/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
MenuItem turn = new MenuItem("Turn Propensity");
MenuItem buried = new MenuItem("Buried Index");
+
+ MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
MenuItem user = new MenuItem("User Defined Colours");
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);
strand.addActionListener(this);
turn.addActionListener(this);
buried.addActionListener(this);
+ purinepyrimidine.addActionListener(this);
user.addActionListener(this);
- jmolColour.addActionListener(this);
jmolHelp.addActionListener(this);
coloursMenu.add(strand);
coloursMenu.add(turn);
coloursMenu.add(buried);
+ coloursMenu.add(purinepyrimidine);
coloursMenu.add(user);
coloursMenu.add(jmolColour);
helpMenu.add(jmolHelp);
{
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");
}
setEnabled(buried);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ else if(evt.getSource() == purinepyrimidine)
+ {
+ jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
else if (evt.getSource() == user)
{
setEnabled(user);