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 \r
  11 public class PDBViewer extends JInternalFrame implements Runnable\r
  12 {\r
  13   PDBEntry pdb;\r
  14   Sequence sequence;\r
  15   PDBCanvas pdbcanvas;\r
  16 \r
  17 \r
  18   public PDBViewer(PDBEntry entry,\r
  19                    Sequence seq,\r
  20                    SeqCanvas seqcanvas)\r
  21   {\r
  22     pdb = entry;\r
  23     sequence = seq;\r
  24 \r
  25     try\r
  26     {\r
  27       jbInit();\r
  28     }\r
  29     catch (Exception ex)\r
  30     {\r
  31       ex.printStackTrace();\r
  32     }\r
  33 \r
  34     pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
  35 \r
  36     setContentPane(pdbcanvas);\r
  37     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
  38     if(pdb.getProperty()!=null)\r
  39     {\r
  40       title.append( " Method: " );\r
  41       title.append(pdb.getProperty().get("method"));\r
  42       title.append( " Chain:" );\r
  43       title.append( pdb.getProperty().get("chains"));\r
  44     }\r
  45     Desktop.addInternalFrame(this,title.toString(),400, 400);\r
  46 \r
  47      Thread worker = new Thread(this);\r
  48      worker.start();\r
  49   }\r
  50 \r
  51   public void run()\r
  52   {\r
  53     try\r
  54     {\r
  55       EBIFetchClient ebi = new EBIFetchClient();\r
  56       String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,\r
  57                                       null);\r
  58 \r
  59       PDBfile pdbfile = new PDBfile(result);\r
  60 \r
  61       pdbcanvas.setPDBFile(pdbfile);\r
  62 \r
  63     }\r
  64     catch (Exception ex)\r
  65     {\r
  66       ex.printStackTrace();\r
  67     }\r
  68   }\r
  69 \r
  70   private void jbInit()\r
  71       throws Exception\r
  72   {\r
  73     this.addKeyListener(new KeyAdapter()\r
  74         {\r
  75             public void keyPressed(KeyEvent evt)\r
  76             {\r
  77               pdbcanvas.keyPressed(evt);\r
  78             }\r
  79         });\r
  80 \r
  81     this.setJMenuBar(jMenuBar1);\r
  82     fileMenu.setText("File");\r
  83     coloursMenu.setText("Colours");\r
  84     saveMenu.setActionCommand("Save Image");\r
  85     saveMenu.setText("Save As");\r
  86     png.setText("PNG");\r
  87     png.addActionListener(new ActionListener()\r
  88     {\r
  89       public void actionPerformed(ActionEvent e)\r
  90       {\r
  91         png_actionPerformed(e);\r
  92       }\r
  93     });\r
  94     eps.setText("EPS");\r
  95     eps.addActionListener(new ActionListener()\r
  96     {\r
  97       public void actionPerformed(ActionEvent e)\r
  98       {\r
  99         eps_actionPerformed(e);\r
 100       }\r
 101     });\r
 102     mapping.setText("View Mapping");\r
 103     mapping.addActionListener(new ActionListener()\r
 104     {\r
 105       public void actionPerformed(ActionEvent e)\r
 106       {\r
 107         mapping_actionPerformed(e);\r
 108       }\r
 109     });\r
 110     wire.setText("Wireframe");\r
 111     wire.addActionListener(new ActionListener()\r
 112     {\r
 113       public void actionPerformed(ActionEvent e)\r
 114       {\r
 115         wire_actionPerformed(e);\r
 116       }\r
 117     });\r
 118     depth.setSelected(true);\r
 119     depth.setText("Depthcue");\r
 120     depth.addActionListener(new ActionListener()\r
 121     {\r
 122       public void actionPerformed(ActionEvent e)\r
 123       {\r
 124         depth_actionPerformed(e);\r
 125       }\r
 126     });\r
 127     zbuffer.setSelected(true);\r
 128     zbuffer.setText("Z Buffering");\r
 129     zbuffer.addActionListener(new ActionListener()\r
 130     {\r
