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 \r
  23     pdb = entry;\r
  24     sequence = seq;\r
  25 \r
  26     Thread worker = new Thread(this);\r
  27     worker.start();\r
  28 \r
  29     try\r
  30     {\r
  31       jbInit();\r
  32     }\r
  33     catch (Exception ex)\r
  34     {\r
  35       ex.printStackTrace();\r
  36     }\r
  37 \r
  38     pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
  39 \r
  40     setContentPane(pdbcanvas);\r
  41     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
  42     if(pdb.getProperty()!=null)\r
  43     {\r
  44       title.append( " Method: " );\r
  45       title.append(pdb.getProperty().get("method"));\r
  46       title.append( " Chain:" );\r
  47       title.append( pdb.getProperty().get("chains"));\r
  48     }\r
  49 \r
  50      Desktop.addInternalFrame(this,title.toString(),400, 400);\r
  51   }\r
  52 \r
  53   public void run()\r
  54   {\r
  55     try\r
  56     {\r
  57       EBIFetchClient ebi = new EBIFetchClient();\r
  58       String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
  59 \r
  60       PDBfile pdbfile = new PDBfile(result);\r
  61 \r
  62       pdbcanvas.setPDBFile(pdbfile);\r
  63 \r
  64     }\r
  65     catch (Exception ex)\r
  66     {\r
  67       ex.printStackTrace();\r
  68     }\r
  69   }\r
  70 \r
  71   private void jbInit()\r
  72       throws Exception\r
  73   {\r
  74     this.addKeyListener(new KeyAdapter()\r
  75         {\r
  76             public void keyPressed(KeyEvent evt)\r
  77             {\r
  78               pdbcanvas.keyPressed(evt);\r
  79             }\r
  80         });\r
  81 \r
  82     this.setJMenuBar(jMenuBar1);\r
  83     fileMenu.setText("File");\r
  84     coloursMenu.setText("Colours");\r
  85     saveMenu.setActionCommand("Save Image");\r
  86     saveMenu.setText("Save As");\r
  87     png.setText("PNG");\r
  88     png.addActionListener(new ActionListener()\r
  89     {\r
  90       public void actionPerformed(ActionEvent e)\r
  91       {\r
  92         png_actionPerformed(e);\r
  93       }\r
  94     });\r
  95     eps.setText("EPS");\r
  96     eps.addActionListener(new ActionListener()\r
  97     {\r
  98       public void actionPerformed(ActionEvent e)\r
  99       {\r
 100         eps_actionPerformed(e);\r
 101       }\r
 102     });\r
 103     mapping.setText("View Mapping");\r
 104     mapping.addActionListener(new ActionListener()\r
 105     {\r
 106       public void actionPerformed(ActionEvent e)\r
 107       {\r
 108         mapping_actionPerformed(e);\r
 109       }\r
 110     });\r
 111     wire.setText("Wireframe");\r
 112     wire.addActionListener(new ActionListener()\r
 113     {\r
 114       public void actionPerformed(ActionEvent e)\r
 115       {\r
 116         wire_actionPerformed(e);\r
 117       }\r
 118     });\r
 119     depth.setSelected(true);\r
 120     depth.setText("Depthcue");\r
 121     depth.addActionListener(new ActionListener()\r
 122     {\r
 123       public void actionPerformed(ActionEvent e)\r
 124       {\r
 125         depth_actionPerformed(e);\r
 126       }\r
 127     });\r
 128     zbuffer.setSelected(true);\r
 129     zbuffer.setText("Z Buffering");\r
 130     zbuffer.addActionListener(new ActionListener()\r
 131     {\r
 132       public void actionPerformed(ActionEvent e)\r
 133       {\r
 134         zbuffer_actionPerformed(e);\r
 135       }\r
 136     });\r
 137     charge.setText("Charge & Cysteine");\r
 138     charge.addActionListener(new ActionListener()\r
 139     {\r
