import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
+
import org.jmol.popup.*;
import jalview.schemes.*;
-public class AppletJmol extends Frame
+public class AppletJmol extends EmbmenuFrame
implements StructureListener, JmolStatusListener,
KeyListener, ActionListener, ItemListener
TextField inputLine;
TextArea history;
SequenceI[] sequence;
+ String [] chains;
StructureSelectionManager ssm;
RenderPanel renderPanel;
AlignmentPanel ap;
public AppletJmol(PDBEntry pdbentry,
SequenceI[] seq,
+ String[] chains,
AlignmentPanel ap,
String protocol)
{
this.ap = ap;
this.sequence = seq;
+ this.chains = chains;
this.pdbentry = pdbentry;
String alreadyMapped = StructureSelectionManager
if (alreadyMapped != null)
{
StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, pdbentry.getFile(), protocol);
- return;
+ .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
+ //FOR NOW, LETS JUST OPEN A NEW WINDOW
}
-
- renderPanel = new RenderPanel();
-
- this.add(renderPanel, BorderLayout.CENTER);
-
- viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
-
- viewer.setAppletContext("jalview",
- ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(),
- null);
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeViewer();
- }
- });
-
MenuBar menuBar = new MenuBar();
menuBar.add(fileMenu);
fileMenu.add(mappingMenuItem);
helpMenu.add(jmolHelp);
- this.setMenuBar(menuBar);
+ setMenuBar(menuBar);
+
+ renderPanel = new RenderPanel();
+ embedMenuIfNeeded(renderPanel);
+ this.add(renderPanel, BorderLayout.CENTER);
+ viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
+
+ viewer.setAppletContext("jalview",
+ ap.av.applet.getDocumentBase(),
+ ap.av.applet.getCodeBase(),
+ null);
+
+ viewer.setJmolStatusListener(this);
+
+ jmolpopup = JmolPopup.newJmolPopup(viewer);
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ closeViewer();
+ }
+ });
+
if(pdbentry.getFile()!=null)
{
+ // import structure data from pdbentry.getFile based on given protocol
if (protocol.equals(AppletFormatAdapter.PASTE))
+ {
loadInline(pdbentry.getFile());
- else
+ } else
+ if (protocol.equals(AppletFormatAdapter.FILE) || protocol.equals(AppletFormatAdapter.URL)){
viewer.openFile(pdbentry.getFile());
+ }
+ else
+ {
+ // probably CLASSLOADER based datasource..
+ // Try and get a reader on the datasource, and pass that to Jmol
+ try {
+ FileParse fparser = new jalview.io.FileParse(protocol, pdbentry.getFile());
+ if (!fparser.isValid())
+ {
+ throw new Exception("Invalid datasource. "+fparser.getWarningMessage());
+ }
+ viewer.openReader(pdbentry.getFile(), pdbentry.getId(), fparser.getReader());
+ } catch (Exception e)
+ {
+ // give up!
+ System.err.println("Couldn't access pdbentry id="+pdbentry.getId()+" and file="+pdbentry.getFile()+" using protocol="+protocol);
+ e.printStackTrace();
+ }
+ }
}
-
- this.setBounds(400, 400, 400, 400);
-
- this.setVisible(true);
+
+ jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
}
public void loadInline(String string)
{
if (evt.getSource() == seqColour)
{
+ lastCommand = null;
colourBySequence = seqColour.getState();
colourBySequence(ap);
}
resetLastRes.append(":" + chain);
}
- eval.append(";color gold;wireframe 100");
+ eval.append(";wireframe 100;"+eval.toString()+".CA;");
- Color col = new Color(viewer.getAtomArgb(atomIndex));
+ resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
- resetLastRes.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];wireframe 0");
+ eval.append("spacefill 200;select none");
viewer.evalStringQuiet(eval.toString());
//End StructureListener
////////////////////////////
- FeatureRenderer fr;
- public void colourBySequence(AlignmentPanel ap)
+ public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
{
- if(!colourBySequence)
- return;
+ if (!pdbfile.equals(pdbentry.getFile()))
+ return null;
+
+ return new Color(viewer.getAtomArgb(atomIndex));
+ }
+ String lastCommand;
+ FeatureRenderer fr=null;
+ public void colourBySequence(AlignmentPanel sourceap)
+ {
+ this.ap = sourceap;
+
+ if (!colourBySequence)
+ return;
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
if (mapping.length < 1)
return;
- SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+ SequenceRenderer sr = new SequenceRenderer(ap.av);
boolean showFeatures = false;
+
if (ap.av.showSequenceFeatures)
{
showFeatures = true;
int lastPos = -1;
for (int s = 0; s < sequence.length; s++)
{
- for (int m = 0; m < mapping.length; m++)
+ for (int sp,m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s])
+ if (mapping[m].getSequence() == sequence[s]
+ && (sp=ap.av.alignment.findIndex(sequence[s])) > -1)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ SequenceI asp = ap.av.alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
{
+ // no mapping to gaps in sequence
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
+ asp.findPosition(r));
+
- if (pos < 1 || pos==lastPos)
+ if (pos < 1 || pos == lastPos)
continue;
lastPos = pos;
if (showFeatures)
col = fr.findFeatureColour(col, sequence[s], r);
- if (command.toString().endsWith(":" + mapping[m].getChain()+
+ if (command.toString().endsWith(":" + mapping[m].getChain() +
";color["
+ col.getRed() + ","
+ col.getGreen() + ","
}
command.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]");
-
+ + col.getRed() + ","
+ + col.getGreen() + ","
+ + col.getBlue() + "]");
}
break;
}
}
}
- viewer.evalStringQuiet(command.toString());
+ if (lastCommand == null || !lastCommand.equals(command.toString()))
+ {
+ viewer.evalStringQuiet(command.toString());
+ }
+ lastCommand = command.toString();
}
+
StringBuffer condenseCommand(String command, int pos)
{
MCview.PDBfile pdb;
if (loadedInline)
{
- pdb = ssm.setMapping(sequence,
+ pdb = ssm.setMapping(sequence,chains,
pdbentry.getFile(),
AppletFormatAdapter.PASTE);
pdbentry.setFile("INLINE"+pdb.id);
}
else
{
- pdb = ssm.setMapping(sequence,
+ pdb = ssm.setMapping(sequence,chains,
pdbentry.getFile(),
AppletFormatAdapter.URL);
}
pdbentry.setId(pdb.id);
ssm.addStructureViewerListener(this);
- if (fr!=null)
- fr.featuresAdded();
+
Vector chains = new Vector();
for (int i = 0; i < pdb.chains.size(); i++)
{
picked+=strInfo.substring(strInfo.indexOf(":")+1,
strInfo.indexOf("."));
- picked+=".C";
+ picked+=".CA";
if (!atomsPicked.contains(picked))
{
git://source.jalview.org / jalview.git / blobdiff