src/jalview/bin/JalviewLite.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 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.TreePanel;\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     static int lastFrameX = 200;\r
  43     static int lastFrameY = 200;\r
  44     boolean fileFound = true;\r
  45     String file = "No file";\r
  46     Button launcher = new Button("Start Jalview");\r
  47 \r
  48     static AlignFrame currentAlignFrame;\r
  49     boolean embedded = false;\r
  50 \r
  51 \r
  52     /**\r
  53      * init method for Jalview Applet\r
  54      */\r
  55     public void init()\r
  56     {\r
  57         int r = 255;\r
  58         int g = 255;\r
  59         int b = 255;\r
  60         String param = getParameter("RGB");\r
  61 \r
  62         if (param != null)\r
  63         {\r
  64             try\r
  65             {\r
  66                 r = Integer.parseInt(param.substring(0, 2), 16);\r
  67                 g = Integer.parseInt(param.substring(2, 4), 16);\r
  68                 b = Integer.parseInt(param.substring(4, 6), 16);\r
  69             }\r
  70             catch (Exception ex)\r
  71             {\r
  72                 r = 255;\r
  73                 g = 255;\r
  74                 b = 255;\r
  75             }\r
  76         }\r
  77 \r
  78         param = getParameter("label");\r
  79         if(param != null)\r
  80           launcher.setLabel(param);\r
  81 \r
  82         this.setBackground(new Color(r, g, b));\r
  83 \r
  84         file = getParameter("file");\r
  85         if(file.indexOf("://")==-1)\r
  86                file = getCodeBase() + file;\r
  87 \r
  88         final JalviewLite applet = this;\r
  89         if(getParameter("embedded")!=null\r
  90            && getParameter("embedded").equalsIgnoreCase("true"))\r
  91         {\r
  92           embedded = true;\r
  93           LoadingThread loader = new LoadingThread(file,\r
  94                             "URL",\r
  95                             applet);\r
  96           loader.start();\r
  97         }\r
  98         else if (file != null)\r
  99         {\r
 100             add(launcher);\r
 101 \r
 102             launcher.addActionListener(new java.awt.event.ActionListener()\r
 103                 {\r
 104                     public void actionPerformed(ActionEvent e)\r
 105                     {\r
 106                         LoadingThread loader = new LoadingThread(file,\r
 107                             "URL",\r
 108                             applet);\r
 109                         loader.start();\r
 110                       }\r
 111                 });\r
 112         }\r
 113         else\r
 114         {\r
 115             file = "NO FILE";\r
 116             fileFound = false;\r
 117         }\r
 118     }\r
 119 \r
 120 \r
 121     public static void main(String [] args)\r
 122     {\r
 123       if(args.length!=1)\r
 124       {\r
 125         System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");\r
 126         System.exit(1);\r
 127       }\r
 128 \r
 129       String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
 130       SequenceI[] sequences = null;\r
 131      try{\r
 132        sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
 133      }catch(java.io.IOException ex)\r
 134      {\r
 135        ex.printStackTrace();\r
 136      }\r
 137       if ( (sequences != null) && (sequences.length > 0))\r
 138       {\r
 139         AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
 140         af.statusBar.setText("Successfully loaded file " + args[0]);\r
 141       }\r
 142     }\r
 143 \r
 144 \r
 145     /**\r
 146      * Initialises and displays a new java.awt.Frame\r
 147      *\r
 148      * @param frame java.awt.Frame to be displayed\r
 149      * @param title title of new frame\r
 150      * @param width width if new frame\r
 151      * @param height height of new frame\r
 152      */\r
 153     public static void addFrame(final Frame frame, String title, int width,\r
 154         int height)\r
 155     {\r
 156         frame.setLocation(lastFrameX, lastFrameY);\r
 157         lastFrameX += 40;\r
 158         lastFrameY += 40;\r
 159         frame.setSize(width, height);\r
 160         frame.setTitle(title);\r
 161         frame.addWindowListener(new WindowAdapter()\r
 162             {\r
 163                 public void windowClosing(WindowEvent e)\r
 164                 {\r
 165                     if(currentAlignFrame == frame)\r
 166                     {\r
 167                       currentAlignFrame = null;\r
 168                     }\r
 169                     lastFrameX -=40;\r
 170                     lastFrameY-=40;\r
 171                     frame.setMenuBar(null);\r
 172                     frame.dispose();\r
 173                 }\r
 174                 public void windowActivated(WindowEvent e)\r
 175                 {\r
 176                   if(frame instanceof AlignFrame)\r
 177                     currentAlignFrame = (AlignFrame)frame;\r
 178                 }\r
 179 \r
 180             });\r
 181         frame.setVisible(true);\r
 182     }\r
 183 \r
 184     public String getAlignment(String format)\r
 185     {\r
 186       return getAlignment(format, "true");\r
 187     }\r
 188 \r
 189     public String getAlignment(String format, String suffix)\r
 190     {\r
 191       try\r
 192       {\r
 193         boolean seqlimits = suffix.equalsIgnoreCase("true");\r
 194 \r
 195         String reply = new AppletFormatAdapter().formatSequences(format,\r
 196             currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
 197         return reply;\r
 198       }\r
 199       catch (Exception ex)\r
