| 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 comparator for vectors of SIPPeptides based on their size. Used to sort by group size. 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< IsotopePattern > | IsotopePatterns

## 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 comparator for vectors of SIPPeptides based on their size. Used to sort by group size.

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

typedef vector<IsotopePattern> IsotopePatterns

## ◆ MapRateToScoreType

typedef map<double, double> MapRateToScoreType