+ // TODO obtain config value from preference settings.
+ // Set value to 'true' to test PDB processing with Jmol: JAL-1213
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ if (isParseWithJMOL)
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ type);
+ }
+ else
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ type);
+ }
+ ((StructureFile) alignFile).setDbRefType(format);
+ }
+ else if (format.equalsIgnoreCase("mmCIF"))
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,