27#include "boost/filesystem/path.hpp"
36namespace bfs = boost::filesystem;
52 *
os_ <<
"[verifyPrecursorInfo] " << spectrum.
index <<
" " << spectrum.
id <<
" "
53 << precursorMZ <<
" " << precursorCharge <<
": "
59 if (precursorCharge != 0)
66 MSDataFile msd((datadir /
"5peptideFT.mzML").
string());
69 if (
os_) *
os_ <<
"original spectra:\n";
76 shared_ptr<SpectrumList_PrecursorRecalculator> spectrumListRecalculated(
80 if (
os_) *
os_ <<
"recalculated spectra:\n";
89void test(
const bfs::path& datadir)
95int main(
int argc,
char* argv[])
101 bfs::path datadir =
".";
103 for (
int i=1; i<argc; i++)
105 if (!strcmp(argv[i],
"-v"))
111 datadir = bfs::path(argv[i]).branch_path();
114 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
int main(int argc, char *argv[])
void verifyPrecursorInfo(const Spectrum &spectrum, double precursorMZ, int precursorCharge)
void test5peptideFT(const bfs::path &datadir)
SpectrumList wrapper that recalculates precursor info on spectrum() requests.
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged.
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
value_type valueAs() const
templated value access with type conversion
CVParam cvParam(CVID cvid) const
finds cvid in the container:
MSData object plus file I/O.
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
The method of precursor ion selection and activation.
std::vector< SelectedIon > selectedIons
this list of precursor ions that were selected.
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
The structure that captures the generation of a peak list (including the underlying acquisitions)
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
#define unit_assert_equal(x, y, epsilon)
#define TEST_PROLOG(argc, argv)