- afile = new MCview.PDBfile(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ // TODO obtain config value from preference settings
+ boolean isParseWithJMOL = false;
+ if (isParseWithJMOL)
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
+ }
+ else if (format.equalsIgnoreCase("mmCIF"))
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
+ ((StructureFile) alignFile).setDbRefType(Type.MMCIF);