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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)
 

Function Documentation

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

Definition at line 36 of file SpectrumList_ChargeStateCalculatorTest.cpp.

37 {
38  os << "(";
39  for (size_t i=0; i < v.size(); ++i)
40  os << " " << v[i];
41  os << " )";
42  return os;
43 }
vector<double> parseDoubleArray ( const string &  doubleArray)

Definition at line 268 of file SpectrumList_ChargeStateCalculatorTest.cpp.

Referenced by test().

269 {
270  vector<double> doubleVector;
271  vector<string> tokens;
272  bal::split(tokens, doubleArray, bal::is_space(), bal::token_compress_on);
273  if (!tokens.empty())
274  for (size_t i=0; i < tokens.size(); ++i)
275  if (!tokens[i].empty())
276  doubleVector.push_back(lexical_cast<double>(tokens[i]));
277  return doubleVector;
278 }
vector<CVID> parseCVTermArray ( const string &  cvTermArray)

Definition at line 280 of file SpectrumList_ChargeStateCalculatorTest.cpp.

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

Referenced by test().

281 {
282  static pwiz::data::CVTranslator cvTranslator;
283  vector<CVID> cvTermVector;
284  vector<string> tokens;
285  bal::split(tokens, cvTermArray, bal::is_space());
286  if (!tokens.empty() && !tokens[0].empty())
287  for (size_t i=0; i < tokens.size(); ++i)
288  cvTermVector.push_back(cvTranslator.translate(tokens[i]));
289  return cvTermVector;
290 }
translates text to CV terms
cv::CVID translate(const std::string &text) const
translate text -> CVID
int test ( )

Definition at line 292 of file SpectrumList_ChargeStateCalculatorTest.cpp.

References TestChargeStateCalculator::chargeStateArray, pwiz::data::CVParam::cvid, 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().

Referenced by main().

293 {
294  int failedTests = 0;
295  for (size_t i=0; i < testChargeStateCalculatorsSize; ++i)
296  {
298  SpectrumListPtr originalList(sl);
299  SpectrumPtr s(new Spectrum);
300  s->set(MS_MSn_spectrum);
301  s->set(MS_ms_level, 2);
302  sl->spectra.push_back(s);
303 
304  try
305  {
307 
308  vector<double> inputMZArray = parseDoubleArray(t.inputMZArray);
309  vector<double> inputIntensityArray = parseDoubleArray(t.inputIntensityArray);
310  s->setMZIntensityArrays(inputMZArray, inputIntensityArray, MS_number_of_counts);
311 
312  s->precursors.push_back(Precursor(t.inputPrecursorMZ));
313  vector<double> inputChargeStateArray = parseDoubleArray(t.inputChargeStateArray);
314  CVID inputChargeStateTerm = inputChargeStateArray.size() > 1 ? MS_possible_charge_state : MS_charge_state;
315  BOOST_FOREACH(int z, inputChargeStateArray)
316  s->precursors[0].selectedIons[0].cvParams.push_back(CVParam(inputChargeStateTerm, z));
317 
318  vector<CVID> inputActivationTypes = parseCVTermArray(t.inputActivationTypeArray);
319  BOOST_FOREACH(CVID cvid, inputActivationTypes)
320  s->precursors[0].activation.set(cvid);
321 
323  originalList,
324  t.overrideExistingChargeState,
325  t.maxMultipleCharge,
326  t.minMultipleCharge,
327  t.singlyChargedFraction,
328  t.useMakeMS2Behavior));
329 
330  vector<double> outputChargeStateArray = parseDoubleArray(t.chargeStateArray);
331  CVID outputChargeStateTerm = outputChargeStateArray.size() > 1 ? MS_possible_charge_state : MS_charge_state;
332  SpectrumPtr calculatedSpectrum = calculator->spectrum(0, true);
333  BOOST_FOREACH(const CVParam& cvParam, calculatedSpectrum->precursors[0].selectedIons[0].cvParams)
334  {
335  if (cvParam.cvid != MS_charge_state && cvParam.cvid != MS_possible_charge_state)
336  continue;
337  unit_assert_operator_equal(outputChargeStateTerm, cvParam.cvid);
338  unit_assert(find(outputChargeStateArray.begin(), outputChargeStateArray.end(), cvParam.valueAs<int>()) != outputChargeStateArray.end());
339  }
340  }
341  catch (exception& e)
342  {
343  cerr << "Test case " << (i+1) << " failed:\n" << e.what() << endl;
344  ++failedTests;
345  }
346  }
347  return failedTests;
348 }
vector< CVID > parseCVTermArray(const string &cvTermArray)
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged...
Definition: cv.hpp:227
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS/MS experiments designed to record product ion spectra wher...
Definition: cv.hpp:2204
The method of precursor ion selection and activation.
Definition: MSData.hpp:310
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: MSData.hpp:565
TestChargeStateCalculator testChargeStateCalculators[]
SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.
vector< double > parseDoubleArray(const string &doubleArray)
const size_t testChargeStateCalculatorsSize
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
Definition: cv.hpp:1979
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:86
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition: MSData.hpp:712
MS_possible_charge_state
possible charge state: A possible charge state of the ion in a situation where the charge of an ion i...
Definition: cv.hpp:2411
std::vector< SpectrumPtr > spectra
Definition: MSData.hpp:719
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: MSData.hpp:504
Simple writeable in-memory implementation of SpectrumList.
Definition: MSData.hpp:717
#define unit_assert(x)
Definition: unit.hpp:82
MS_number_of_counts
number of counts: The number of counted events observed in one or a group of elements of a detector...
Definition: cv.hpp:572
represents a tag-value pair, where the tag comes from the controlled vocabulary
Definition: ParamTypes.hpp:44
int main ( int  argc,
char *  argv[] 
)

Definition at line 351 of file SpectrumList_ChargeStateCalculatorTest.cpp.

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

352 {
353  TEST_PROLOG(argc, argv)
354 
355  try
356  {
357  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
358  int failedTests = test();
359  unit_assert_operator_equal(0, failedTests);
360  }
361  catch (exception& e)
362  {
363  TEST_FAILED(e.what())
364  }
365  catch (...)
366  {
367  TEST_FAILED("Caught unknown exception.")
368  }
369 
371 }
#define TEST_EPILOG
Definition: unit.hpp:166
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:86
#define TEST_FAILED(x)
Definition: unit.hpp:160
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:158

Variable Documentation

ostream* os_ = 0

Definition at line 34 of file SpectrumList_ChargeStateCalculatorTest.cpp.

Referenced by main().

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().