Loads a Swath run from a list of split mzML files
| 29 | |
| 30 | /// Loads a Swath run from a list of split mzML files |
| 31 | std::vector<OpenSwath::SwathMap> SwathFile::loadSplit(StringList file_list, |
| 32 | const String& tmp, |
| 33 | boost::shared_ptr<ExperimentalSettings>& exp_meta, |
| 34 | const String& readoptions) |
| 35 | { |
| 36 | int progress = 0; |
| 37 | startProgress(0, file_list.size(), "Loading data"); |
| 38 | |
| 39 | std::vector<OpenSwath::SwathMap> swath_maps(file_list.size()); |
| 40 | #ifdef _OPENMP |
| 41 | #pragma omp parallel for |
| 42 | #endif |
| 43 | for (SignedSize i = 0; i < boost::numeric_cast<SignedSize>(file_list.size()); ++i) |
| 44 | { |
| 45 | |
| 46 | #ifdef _OPENMP |
| 47 | #pragma omp critical (OPENMS_SwathFile_loadSplit) |
| 48 | #endif |
| 49 | { |
| 50 | std::cout << "Loading file " << i << " with name " << file_list[i] << " using readoptions " << readoptions << std::endl; |
| 51 | } |
| 52 | |
| 53 | String tmp_fname = "openswath_tmpfile_" + String(i) + ".mzML"; |
| 54 | |
| 55 | boost::shared_ptr<PeakMap > exp(new PeakMap); |
| 56 | OpenSwath::SpectrumAccessPtr spectra_ptr; |
| 57 | |
| 58 | // Populate meta-data |
| 59 | if (i == 0) |
| 60 | { |
| 61 | exp_meta = populateMetaData_(file_list[i]); |
| 62 | } |
| 63 | |
| 64 | if (readoptions == "normal") |
| 65 | { |
| 66 | MzMLFile().load(file_list[i], *exp.get()); |
| 67 | spectra_ptr = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp); |
| 68 | } |
| 69 | else if (readoptions == "cache") |
| 70 | { |
| 71 | // Cache and load the exp (metadata only) file again |
| 72 | spectra_ptr = doCacheFile_(file_list[i], tmp, tmp_fname, exp); |
| 73 | } |
| 74 | else |
| 75 | { |
| 76 | throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, |
| 77 | "Unknown option " + readoptions); |
| 78 | } |
| 79 | |
| 80 | OpenSwath::SwathMap swath_map; |
| 81 | |
| 82 | bool ms1 = false; |
| 83 | double upper = -1, lower = -1, center = -1; |
| 84 | if (exp->empty()) |
| 85 | { |
| 86 | std::cerr << "WARNING: File " << file_list[i] << "\n does not have any scans - I will skip it" << std::endl; |
| 87 | continue; |
| 88 | } |