SequenceI[][] seqs)
{
createProgressBar();
+ // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
.getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
+ // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+ // ChimeraViewFrame. Is this even used ???
+
chain = pdbrefs.get(0).getChainCode();
}
}
{
int pos = filePDBpos.get(num).intValue();
long startTime = startProgressBar("Chimera "
- + MessageManager.getString("status.opening_file"));
+ + MessageManager.getString("status.opening_file_for")
+ + " " + pe.getId());
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
*/
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
+ // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;