 140       public void actionPerformed(ActionEvent e)\r
 141       {\r
 142         charge_actionPerformed(e);\r
 143       }\r
 144     });\r
 145     hydro.setText("Hydrophobicity");\r
 146     hydro.addActionListener(new ActionListener()\r
 147     {\r
 148       public void actionPerformed(ActionEvent e)\r
 149       {\r
 150         hydro_actionPerformed(e);\r
 151       }\r
 152     });\r
 153     chain.setText("By Chain");\r
 154     chain.addActionListener(new ActionListener()\r
 155     {\r
 156       public void actionPerformed(ActionEvent e)\r
 157       {\r
 158         chain_actionPerformed(e);\r
 159       }\r
 160     });\r
 161     seqButton.setSelected(true);\r
 162     seqButton.setText("By Sequence");\r
 163     seqButton.addActionListener(new ActionListener()\r
 164     {\r
 165       public void actionPerformed(ActionEvent e)\r
 166       {\r
 167         seqButton_actionPerformed(e);\r
 168       }\r
 169     });\r
 170     molecule.setText("By Molecule");\r
 171     molecule.addActionListener(new ActionListener()\r
 172     {\r
 173       public void actionPerformed(ActionEvent e)\r
 174       {\r
 175         molecule_actionPerformed(e);\r
 176       }\r
 177     });\r
 178     allchains.setSelected(true);\r
 179     allchains.setText("Show All Chains");\r
 180     allchains.addItemListener(new ItemListener()\r
 181     {\r
 182       public void itemStateChanged(ItemEvent e)\r
 183       {\r
 184         allchains_itemStateChanged(e);\r
 185       }\r
 186     });\r
 187     jMenuBar1.add(fileMenu);\r
 188     jMenuBar1.add(coloursMenu);\r
 189     fileMenu.add(saveMenu);\r
 190     fileMenu.add(mapping);\r
 191     saveMenu.add(png);\r
 192     saveMenu.add(eps);\r
 193     coloursMenu.add(seqButton);\r
 194     coloursMenu.add(chain);\r
 195     coloursMenu.add(hydro);\r
 196     coloursMenu.add(charge);\r
 197     coloursMenu.addSeparator();\r
 198     coloursMenu.add(wire);\r
 199     coloursMenu.add(depth);\r
 200     coloursMenu.add(zbuffer);\r
 201     coloursMenu.add(molecule);\r
 202     coloursMenu.add(allchains);\r
 203     ButtonGroup bg = new ButtonGroup();\r
 204     bg.add(seqButton);\r
 205     bg.add(chain);\r
 206     bg.add(hydro);\r
 207     bg.add(charge);\r
 208   }\r
 209 \r
 210   JMenuBar jMenuBar1 = new JMenuBar();\r
 211   JMenu fileMenu = new JMenu();\r
 212   JMenu coloursMenu = new JMenu();\r
 213   JMenu saveMenu = new JMenu();\r
 214   JMenuItem png = new JMenuItem();\r
 215   JMenuItem eps = new JMenuItem();\r
 216   JMenuItem mapping = new JMenuItem();\r
 217   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
 218   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
 219   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
 220   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
 221   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
 222   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
 223   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
 224   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
 225   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
 226 \r
 227   /**\r
 228    * DOCUMENT ME!\r
 229    *\r
 230    * @param e DOCUMENT ME!\r
 231    */\r
 232   public void eps_actionPerformed(ActionEvent e)\r
 233   {\r
 234     makePDBImage(jalview.util.ImageMaker.EPS);\r
 235   }\r
 236 \r
 237   /**\r
 238    * DOCUMENT ME!\r
 239    *\r
 240    * @param e DOCUMENT ME!\r
 241    */\r
 242   public void png_actionPerformed(ActionEvent e)\r
 243   {\r
