* Loads the input file depending on the type. Returns 0 if the loading of the input was successful, error * code otherwise * @return 0 if the loading of the input was successful, error code otherwise */
| 194 | * @return 0 if the loading of the input was successful, error code otherwise |
| 195 | */ |
| 196 | ExitCodes loadInputFile_(std::vector<PeptideIdentification>& peptide_ids, ProteinIdentification& protein_id) |
| 197 | { |
| 198 | //------------------------------------------------------------ |
| 199 | // Determine type of input file |
| 200 | //------------------------------------------------------------- |
| 201 | // const String arg_in_type = getStringOption_(TOPPXFDR::param_in_type); |
| 202 | const FileTypes::Type in_type = arg_in_type_.empty() ? |
| 203 | FileHandler::getType(this->arg_in_) : FileTypes::nameToType(arg_in_type_); |
| 204 | |
| 205 | std::vector<ProteinIdentification> protein_ids; |
| 206 | if (in_type == FileTypes::XQUESTXML) |
| 207 | { |
| 208 | XQuestResultXMLFile xquest_file; |
| 209 | xquest_file.load(arg_in_, peptide_ids, protein_ids); |
| 210 | |
| 211 | writeLogInfo_("\nTotal number of hits in xQuest input: " + String(xquest_file.getNumberOfHits())); |
| 212 | } |
| 213 | else if (in_type == FileTypes::MZIDENTML) |
| 214 | { |
| 215 | MzIdentMLFile().load(arg_in_, protein_ids, peptide_ids); |
| 216 | } |
| 217 | else if (in_type == FileTypes::IDXML) |
| 218 | { |
| 219 | IdXMLFile().load(arg_in_, protein_ids, peptide_ids); |
| 220 | } |
| 221 | else |
| 222 | { |
| 223 | logFatal("Input file type not recognized."); |
| 224 | return ILLEGAL_PARAMETERS; |
| 225 | } |
| 226 | const Size n_pep_ids = peptide_ids.size(); |
| 227 | const Size n_prot_ids = protein_ids.size(); |
| 228 | |
| 229 | writeLogInfo_("Number of Peptide IDs in input file: " + String(n_pep_ids)); |
| 230 | writeLogInfo_("Number of Protein IDs in input file: " + String(n_prot_ids)); |
| 231 | |
| 232 | // Terminate if no hits could be found |
| 233 | if (n_pep_ids == 0) |
| 234 | { |
| 235 | logFatal("Input file does not contain any identifications."); |
| 236 | return INPUT_FILE_EMPTY; |
| 237 | } |
| 238 | |
| 239 | // Terminate if do not exactly encounter one protein id |
| 240 | if (n_prot_ids != 1) |
| 241 | { |
| 242 | logFatal("There is not exactly one protein identification in the input file. This is unsupported!"); |
| 243 | return INPUT_FILE_CORRUPT; |
| 244 | } |
| 245 | protein_id = protein_ids[0]; |
| 246 | |
| 247 | return EXECUTION_OK; |
| 248 | } |
| 249 | |
| 250 | void logFatal(const String &message) const |
| 251 | { |