src/MCview/PDBViewer.java

   1 package MCview;\r
   2 \r
   3 import javax.swing.*;\r
   4 import java.awt.event.*;\r
   5 import jalview.datamodel.*;\r
   6 import jalview.gui.*;\r
   7 import jalview.io.EBIFetchClient;\r
   8 import java.awt.event.ActionListener;\r
   9 import java.awt.event.ActionEvent;\r
  10 import java.io.FileOutputStream;\r
  11 import org.jibble.epsgraphics.EpsGraphics2D;\r
  12 import javax.imageio.ImageIO;\r
  13 import java.awt.image.BufferedImage;\r
  14 import java.awt.Graphics;\r
  15 import java.awt.Graphics2D;\r
  16 import java.awt.RenderingHints;\r
  17 \r
  18 public class PDBViewer extends JInternalFrame implements Runnable\r
  19 {\r
  20   PDBEntry pdb;\r
  21   Sequence sequence;\r
  22   PDBCanvas pdbcanvas;\r
  23 \r
  24 \r
  25   public PDBViewer(PDBEntry entry,\r
  26                    Sequence seq,\r
  27                    SeqCanvas seqcanvas)\r
  28   {\r
  29     pdb = entry;\r
  30     sequence = seq;\r
  31 \r
  32     try\r
  33     {\r
  34       jbInit();\r
  35     }\r
  36     catch (Exception ex)\r
  37     {\r
  38       ex.printStackTrace();\r
  39     }\r
  40 \r
  41     pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
  42 \r
  43     setContentPane(pdbcanvas);\r
  44     Desktop.addInternalFrame(this,\r
  45                          sequence.getName() + ":" + pdb.getId()\r
  46                          + " Method: " + pdb.getProperty().get("method")\r
  47                          + " Chain:" + pdb.getProperty().get("chains"),\r
  48                          400, 400);\r
  49 \r
  50      Thread worker = new Thread(this);\r
  51      worker.start();\r
  52   }\r
  53 \r
  54   public void run()\r
  55   {\r
  56     try\r
  57     {\r
  58       EBIFetchClient ebi = new EBIFetchClient();\r
  59       String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,\r
  60                                       null);\r
  61 \r
  62       PDBfile pdbfile = new PDBfile(result);\r
  63 \r
  64       pdbcanvas.setPDBFile(pdbfile);\r
  65 \r
  66     }\r
  67     catch (Exception ex)\r
  68     {\r
  69       ex.printStackTrace();\r
  70     }\r
  71   }\r
  72 \r
  73   private void jbInit()\r
  74       throws Exception\r
  75   {\r
  76     this.addKeyListener(new KeyAdapter()\r
  77         {\r
  78             public void keyPressed(KeyEvent evt)\r
  79             {\r
  80               pdbcanvas.keyPressed(evt);\r
  81             }\r
  82         });\r
  83 \r
  84     this.setJMenuBar(jMenuBar1);\r
  85     fileMenu.setText("File");\r
  86     coloursMenu.setText("Colours");\r
  87     saveMenu.setActionCommand("Save Image");\r
  88     saveMenu.setText("Save As");\r
  89     png.setText("PNG");\r
  90     png.addActionListener(new ActionListener()\r
  91     {\r
  92       public void actionPerformed(ActionEvent e)\r
  93       {\r
  94         png_actionPerformed(e);\r
  95       }\r
  96     });\r
  97     eps.setText("EPS");\r
  98     eps.addActionListener(new ActionListener()\r
  99     {\r
 100       public void actionPerformed(ActionEvent e)\r
 101       {\r
 102         eps_actionPerformed(e);\r
 103       }\r
 104     });\r
 105     mapping.setText("View Mapping");\r
 106     mapping.addActionListener(new ActionListener()\r
 107     {\r
 108       public void actionPerformed(ActionEvent e)\r
 109       {\r
 110         mapping_actionPerformed(e);\r
 111       }\r
 112     });\r
 113     wire.setText("Wireframe");\r
 114     wire.addActionListener(new ActionListener()\r
 115     {\r
 116       public void actionPerformed(ActionEvent e)\r
 117       {\r
 118         wire_actionPerformed(e);\r
 119       }\r
 120     });\r
 121     depth.setSelected(true);\r
 122     depth.setText("Depthcue");\r
 123     depth.addActionListener(new ActionListener()\r
 124     {\r
 125       public void actionPerformed(ActionEvent e)\r
 126       {\r
 127         depth_actionPerformed(e);\r
 128       }\r
 129     });\r
 130     zbuffer.setSelected(true);\r
 131     zbuffer.setText("Z Buffering");\r
 132     zbuffer.addActionListener(new ActionListener()\r
 133     {\r
 134       public void actionPerformed(ActionEvent e)\r
 135       {\r
 136         zbuffer_actionPerformed(e);\r
 137       }\r
 138     });\r
 139     charge.setText("Charge & Cysteine");\r
 140     charge.addActionListener(new ActionListener()\r
 141     {\r
 142       public void actionPerformed(ActionEvent e)\r
 143       {\r
 144         charge_actionPerformed(e);\r
 145       }\r
 146     });\r
 147     hydro.setText("Hydrophobicity");\r