 131       public void actionPerformed(ActionEvent e)\r
 132       {\r
 133         zbuffer_actionPerformed(e);\r
 134       }\r
 135     });\r
 136     charge.setText("Charge & Cysteine");\r
 137     charge.addActionListener(new ActionListener()\r
 138     {\r
 139       public void actionPerformed(ActionEvent e)\r
 140       {\r
 141         charge_actionPerformed(e);\r
 142       }\r
 143     });\r
 144     hydro.setText("Hydrophobicity");\r
 145     hydro.addActionListener(new ActionListener()\r
 146     {\r
 147       public void actionPerformed(ActionEvent e)\r
 148       {\r
 149         hydro_actionPerformed(e);\r
 150       }\r
 151     });\r
 152     chain.setText("By Chain");\r
 153     chain.addActionListener(new ActionListener()\r
 154     {\r
 155       public void actionPerformed(ActionEvent e)\r
 156       {\r
 157         chain_actionPerformed(e);\r
 158       }\r
 159     });\r
 160     seqButton.setSelected(true);\r
 161     seqButton.setText("By Sequence");\r
 162     seqButton.addActionListener(new ActionListener()\r
 163     {\r
 164       public void actionPerformed(ActionEvent e)\r
 165       {\r
 166         seqButton_actionPerformed(e);\r
 167       }\r
 168     });\r
 169     molecule.setText("By Molecule");\r
 170     molecule.addActionListener(new ActionListener()\r
 171     {\r
 172       public void actionPerformed(ActionEvent e)\r
 173       {\r
 174         molecule_actionPerformed(e);\r
 175       }\r
 176     });\r
 177     allchains.setSelected(true);\r
 178     allchains.setText("Show All Chains");\r
 179     allchains.addItemListener(new ItemListener()\r
 180     {\r
 181       public void itemStateChanged(ItemEvent e)\r
 182       {\r
 183         allchains_itemStateChanged(e);\r
 184       }\r
 185     });\r
 186     jMenuBar1.add(fileMenu);\r
 187     jMenuBar1.add(coloursMenu);\r
 188     fileMenu.add(saveMenu);\r
 189     fileMenu.add(mapping);\r
 190     saveMenu.add(png);\r
 191     saveMenu.add(eps);\r
 192     coloursMenu.add(seqButton);\r
 193     coloursMenu.add(chain);\r
 194     coloursMenu.add(hydro);\r
 195     coloursMenu.add(charge);\r
 196     coloursMenu.addSeparator();\r
 197     coloursMenu.add(wire);\r
 198     coloursMenu.add(depth);\r
 199     coloursMenu.add(zbuffer);\r
 200     coloursMenu.add(molecule);\r
 201     coloursMenu.add(allchains);\r
 202     ButtonGroup bg = new ButtonGroup();\r
 203     bg.add(seqButton);\r
 204     bg.add(chain);\r
 205     bg.add(hydro);\r
 206     bg.add(charge);\r
 207   }\r
 208 \r
 209   JMenuBar jMenuBar1 = new JMenuBar();\r
 210   JMenu fileMenu = new JMenu();\r
 211   JMenu coloursMenu = new JMenu();\r
 212   JMenu saveMenu = new JMenu();\r
 213   JMenuItem png = new JMenuItem();\r
 214   JMenuItem eps = new JMenuItem();\r
 215   JMenuItem mapping = new JMenuItem();\r
 216   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
 217   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
 218   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
 219   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
 220   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
 221   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
 222   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
 223   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
 224   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
 225 \r
 226   /**\r
 227    * DOCUMENT ME!\r
 228    *\r
 229    * @param e DOCUMENT ME!\r
 230    */\r
 231   public void eps_actionPerformed(ActionEvent e)\r
 232   {\r
 233     makePDBImage(jalview.util.ImageMaker.EPS);\r
 234   }\r
 235 \r
 236   /**\r
 237    * DOCUMENT ME!\r
 238    *\r