 244      makePDBImage(jalview.util.ImageMaker.PNG);\r
 245   }\r
 246 \r
 247   void makePDBImage(int type)\r
 248   {\r
 249     int width = pdbcanvas.getWidth();\r
 250     int height = pdbcanvas.getHeight();\r
 251 \r
 252     jalview.util.ImageMaker im;\r
 253 \r
 254     if (type == jalview.util.ImageMaker.PNG)\r
 255       im = new jalview.util.ImageMaker(this,\r
 256                                        jalview.util.ImageMaker.PNG,\r
 257                                        "Make PNG image from view",\r
 258                                        width, height,\r
 259                                        null, null);\r
 260     else\r
 261       im = new jalview.util.ImageMaker(this,\r
 262                                        jalview.util.ImageMaker.EPS,\r
 263                                        "Make EPS file from view",\r
 264                                        width, height,\r
 265                                        null, this.getTitle());\r
 266 \r
 267     if (im.getGraphics() != null)\r
 268     {\r
 269       pdbcanvas.drawAll(im.getGraphics(), width, height);\r
 270       im.writeImage();\r
 271     }\r
 272   }\r
 273   public void charge_actionPerformed(ActionEvent e)\r
 274   {\r
 275     clearButtonGroup();\r
 276     pdbcanvas.pdb.setChargeColours();\r
 277     pdbcanvas.redrawneeded=true;\r
 278     pdbcanvas.repaint();\r
 279   }\r
 280 \r
 281   public void hydro_actionPerformed(ActionEvent e)\r
 282   {\r
 283     clearButtonGroup();\r
 284     pdbcanvas.pdb.setHydrophobicityColours();\r
 285     pdbcanvas.redrawneeded=true;\r
 286     pdbcanvas.repaint();\r
 287   }\r
 288 \r
 289   public void chain_actionPerformed(ActionEvent e)\r
 290   {\r
 291     clearButtonGroup();\r
 292     pdbcanvas.pdb.setChainColours();\r
 293     pdbcanvas.redrawneeded=true;\r
 294     pdbcanvas.repaint();\r
 295   }\r
 296 \r
 297   public void zbuffer_actionPerformed(ActionEvent e)\r
 298   {\r
 299     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 300     pdbcanvas.redrawneeded=true;\r
 301     pdbcanvas.repaint();\r
 302   }\r
 303 \r
 304   public void molecule_actionPerformed(ActionEvent e)\r
 305   {\r
 306     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 307     pdbcanvas.redrawneeded=true;\r
 308     pdbcanvas.repaint();\r
 309   }\r
 310 \r
 311   public void depth_actionPerformed(ActionEvent e)\r
 312   {\r
 313   pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 314   pdbcanvas.redrawneeded=true;\r
 315     pdbcanvas.repaint();\r
 316   }\r
 317 \r
 318   public void wire_actionPerformed(ActionEvent e)\r
 319   {\r
 320     pdbcanvas.wire = ! pdbcanvas.wire;\r
 321     pdbcanvas.redrawneeded=true;\r
 322     pdbcanvas.repaint();\r
 323   }\r
 324 \r
 325   public void seqButton_actionPerformed(ActionEvent e)\r
 326   {\r
 327     clearButtonGroup();\r
 328     pdbcanvas.bysequence = seqButton.isSelected();\r
 329     pdbcanvas.updateSeqColours();\r
 330   }\r
 331 \r
 332   void clearButtonGroup()\r
 333   {\r
 334    pdbcanvas.bysequence = false;\r
 335    pdbcanvas.bymolecule = false;\r
 336   }\r
 337 \r
 338   public void mapping_actionPerformed(ActionEvent e)\r
 339   {\r
 340     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
 341     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
 342     cap.setText(pdbcanvas.mappingDetails.toString());\r
 343   }\r
 344 \r
 345   public void allchains_itemStateChanged(ItemEvent e)\r
 346   {\r
 347     pdbcanvas.setAllchainsVisible(allchains.getState());\r
 348   }\r
 349 }\r