 148     hydro.addActionListener(new ActionListener()\r
 149     {\r
 150       public void actionPerformed(ActionEvent e)\r
 151       {\r
 152         hydro_actionPerformed(e);\r
 153       }\r
 154     });\r
 155     chain.setText("By Chain");\r
 156     chain.addActionListener(new ActionListener()\r
 157     {\r
 158       public void actionPerformed(ActionEvent e)\r
 159       {\r
 160         chain_actionPerformed(e);\r
 161       }\r
 162     });\r
 163     seqButton.setSelected(true);\r
 164     seqButton.setText("By Sequence");\r
 165     seqButton.addActionListener(new ActionListener()\r
 166     {\r
 167       public void actionPerformed(ActionEvent e)\r
 168       {\r
 169         seqButton_actionPerformed(e);\r
 170       }\r
 171     });\r
 172     molecule.setText("By Molecule");\r
 173     molecule.addActionListener(new ActionListener()\r
 174     {\r
 175       public void actionPerformed(ActionEvent e)\r
 176       {\r
 177         molecule_actionPerformed(e);\r
 178       }\r
 179     });\r
 180     jMenuBar1.add(fileMenu);\r
 181     jMenuBar1.add(coloursMenu);\r
 182     fileMenu.add(saveMenu);\r
 183     fileMenu.add(mapping);\r
 184     saveMenu.add(png);\r
 185     saveMenu.add(eps);\r
 186     coloursMenu.add(seqButton);\r
 187     coloursMenu.add(chain);\r
 188     coloursMenu.add(hydro);\r
 189     coloursMenu.add(charge);\r
 190     coloursMenu.addSeparator();\r
 191     coloursMenu.add(wire);\r
 192     coloursMenu.add(depth);\r
 193     coloursMenu.add(zbuffer);\r
 194     coloursMenu.add(molecule);\r
 195     ButtonGroup bg = new ButtonGroup();\r
 196     bg.add(seqButton);\r
 197     bg.add(chain);\r
 198     bg.add(hydro);\r
 199     bg.add(charge);\r
 200   }\r
 201 \r
 202   JMenuBar jMenuBar1 = new JMenuBar();\r
 203   JMenu fileMenu = new JMenu();\r
 204   JMenu coloursMenu = new JMenu();\r
 205   JMenu saveMenu = new JMenu();\r
 206   JMenuItem png = new JMenuItem();\r
 207   JMenuItem eps = new JMenuItem();\r
 208   JMenuItem mapping = new JMenuItem();\r
 209   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
 210   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
 211   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
 212   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
 213   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
 214   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
 215   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
 216   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
 217 \r
 218   public void png_actionPerformed(ActionEvent e)\r
 219   {\r
 220     int width =  pdbcanvas.getWidth();\r
 221     int height = pdbcanvas.getHeight();\r
 222 \r
 223     try\r
 224     {\r
 225         jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 226                     "LAST_DIRECTORY"), new String[] { "png" },\r
 227                 new String[] { "Portable network graphics" },\r
 228                 "Portable network graphics");\r
 229 \r
 230         chooser.setFileView(new jalview.io.JalviewFileView());\r
 231         chooser.setDialogTitle("Create PNG Image of Molecule");\r
 232         chooser.setToolTipText("Save");\r
 233 \r
 234         int value = chooser.showSaveDialog(this);\r
 235 \r
 236         if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 237         {\r
 238             return;\r
 239         }\r
 240 \r
 241         jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 242             chooser.getSelectedFile().getParent());\r
 243 \r
 244         FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 245 \r
 246         BufferedImage bi = new BufferedImage(width, height,\r
 247                 BufferedImage.TYPE_INT_RGB);\r
 248         Graphics png = bi.getGraphics();\r
 249         Graphics2D ig2 = (Graphics2D) png;\r
 250         ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 251                                  RenderingHints.VALUE_ANTIALIAS_ON);\r
 252 \r
 253 \r
 254         pdbcanvas.drawAll(png, width, height);\r
 255 \r
 256         ImageIO.write(bi, "png", out);\r
 257         out.close();\r
 258     }\r
 259     catch (Exception ex)\r
 260     {\r
 261         ex.printStackTrace();\r
 262     }\r
 263   }\r
 264 \r
 265   public void eps_actionPerformed(ActionEvent e)\r
 266   {\r
 267     boolean accurateText = true;\r
 268 \r
 269     String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
 270         "Prompt each time");\r
 271 \r
 272   // If we need to prompt, and if the GUI is visible then\r
