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
11 public class PDBViewer extends JInternalFrame implements Runnable
\r
15 PDBCanvas pdbcanvas;
\r
18 public PDBViewer(PDBEntry entry,
\r
20 SeqCanvas seqcanvas)
\r
29 catch (Exception ex)
\r
31 ex.printStackTrace();
\r
34 pdbcanvas = new PDBCanvas(seqcanvas, seq);
\r
36 setContentPane(pdbcanvas);
\r
37 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
\r
38 if(pdb.getProperty()!=null)
\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
45 Desktop.addInternalFrame(this,title.toString(),400, 400);
\r
47 Thread worker = new Thread(this);
\r
55 EBIFetchClient ebi = new EBIFetchClient();
\r
56 String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
\r
59 PDBfile pdbfile = new PDBfile(result);
\r
61 pdbcanvas.setPDBFile(pdbfile);
\r
64 catch (Exception ex)
\r
66 ex.printStackTrace();
\r
70 private void jbInit()
\r
73 this.addKeyListener(new KeyAdapter()
\r
75 public void keyPressed(KeyEvent evt)
\r
77 pdbcanvas.keyPressed(evt);
\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
87 png.addActionListener(new ActionListener()
\r
89 public void actionPerformed(ActionEvent e)
\r
91 png_actionPerformed(e);
\r
95 eps.addActionListener(new ActionListener()
\r
97 public void actionPerformed(ActionEvent e)
\r
99 eps_actionPerformed(e);
\r
102 mapping.setText("View Mapping");
\r
103 mapping.addActionListener(new ActionListener()
\r
105 public void actionPerformed(ActionEvent e)
\r
107 mapping_actionPerformed(e);
\r
110 wire.setText("Wireframe");
\r
111 wire.addActionListener(new ActionListener()
\r
113 public void actionPerformed(ActionEvent e)
\r
115 wire_actionPerformed(e);
\r
118 depth.setSelected(true);
\r
119 depth.setText("Depthcue");
\r
120 depth.addActionListener(new ActionListener()
\r
122 public void actionPerformed(ActionEvent e)
\r
124 depth_actionPerformed(e);
\r
127 zbuffer.setSelected(true);
\r
128 zbuffer.setText("Z Buffering");
\r
129 zbuffer.addActionListener(new ActionListener()
\r
131 public void actionPerformed(ActionEvent e)
\r
133 zbuffer_actionPerformed(e);
\r
136 charge.setText("Charge & Cysteine");
\r
137 charge.addActionListener(new ActionListener()
\r
139 public void actionPerformed(ActionEvent e)
\r
141 charge_actionPerformed(e);
\r
144 hydro.setText("Hydrophobicity");
\r
145 hydro.addActionListener(new ActionListener()
\r
147 public void actionPerformed(ActionEvent e)
\r
149 hydro_actionPerformed(e);
\r
152 chain.setText("By Chain");
\r
153 chain.addActionListener(new ActionListener()
\r
155 public void actionPerformed(ActionEvent e)
\r
157 chain_actionPerformed(e);
\r
160 seqButton.setSelected(true);
\r
161 seqButton.setText("By Sequence");
\r
162 seqButton.addActionListener(new ActionListener()
\r
164 public void actionPerformed(ActionEvent e)
\r
166 seqButton_actionPerformed(e);
\r
169 molecule.setText("By Molecule");
\r
170 molecule.addActionListener(new ActionListener()
\r
172 public void actionPerformed(ActionEvent e)
\r
174 molecule_actionPerformed(e);
\r
177 allchains.setSelected(true);
\r
178 allchains.setText("Show All Chains");
\r
179 allchains.addItemListener(new ItemListener()
\r
181 public void itemStateChanged(ItemEvent e)
\r
183 allchains_itemStateChanged(e);
\r
186 jMenuBar1.add(fileMenu);
\r
187 jMenuBar1.add(coloursMenu);
\r
188 fileMenu.add(saveMenu);
\r
189 fileMenu.add(mapping);
\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
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
229 * @param e DOCUMENT ME!
\r
231 public void eps_actionPerformed(ActionEvent e)
\r
233 makePDBImage(jalview.util.ImageMaker.EPS);
\r
239 * @param e DOCUMENT ME!
\r
241 public void png_actionPerformed(ActionEvent e)
\r
243 makePDBImage(jalview.util.ImageMaker.PNG);
\r
246 void makePDBImage(int type)
\r
248 int width = pdbcanvas.getWidth();
\r
249 int height = pdbcanvas.getHeight();
\r
251 jalview.util.ImageMaker im;
\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
260 im = new jalview.util.ImageMaker(this,
\r
261 jalview.util.ImageMaker.EPS,
\r
262 "Make EPS file from view",
\r
264 null, this.getTitle());
\r
266 if (im.getGraphics() != null)
\r
268 pdbcanvas.drawAll(im.getGraphics(), width, height);
\r
272 public void charge_actionPerformed(ActionEvent e)
\r
274 clearButtonGroup();
\r
275 pdbcanvas.pdb.setChargeColours();
\r
276 pdbcanvas.redrawneeded=true;
\r
277 pdbcanvas.repaint();
\r
280 public void hydro_actionPerformed(ActionEvent e)
\r
282 clearButtonGroup();
\r
283 pdbcanvas.pdb.setHydrophobicityColours();
\r
284 pdbcanvas.redrawneeded=true;
\r
285 pdbcanvas.repaint();
\r
288 public void chain_actionPerformed(ActionEvent e)
\r
290 clearButtonGroup();
\r
291 pdbcanvas.pdb.setChainColours();
\r
292 pdbcanvas.redrawneeded=true;
\r
293 pdbcanvas.repaint();
\r
296 public void zbuffer_actionPerformed(ActionEvent e)
\r
298 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
\r
299 pdbcanvas.redrawneeded=true;
\r
300 pdbcanvas.repaint();
\r
303 public void molecule_actionPerformed(ActionEvent e)
\r
305 pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
\r
306 pdbcanvas.redrawneeded=true;
\r
307 pdbcanvas.repaint();
\r
310 public void depth_actionPerformed(ActionEvent e)
\r
312 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
\r
313 pdbcanvas.redrawneeded=true;
\r
314 pdbcanvas.repaint();
\r
317 public void wire_actionPerformed(ActionEvent e)
\r
319 pdbcanvas.wire = ! pdbcanvas.wire;
\r
320 pdbcanvas.redrawneeded=true;
\r
321 pdbcanvas.repaint();
\r
324 public void seqButton_actionPerformed(ActionEvent e)
\r
326 clearButtonGroup();
\r
327 pdbcanvas.bysequence = seqButton.isSelected();
\r
328 pdbcanvas.updateSeqColours();
\r
331 void clearButtonGroup()
\r
333 pdbcanvas.bysequence = false;
\r
334 pdbcanvas.bymolecule = false;
\r
337 public void mapping_actionPerformed(ActionEvent e)
\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
344 public void allchains_itemStateChanged(ItemEvent e)
\r
346 pdbcanvas.setAllchainsVisible(allchains.getState());
\r