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SpectrumList_PeakFilterTest.cpp File Reference
#include "pwiz/data/msdata/MSData.hpp"
#include "PrecursorMassFilter.hpp"
#include "ThresholdFilter.hpp"
#include "MS2Deisotoper.hpp"
#include "MS2NoiseFilter.hpp"
#include "SpectrumList_PeakFilter.hpp"
#include "SpectrumList_ZeroSamplesFilter.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/data/msdata/examples.hpp"
#include "pwiz/data/msdata/TextWriter.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Classes

struct  TestETDMassFilter
struct  TestThresholder
struct  TestDeisotoper
struct  TestMS2Denoise

Macros

#define PRECURSOR_CHARGE   3
#define PRECURSOR_MZ   445.34

Functions

ostream & operator<< (ostream &os, const vector< double > &v)
vector< double > parseDoubleArray (const string &doubleArray)
void testPrecursorMassRemoval ()
void testIntensityThresholding ()
void testDeisotoping ()
void testMS2Denoising ()
void testZeroSamplesFilter ()
void test ()
int main (int argc, char *argv[])

Variables

ostream * os_ = 0
TestETDMassFilter testETDMassFilterData []
const size_t testETDMassFilterDataSize = sizeof(testETDMassFilterData) / sizeof(TestETDMassFilter)
TestThresholder testThresholders []
const size_t testThresholdersSize = sizeof(testThresholders) / sizeof(TestThresholder)
TestDeisotoper TestDeisotopers []
const size_t testDeisotopersSize = sizeof(TestDeisotopers) / sizeof(TestDeisotoper)
TestMS2Denoise TestMS2DenoiseArr []
const size_t testMS2DenoiseSize = sizeof(TestMS2DenoiseArr) / sizeof(TestMS2Denoise)

Macro Definition Documentation

#define PRECURSOR_CHARGE   3

Definition at line 82 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testDeisotoping(), and testPrecursorMassRemoval().

#define PRECURSOR_MZ   445.34

Definition at line 83 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testDeisotoping(), and testPrecursorMassRemoval().


Function Documentation

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

Definition at line 41 of file SpectrumList_PeakFilterTest.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 50 of file SpectrumList_PeakFilterTest.cpp.

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

Definition at line 147 of file SpectrumList_PeakFilterTest.cpp.

References TestETDMassFilter::blanketRemovalofNeutralLoss, TestETDMassFilter::hasCharge, TestETDMassFilter::inputIntensityArray, TestETDMassFilter::inputMZArray, TestETDMassFilter::matchingTolerance, MS_charge_state, MS_electron_transfer_dissociation, MS_m_z, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_selected_ion_m_z, TestETDMassFilter::outputIntensityArray, TestETDMassFilter::outputMZArray, parseDoubleArray(), PRECURSOR_CHARGE, PRECURSOR_MZ, TestETDMassFilter::removeNeutralLossPrecursors, TestETDMassFilter::removePrecursor, TestETDMassFilter::removeReducedChargePrecursors, pwiz::msdata::SpectrumListSimple::spectra, testETDMassFilterData, testETDMassFilterDataSize, unit_assert, unit_assert_equal, and TestETDMassFilter::usePPM.

Referenced by test().

