OpenMS  2.5.0
Classes | Typedefs
MetaProSIP.cpp File Reference
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/CHEMISTRY/Element.h>
#include <OpenMS/CHEMISTRY/ElementDB.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/MATH/MISC/NonNegativeLeastSquaresSolver.h>
#include <OpenMS/FORMAT/SVOutStream.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/GaussModel.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/FILTERING/TRANSFORMERS/ThresholdMower.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/SYSTEM/File.h>
#include <boost/math/distributions/normal.hpp>
#include <QtCore/QStringList>
#include <QtCore/QFile>
#include <QtCore/QDir>
#include <QtCore/QFileInfo>
#include <QtCore/QProcess>
#include <algorithm>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <map>
#include <cmath>

Classes

struct  RateScorePair
 
struct  SIPIncorporation
 datastructure for reporting an incorporation event More...
 
struct  SIPPeptide
 datastructure for reporting a peptide with one or more incorporation rates More...
 
struct  SizeLess
 
struct  SequenceLess
 
struct  RIALess
 
class  MetaProSIPInterpolation
 
class  MetaProSIPClustering
 
class  MetaProSIPReporting
 
class  MetaProSIPDecomposition
 
class  MetaProSIPXICExtraction
 
class  RIntegration
 

Typedefs

typedef map< double, double > MapRateToScoreType
 
typedef pair< double, vector< double > > IsotopePattern
 
typedef vector< IsotopePatternIsotopePatterns
 

Class Documentation

◆ RateScorePair

struct RateScorePair
Class Members
double rate
double score

◆ SIPIncorporation

struct SIPIncorporation

datastructure for reporting an incorporation event

Class Members
double abundance abundance of isotopologue
double correlation correlation coefficient
double rate rate

◆ SIPPeptide

struct SIPPeptide

datastructure for reporting a peptide with one or more incorporation rates

Class Members
vector< String > accessions protein accessions of the peptide
PeakSpectrum accumulated
Int charge charge of the peptide feature
MapRateToScoreType correlation_map
vector< RateScorePair > correlation_maxima
MapRateToScoreType decomposition_map
double explained_TIC_fraction fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights
double feature_mz mz of feature apex [s]
double feature_rt measurement time of feature apex [s]
String feature_type used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reporting
double global_LR labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities. (15N analogous)
vector< SIPIncorporation > incorporations
double mass_diff
double mass_theo uncharged theoretical mass
double mz_theo theoretical mz
Size non_zero_decomposition_coefficients decomposition coefficients significantly larger than 0
IsotopePatterns patterns
PeakSpectrum reconstruction signal reconstruction (debugging)
vector< double > reconstruction_monoistopic signal reconstruction of natural peptide (at mono-isotopic peak)
double RR R squared of NNLS fit.
double score search engine score or q-value if fdr filtering is applied
AASequence sequence sequence of the peptide
bool unique if the peptide is unique and therefor identifies the protein umambigously

Typedef Documentation

◆ IsotopePattern

typedef pair<double, vector<double> > IsotopePattern

◆ IsotopePatterns

◆ MapRateToScoreType

typedef map<double, double> MapRateToScoreType