 200       {\r
 201         ex.printStackTrace();\r
 202         return "Error retrieving alignment in " + format + " format. ";\r
 203       }\r
 204     }\r
 205 \r
 206     /**\r
 207      * This paints the background surrounding the "Launch Jalview button"\r
 208      * <br>\r
 209      * <br>If file given in parameter not found, displays error message\r
 210      *\r
 211      * @param g graphics context\r
 212      */\r
 213     public void paint(Graphics g)\r
 214     {\r
 215         if (!fileFound)\r
 216         {\r
 217             g.setColor(new Color(200, 200, 200));\r
 218             g.setColor(Color.cyan);\r
 219             g.fillRect(0, 0, getSize().width, getSize().height);\r
 220             g.setColor(Color.red);\r
 221             g.drawString("Jalview can't open file", 5, 15);\r
 222             g.drawString("\"" + file + "\"", 5, 30);\r
 223         }\r
 224         else if(embedded)\r
 225         {\r
 226           g.setColor(Color.black);\r
 227           g.setFont(new Font("Arial", Font.BOLD, 24));\r
 228           g.drawString("Jalview Applet", 50, this.size().height/2 -30);\r
 229           g.drawString("Loading Data...", 50, this.size().height/2);\r
 230         }\r
 231 \r
 232 \r
 233     }\r
 234 \r
 235     class LoadingThread extends Thread\r
 236     {\r
 237         String file;\r
 238         String protocol;\r
 239         String format;\r
 240         JalviewLite applet;\r
 241 \r
 242         public LoadingThread(String file,\r
 243                              String protocol,\r
 244                              JalviewLite applet)\r
 245         {\r
 246             this.file = file;\r
 247             this.protocol = protocol;\r
 248             format = jalview.io.IdentifyFile.Identify(file, "URL");\r
 249             this.applet = applet;\r
 250         }\r
 251 \r
 252         public void run()\r
 253         {\r
 254             SequenceI[] sequences = null;\r
 255             try{\r
 256               sequences = new AppletFormatAdapter().readFile(file, protocol,\r
 257                   format);\r
 258             }catch(java.io.IOException ex)\r
 259             {\r
 260               ex.printStackTrace();\r
 261             }\r
 262             if ((sequences != null) && (sequences.length > 0))\r
 263             {\r
 264               currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
 265                                                  applet, file);\r
 266               if (embedded)\r
 267                 currentAlignFrame.setEmbedded();\r
 268 \r
 269               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
 270 \r
 271 \r
 272                 String treeFile = applet.getParameter("treeFile");\r
 273                 if (treeFile != null)\r
 274                 {\r
 275                   if (treeFile.indexOf("://") == -1)\r
 276                     treeFile = getCodeBase() + treeFile;\r
 277 \r
 278                   try\r
 279                   {\r
 280                     jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");\r
 281                     fin.parse();\r
 282 \r
 283                     if (fin.getTree() != null)\r
 284                     {\r
 285                       TreePanel tp = null;\r
 286                       tp = new TreePanel(currentAlignFrame.viewport,\r
 287                                          currentAlignFrame.viewport.getAlignment().getSequences(),\r
 288                                          fin, "FromFile", treeFile);\r
 289                       addFrame(tp, treeFile, 600, 500);\r
 290                       currentAlignFrame.addTreeMenuItem(tp, treeFile);\r
 291                     }\r
 292                   }\r
 293                   catch (Exception ex)\r
 294                   {\r
 295                     ex.printStackTrace();\r
 296                   }\r
 297               }\r
 298 \r
 299               String param = getParameter("features");\r
 300               if (param != null)\r
 301               {\r
 302                 if (param.indexOf("://") == -1)\r
 303                   param = getCodeBase() + param;\r
 304 \r
 305                 currentAlignFrame.parseFeaturesFile(param);\r
 306               }\r
 307 \r
 308              param = getParameter("annotations");\r
 309              if (param != null)\r
 310              {\r
 311                if (param.indexOf("://") == -1)\r
 312                  param = getCodeBase() + param;\r
 313 \r
 314                new AnnotationReader().readAnnotationFile(\r
 315                    currentAlignFrame.viewport.getAlignment(),\r
 316                    param);\r
 317 \r
 318                currentAlignFrame.alignPanel.fontChanged();\r
 319              }\r
 320 \r
 321 \r
 322                 String pdbfile = applet.getParameter("PDBFILE");\r
 323                 if(pdbfile!=null)\r
 324                 {\r
 325                   if(pdbfile.indexOf("://")==-1)\r
 326                        pdbfile = getCodeBase() + pdbfile;\r
 327 \r
 328                   String sequence = applet.getParameter("PDBSEQ");\r
 329 \r
 330                   if(sequence!=null)\r
 331                   {\r
 332                     new MCview.AppletPDBViewer(pdbfile, "URL",\r
 333                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
 334                                                currentAlignFrame.getSeqcanvas());\r
 335                   }\r
 336 \r
 337                 }\r
 338             }\r
 339             else\r
 340             {\r
 341                 fileFound = false;\r
 342                 remove(launcher);\r
 343                 repaint();\r
 344             }\r
 345         }\r
 346     }\r
 347 }\r