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27 #include "boost/filesystem/path.hpp"
36 namespace bfs = boost::filesystem;
55 *
os_ <<
"[verifyPrecursorMZ] " << spectrum.
index <<
" " << spectrum.
id <<
" "
56 << precursorMZ <<
": "
67 MSDataFile msd((datadir /
"PrecursorRefineOrbi.mzML").
string());
70 if (
os_) *
os_ <<
"original spectra:\n";
77 shared_ptr<SpectrumList_PrecursorRefine> spectrumListRecalculated(
80 unit_assert(spectrumListRecalculated->size() == 51);
81 if (
os_) *
os_ <<
"recalculated spectra:\n";
90 void test(
const bfs::path& datadir)
96 int main(
int argc,
char* argv[])
102 bfs::path datadir =
".";
104 for (
int i=1; i<argc; i++)
106 if (!strcmp(argv[i],
"-v"))
112 datadir = bfs::path(argv[i]).branch_path();
115 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged.
The structure that captures the generation of a peak list (including the underlying acquisitions)
#define unit_assert_equal(x, y, epsilon)
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
void test(const bfs::path &datadir)
value_type valueAs() const
templated value access with type conversion
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
CVParam cvParam(CVID cvid) const
finds cvid in the container:
void testPrecursorRefine(const bfs::path &datadir)
int main(int argc, char *argv[])
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
#define TEST_PROLOG(argc, argv)
MSData object plus file I/O.
SpectrumList wrapper that recalculates precursor info on spectrum() requests.
void verifyPrecursorMZ(const Spectrum &spectrum, double precursorMZ)
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
std::vector< SelectedIon > selectedIons
this list of precursor ions that were selected.
The method of precursor ion selection and activation.