void hackInMemoryMSData(MSData& msd)
{
// remove metadata ptrs appended on read
vector<SourceFilePtr>& sfs = msd.fileDescription.sourceFilePtrs;
if (!sfs.empty()) sfs.erase(sfs.end()-1);
vector<SoftwarePtr>& sws = msd.softwarePtrs;
if (!sws.empty()) sws.erase(sws.end()-1);
// remove current DataProcessing created on read
SpectrumListBase* sl = dynamic_cast<SpectrumListBase*>(msd.run.spectrumListPtr.get());
ChromatogramListBase* cl = dynamic_cast<ChromatogramListBase*>(msd.run.chromatogramListPtr.get());
if (sl) sl->setDataProcessingPtr(DataProcessingPtr());
if (cl) cl->setDataProcessingPtr(DataProcessingPtr());
}
void fillInCommonMetadata(const string& filename, MSData& msd)
{
appendSourceFile(filename, msd);
msd.cvs = defaultCVList();
SoftwarePtr softwarePwiz = getSoftwarePwiz(msd.softwarePtrs);
DataProcessingPtr dpPwiz(new DataProcessing);
dpPwiz->id = "pwiz_Reader_conversion";
dpPwiz->processingMethods.push_back(ProcessingMethod());
dpPwiz->processingMethods.back().softwarePtr = softwarePwiz;
dpPwiz->processingMethods.back().cvParams.push_back(MS_Conversion_to_mzML);
// give ownership of dpPwiz to the SpectrumList (and ChromatogramList)
SpectrumListBase* sl = dynamic_cast<SpectrumListBase*>(msd.run.spectrumListPtr.get());
ChromatogramListBase* cl = dynamic_cast<ChromatogramListBase*>(msd.run.chromatogramListPtr.get());
if (sl) sl->setDataProcessingPtr(dpPwiz);
if (cl) cl->setDataProcessingPtr(dpPwiz);
// the file-level ids can't be empty
if (msd.id.empty() || msd.run.id.empty())
msd.id = msd.run.id = bfs::basename(filename);
}