/*
- * 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, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* @param ap
*/
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
// ////////////////////////////////
{
if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
+ final AppJmol topJmol = ((AppJmol) frames[i]);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
break;
}
}
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
- boolean promptUser=pdbentrys.length==1;
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
worker=null;
- String filelist="";
-// for (PDBEntry pe: pdbentrys)
-// {
-// if (pe.getFile()==null)
{
addingStructures = false;
worker = new Thread(this);
worker.start();
-// break;
}
-// filelist+=" \""+pe.getFile()+"\"";
-
-/* }
- if (worker==null)
- {
- initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
- }
-*/
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
// just transfer the file name from the first sequence's first
// PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+ file = new File(((PDBEntry) pdbseq
+ .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).toURI().getPath().substring(1);
+ jmb.pdbentry[pi].setFile(file);
+
files.append(" \"" + file + "\"");
}
else