27 #include "boost/filesystem/path.hpp"
33 using namespace pwiz::msdata;
34 using namespace pwiz::util;
35 using namespace pwiz::analysis;
36 namespace bfs = boost::filesystem;
47 const SelectedIon& selectedIon = precursor.selectedIons[0];
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;
void testPrecursorRefine(const bfs::path &datadir)
int main(int argc, char *argv[])
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged...
value_type valueAs() const
templated value access with type conversion
PWIZ_API_DECL const CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO ...
The method of precursor ion selection and activation.
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
#define unit_assert_equal(x, y, epsilon)
void test(const bfs::path &datadir)
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of the ion selected for fragmentation.
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
void verifyPrecursorMZ(const Spectrum &spectrum, double precursorMZ)
MSData object plus file I/O.
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.
SpectrumList wrapper that recalculates precursor info on spectrum() requests.
#define TEST_PROLOG(argc, argv)
CVParam cvParam(CVID cvid) const
finds cvid in the container:
The structure that captures the generation of a peak list (including the underlying acquisitions) ...