| 184 | } |
| 185 | |
| 186 | void MascotGenericFile::writeHeader_(ostream& os) |
| 187 | { |
| 188 | // search title |
| 189 | if (param_.getValue("search_title") != "") |
| 190 | { |
| 191 | writeParameterHeader_("COM", os); |
| 192 | os << param_.getValue("search_title") << "\n"; |
| 193 | } |
| 194 | |
| 195 | // user name |
| 196 | writeParameterHeader_("USERNAME", os); |
| 197 | os << param_.getValue("username") << "\n"; |
| 198 | |
| 199 | // email |
| 200 | if (!param_.getValue("email").toString().empty()) |
| 201 | { |
| 202 | writeParameterHeader_("USEREMAIL", os); |
| 203 | os << param_.getValue("email") << "\n"; |
| 204 | } |
| 205 | |
| 206 | // format |
| 207 | writeParameterHeader_("FORMAT", os); // make sure this stays within the first 5 lines of the file, since we use it to recognize our own MGF files in case their file suffix is not MGF |
| 208 | os << param_.getValue("internal:format") << "\n"; |
| 209 | |
| 210 | // precursor mass tolerance unit : Da |
| 211 | writeParameterHeader_("TOLU", os); |
| 212 | os << param_.getValue("precursor_error_units") << "\n"; |
| 213 | |
| 214 | // ion mass tolerance unit : Da |
| 215 | writeParameterHeader_("ITOLU", os); |
| 216 | os << param_.getValue("fragment_error_units") << "\n"; |
| 217 | |
| 218 | // format version |
| 219 | writeParameterHeader_("FORMVER", os); |
| 220 | os << "1.01" << "\n"; |
| 221 | |
| 222 | // db name |
| 223 | writeParameterHeader_("DB", os); |
| 224 | os << param_.getValue("database") << "\n"; |
| 225 | |
| 226 | // decoys |
| 227 | if (param_.getValue("decoy").toBool() == true) |
| 228 | { |
| 229 | writeParameterHeader_("DECOY", os); |
| 230 | os << 1 << "\n"; |
| 231 | } |
| 232 | |
| 233 | // search type |
| 234 | writeParameterHeader_("SEARCH", os); |
| 235 | os << param_.getValue("search_type") << "\n"; |
| 236 | |
| 237 | // number of peptide candidates in the list |
| 238 | writeParameterHeader_("REPORT", os); |
| 239 | UInt num_hits((UInt)param_.getValue("number_of_hits")); |
| 240 | if (num_hits != 0) |
| 241 | { |
| 242 | os << param_.getValue("number_of_hits") << "\n"; |
| 243 | } |