{
for (size_t i=0; i < testETDMassFilterDataSize; ++i)
{
SpectrumListPtr originalList(sl);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
s->set(MS_MSn_spectrum);
s->set(MS_ms_level, 2);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
s->precursors.resize(1);
s->precursors[0].activation.set(MS_electron_transfer_dissociation);
s->precursors[0].selectedIons.resize(1);
s->precursors[0].selectedIons[0].set(MS_selected_ion_m_z, PRECURSOR_MZ, MS_m_z);
if (t.hasCharge)
s->precursors[0].selectedIons[0].set(MS_charge_state, PRECURSOR_CHARGE);
MZTolerance tol(t.matchingTolerance, t.usePPM ? MZTolerance::PPM : MZTolerance::MZ);
{
filter.reset(new PrecursorMassFilter(params));
}
else
{
filter.reset(new PrecursorMassFilter(params));
}
SpectrumListPtr peakFilter(new SpectrumList_PeakFilter(originalList, filter));
SpectrumPtr pFiltered = peakFilter->spectrum(0, true);
vector<double> outputMZArray = parseDoubleArray(t.outputMZArray);
vector<double> outputIntensityArray = parseDoubleArray(t.outputIntensityArray);
vector<double>& resultMZArray = pFiltered->getMZArray()->data;
vector<double>& resultIntensityArray = pFiltered->getIntensityArray()->data;
unit_assert(resultMZArray.size() == outputMZArray.size());
unit_assert(resultIntensityArray.size() == outputIntensityArray.size());
for (size_t ii=0; ii < outputMZArray.size(); ++ii)
{
unit_assert_equal(resultMZArray[ii], outputMZArray[ii], 0.001);
unit_assert_equal(resultIntensityArray[ii], outputIntensityArray[ii], 0.001);
}
}
}
void testIntensityThresholding ( )

Definition at line 350 of file SpectrumList_PeakFilterTest.cpp.

References TestThresholder::byType, TestThresholder::inputIntensityArray, TestThresholder::inputMZArray, MS_ms_level, MS_number_of_counts, TestThresholder::orientation, TestThresholder::outputIntensityArray, TestThresholder::outputMZArray, parseDoubleArray(), pwiz::msdata::SpectrumListSimple::spectra, testThresholders, testThresholdersSize, TestThresholder::threshold, and unit_assert.

Referenced by test().

{
// default msLevelsToThreshold should include all levels
for (size_t i=0; i < testThresholdersSize; ++i)
{
SpectrumListPtr originalList(sl);
s->set(MS_ms_level, 2);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
SpectrumListPtr thresholder(new SpectrumList_PeakFilter(originalList, pFilter));
vector<double> outputMZArray = parseDoubleArray(t.outputMZArray);
vector<double> outputIntensityArray = parseDoubleArray(t.outputIntensityArray);
SpectrumPtr thresholdedSpectrum = thresholder->spectrum(0, true);
//if (os_) cout << s1->defaultArrayLength << ": " << s1->getMZArray()->data << " " << s1->getIntensityArray()->data << endl;
unit_assert(thresholdedSpectrum->defaultArrayLength == outputMZArray.size());
for (size_t i=0; i < outputMZArray.size(); ++i)
{
unit_assert(thresholdedSpectrum->getMZArray()->data[i] == outputMZArray[i]);
unit_assert(thresholdedSpectrum->getIntensityArray()->data[i] == outputIntensityArray[i]);
}
}
// test that msLevelsToThreshold actually works
for (size_t i=0; i < testThresholdersSize; ++i)
{
SpectrumListPtr originalList(sl);
s->set(MS_ms_level, 1);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
SpectrumListPtr thresholder(new SpectrumList_PeakFilter(originalList, pFilter));
SpectrumPtr unthresholdedSpectrum = thresholder->spectrum(0, true);
//if (os_) cout << s1->defaultArrayLength << ": " << s1->getMZArray()->data << " " << s1->getIntensityArray()->data << endl;
unit_assert(unthresholdedSpectrum->defaultArrayLength == inputMZArray.size());
for (size_t i=0; i < inputMZArray.size(); ++i)
{
unit_assert(unthresholdedSpectrum->getMZArray()->data[i] == inputMZArray[i]);
unit_assert(unthresholdedSpectrum->getIntensityArray()->data[i] == inputIntensityArray[i]);
}
}
}
void testDeisotoping ( )

Definition at line 443 of file SpectrumList_PeakFilterTest.cpp.

