String fileLoadingError;
boolean colourBySequence = true;
boolean loadingFromArchive = false;
+ Vector atomsPicked = new Vector();
public AppJMol(String file, String id,
SequenceI[] seq,
});
}
+public synchronized void addSequence(SequenceI [] seq)
+ {
+ Vector v = new Vector();
+ for(int i=0; i<sequence.length; i++)
+ v.addElement(sequence[i]);
+
+ for(int i=0; i<seq.length; i++)
+ if(!v.contains(seq[i]))
+ v.addElement(seq[i]);
+
+ SequenceI [] tmp = new SequenceI[v.size()];
+ v.copyInto(tmp);
+ sequence = tmp;
+ }
+
public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap)
{
//////////////////////////////////
});
}
+
void initJmol(String command)
{
renderPanel = new RenderPanel();
public void notifyAtomPicked(int atomIndex, String strInfo)
{
+ Matcher matcher = pattern.matcher(strInfo);
+ matcher.find();
+
+ matcher.group(1);
+ String resnum = new String(matcher.group(2));
+ String chainId = matcher.group(3);
+
+ String picked = resnum;
+
+ if (chainId != null)
+ picked+=(":"+chainId.substring(1, chainId.length()));
+
+ picked+=".C";
+
+ if (!atomsPicked.contains(picked))
+ {
+ viewer.evalString("select "+picked+";label %n %r:%c");
+ atomsPicked.addElement(picked);
+ }
+ else
+ {
+ viewer.evalString("select "+picked+";label off");
+ atomsPicked.removeElement(picked);
+ }
+
if (scriptWindow != null)
{
scriptWindow.sendConsoleMessage(strInfo);