SpectrumIteratorTest.cpp File Reference

#include "SpectrumIterator.hpp"
#include "MSData.hpp"
#include "pwiz/utility/misc/IntegerSet.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Classes
class	FTSieve

Functions
void	initializeSpectrumList (SpectrumListSimple &spectrumList)
const char *	anal (const CVParam &cvParam)
void	printSpectrumList (ostream &os, const SpectrumList &sl)
void	testBasic (const SpectrumList &sl)
void	doSomething (const Spectrum &spectrum)
void	testForEach (const SpectrumList &spectrumList)
void	testIntegerSet (const SpectrumList &spectrumList)
int	getScanNumber (const Spectrum &spectrum)
void	testSieve (const SpectrumList &spectrumList)
void	testIteratorEquality (const SpectrumList &spectrumList)
void	testMSDataConstruction ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void initializeSpectrumList

(

SpectrumListSimple &

spectrumList

)

Definition at line 40 of file SpectrumIteratorTest.cpp.

References boost::lexical_cast(), MS_FT_ICR, MS_intensity_array, MS_ion_trap, MS_m_z_array, and pwiz::msdata::SpectrumListSimple::spectra.

Referenced by main(), and testMSDataConstruction().

{
    // initialize with scans:
    // scan  0: IT
    // scan  5: FT (1,100)
    // scan 10: IT (1,100), (2,200)
    // scan 15: FT (1,100), (2,200), (3,300)
    // scan 20: IT (1,100), (2,200), (3,300), (4,400)
    // ...

    for (int i=0; i<=10; i++)
    {
        SpectrumPtr spectrum(new Spectrum);
        spectrum->id = lexical_cast<string>(i*5);
        
        spectrum->cvParams.push_back(i%2 ? 
            MS_FT_ICR :
            MS_ion_trap);

        BinaryDataArrayPtr bdMZ(new BinaryDataArray);
        bdMZ->cvParams.push_back(MS_m_z_array);
        spectrum->binaryDataArrayPtrs.push_back(bdMZ);

        BinaryDataArrayPtr bdIntensity(new BinaryDataArray);
        bdIntensity->cvParams.push_back(MS_intensity_array);
        spectrum->binaryDataArrayPtrs.push_back(bdIntensity);

        for (int j=1; j<=i; j++)
        {
            bdMZ->data.push_back(j);
            bdIntensity->data.push_back(100*j);
        }

        spectrum->defaultArrayLength = i;
        spectrumList.spectra.push_back(spectrum);
    }
}

const char* anal

(

const CVParam &

cvParam

)

Definition at line 79 of file SpectrumIteratorTest.cpp.

References MS_FT_ICR, and MS_ion_trap.

Referenced by doSomething(), printSpectrumList(), test(), and testMSDataConstruction().

{
    if (cvParam == MS_FT_ICR)
        return "FT";
    else if (cvParam == MS_ion_trap)
        return "IT";
    else 
        return "Unknown";
}

void printSpectrumList	(	ostream &	os,
		const SpectrumList &	sl
	)

Definition at line 90 of file SpectrumIteratorTest.cpp.

References anal(), MS_mass_analyzer, os_, pwiz::msdata::SpectrumList::size(), and pwiz::msdata::SpectrumList::spectrum().

{
    if (os_) *os_ << "printSpectrumList()\n";

    for (unsigned int i=0; i<sl.size(); i++)
    {
        SpectrumPtr spectrum = sl.spectrum(i);
        os << spectrum->id << " "
           << anal(spectrum->cvParamChild(MS_mass_analyzer)) << endl;

        vector<MZIntensityPair> mziPairs;
        spectrum->getMZIntensityPairs(mziPairs);
        copy(mziPairs.begin(), mziPairs.end(), ostream_iterator<MZIntensityPair>(os,""));
        os << endl;
    }
}

void testBasic

(

const SpectrumList &

sl

)

Definition at line 108 of file SpectrumIteratorTest.cpp.

References pwiz::msdata::Spectrum::binaryDataArrayPtrs, pwiz::msdata::SpectrumIdentity::id, MS_FT_ICR, MS_ion_trap, MS_mass_analyzer_type, os_, and unit_assert.

{
    if (os_) *os_ << "testBasic()\n";

    SpectrumIterator it(sl);

    unit_assert(it->id == "0");
    unit_assert((*it).cvParamChild(MS_mass_analyzer_type) == MS_ion_trap);
    unit_assert(it->binaryDataArrayPtrs.size() == 2);

    ++it; ++it; ++it; ++it; ++it; // advance to scan 5

    unit_assert(it->id == "25");
    unit_assert(it->cvParamChild(MS_mass_analyzer_type) == MS_FT_ICR);
    unit_assert(it->binaryDataArrayPtrs.size() == 2 &&
                it->binaryDataArrayPtrs[0]->data.size() == 5);
}

void doSomething

(

const Spectrum &

spectrum

)

Definition at line 127 of file SpectrumIteratorTest.cpp.

References anal(), pwiz::data::ParamContainer::cvParamChild(), pwiz::msdata::Spectrum::getMZIntensityPairs(), pwiz::msdata::SpectrumIdentity::id, boost::lexical_cast(), MS_mass_analyzer, os_, and unit_assert.

Referenced by testForEach(), and testIntegerSet().