References TestDeisotoper::hires, TestDeisotoper::inputIntensityArray, TestDeisotoper::inputMZArray, MS_charge_state, MS_electron_transfer_dissociation, MS_m_z, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_selected_ion_m_z, TestDeisotoper::outputIntensityArray, TestDeisotoper::outputMZArray, parseDoubleArray(), PRECURSOR_CHARGE, PRECURSOR_MZ, pwiz::msdata::SpectrumListSimple::spectra, TestDeisotopers, testDeisotopersSize, TestDeisotoper::tol, and unit_assert.

Referenced by test().

{
for (size_t i=0; i < testDeisotopersSize; ++i)
{
SpectrumListPtr originalList(sl);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
s->set(MS_MSn_spectrum);
s->set(MS_ms_level, 2);
s->precursors.resize(1);
s->precursors[0].activation.set(MS_electron_transfer_dissociation);
s->precursors[0].selectedIons.resize(1);
s->precursors[0].selectedIons[0].set(MS_selected_ion_m_z, PRECURSOR_MZ, MS_m_z);
s->precursors[0].selectedIons[0].set(MS_charge_state, PRECURSOR_CHARGE);
SpectrumListPtr deisotopedList(new SpectrumList_PeakFilter(originalList, pFilter));
vector<double> outputMZArray = parseDoubleArray(t.outputMZArray);
vector<double> outputIntensityArray = parseDoubleArray(t.outputIntensityArray);
SpectrumPtr deisotopedSpectrum = deisotopedList->spectrum(0, true);
unit_assert(deisotopedSpectrum->defaultArrayLength == outputMZArray.size());
for (size_t i=0; i < outputMZArray.size(); ++i)
{
unit_assert(deisotopedSpectrum->getMZArray()->data[i] == outputMZArray[i]);
unit_assert(deisotopedSpectrum->getIntensityArray()->data[i] == outputIntensityArray[i]);
}
}
}
void testMS2Denoising ( )

Definition at line 529 of file SpectrumList_PeakFilterTest.cpp.

References TestMS2Denoise::inputIntensityArray, TestMS2Denoise::inputMZArray, TestMS2Denoise::keepTopN, MS_charge_state, MS_electron_transfer_dissociation, MS_m_z, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_selected_ion_m_z, TestMS2Denoise::outputIntensityArray, TestMS2Denoise::outputMZArray, parseDoubleArray(), TestMS2Denoise::precursorCharge, TestMS2Denoise::precursorMass, TestMS2Denoise::relaxLowMass, pwiz::msdata::SpectrumListSimple::spectra, TestMS2DenoiseArr, testMS2DenoiseSize, unit_assert, and TestMS2Denoise::windowSize.

Referenced by test().

{
for (size_t i=0; i < testMS2DenoiseSize; ++i)
{
SpectrumListPtr originalList(sl);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
s->set(MS_MSn_spectrum);
s->set(MS_ms_level, 2);
s->precursors.resize(1);
s->precursors[0].activation.set(MS_electron_transfer_dissociation);
s->precursors[0].selectedIons.resize(1);
s->precursors[0].selectedIons[0].set(MS_selected_ion_m_z, t.precursorMass, MS_m_z);
s->precursors[0].selectedIons[0].set(MS_charge_state, t.precursorCharge);
SpectrumListPtr filteredList(new SpectrumList_PeakFilter(originalList, pFilter));
vector<double> outputMZArray = parseDoubleArray(t.outputMZArray);
vector<double> outputIntensityArray = parseDoubleArray(t.outputIntensityArray);
SpectrumPtr filteredSpectrum = filteredList->spectrum(0, true);
unit_assert(filteredSpectrum->defaultArrayLength == outputMZArray.size());
for (size_t i=0; i < outputMZArray.size(); ++i)
{
unit_assert(filteredSpectrum->getMZArray()->data[i] == outputMZArray[i]);
unit_assert(filteredSpectrum->getIntensityArray()->data[i] == outputIntensityArray[i]);
}
}
}
void testZeroSamplesFilter ( )

Definition at line 569 of file SpectrumList_PeakFilterTest.cpp.

