SpectrumList_ChargeStateCalculatorTest.cpp File Reference

#include "SpectrumList_ChargeStateCalculator.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/data/msdata/examples.hpp"
#include "pwiz/data/msdata/TextWriter.hpp"
#include "pwiz/data/common/CVTranslator.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Classes
struct	TestChargeStateCalculator

Functions
ostream &	operator<< (ostream &os, const vector< double > &v)
vector< double >	parseDoubleArray (const string &doubleArray)
vector< CVID >	parseCVTermArray (const string &cvTermArray)
int	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
TestChargeStateCalculator	testChargeStateCalculators []
const size_t	testChargeStateCalculatorsSize = sizeof(testChargeStateCalculators) / sizeof(TestChargeStateCalculator)

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Function Documentation

ostream& operator<<	(	ostream &	os,
		const vector< double > &	v
	)

Definition at line 36 of file SpectrumList_ChargeStateCalculatorTest.cpp.

{
    os << "(";
    for (size_t i=0; i < v.size(); ++i)
        os << " " << v[i];
    os << " )";
    return os;
}

vector<double> parseDoubleArray

(

const string &

doubleArray

)

Definition at line 268 of file SpectrumList_ChargeStateCalculatorTest.cpp.

{
    vector<double> doubleVector;
    vector<string> tokens;
    bal::split(tokens, doubleArray, bal::is_space(), bal::token_compress_on);
    if (!tokens.empty())
        for (size_t i=0; i < tokens.size(); ++i)
            if (!tokens[i].empty())
                doubleVector.push_back(lexical_cast<double>(tokens[i]));
    return doubleVector;
}

vector<CVID> parseCVTermArray

(

const string &

cvTermArray

)

Definition at line 280 of file SpectrumList_ChargeStateCalculatorTest.cpp.

References pwiz::data::CVTranslator::translate().

Referenced by test().

{
    static pwiz::data::CVTranslator cvTranslator;
    vector<CVID> cvTermVector;
    vector<string> tokens;
    bal::split(tokens, cvTermArray, bal::is_space());
    if (!tokens.empty() && !tokens[0].empty())
        for (size_t i=0; i < tokens.size(); ++i)
            cvTermVector.push_back(cvTranslator.translate(tokens[i]));
    return cvTermVector;
}

int test

(

)

Definition at line 292 of file SpectrumList_ChargeStateCalculatorTest.cpp.

References TestChargeStateCalculator::chargeStateArray, pwiz::data::CVParam::cvid, e(), TestChargeStateCalculator::inputActivationTypeArray, TestChargeStateCalculator::inputChargeStateArray, TestChargeStateCalculator::inputIntensityArray, TestChargeStateCalculator::inputMZArray, TestChargeStateCalculator::inputPrecursorMZ, TestChargeStateCalculator::maxMultipleCharge, TestChargeStateCalculator::minMultipleCharge, MS_charge_state, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_possible_charge_state, TestChargeStateCalculator::overrideExistingChargeState, parseCVTermArray(), parseDoubleArray(), TestChargeStateCalculator::singlyChargedFraction, pwiz::msdata::SpectrumListSimple::spectra, testChargeStateCalculators, testChargeStateCalculatorsSize, unit_assert, unit_assert_operator_equal, TestChargeStateCalculator::useMakeMS2Behavior, and pwiz::data::CVParam::valueAs().

{
    int failedTests = 0;
    for (size_t i=0; i < testChargeStateCalculatorsSize; ++i)
    {
        SpectrumListSimple* sl = new SpectrumListSimple;
        SpectrumListPtr originalList(sl);
        SpectrumPtr s(new Spectrum);
        s->set(MS_MSn_spectrum);
        s->set(MS_ms_level, 2);
        sl->spectra.push_back(s);

        try
        {
            TestChargeStateCalculator& t = testChargeStateCalculators[i];

            vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
            vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
            s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);

            s->precursors.push_back(Precursor(t.inputPrecursorMZ));
            vector<double> inputChargeStateArray = parseDoubleArray(t.inputChargeStateArray);
            CVID inputChargeStateTerm = inputChargeStateArray.size() > 1 ? MS_possible_charge_state : MS_charge_state;
            BOOST_FOREACH(int z, inputChargeStateArray)
                s->precursors[0].selectedIons[0].cvParams.push_back(CVParam(inputChargeStateTerm, z));

            vector<CVID> inputActivationTypes = parseCVTermArray(t.inputActivationTypeArray);
            BOOST_FOREACH(CVID cvid, inputActivationTypes)
                s->precursors[0].activation.set(cvid);

            SpectrumListPtr calculator(new SpectrumList_ChargeStateCalculator(
                originalList,
                t.overrideExistingChargeState,
                t.maxMultipleCharge,
                t.minMultipleCharge,
                t.singlyChargedFraction,
                t.useMakeMS2Behavior));

            vector<double> outputChargeStateArray = parseDoubleArray(t.chargeStateArray);
            CVID outputChargeStateTerm = outputChargeStateArray.size() > 1 ? MS_possible_charge_state : MS_charge_state;
            SpectrumPtr calculatedSpectrum = calculator->spectrum(0, true);
            BOOST_FOREACH(const CVParam& cvParam, calculatedSpectrum->precursors[0].selectedIons[0].cvParams)
            {
                if (cvParam.cvid != MS_charge_state && cvParam.cvid != MS_possible_charge_state)
                    continue;
                unit_assert_operator_equal(outputChargeStateTerm, cvParam.cvid);
                unit_assert(find(outputChargeStateArray.begin(), outputChargeStateArray.end(), cvParam.valueAs<int>()) != outputChargeStateArray.end());
            }
        }
        catch (exception& e)
        {
            cerr << "Test case " << (i+1) << " failed:\n" << e.what() << endl;
            ++failedTests;
        }
    }
    return failedTests;
}

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

Definition at line 351 of file SpectrumList_ChargeStateCalculatorTest.cpp.

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

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        int failedTests = test();
        unit_assert_operator_equal(0, failedTests);
    }
    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 34 of file SpectrumList_ChargeStateCalculatorTest.cpp.

TestChargeStateCalculator testChargeStateCalculators[]

Definition at line 63 of file SpectrumList_ChargeStateCalculatorTest.cpp.

Referenced by test().

const size_t testChargeStateCalculatorsSize = sizeof(testChargeStateCalculators) / sizeof(TestChargeStateCalculator)

Definition at line 266 of file SpectrumList_ChargeStateCalculatorTest.cpp.

Referenced by test().