{
    if (os_) *os_ << "spectrum: " << spectrum.id << " "
                  << anal(spectrum.cvParamChild(MS_mass_analyzer)) << endl; 
    
    vector<MZIntensityPair> pairs;
    spectrum.getMZIntensityPairs(pairs);

    if (os_)
    {
        copy(pairs.begin(), pairs.end(), ostream_iterator<MZIntensityPair>(*os_,"")); 
        *os_ << endl;
    }
  
    unit_assert((int)pairs.size()*5 == lexical_cast<int>(spectrum.id));
}

void testForEach

(

const SpectrumList &

spectrumList

)

Definition at line 145 of file SpectrumIteratorTest.cpp.

References doSomething(), and os_.

Referenced by main().

{
    if (os_) *os_ << "testForEach(): \n";
    for_each(SpectrumIterator(spectrumList), SpectrumIterator(), doSomething);
}

void testIntegerSet

(

const SpectrumList &

spectrumList

)

Definition at line 152 of file SpectrumIteratorTest.cpp.

References doSomething(), pwiz::util::IntegerSet::insert(), and os_.

Referenced by main().

{
    // iterate through even scan numbers 

    if (os_) *os_ << "testIntegerSet():\n";

    IntegerSet scanNumbers;
    for (int i=2; i<=50; i+=2) // note that some scan numbers don't exist in spectrumList 
        scanNumbers.insert(i);
    
    // loop written for illustration
    // note automatic conversion from IntegerSet to SpectrumIterator::Config
    for (SpectrumIterator it(spectrumList, scanNumbers); it!=SpectrumIterator(); ++it)
        doSomething(*it); 

    // using for_each: 
    for_each(SpectrumIterator(spectrumList, scanNumbers), SpectrumIterator(), doSomething);
}

int getScanNumber ( const Spectrum &  spectrum )

inline

Definition at line 172 of file SpectrumIteratorTest.cpp.

References pwiz::msdata::SpectrumIdentity::id, and boost::lexical_cast().

Referenced by testSieve().

{
    return lexical_cast<int>(spectrum.id);
}

void testSieve

(

const SpectrumList &

spectrumList

)

Definition at line 188 of file SpectrumIteratorTest.cpp.

References getScanNumber(), os_, and unit_assert.

Referenced by main().

{
    vector<int> ftScanNumbers;

    FTSieve sieve;
    SpectrumIterator::Config config(sieve, false);

    transform(SpectrumIterator(spectrumList, config),
              SpectrumIterator(), 
              back_inserter(ftScanNumbers), 
              getScanNumber);

    if (os_)
    {
        *os_ << "testSieve():\n"; 
        copy(ftScanNumbers.begin(), ftScanNumbers.end(), ostream_iterator<int>(*os_, " "));
        *os_ << endl;
    }

    unit_assert(ftScanNumbers.size() == 5);
    unit_assert(ftScanNumbers[0] == 5);
    unit_assert(ftScanNumbers[1] == 15);
    unit_assert(ftScanNumbers[2] == 25);
    unit_assert(ftScanNumbers[3] == 35);
    unit_assert(ftScanNumbers[4] == 45);
}

void testIteratorEquality

(

const SpectrumList &

spectrumList

)

Definition at line 216 of file SpectrumIteratorTest.cpp.

References os_, and unit_assert.

Referenced by main().

{
    if (os_) *os_ << "testIteratorEquality()\n";

    SpectrumIterator it(spectrumList);
    ++it; ++it; ++it;

    SpectrumIterator jt(spectrumList);
    unit_assert(it!=jt);
    ++jt;
    unit_assert(it!=jt);
    ++jt;
    unit_assert(it!=jt);
    ++jt;
    unit_assert(it==jt);
}

void testMSDataConstruction

(

)

Definition at line 234 of file SpectrumIteratorTest.cpp.

References anal(), initializeSpectrumList(), MS_mass_analyzer, os_, pwiz::msdata::MSData::run, pwiz::msdata::Run::spectrumListPtr, and unit_assert.

Referenced by main().

{
    if (os_) *os_ << "testMSDataConstruction()\n";

    SpectrumListSimplePtr sl(new SpectrumListSimple());
    initializeSpectrumList(*sl);

    MSData msd;
    msd.run.spectrumListPtr = sl; 

    int i = 0;
    FTSieve sieve;
    for (SpectrumIterator it(msd, sieve); it!=SpectrumIterator(); ++it, ++i)
    {
        if (os_) *os_ << it->id << " "
                      << anal(it->cvParamChild(MS_mass_analyzer)) << endl;

        unit_assert(it->id == lexical_cast<string>(5+i*10));
    }
}

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

Definition at line 256 of file SpectrumIteratorTest.cpp.

References e(), initializeSpectrumList(), os_, printSpectrumList(), TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testBasic(), testForEach(), testIntegerSet(), testIteratorEquality(), testMSDataConstruction(), and testSieve().

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;

        SpectrumListSimple spectrumList;
        initializeSpectrumList(spectrumList);
        if (os_) printSpectrumList(*os_, spectrumList);

        testBasic(spectrumList);
        testForEach(spectrumList);
        testIntegerSet(spectrumList);
        testSieve(spectrumList);
        testIteratorEquality(spectrumList);
        testMSDataConstruction();

    }
    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 37 of file SpectrumIteratorTest.cpp.