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