 273   // Prompt for EPS rendering style\r
 274     if (renderStyle.equalsIgnoreCase("Prompt each time")\r
 275         && !\r
 276         (System.getProperty("java.awt.headless") != null\r
 277          && System.getProperty("java.awt.headless").equals("true")))\r
 278     {\r
 279       EPSOptions eps = new EPSOptions();\r
 280       renderStyle = eps.getValue();\r
 281 \r
 282       if (renderStyle==null || eps.cancelled)\r
 283         return;\r
 284 \r
 285 \r
 286     }\r
 287 \r
 288     if (renderStyle.equalsIgnoreCase("text"))\r
 289     {\r
 290       accurateText = false;\r
 291     }\r
 292 \r
 293       int width = getWidth();\r
 294       int height = getHeight();\r
 295 \r
 296       try\r
 297       {\r
 298           jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 299                       "LAST_DIRECTORY"), new String[] { "eps" },\r
 300                   new String[] { "Encapsulated Postscript" },\r
 301                   "Encapsulated Postscript");\r
 302           chooser.setFileView(new jalview.io.JalviewFileView());\r
 303           chooser.setDialogTitle("Create EPS file from tree");\r
 304           chooser.setToolTipText("Save");\r
 305 \r
 306           int value = chooser.showSaveDialog(this);\r
 307 \r
 308           if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 309           {\r
 310               return;\r
 311           }\r
 312 \r
 313           jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 314                                         chooser.getSelectedFile().getParent());\r
 315 \r
 316           FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 317           EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
 318                                                height);\r
 319           Graphics2D ig2 = (Graphics2D) pg;\r
 320           ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 321                          RenderingHints.VALUE_ANTIALIAS_ON);\r
 322 \r
 323 \r
 324           pg.setAccurateTextMode(accurateText);\r
 325 \r
 326           pdbcanvas.drawAll(pg, width, height);\r
 327 \r
 328           pg.flush();\r
 329           pg.close();\r
 330       }\r
 331       catch (Exception ex)\r
 332       {\r
 333           ex.printStackTrace();\r
 334         }\r
 335 \r
 336   }\r
 337 \r
 338   public void charge_actionPerformed(ActionEvent e)\r
 339   {\r
 340     clearButtonGroup();\r
 341     pdbcanvas.pdb.setChargeColours();\r
 342     pdbcanvas.redrawneeded=true;\r
 343     pdbcanvas.repaint();\r
 344   }\r
 345 \r
 346   public void hydro_actionPerformed(ActionEvent e)\r
 347   {\r
 348     clearButtonGroup();\r
 349     pdbcanvas.pdb.setHydrophobicityColours();\r
 350     pdbcanvas.redrawneeded=true;\r
 351     pdbcanvas.repaint();\r
 352   }\r
 353 \r
 354   public void chain_actionPerformed(ActionEvent e)\r
 355   {\r
 356     clearButtonGroup();\r
 357     pdbcanvas.pdb.setChainColours();\r
 358     pdbcanvas.redrawneeded=true;\r
 359     pdbcanvas.repaint();\r
 360   }\r
 361 \r
 362   public void zbuffer_actionPerformed(ActionEvent e)\r
 363   {\r
 364     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 365     pdbcanvas.redrawneeded=true;\r
 366     pdbcanvas.repaint();\r
 367   }\r
 368 \r
 369   public void molecule_actionPerformed(ActionEvent e)\r
 370   {\r
 371     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 372     pdbcanvas.redrawneeded=true;\r
 373     pdbcanvas.repaint();\r
 374   }\r
 375 \r
 376   public void depth_actionPerformed(ActionEvent e)\r
 377   {\r
 378   pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 379   pdbcanvas.redrawneeded=true;\r
 380     pdbcanvas.repaint();\r
 381   }\r
 382 \r
 383   public void wire_actionPerformed(ActionEvent e)\r
 384   {\r
 385     pdbcanvas.wire = ! pdbcanvas.wire;\r
 386     pdbcanvas.redrawneeded=true;\r
 387     pdbcanvas.repaint();\r
 388   }\r
 389 \r
 390   public void seqButton_actionPerformed(ActionEvent e)\r
 391   {\r
 392     clearButtonGroup();\r
 393     pdbcanvas.bysequence = seqButton.isSelected();\r
 394     pdbcanvas.updateSeqColours();\r
 395   }\r
 396 \r
 397   void clearButtonGroup()\r
 398   {\r
 399    pdbcanvas.bysequence = false;\r
 400    pdbcanvas.bymolecule = false;\r
 401   }\r
 402 \r
 403   public void mapping_actionPerformed(ActionEvent e)\r
 404   {\r
 405     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
 406     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);\r
 407     cap.setText(pdbcanvas.mappingDetails.toString());\r
 408   }\r
 409 }\r