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];
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";
89 void test(
const bfs::path& datadir)
95 int 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;
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged...
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 ...
void test5peptideFT(const bfs::path &datadir)
SpectrumList wrapper that recalculates precursor info on spectrum() requests.
The method of precursor ion selection and activation.
void verifyPrecursorInfo(const Spectrum &spectrum, double precursorMZ, int precursorCharge)
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
#define unit_assert_equal(x, y, epsilon)
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.
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.
#define TEST_PROLOG(argc, argv)
The structure that captures the generation of a peak list (including the underlying acquisitions) ...