References MS_charge_state, MS_electron_transfer_dissociation, MS_m_z, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_selected_ion_m_z, parseDoubleArray(), pwiz::msdata::SpectrumListSimple::spectra, and unit_assert.

Referenced by test().

{
const char* RawX =
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const char* RawY =
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"164.043045043945 0 0 0 0 0 0 0 0 101.22346496582 199.961135864258 181.580459594727 0 0 0 0 0 0 0 0 171.627029418945 216.893325805664 165.188735961914 0 0 0 0 0 0 0 0 184.577438354492 315.924865722656 400.736938476563 401.748779296875 309.456359863281 177.526077270508 0 0 0 0 0 0 0 0 71.3968505859375 196.379440307617 317.622741699219 323.017578125 218.84977722168 108.977661132813 0 0 0 0 0 0 0 0 143.710311889648 248.819686889648 318.435913085938 338.807861328125 306.490661621094 239.977798461914 197.418716430664 128.426620483398 0 0 0 0 0 0 0 0 126.655654907227 226.479202270508 229.53288269043 179.628677368164 0 0 0 0 0 0 0 0 144.30647277832 214.861099243164 189.256454467773 0 0 0 0 0 0 0 0 188.085342407227 308.395935058594 374.08056640625 337.305053710938 193.459030151367 33.2561950683594 0 0 0 0 0 0 0 0 101.20735168457 200.764785766602 247.183944702148 206.08268737793 87.9416961669922 0 0 0 0 0 0 0 0 95.3595581054688 225.91584777832 248.077072143555 250.59260559082 257.277648925781 180.943740844727 0 0 0 0 0 0 0 0 155.655776977539 238.868362426758 250.283981323242 157.468978881836 0 0 0 0 0 0 0 0 165.849624633789 341.285217285156 449.087829589844 465.197448730469 414.669006347656 350.80908203125 287.216369628906 202.29280090332 102.295700073242 0 0 0 0 0 0 0 0 122.961654663086 216.524826049805 227.398483276367 197.743057250977 252.932815551758 368.044921875 412.497924804688 332.376770019531 189.94221496582 0 0 0 0 0 0 0 0 110.821487426758 205.431838989258 197.784744262695 165.351150512695 0 0 0 0 0 0 0 0 148.747482299805 197.384048461914 222.412368774414 130.84407043457 0 0 0 0 0 0 0 0 186.619369506836 231.119979858398 185.139663696289 0 0 0 0 0 0 0 0 129.717819213867 224.055252075195 180.142196655273 0 0 0 0 0 0 0 0 176.265243530273 223.66975402832 295.446105957031 361.572326660156 360.102111816406 244.047714233398 41.8561553955078 0 0 0 0 0 0 0 0 160.23698425293 238.57145690918 249.646987915039 191.794631958008 0 0 0 0 0 0 0 0 177.559341430664 308.058898925781 "
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SpectrumListPtr originalList(sl);
sl->spectra.push_back(s);
vector<double> inputMZArray = parseDoubleArray(RawX);
vector<double> inputIntensityArray = parseDoubleArray(RawY);
s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
s->set(MS_MSn_spectrum);
s->set(MS_ms_level, 2);
s->precursors.resize(1);
s->precursors[0].activation.set(MS_electron_transfer_dissociation);
s->precursors[0].selectedIons.resize(1);
s->precursors[0].selectedIons[0].set(MS_selected_ion_m_z, 1000, MS_m_z);
s->precursors[0].selectedIons[0].set(MS_charge_state, 2);
// should be no change if we specify MS3
SpectrumListPtr filteredList2(new
SpectrumList_ZeroSamplesFilter(originalList,IntegerSet(3),SpectrumList_ZeroSamplesFilter::Mode_RemoveExtraZeros,0));
SpectrumPtr filteredSpectrum2 = filteredList2->spectrum(0, true);
unit_assert(filteredSpectrum2->getIntensityArray()->data[9] == inputIntensityArray[9]);
SpectrumListPtr filteredList(new
SpectrumList_ZeroSamplesFilter(originalList,IntegerSet(2),SpectrumList_ZeroSamplesFilter::Mode_RemoveExtraZeros,0));
SpectrumPtr filteredSpectrum = filteredList->spectrum(0, true);
unit_assert(filteredSpectrum->getIntensityArray()->data.size() == filteredSpectrum->getMZArray()->data.size());
unit_assert(filteredSpectrum->getIntensityArray()->data[0]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[1]!=0);
unit_assert(filteredSpectrum->getIntensityArray()->data[filteredSpectrum->getIntensityArray()->data.size()-1]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[filteredSpectrum->getIntensityArray()->data.size()-2]!=0);
unit_assert(filteredSpectrum->getIntensityArray()->data[1] == inputIntensityArray[9]);
// now add missing zeros
int nzeros=10;
SpectrumListPtr filteredList3(new
SpectrumList_ZeroSamplesFilter(originalList,IntegerSet(2),SpectrumList_ZeroSamplesFilter::Mode_AddMissingZeros,nzeros));
filteredSpectrum = filteredList3->spectrum(0, true);
unit_assert(filteredSpectrum->getIntensityArray()->data[0]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[1]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[filteredSpectrum->getIntensityArray()->data.size()-1]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[filteredSpectrum->getIntensityArray()->data.size()-2]==0);
unit_assert(filteredSpectrum->getIntensityArray()->data[nzeros] == inputIntensityArray[9]);
}
void test ( )
int main ( int  argc,
char *  argv[] 
)

