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();
viewer.openFile(pdbentry.getFile());
}
- this.setBounds(400, 400, 400, 400);
-
- this.setVisible(true);
+ jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
}
public void loadInline(String string)
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
////////////////////////////
+ public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ {
+ if (!pdbfile.equals(pdbentry.getFile()))
+ return null;
+
+ return new Color(viewer.getAtomArgb(atomIndex));
+ }
+
FeatureRenderer fr;
+ String lastCommand;
public void colourBySequence(AlignmentPanel ap)
{
if(!colourBySequence)
if (mapping.length < 1)
return;
- SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+ SequenceRenderer sr = new SequenceRenderer(ap.av);
boolean showFeatures = false;
if (ap.av.showSequenceFeatures)
{
for (int m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s])
+ if (mapping[m].getSequence() == sequence[s]
+ && ap.av.alignment.findIndex(sequence[s])>-1)
{
for (int r = 0; r < sequence[s].getLength(); r++)
{
}
}
- 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);
}
picked+=strInfo.substring(strInfo.indexOf(":")+1,
strInfo.indexOf("."));
- picked+=".C";
+ picked+=".CA";
if (!atomsPicked.contains(picked))
{