ProteoWizard
Classes | Public Types | Public Member Functions | List of all members
DemuxTest Struct Reference

Classes

struct  MSDPair
 

Public Types

typedef boost::shared_ptr< MSDataMSDataPtr
 

Public Member Functions

MSDPair GenerateSpectrumList (const string &inputFile, bool demux=false, const SpectrumList_Demux::Params &params=SpectrumList_Demux::Params()) const
 
void GetMask (const vector< double > &original, const vector< double > &derived, vector< size_t > &mask) const
 

Detailed Description

Definition at line 52 of file SpectrumList_DemuxTest.cpp.

Member Typedef Documentation

◆ MSDataPtr

typedef boost::shared_ptr<MSData> DemuxTest::MSDataPtr

Definition at line 53 of file SpectrumList_DemuxTest.cpp.

Member Function Documentation

◆ GenerateSpectrumList()

DemuxTest::MSDPair DemuxTest::GenerateSpectrumList ( const string &  inputFile,
bool  demux = false,
const SpectrumList_Demux::Params params = SpectrumList_Demux::Params() 
) const

Definition at line 68 of file SpectrumList_DemuxTest.cpp.

Referenced by testMSXOnly(), and testOverlapOnly().

71 {
72  FullReaderList readers;
73  MSDataPtr msdPtr = boost::make_shared<MSDataFile>(inputFile, &readers);
74  IntegerSet levelsToCentroid(1, 2);
75  SpectrumListPtr centroidedPtr(
76  new SpectrumList_PeakPicker(msdPtr->run.spectrumListPtr,
77  PeakDetectorPtr(boost::make_shared<LocalMaximumPeakDetector>(3)),
78  true,
79  levelsToCentroid));
80  msdPtr->filterApplied();
81 
82  if (!demux)
83  return MSDPair(msdPtr, centroidedPtr);
84 
85  SpectrumListPtr demuxList(new SpectrumList_Demux(centroidedPtr, params));
86  msdPtr->filterApplied();
87  msdPtr->run.spectrumListPtr = demuxList;
88  return MSDPair(msdPtr, demuxList);
89 }
boost::shared_ptr< PeakDetector > PeakDetectorPtr
a virtual container of integers, accessible via an iterator interface, stored as union of intervals ...
Definition: IntegerSet.hpp:37
SpectrumList decorator implementation that can demultiplex spectra of several precursor windows acqui...
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition: MSData.hpp:707
boost::shared_ptr< MSData > MSDataPtr
Definition: MSData.hpp:909
SpectrumList implementation to replace peak profiles with picked peaks.

◆ GetMask()

void DemuxTest::GetMask ( const vector< double > &  original,
const vector< double > &  derived,
vector< size_t > &  mask 
) const

Definition at line 91 of file SpectrumList_DemuxTest.cpp.

References unit_assert, and unit_assert_operator_equal.

Referenced by testMSXOnly(), and testOverlapOnly().

92 {
93  unit_assert(std::is_sorted(original.begin(), original.end()));
94  unit_assert(std::is_sorted(derived.begin(), derived.end()));
95  mask.clear();
96  auto originalIt = original.begin();
97  for (auto derivedIt = derived.begin(); derivedIt != derived.end(); ++derivedIt)
98  {
99  for (; originalIt != original.end(); ++originalIt)
100  {
101  if (abs(*originalIt - *derivedIt) < 1.0e-5)
102  {
103  mask.push_back(originalIt - original.begin());
104  break;
105  }
106  unit_assert(*originalIt < *derivedIt);
107  }
108  }
109  unit_assert_operator_equal(derived.size(), mask.size());
110 }
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
#define unit_assert(x)
Definition: unit.hpp:85

The documentation for this struct was generated from the following file: