- * 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
* @param ap
*/
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
* @param ap
*/
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
// 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);
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- 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);
+