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