-
- boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser().equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
- if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+ pdb = new JmolParser(pdbFile, sourceType);