208             launcher.addActionListener(new java.awt.event.ActionListener()\r
 209                 {\r
 210                     public void actionPerformed(ActionEvent e)\r
 211                     {\r
 212                         LoadingThread loader = new LoadingThread(file,\r
 213                             applet);\r
 214                         loader.start();\r
 215                       }\r
 216                 });\r
 217         }\r
 218         else\r
 219         {\r
 220             file = "NO FILE";\r
 221             fileFound = false;\r
 222         }\r
 223     }\r
 224 \r
 225 \r
 226     public static void main(String [] args)\r
 227     {\r
 228       if(args.length!=1)\r
 229       {\r
 230         System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");\r
 231         System.exit(1);\r
 232       }\r
 233 \r
 234       String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);\r
 235 \r
 236      Alignment al = null;\r
 237      try{\r
 238        al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);\r
 239      }catch(java.io.IOException ex)\r
 240      {\r
 241        ex.printStackTrace();\r
 242      }\r
 243       if ( (al != null) && (al.getHeight() > 0))\r
 244       {\r
 245         AlignFrame af = new AlignFrame(al, null, args[0], false);\r
 246         af.statusBar.setText("Successfully loaded file " + args[0]);\r
 247       }\r
 248     }\r
 249 \r
 250 \r
 251     /**\r
 252      * Initialises and displays a new java.awt.Frame\r
 253      *\r
 254      * @param frame java.awt.Frame to be displayed\r
 255      * @param title title of new frame\r
 256      * @param width width if new frame\r
 257      * @param height height of new frame\r
 258      */\r
 259     public static void addFrame(final Frame frame, String title, int width,\r
 260         int height)\r
 261     {\r
 262         frame.setLocation(lastFrameX, lastFrameY);\r
 263         lastFrameX += 40;\r
 264         lastFrameY += 40;\r
 265         frame.setSize(width, height);\r
 266         frame.setTitle(title);\r
 267         frame.addWindowListener(new WindowAdapter()\r
 268             {\r
 269                 public void windowClosing(WindowEvent e)\r
 270                 {\r
 271                   if(frame instanceof AlignFrame)\r
 272                     ((AlignFrame)frame).closeMenuItem_actionPerformed();\r
 273                     if(currentAlignFrame == frame)\r
 274                     {\r
 275                       currentAlignFrame = null;\r
 276                     }\r
 277                     lastFrameX -=40;\r
 278                     lastFrameY -=40;\r
 279                     frame.setMenuBar(null);\r
 280                     frame.dispose();\r
 281                 }\r
 282                 public void windowActivated(WindowEvent e)\r
 283                 {\r
 284                   if(frame instanceof AlignFrame)\r
 285                     currentAlignFrame = (AlignFrame)frame;\r
 286                 }\r
 287 \r
 288             });\r
 289         frame.setVisible(true);\r
 290     }\r
 291 \r
 292 \r
 293 \r
 294     /**\r
 295      * This paints the background surrounding the "Launch Jalview button"\r
 296      * <br>\r
 297      * <br>If file given in parameter not found, displays error message\r
 298      *\r
 299      * @param g graphics context\r
 300      */\r
 301     public void paint(Graphics g)\r
 302     {\r
 303         if (!fileFound)\r
 304         {\r
 305             g.setColor(new Color(200, 200, 200));\r
 306             g.setColor(Color.cyan);\r
 307             g.fillRect(0, 0, getSize().width, getSize().height);\r
 308             g.setColor(Color.red);\r
 309             g.drawString("Jalview can't open file", 5, 15);\r
 310             g.drawString("\"" + file + "\"", 5, 30);\r
 311         }\r
 312         else if(embedded)\r
 313         {\r
 314           g.setColor(Color.black);\r
 315           g.setFont(new Font("Arial", Font.BOLD, 24));\r
 316           g.drawString("Jalview Applet", 50, this.getSize().height/2 -30);\r
 317           g.drawString("Loading Data...", 50, this.getSize().height/2);\r
 318         }\r
 319 \r
 320 \r
 321     }\r
 322 \r
 323     class LoadingThread extends Thread\r
 324     {\r
 325         String file;\r
 326         String protocol;\r
 327         String format;\r
 328         JalviewLite applet;\r
 329 \r
 330         public LoadingThread(String _file,\r
