FeatureDetectorPeakelTest.cpp File Reference

#include "FeatureDetectorPeakel.hpp"
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/filesystem/path.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions
void	verifyBombesinFeatures (const FeatureField &featureField)
shared_ptr< FeatureDetectorPeakel >	createFeatureDetectorPeakel ()
void	testBombesin (const string &filename)
void	test (const bfs::path &datadir)
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void verifyBombesinFeatures

(

const FeatureField &

featureField

)

Definition at line 42 of file FeatureDetectorPeakelTest.cpp.

References epsilon, pwiz::analysis::MZRTField< T >::find(), unit_assert, and unit_assert_equal.

Referenced by testBombesin().

{
    const double epsilon = .01;

    const double mz_bomb2 = 810.415;
    vector<FeaturePtr> bombesin_2_found = featureField.find(mz_bomb2, epsilon, 
        RTMatches_Contains<Feature>(1865));
    unit_assert(bombesin_2_found.size() == 1);
    const Feature& bombesin_2 = *bombesin_2_found[0];
    unit_assert(bombesin_2.charge == 2);
    unit_assert(bombesin_2.peakels.size() == 5);
    unit_assert_equal(bombesin_2.peakels[0]->mz, mz_bomb2, epsilon);
    unit_assert_equal(bombesin_2.peakels[1]->mz, mz_bomb2+.5, epsilon);
    unit_assert_equal(bombesin_2.peakels[2]->mz, mz_bomb2+1, epsilon);
    unit_assert_equal(bombesin_2.peakels[3]->mz, mz_bomb2+1.5, epsilon);
    unit_assert_equal(bombesin_2.peakels[4]->mz, mz_bomb2+2, epsilon);
    //TODO: verify feature metadata

    const double mz_bomb3 = 540.612;
    vector<FeaturePtr> bombesin_3_found = featureField.find(mz_bomb3, epsilon, 
        RTMatches_Contains<Feature>(1865));
    unit_assert(bombesin_3_found.size() == 1);
    const Feature& bombesin_3 = *bombesin_3_found[0];
    unit_assert(bombesin_3.charge == 3);
    unit_assert(bombesin_3.peakels.size() == 3);
    unit_assert_equal(bombesin_3.peakels[0]->mz, mz_bomb3, epsilon);
    unit_assert_equal(bombesin_3.peakels[1]->mz, mz_bomb3+1./3, epsilon);
    unit_assert_equal(bombesin_3.peakels[2]->mz, mz_bomb3+2./3, epsilon);
    //TODO: verify feature metadata
}

shared_ptr<FeatureDetectorPeakel> createFeatureDetectorPeakel

(

)

Definition at line 74 of file FeatureDetectorPeakelTest.cpp.

References pwiz::analysis::PeakelPicker_Basic::Config::log, pwiz::analysis::PeakelPicker_Basic::Config::maxCharge, pwiz::analysis::PeakelPicker_Basic::Config::minCharge, pwiz::analysis::PeakelPicker_Basic::Config::minMonoisotopicPeakelSize, pwiz::analysis::PeakelPicker_Basic::Config::minPeakelCount, pwiz::analysis::PeakelPicker_Basic::Config::mzTolerance, pwiz::analysis::PeakelGrower_Proximity::Config::mzTolerance, pwiz::analysis::FeatureDetectorPeakel::Config::noiseCalculator_2Pass, pwiz::analysis::FeatureDetectorPeakel::Config::peakelGrower_Proximity, pwiz::analysis::FeatureDetectorPeakel::Config::peakelPicker_Basic, pwiz::analysis::FeatureDetectorPeakel::Config::peakFinder_SNR, pwiz::analysis::FeatureDetectorPeakel::Config::peakFitter_Parabola, pwiz::analysis::PeakFinder_SNR::Config::preprocessWithLogarithm, pwiz::analysis::PeakelPicker_Basic::Config::rtTolerance, pwiz::analysis::PeakelGrower_Proximity::Config::rtTolerance, pwiz::analysis::PeakFinder_SNR::Config::windowRadius, pwiz::analysis::PeakFitter_Parabola::Config::windowRadius, pwiz::analysis::NoiseCalculator_2Pass::Config::zValueCutoff, and pwiz::analysis::PeakFinder_SNR::Config::zValueThreshold.

Referenced by testBombesin().

{
    FeatureDetectorPeakel::Config config;

    // these are just the defaults, to demonstrate usage

    config.noiseCalculator_2Pass.zValueCutoff = 1;

    config.peakFinder_SNR.windowRadius = 2;
    config.peakFinder_SNR.zValueThreshold = 3;
    config.peakFinder_SNR.preprocessWithLogarithm = true;

    config.peakFitter_Parabola.windowRadius = 1;

    config.peakelGrower_Proximity.mzTolerance = .01;
    config.peakelGrower_Proximity.rtTolerance = 10;

    config.peakelPicker_Basic.log = 0; // ostream*
    config.peakelPicker_Basic.minCharge = 2;
    config.peakelPicker_Basic.maxCharge = 5;
    config.peakelPicker_Basic.minMonoisotopicPeakelSize = 2;
    config.peakelPicker_Basic.mzTolerance = MZTolerance(10, MZTolerance::PPM);
    config.peakelPicker_Basic.rtTolerance = 5;
    config.peakelPicker_Basic.minPeakelCount = 3;

    return FeatureDetectorPeakel::create(config);
}

void testBombesin

(

const string &

filename

)

Definition at line 103 of file FeatureDetectorPeakelTest.cpp.

References createFeatureDetectorPeakel(), os_, pwiz::msdata::MSData::run, pwiz::msdata::Run::spectrumListPtr, unit_assert, and verifyBombesinFeatures().

Referenced by test().

{
    if (os_) *os_ << "testBombesin()" << endl;

    // open data file and check sanity

    MSDataFile msd(filename);
    unit_assert(msd.run.spectrumListPtr.get());
    unit_assert(msd.run.spectrumListPtr->size() == 8);

    // instantiate FeatureDetector

    shared_ptr<FeatureDetectorPeakel> featureDetectorPeakel = createFeatureDetectorPeakel();

    FeatureField featureField;
    featureDetectorPeakel->detect(msd, featureField);
    
    if (os_) *os_ << "featureField:\n" << featureField << endl;
    verifyBombesinFeatures(featureField);
}

void test

(

const bfs::path &

datadir

)

Definition at line 125 of file FeatureDetectorPeakelTest.cpp.

References testBombesin().

{
    testBombesin((datadir / "FeatureDetectorTest_Bombesin.mzML").string());
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 131 of file FeatureDetectorPeakelTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

{
    TEST_PROLOG(argc, argv)

    try
    {
        bfs::path datadir = ".";

        for (int i=1; i<argc; i++)
        {
            if (!strcmp(argv[i],"-v")) 
                os_ = &cout;
            else
                // hack to allow running unit test from a different directory:
                // Jamfile passes full path to specified input file.
                // we want the path, so we can ignore filename
                datadir = bfs::path(argv[i]).branch_path(); 
        }   
        
        test(datadir);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

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Variable Documentation

ostream* os_ = 0

Definition at line 39 of file FeatureDetectorPeakelTest.cpp.