| 208 | } |
| 209 | |
| 210 | ExperimentalDesign ExperimentalDesign::fromIdentifications(const vector <ProteinIdentification> &proteins) |
| 211 | { |
| 212 | ExperimentalDesign experimental_design; |
| 213 | // path of the original MS files (mzML / raw file) |
| 214 | StringList ms_run_paths; |
| 215 | for (const auto &protein : proteins) |
| 216 | { |
| 217 | // Due to merging it is valid to have multiple origins in a ProteinIDRun |
| 218 | StringList tmp_ms_run_paths; |
| 219 | protein.getPrimaryMSRunPath(tmp_ms_run_paths); |
| 220 | ms_run_paths.insert(ms_run_paths.end(), tmp_ms_run_paths.begin(), tmp_ms_run_paths.end()); |
| 221 | //TODO think about uniquifying or warning if duplicates occur |
| 222 | } |
| 223 | |
| 224 | // For now and without further info we have to assume a labelfree, unfractionated experiment |
| 225 | // no fractionation -> as many fraction_groups as samples |
| 226 | // each identification run corresponds to one sample abundance |
| 227 | unsigned sample(0); |
| 228 | ExperimentalDesign::MSFileSection rows; |
| 229 | ExperimentalDesign::SampleSection srows; |
| 230 | for (const auto &f : ms_run_paths) |
| 231 | { |
| 232 | ExperimentalDesign::MSFileSectionEntry r; |
| 233 | r.path = f; |
| 234 | r.fraction = 1; |
| 235 | r.sample = sample; |
| 236 | r.sample_name = String(sample); |
| 237 | r.fraction_group = sample; |
| 238 | r.label = 1; |
| 239 | |
| 240 | rows.push_back(r); |
| 241 | srows.addSample(String(sample)); |
| 242 | ++sample; |
| 243 | } |
| 244 | experimental_design.setMSFileSection(rows); |
| 245 | experimental_design.setSampleSection(srows); |
| 246 | OPENMS_LOG_INFO << "Experimental design (Identification derived):\n" |
| 247 | << " files: " << experimental_design.getNumberOfMSFiles() |
| 248 | << " fractions: " << experimental_design.getNumberOfFractions() |
| 249 | << " labels: " << experimental_design.getNumberOfLabels() |
| 250 | << " samples: " << experimental_design.getNumberOfSamples() << "\n" |
| 251 | << endl; |
| 252 | return experimental_design; |
| 253 | } |
| 254 | |
| 255 | map<unsigned, vector<String> > ExperimentalDesign::getFractionToMSFilesMapping() const |
| 256 | { |
nothing calls this directly
no test coverage detected