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