 239    * @param e DOCUMENT ME!\r
 240    */\r
 241   public void png_actionPerformed(ActionEvent e)\r
 242   {\r
 243      makePDBImage(jalview.util.ImageMaker.PNG);\r
 244   }\r
 245 \r
 246   void makePDBImage(int type)\r
 247   {\r
 248     int width = pdbcanvas.getWidth();\r
 249     int height = pdbcanvas.getHeight();\r
 250 \r
 251     jalview.util.ImageMaker im;\r
 252 \r
 253     if (type == jalview.util.ImageMaker.PNG)\r
 254       im = new jalview.util.ImageMaker(this,\r
 255                                        jalview.util.ImageMaker.PNG,\r
 256                                        "Make PNG image from view",\r
 257                                        width, height,\r
 258                                        null, null);\r
 259     else\r
 260       im = new jalview.util.ImageMaker(this,\r
 261                                        jalview.util.ImageMaker.EPS,\r
 262                                        "Make EPS file from view",\r
 263                                        width, height,\r
 264                                        null, this.getTitle());\r
 265 \r
 266     if (im.getGraphics() != null)\r
 267     {\r
 268       pdbcanvas.drawAll(im.getGraphics(), width, height);\r
 269       im.writeImage();\r
 270     }\r
 271   }\r
 272   public void charge_actionPerformed(ActionEvent e)\r
 273   {\r
 274     clearButtonGroup();\r
 275     pdbcanvas.pdb.setChargeColours();\r
 276     pdbcanvas.redrawneeded=true;\r
 277     pdbcanvas.repaint();\r
 278   }\r
 279 \r
 280   public void hydro_actionPerformed(ActionEvent e)\r
 281   {\r
 282     clearButtonGroup();\r
 283     pdbcanvas.pdb.setHydrophobicityColours();\r
 284     pdbcanvas.redrawneeded=true;\r
 285     pdbcanvas.repaint();\r
 286   }\r
 287 \r
 288   public void chain_actionPerformed(ActionEvent e)\r
 289   {\r
 290     clearButtonGroup();\r
 291     pdbcanvas.pdb.setChainColours();\r
 292     pdbcanvas.redrawneeded=true;\r
 293     pdbcanvas.repaint();\r
 294   }\r
 295 \r
 296   public void zbuffer_actionPerformed(ActionEvent e)\r
 297   {\r
 298     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 299     pdbcanvas.redrawneeded=true;\r
 300     pdbcanvas.repaint();\r
 301   }\r
 302 \r
 303   public void molecule_actionPerformed(ActionEvent e)\r
 304   {\r
 305     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 306     pdbcanvas.redrawneeded=true;\r
 307     pdbcanvas.repaint();\r
 308   }\r
 309 \r
 310   public void depth_actionPerformed(ActionEvent e)\r
 311   {\r
 312   pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 313   pdbcanvas.redrawneeded=true;\r
 314     pdbcanvas.repaint();\r
 315   }\r
 316 \r
 317   public void wire_actionPerformed(ActionEvent e)\r
 318   {\r
 319     pdbcanvas.wire = ! pdbcanvas.wire;\r
 320     pdbcanvas.redrawneeded=true;\r
 321     pdbcanvas.repaint();\r
 322   }\r
 323 \r
 324   public void seqButton_actionPerformed(ActionEvent e)\r
 325   {\r
 326     clearButtonGroup();\r
 327     pdbcanvas.bysequence = seqButton.isSelected();\r
 328     pdbcanvas.updateSeqColours();\r
 329   }\r
 330 \r
 331   void clearButtonGroup()\r
 332   {\r
 333    pdbcanvas.bysequence = false;\r
 334    pdbcanvas.bymolecule = false;\r
 335   }\r
 336 \r
 337   public void mapping_actionPerformed(ActionEvent e)\r
 338   {\r
 339     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
 340     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);\r
 341     cap.setText(pdbcanvas.mappingDetails.toString());\r
 342   }\r
 343 \r
 344   public void allchains_itemStateChanged(ItemEvent e)\r
 345   {\r
 346     pdbcanvas.setAllchainsVisible(allchains.getState());\r
 347   }\r
 348 }\r