Definition at line 672 of file SpectrumList_PeakFilterTest.cpp.

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

{
TEST_PROLOG(argc, argv)
try
{
if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
test();
}
catch (exception& e)
{
TEST_FAILED(e.what())
}
catch (...)
{
TEST_FAILED("Caught unknown exception.")
}
}

Variable Documentation

ostream* os_ = 0

Definition at line 39 of file SpectrumList_PeakFilterTest.cpp.

TestETDMassFilter testETDMassFilterData[]

Definition at line 85 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testPrecursorMassRemoval().

const size_t testETDMassFilterDataSize = sizeof(testETDMassFilterData) / sizeof(TestETDMassFilter)

Definition at line 145 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testPrecursorMassRemoval().

TestThresholder testThresholders[]

Definition at line 221 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testIntensityThresholding().

const size_t testThresholdersSize = sizeof(testThresholders) / sizeof(TestThresholder)

Definition at line 348 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testIntensityThresholding().

TestDeisotoper TestDeisotopers[]
Initial value:
{
{
"101 102 103 104 105",
"10 20 30 20 10",
"101 102 103",
"10 20 30",
0.5,
false
},
}

Definition at line 428 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testDeisotoping().

const size_t testDeisotopersSize = sizeof(TestDeisotopers) / sizeof(TestDeisotoper)

Definition at line 441 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testDeisotoping().

TestMS2Denoise TestMS2DenoiseArr[]
Initial value:
{
{
"101 102 103 104 105",
"10 20 30 20 10",
"102 103 104",
"20 30 20",
500.0,
2,
10.0,
3,
false
},
{
"101 102 103 104 105 500 945",
"10 20 30 20 10 10 10",
"102 103 104",
"20 30 20",
500.0,
2,
10.0,
3,
false
},
}

Definition at line 501 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testMS2Denoising().

const size_t testMS2DenoiseSize = sizeof(TestMS2DenoiseArr) / sizeof(TestMS2Denoise)

Definition at line 527 of file SpectrumList_PeakFilterTest.cpp.

Referenced by testMS2Denoising().