- // convert Type.PDB/MMCIF to FileFormat.PDB/MMCIF
- // todo get rid of Type?
- FileFormatI fileFormat = FileFormat.valueOf(pdbFileFormat.toString());
- pdbAlignment = new FormatAdapter().readFile(file,
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
+ : FileFormat.MMCif;
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,