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MS2DeisotoperTest.cpp File Reference
#include "MS2Deisotoper.hpp"
#include "SpectrumList_PeakFilter.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  TestDeisotopeCalculator
 

Functions

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

Variables

ostream * os_ = 0
 
TestDeisotopeCalculator testDeisotopeCalculators []
 
TestDeisotopeCalculator goldStandard []
 
const size_t testDeisotopeSize = sizeof(testDeisotopeCalculators) / sizeof(TestDeisotopeCalculator)
 
const size_t goldStandardSize = sizeof(goldStandard) / sizeof(TestDeisotopeCalculator)
 

Function Documentation

§ operator<<()

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

Definition at line 37 of file MS2DeisotoperTest.cpp.

38 {
39  os << "(";
40  for (size_t i=0; i < v.size(); ++i)
41  os << " " << v[i];
42  os << " )";
43  return os;
44 }

§ parseDoubleArray()

vector<double> parseDoubleArray ( const string &  doubleArray)

Definition at line 86 of file MS2DeisotoperTest.cpp.

Referenced by test().

87 {
88  vector<double> doubleVector;
89  vector<string> tokens;
90  bal::split(tokens, doubleArray, bal::is_space(), bal::token_compress_on);
91  if (!tokens.empty())
92  for (size_t i=0; i < tokens.size(); ++i)
93  if (!tokens[i].empty())
94  doubleVector.push_back(lexical_cast<double>(tokens[i]));
95  return doubleVector;
96 }

§ test()

int test ( )

Definition at line 98 of file MS2DeisotoperTest.cpp.

References ralab::base::filter::filter(), TestDeisotopeCalculator::inputIntensityArray, TestDeisotopeCalculator::inputMZArray, MS_ms_level, MS_MSn_spectrum, MS_number_of_detector_counts, parseDoubleArray(), pwiz::msdata::SpectrumListSimple::spectra, testDeisotopeSize, unit_assert, and unit_assert_equal.

Referenced by main().

99 {
100  int failedTests = 0;
101 
102  // create the spectrum list
104  SpectrumListPtr originalList(sl);
105 
106  for (size_t i=0; i < testDeisotopeSize; ++i)
107  {
109  // attach all the data to the spectrum list
110  SpectrumPtr s(new Spectrum);
111  s->set(MS_MSn_spectrum);
112  s->set(MS_ms_level,2);
113  s->precursors.push_back(Precursor(100.0)); // dummy precursor m/z
114 
115  vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
116  vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
117  s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_detector_counts);
118  s->defaultArrayLength = inputMZArray.size();
119 
120  sl->spectra.push_back(s);
121 
122  }
123 
124  vector<double> goldMZArray = parseDoubleArray(goldStandard[0].inputMZArray);
125  vector<double> goldIntensityArray = parseDoubleArray(goldStandard[0].inputIntensityArray);
126 
127  // construct the filter
128  bool hires = false;
129  MZTolerance mzt(hires? 0.01 : 0.5);
130  bool poisson = true;
131  int maxCharge = 3, minCharge = 1;
132  SpectrumDataFilterPtr filter = SpectrumDataFilterPtr(new MS2Deisotoper(MS2Deisotoper::Config(mzt, hires, poisson, maxCharge, minCharge)));
133 
134  // run spectral summation
135  try
136  {
137 
138  SpectrumListPtr calculator(new SpectrumList_PeakFilter(originalList,filter));
139 
140  for (size_t i=0; i < calculator->size(); ++i)
141  {
142  SpectrumPtr s = calculator->spectrum(i,true);
143  vector<double>& mzs = s->getMZArray()->data;
144  vector<double>& intensities = s->getIntensityArray()->data;
145 
146  vector<double> goldMZArray = parseDoubleArray(goldStandard[i].inputMZArray);
147  vector<double> goldIntensityArray = parseDoubleArray(goldStandard[i].inputIntensityArray);
148 
149  unit_assert(mzs.size() == goldMZArray.size());
150  unit_assert(intensities.size() == goldIntensityArray.size());
151 
152  for (size_t j=0; j < mzs.size(); ++j)
153  {
154  unit_assert_equal(mzs[j], goldMZArray[j], 1e-5);
155  unit_assert_equal(intensities[j], goldIntensityArray[j], 1e-5);
156  }
157 
158  }
159 
160 
161 
162 
163  }
164  catch (exception& e)
165  {
166  cerr << "Test failed:\n" << e.what() << endl;
167  ++failedTests;
168  }
169  return failedTests;
170 }
TestDeisotopeCalculator goldStandard[]
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
Definition: cv.hpp:2212
The method of precursor ion selection and activation.
Definition: MSData.hpp:310
const size_t testDeisotopeSize
boost::shared_ptr< SpectrumDataFilter > SpectrumDataFilterPtr
Definition: DataFilter.hpp:42
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: MSData.hpp:569
SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation appl...
#define unit_assert_equal(x, y, epsilon)
Definition: unit.hpp:99
TestDeisotopeCalculator testDeisotopeCalculators[]
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
Definition: cv.hpp:1987
PrecursorMassFilter&#39;s parameters.
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition: MSData.hpp:707
std::vector< SpectrumPtr > spectra
Definition: MSData.hpp:714
MS_number_of_detector_counts
number of detector counts: The number of counted events observed in one or a group of elements of a d...
Definition: cv.hpp:580
struct for expressing m/z tolerance in either amu or ppm
Definition: MZTolerance.hpp:38
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: MSData.hpp:504
vector< double > parseDoubleArray(const string &doubleArray)
Simple writeable in-memory implementation of SpectrumList.
Definition: MSData.hpp:712
#define unit_assert(x)
Definition: unit.hpp:85
void filter(const TContainer &data, const TContainer &filter, TContainer &result, bool circular=false, uint32_t sides=2)
Applies linear convolution (filtering) to a univariate time series.
Definition: filter.hpp:112

