OpenMS  2.6.0
GoodDiffFilter.h
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31 // $Maintainer: Timo Sachsenberg $
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35 
36 #pragma once
37 
39 
40 #include <map>
41 #include <string>
42 #include <cmath>
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI GoodDiffFilter :
54  public FilterFunctor
55  {
56 public:
57 
58  // @name Constructors and Destructors
59  // @{
62 
64  GoodDiffFilter(const GoodDiffFilter & source);
65 
67  ~GoodDiffFilter() override;
68  // @}
69 
70  // @name Operators
71  // @{
73  GoodDiffFilter & operator=(const GoodDiffFilter & source);
74  // @}
75 
76  // @name Accessors
77  // @{
79  static FilterFunctor * create() { return new GoodDiffFilter(); }
80 
82  template <typename SpectrumType>
83  double apply(SpectrumType & spectrum)
84  {
85  double tolerance = (double)param_.getValue("tolerance");
86  double gooddiff = 0;
87  //iterate over all peaks
88  double totaldiff = 0;
89  for (Size i = 0; i < spectrum.size(); ++i)
90  {
91  //look for each peakdifference that is in range of aa residuemasses (56/187), if it could be a aa (aamass)
92  for (Size j = i; i + j < spectrum.size(); ++j)
93  {
94  double diff = spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0];
95  if (diff < 56)
96  {
97  continue;
98  }
99 
100  if (diff > 187)
101  {
102  j = spectrum.size();
103  }
104  else
105  {
106  totaldiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
107  std::map<double, char>::const_iterator aait = aamass_.lower_bound(diff);
108  if (aait == aamass_.end())
109  {
110  continue;
111  }
112  //look for aamasses that fit diff
113  if (fabs(aait->first - diff) <= tolerance)
114  {
115  gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
116  }
117  else
118  {
119  ++aait;
120  if ((aait) != aamass_.end() && fabs((aait)->first - diff) <= tolerance)
121  {
122  gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
123  }
124  }
125  }
126  }
127  }
128 
129  return gooddiff / totaldiff;
130  }
131 
133  static const String getProductName()
134  {
135  return "GoodDiffFilter";
136  }
137 
138  // @}
139 
140 
141 private:
142 
144  std::map<double, char> aamass_;
145  };
146 }
147 
OpenMS::GoodDiffFilter
GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid ...
Definition: GoodDiffFilter.h:53
ConsensusXMLFile.h
UniqueIdInterface.h
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
BinnedSpectralContrastAngle.h
double
OpenMS::BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES
static constexpr const float DEFAULT_BIN_WIDTH_HIRES
Definition: BinnedSpectrum.h:99
OpenMS::BinnedSpectrum
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:59
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SpectraMerger.h
TOPPGNPSExport::TOPPGNPSExport
TOPPGNPSExport()
Definition: GNPSExport.cpp:82
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
TOPPGNPSExport::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: GNPSExport.cpp:93
FilterFunctor.h
BinnedSpectrum.h
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::ConsensusFeature::end
const_iterator end() const
TOPPGNPSExport
Definition: GNPSExport.cpp:79
TOPPGNPSExport::main_
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: GNPSExport.cpp:115
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
int
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:80
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
main
int main(int argc, const char **argv)
Definition: GNPSExport.cpp:378
MSExperiment.h
OpenMS::GoodDiffFilter::getProductName
static const String getProductName()
Definition: GoodDiffFilter.h:133
OpenMS::ConsensusFeature::begin
const_iterator begin() const
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
OpenMS::GoodDiffFilter::create
static FilterFunctor * create()
Definition: GoodDiffFilter.h:79
OpenMS::GoodDiffFilter::aamass_
std::map< double, char > aamass_
list of unique amino acid masses
Definition: GoodDiffFilter.h:144
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
OpenMS::BinnedSpectralContrastAngle
Compare functor scoring the spectral contrast angle for similarity measurement.
Definition: BinnedSpectralContrastAngle.h:57
PeptideIdentification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::GoodDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: GoodDiffFilter.h:83
OpenMS::TOPPBase::main
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
OpenMS::UniqueIdInterface::getUniqueId
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:105
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::BinnedSpectrum::DEFAULT_BIN_OFFSET_HIRES
static constexpr const float DEFAULT_BIN_OFFSET_HIRES
default bin offset for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
Definition: BinnedSpectrum.h:102
MSSpectrum.h
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:62