// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(file,
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,
DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
}
}
- if (chain == null
- || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim()) || (chain
- .trim().length() == 0 && chid.equals("_")))))
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
{
// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
// TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
- + id + SEPARATOR + pdbcs.getName());
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+ + SEPARATOR + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[] { id,
- ((chain == null) ? "' '" : chain) }));
+ "exception.no_pdb_records_for_chain", new String[]
+ { id, ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file