OpenMS  3.0.0
SpectraSTSimilarityScore.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: David Wojnar $
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
62  class OPENMS_DLLAPI SpectraSTSimilarityScore :
64  {
65 public:
66 
67  // @name Constructors and Destructors
68  // @{
71 
74 
76  ~SpectraSTSimilarityScore() override;
77  // @}
78 
80  SpectraSTSimilarityScore & operator=(const SpectraSTSimilarityScore & source);
81 
85  double operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const override;
89  double operator()(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2) const;
93  double operator()(const PeakSpectrum & spec) const override;
94 
103  bool preprocess(PeakSpectrum & spec, float remove_peak_intensity_threshold = 2.01, UInt cut_peaks_below = 1000, Size min_peak_number = 5, Size max_peak_number = 150);
104 
105 
107  BinnedSpectrum transform(const PeakSpectrum & spec);
108 
116  double dot_bias(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2, double dot_product = -1) const;
117 
128  double delta_D(double top_hit, double runner_up);
129 
138  double compute_F(double dot_product, double delta_D, double dot_bias);
139 
140 
141 
144 
146  static const String getProductName()
147  {
148  return "SpectraSTSimilarityScore";
149  }
150 
151 protected:
152 
153 
154  };
155 
156 }
LogStream.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
OpenMS::SpectraSTSimilarityScore::create
static PeakSpectrumCompareFunctor * create()
Definition: SpectraSTSimilarityScore.h:143
OpenMS::BinnedSpectrum
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:80
OpenMS::File::basename
static String basename(const String &file)
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::SpectraSTSimilarityScore::getProductName
static const String getProductName()
Reimplemented from PeakSpectrumCompareFunctor.
Definition: SpectraSTSimilarityScore.h:146
OpenMS::String
A more convenient string class.
Definition: String.h:58
Int
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PeakSpectrumCompareFunctor
Base class for compare functors of spectra, that return a similarity value for two spectra.
Definition: PeakSpectrumCompareFunctor.h:52
BinnedSpectrum.h
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
QProcess
PeakSpectrumCompareFunctor.h
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::SpectraSTSimilarityScore
Similarity score of SpectraST.
Definition: SpectraSTSimilarityScore.h:62
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::String::hasSuffix
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::StringConversions::append
void append(const T &i, String &target)
Definition: StringConversions.h:118
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::StringUtils::number
static String number(double d, UInt n)
Definition: StringUtils.h:196
OpenMS::FileHandler::stripExtension
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
File.h
TOPPBase.h