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