27#include "boost/filesystem/path.hpp"
36namespace bfs = boost::filesystem;
46 const double mz_bomb2 = 810.415;
47 vector<FeaturePtr> bombesin_2_found = featureField.
find(mz_bomb2,
epsilon,
50 const Feature& bombesin_2 = *bombesin_2_found[0];
60 const double mz_bomb3 = 540.612;
61 vector<FeaturePtr> bombesin_3_found = featureField.
find(mz_bomb3,
epsilon,
64 const Feature& bombesin_3 = *bombesin_3_found[0];
105 if (
os_) *
os_ <<
"testBombesin()" << endl;
118 featureDetectorPeakel->detect(msd, featureField);
120 if (
os_) *
os_ <<
"featureField:\n" << featureField << endl;
125void test(
const bfs::path& datadir)
127 testBombesin((datadir /
"FeatureDetectorTest_Bombesin.mzML").
string());
131int main(
int argc,
char* argv[])
137 bfs::path datadir =
".";
139 for (
int i=1; i<argc; i++)
141 if (!strcmp(argv[i],
"-v"))
147 datadir = bfs::path(argv[i]).branch_path();
void testBombesin(const string &filename)
int main(int argc, char *argv[])
shared_ptr< FeatureDetectorPeakel > createFeatureDetectorPeakel()
void verifyBombesinFeatures(const FeatureField &featureField)
static boost::shared_ptr< FeatureDetectorPeakel > create(Config config)
PeakelGrower_Proximity::Config peakelGrower_Proximity
PeakFinder_SNR::Config peakFinder_SNR
PeakFitter_Parabola::Config peakFitter_Parabola
NoiseCalculator_2Pass::Config noiseCalculator_2Pass
PeakelPicker_Basic::Config peakelPicker_Basic
MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT.
std::vector< TPtr > find(double mz, MZTolerance mzTolerance, RTMatches matches) const
find all objects with a given m/z, within a given m/z tolerance, satisfying the 'matches' predicate
bool preprocessWithLogarithm
size_t minMonoisotopicPeakelSize
predicate returns true iff the object's retention time range contains the specified retention time
struct for expressing m/z tolerance in either amu or ppm
std::vector< PeakelPtr > peakels
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.
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
#define unit_assert_equal(x, y, epsilon)
#define TEST_PROLOG(argc, argv)