AMTDatabaseTest.cpp File Reference

#include "AMTDatabase.hpp"
#include "AMTContainer.hpp"
#include "pwiz/utility/proteome/Ion.hpp"
#include "pwiz/utility/misc/unit.hpp"

Go to the source code of this file.

Typedefs
typedef IslandizedDatabase::Gaussian	Gaussian

Functions
boost::shared_ptr< SpectrumQuery >	makeSpectrumQuery (const double &mass, const int &charge, const double &rt, const string &sequence, const double &score=0.95)
boost::shared_ptr< AMTContainer >	makeAMTContainer ()
void	write (const Gaussian &gaussian)
void	test ()
int	main ()

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Typedef Documentation

typedef IslandizedDatabase::Gaussian Gaussian

Definition at line 37 of file AMTDatabaseTest.cpp.

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Function Documentation

boost::shared_ptr<SpectrumQuery> makeSpectrumQuery	(	const double &	mass,
		const int &	charge,
		const double &	rt,
		const string &	sequence,
		const double &	score = 0.95
	)

Definition at line 39 of file AMTDatabaseTest.cpp.

Referenced by makeAMTContainer(), makeMatch(), makeMSMSRunSummary(), test(), testAdjustRT(), testMerge(), testPeptideID_dataFetcherConstructor(), and testSpectrumQuery().

{
    boost::shared_ptr<SpectrumQuery> result(new SpectrumQuery());
    result->precursorNeutralMass = mass;
    result->assumedCharge = charge;
    result->retentionTimeSec = rt;
    result->searchResult.searchHit.peptide = sequence;
    result->searchResult.searchHit.analysisResult.peptideProphetResult.probability = score;

    return result;

}

boost::shared_ptr<AMTContainer> makeAMTContainer

(

)

Definition at line 52 of file AMTDatabaseTest.cpp.

References makeSpectrumQuery().

Referenced by test().

{
    boost::shared_ptr<AMTContainer> result(new AMTContainer());

    boost::shared_ptr<SpectrumQuery> rag_a = makeSpectrumQuery(3,3,3,"rag");    
    boost::shared_ptr<SpectrumQuery> rag_c = makeSpectrumQuery(3,3,3,"rag");
    boost::shared_ptr<SpectrumQuery> rag_b = makeSpectrumQuery(2,4,0.5,"rag");
    boost::shared_ptr<SpectrumQuery> mallick_a = makeSpectrumQuery(5,1,7,"mallick");
    boost::shared_ptr<SpectrumQuery> mallick_b = makeSpectrumQuery(15,3,7,"mallick");
    
    vector<boost::shared_ptr<SpectrumQuery> > sqs;
    sqs.clear();
    sqs.push_back(rag_a);    
    sqs.push_back(rag_c);
    sqs.push_back(rag_b);
    sqs.push_back(mallick_a);
    sqs.push_back(mallick_b);

    PidfPtr pidf(new PeptideID_dataFetcher(sqs));
    result->_pidf = pidf;
    result->rtAdjusted = true; // don't worry about adjusting RT here
    result->_sqs = sqs;

    return result;

}

void write

(

const Gaussian &

gaussian

)

Definition at line 79 of file AMTDatabaseTest.cpp.

References pwiz::eharmony::IslandizedDatabase::Gaussian::mu, and pwiz::eharmony::IslandizedDatabase::Gaussian::sigma.

Referenced by demo(), pwiz::data::diff_string(), pwiz::identdata::DelimWriter::operator()(), pwiz::data::operator<<(), test(), test_v3(), testBinaryDataArray(), testChromatogram(), testChromatogramListWithPositions(), testIdentData(), testIdentifyFileFormat(), testMSData(), testObject(), testObject_ChromatogramList(), testObject_SpectrumList(), testObjectWithMSData(), testRun(), testSHA1(), testSpectrum(), testSpectrumListWithPositions(), testSpectrumListWriteProgress(), testTraData(), testWriteRead(), validateWriteRead(), and writeTempFile().

{
    cout << gaussian.mu.first << endl;
    cout << gaussian.mu.second << endl;
    cout << gaussian.sigma.first << endl;
    cout << gaussian.sigma.second << endl;

    return;
}

void test

(

)

Definition at line 89 of file AMTDatabaseTest.cpp.

References pwiz::eharmony::IslandizedDatabase::Island::gaussians, pwiz::eharmony::IslandizedDatabase::Island::id, and makeAMTContainer().

{
    boost::shared_ptr<AMTContainer> amtc = makeAMTContainer();
    IslandizedDatabase id(amtc);

    // make the Island that we expect to find
    IslandizedDatabase::Island island;
    island.id = "rag";
    
    IslandizedDatabase::Gaussian gaussian(make_pair(make_pair(1.00727, 3), make_pair(.0009, 90)));
    IslandizedDatabase::Gaussian gaussian_2(make_pair(make_pair(2.00727, 3), make_pair(.0009, 90)));
    island.gaussians.push_back(gaussian);
    island.gaussians.push_back(gaussian_2);
    
    //    write(gaussian);
    //    write(gaussian_2);
    //    write(*(id.islands.begin())->gaussians.begin());

    // create IslandizedDatabase
    // test existence of the islands and correctness of their mu and sigmas

}

int main

(

)

Definition at line 112 of file AMTDatabaseTest.cpp.

References test().

{
    test();
    return 0;
}