28 #include "boost/filesystem/path.hpp" 37 namespace bfs = boost::filesystem;
43 void verifyScanInfo(
const Spectrum& spectrum,
const double&
epsilon,
double basePeakMZ,
double lowestObservedMZ,
double highestObservedMZ,
int mzArrayIndex1,
double mzArrayValue1,
int mzArrayIndex2,
double mzArrayValue2)
50 *
os_ <<
"[verifyScanInfo] " << spectrum.
index <<
" " << spectrum.
id <<
" " 51 << basePeakMZ <<
" " << lowestObservedMZ <<
" " << highestObservedMZ <<
" " 52 << mzArrayValue1 <<
" " << mzArrayValue2 <<
": " 55 << binaryData->data[mzArrayIndex2] << endl;
71 const SelectedIon& selectedIon = precursor.selectedIons[0];
77 *
os_ <<
"[verifyPrecursorInfo] " << spectrum.
index <<
" " << spectrum.
id <<
" " 78 << precursorMZ <<
" " << isolationWindowTarget <<
": " 88 MSDataFile msd((datadir /
"JD_06232014_sample4_C.mzML").
string());
91 if (
os_) *
os_ <<
"original spectra:\n";
108 shared_ptr<SpectrumList_MZRefiner> spectrumListMZRefined(
112 if (
os_) *
os_ <<
"refined spectra:\n";
129 void test(
const bfs::path& datadir)
135 int main(
int argc,
char* argv[])
141 bfs::path datadir =
".";
144 for (
int i=1; i<argc; i++)
146 if (!strcmp(argv[i],
"-v"))
152 datadir = bfs::path(argv[i]).branch_path();
155 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
CVParam cvParam(CVID cvid) const
finds cvid in the container:
a virtual container of integers, accessible via an iterator interface, stored as union of intervals ...
The method of precursor ion selection and activation.
MS_highest_observed_m_z
highest observed m/z: Highest m/z value observed in the m/z array.
void verifyScanInfo(const Spectrum &spectrum, const double &epsilon, double basePeakMZ, double lowestObservedMZ, double highestObservedMZ, int mzArrayIndex1, double mzArrayValue1, int mzArrayIndex2, double mzArrayValue2)
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 an selected ion.
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
MS_base_peak_m_z
base peak m/z: M/z value of the signal of highest intensity in the mass spectrum. ...
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
bool hasBinaryData() const
returns true iff has nonnull and nonempty BinaryDataArrayPtr
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
MS_isolation_window_target_m_z
isolation window target m/z: The primary or reference m/z about which the isolation window is defined...
This element captures the isolation (or 'selection') window configured to isolate one or more precurs...
MSData object plus file I/O.
void verifyPrecursorInfo(const Spectrum &spectrum, const double &epsilon, double precursorMZ, double isolationWindowTarget)
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.
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
#define TEST_PROLOG(argc, argv)
void testShift(const bfs::path &datadir)
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
value_type valueAs() const
templated value access with type conversion
int main(int argc, char *argv[])
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
void test(const bfs::path &datadir)