§ main()

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

Definition at line 173 of file MS2DeisotoperTest.cpp.

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

174 {
175  TEST_PROLOG(argc, argv)
176 
177  try
178  {
179  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
180  int failedTests = test();
181  unit_assert_operator_equal(0, failedTests);
182  }
183  catch (exception& e)
184  {
185  TEST_FAILED(e.what())
186  }
187  catch (...)
188  {
189  TEST_FAILED("Caught unknown exception.")
190  }
191 
193 }
#define TEST_EPILOG
Definition: unit.hpp:182
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
ostream * os_
#define TEST_FAILED(x)
Definition: unit.hpp:176
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:174
int test()

Variable Documentation

§ os_

ostream* os_ = 0

Definition at line 35 of file MS2DeisotoperTest.cpp.

Referenced by main().

§ testDeisotopeCalculators

TestDeisotopeCalculator testDeisotopeCalculators[]
Initial value:
=
{
{ "300.0 302.1 303.11 304.12 305.20",
"1.0 85.0 15.0 3.0 3.0"},
{ "299.5 300.01 300.52 301.03",
"10.0 75.0 25.0 40.0"},
{ "302.1 302.435 302.77 302.94 303.11",
"61.0 31.0 8.0 45.0 40.0"},
}

Definition at line 54 of file MS2DeisotoperTest.cpp.

§ goldStandard

TestDeisotopeCalculator goldStandard[]
Initial value:
=
{
{ "300.0 302.1 305.20",
"1.0 85.0 3.0"},
{ "299.5 300.01 301.03",
"10.0 75.0 40.0"},
{ "302.1 302.94 303.11",
"61.0 45.0 40.0"},
}

Definition at line 68 of file MS2DeisotoperTest.cpp.

§ testDeisotopeSize

const size_t testDeisotopeSize = sizeof(testDeisotopeCalculators) / sizeof(TestDeisotopeCalculator)

Definition at line 83 of file MS2DeisotoperTest.cpp.

Referenced by test().

§ goldStandardSize

const size_t goldStandardSize = sizeof(goldStandard) / sizeof(TestDeisotopeCalculator)

Definition at line 84 of file MS2DeisotoperTest.cpp.