 331                              JalviewLite _applet)\r
 332         {\r
 333             file = _file;\r
 334             if(file.startsWith("PASTE"))\r
 335             {\r
 336               file = file.substring(5);\r
 337               protocol = AppletFormatAdapter.PASTE;\r
 338             }\r
 339             else if(inArchive(file))\r
 340               protocol = AppletFormatAdapter.CLASSLOADER;\r
 341             else\r
 342             {\r
 343               file = addProtocol(file);\r
 344               protocol = AppletFormatAdapter.URL;\r
 345             }\r
 346             format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
 347             applet = _applet;\r
 348         }\r
 349 \r
 350         public void run()\r
 351         {\r
 352             Alignment al = null;\r
 353             try{\r
 354               al = new AppletFormatAdapter().readFile(file, protocol,\r
 355                   format);\r
 356             }catch(java.io.IOException ex)\r
 357             {\r
 358               ex.printStackTrace();\r
 359             }\r
 360             if ((al != null) && (al.getHeight() > 0))\r
 361             {\r
 362               currentAlignFrame = new AlignFrame(al,\r
 363                                                  applet,\r
 364                                                  file,\r
 365                                                  embedded);\r
 366 \r
 367               if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
 368                 currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
 369 \r
 370               initialAlignFrame = currentAlignFrame;\r
 371 \r
 372               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
 373 \r
 374 \r
 375                 String treeFile = applet.getParameter("tree");\r
 376                 if(treeFile==null)\r
 377                   treeFile = applet.getParameter("treeFile");\r
 378 \r
 379                 if (treeFile != null)\r
 380                 {\r
 381                   try\r
 382                   {\r
 383                     if(inArchive(treeFile))\r
 384                       protocol = AppletFormatAdapter.CLASSLOADER;\r
 385                     else\r
 386                     {\r
 387                       protocol = AppletFormatAdapter.URL;\r
 388                       treeFile = addProtocol(treeFile);\r
 389                     }\r
 390 \r
 391                     jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol);\r
 392 \r
 393                     fin.parse();\r
 394 \r
 395                     if (fin.getTree() != null)\r
 396                     {\r
 397                       currentAlignFrame.loadTree(fin, treeFile);\r
 398                     }\r
 399                   }\r
 400                   catch (Exception ex)\r
 401                   {\r
 402                     ex.printStackTrace();\r
 403                   }\r
 404               }\r
 405 \r
 406               String param = getParameter("features");\r
 407               if (param != null)\r
 408               {\r
 409                 if( !inArchive(param) )\r
 410                   param = addProtocol( param );\r
 411 \r
 412                 currentAlignFrame.parseFeaturesFile(param, protocol);\r
 413               }\r
 414 \r
 415               param = getParameter("showFeatureSettings");\r
 416               if(param !=null && param.equalsIgnoreCase("true"))\r
 417               {\r
 418                 currentAlignFrame.viewport.showSequenceFeatures(true);\r
 419                 new FeatureSettings(currentAlignFrame.alignPanel);\r
 420               }\r
 421 \r
 422              param = getParameter("annotations");\r
 423              if (param != null)\r
 424              {\r
 425                if( !inArchive(param) )\r
 426                   param = addProtocol( param );\r
 427 \r
 428                new AnnotationFile().readAnnotationFile(\r
 429                    currentAlignFrame.viewport.getAlignment(),\r
 430                    param,\r
 431                    protocol);\r
 432 \r
 433                currentAlignFrame.alignPanel.fontChanged();\r
 434                currentAlignFrame.alignPanel.setScrollValues(0,0);\r
 435 \r
 436              }\r
 437 \r
 438              param = getParameter("jnetfile");\r
 439              if (param != null)\r
 440              {\r
 441                try\r
 442                {\r
 443                  if (inArchive(param))\r
