| 356 | } |
| 357 | |
| 358 | void readPoutAsMap_(const String& pout_file, std::map<String, PercolatorResult>& pep_map) |
| 359 | { |
| 360 | CsvFile csv_file(pout_file, '\t'); |
| 361 | StringList row; |
| 362 | |
| 363 | for (Size i = 1; i < csv_file.rowCount(); ++i) |
| 364 | { |
| 365 | csv_file.getRow(i, row); |
| 366 | PercolatorResult res(row); |
| 367 | // note: Since we create our pin file in a way that the SpecID (=PSMId) is composed of filename + spectrum native id |
| 368 | // this will be passed through Percolator and we use it again to read it back in. |
| 369 | String spec_ref = res.PSMId + res.peptide; |
| 370 | writeDebug_("PSM identifier in pout file: " + spec_ref, 10); |
| 371 | |
| 372 | // retain only the best result in the unlikely case that a PSMId+peptide combination occurs multiple times |
| 373 | if (pep_map.find(spec_ref) == pep_map.end()) |
| 374 | { |
| 375 | pep_map.insert( map<String, PercolatorResult>::value_type ( spec_ref, res ) ); |
| 376 | } |
| 377 | } |
| 378 | } |
| 379 | |
| 380 | /// We only read the q-value for protein groups since Percolator has a more elaborate FDR estimation. |
| 381 | /// For proteins we add q-value as main score and PEP as metavalue. |