CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+
MenuItem chain = new MenuItem("By Chain");
MenuItem charge = new MenuItem("Charge & Cysteine");
RenderPanel renderPanel;
AlignmentPanel ap;
+ ArrayList _aps = new ArrayList();
String fileLoadingError;
AlignmentPanel ap, String protocol)
{
this.ap = ap;
- jmb = new AppletJmolBinding(this, new PDBEntry[]
+ jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq }, new String[][]
{ chains }, protocol);
}
String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
+ .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile(
pdbentry.getId());
MCview.PDBfile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager()
+ reader = StructureSelectionManager.getStructureSelectionManager(ap.av.applet)
.setMapping(seq, chains, pdbentry.getFile(), protocol);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
hydro.addActionListener(this);
chain.addActionListener(this);
seqColour.addItemListener(this);
+ jmolColour.addItemListener(this);
zappo.addActionListener(this);
taylor.addActionListener(this);
helix.addActionListener(this);
turn.addActionListener(this);
buried.addActionListener(this);
user.addActionListener(this);
-
+
jmolHelp.addActionListener(this);
coloursMenu.add(seqColour);
coloursMenu.add(turn);
coloursMenu.add(buried);
coloursMenu.add(user);
-
+ coloursMenu.add(jmolColour);
helpMenu.add(jmolHelp);
this.setLayout(new BorderLayout());
{
for (int s = 0; s < jmb.pdbentry.length; s++)
{
- sb.append(StructureSelectionManager
- .getStructureSelectionManager().printMapping(
+ sb.append(jmb.printMapping(
jmb.pdbentry[s].getFile()));
sb.append("\n");
}
}
/**
- * tick or untick the seqColour menu entry depending upon if it was selected
+ * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected
* or not.
*
* @param itm
*/
private void setEnabled(MenuItem itm)
{
+ jmolColour.setState(itm == jmolColour);
seqColour.setState(itm == seqColour);
jmb.setColourBySequence(itm == seqColour);
}
public void itemStateChanged(ItemEvent evt)
{
+ if (evt.getSource() == jmolColour)
+ {
+ setEnabled(jmolColour);
+ jmb.setColourBySequence(false);
+ } else
if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
else if (!allChainsSelected)
centerViewer();
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
public void updateTitleAndMenus()
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
setTitle(jmb.getViewerTitle());
}
{
jmb.setJalviewColourScheme(ucs);
}
+
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (int i=0;i<_aps.size();i++)
+ {
+ if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
+ {
+ return ((AlignmentPanel)_aps.get(i));
+ }
+ }
+ return ap;
+ }
}