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;
value_type valueAs() const
templated value access with type conversion
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)
bool hasBinaryData() const
returns true iff has nonnull and nonempty BinaryDataArrayPtr
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...
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.
#define TEST_PROLOG(argc, argv)
CVParam cvParam(CVID cvid) const
finds cvid in the container:
void testShift(const bfs::path &datadir)
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
int main(int argc, char *argv[])
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
void test(const bfs::path &datadir)