 444                    protocol = AppletFormatAdapter.CLASSLOADER;\r
 445                  else\r
 446                  {\r
 447                    protocol = AppletFormatAdapter.URL;\r
 448                    param = addProtocol(param);\r
 449                  }\r
 450 \r
 451                  jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
 452                      param, protocol);\r
 453                  new JnetAnnotationMaker().add_annotation(predictions,\r
 454                      currentAlignFrame.viewport.getAlignment(),\r
 455                      0,false); // do not add sequence profile from concise output\r
 456                  currentAlignFrame.alignPanel.fontChanged();\r
 457                  currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
 458                } catch (Exception ex) {\r
 459                  ex.printStackTrace();\r
 460                }\r
 461              }\r
 462 \r
 463 \r
 464                 param = getParameter("PDBFILE");\r
 465                 if(param!=null)\r
 466                 {\r
 467                   if( inArchive(param) )\r
 468                     protocol = AppletFormatAdapter.CLASSLOADER;\r
 469                   else\r
 470                   {\r
 471                     protocol = AppletFormatAdapter.URL;\r
 472                     param = addProtocol(param);\r
 473                   }\r
 474 \r
 475                   String sequence = applet.getParameter("PDBSEQ");\r
 476 \r
 477                   if(sequence!=null)\r
 478                   {\r
 479                     new MCview.AppletPDBViewer(param, protocol,\r
 480                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
 481                                                currentAlignFrame.getSeqcanvas());\r
 482                   }\r
 483 \r
 484                 }\r
 485 \r
 486                 int gIndex = 1;\r
 487                 param = getParameter("SEQUENCE_GROUP"+gIndex);\r
 488                 if(param!=null)\r
 489                 do{\r
 490                   new AnnotationFile().readAnnotationFile(\r
 491                    currentAlignFrame.viewport.getAlignment(),\r
 492                    "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\t"+param,\r
 493                    AppletFormatAdapter.PASTE);\r
 494                   gIndex++;\r
 495                   param = applet.getParameter("SEQUENCE_GROUP"+gIndex);\r
 496                   currentAlignFrame.alignPanel.repaint();\r
 497                 }while(param!=null);\r
 498 \r
 499               gIndex = 1;\r
 500               param = getParameter("PROPERTIES" + gIndex);\r
 501               if (param != null)\r
 502                 do\r
 503                 {\r
 504                   new AnnotationFile().readAnnotationFile(\r
 505                       currentAlignFrame.viewport.getAlignment(),\r
 506                       "JALVIEW_ANNOTATION\nPROPERTIES\t" + param,\r
 507                       AppletFormatAdapter.PASTE);\r
 508                   gIndex++;\r
 509                   param = applet.getParameter("PROPERTIES" + gIndex);\r
 510                   currentAlignFrame.alignPanel.repaint();\r
 511                 }\r
 512                 while (param != null);\r
 513             }\r
 514             else\r
 515             {\r
 516                 fileFound = false;\r
 517                 remove(launcher);\r
 518                 repaint();\r
 519             }\r
 520         }\r
 521 \r
 522         /**\r
 523          * Discovers whether the given file is in the Applet Archive\r
 524          * @param file String\r
 525          * @return boolean\r
 526          */\r
 527         boolean inArchive(String file)\r
 528         {\r
 529           //This might throw a security exception in certain browsers\r
 530           //Netscape Communicator for instance.\r
 531           try{\r
 532             return (getClass().getResourceAsStream("/" + file) != null);\r
 533           }catch(Exception ex)\r
 534           {\r
 535             System.out.println("Exception checking resources: "+file+" "+ex);\r
 536             return false;\r
 537           }\r
 538         }\r
 539 \r
 540         String addProtocol(String file)\r
 541         {\r
 542           if (file.indexOf("://") == -1)\r
 543              file = getCodeBase() + file;\r
 544 \r
 545           return file;\r
 546         }\r
 547 \r
 548     }\r
 549 }\r