OpenMS  2.8.0
Classes | Public Member Functions | Private Attributes | List of all members
TIC Class Reference

#include <OpenMS/QC/TIC.h>

Inheritance diagram for TIC:
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Collaboration diagram for TIC:
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Classes

struct  Result
 

Public Member Functions

 TIC ()=default
 Constructor. More...
 
virtual ~TIC ()=default
 Destructor. More...
 
Result compute (const MSExperiment &exp, float bin_size=0, UInt ms_level=1)
 Compute Total Ion Count and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given. More...
 
const StringgetName () const override
 Returns the name of the metric. More...
 
const std::vector< MSChromatogram > & getResults () const
 
QCBase::Status requires () const override
 Returns the input data requirements of the compute(...) function. More...
 
void addMetaDataMetricsToMzTab (MzTabMetaData &meta, std::vector< Result > &tics)
 append QC data for given metrics to mzTab's MTD section More...
 
- Public Member Functions inherited from QCBase
bool isRunnable (const Status &s) const
 

Private Attributes

const String name_ = "TIC"
 

Additional Inherited Members

- Public Types inherited from QCBase
enum class  Requires : UInt64 {
  NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,
  CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES
}
 Enum to encode a file type as a bit. More...
 
enum class  ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
 
using Status = FlagSet< Requires >
 
- Static Public Member Functions inherited from QCBase
static bool isLabeledExperiment (const ConsensusMap &cm)
 check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
 
template<typename MAP >
static bool hasPepID (const MAP &fmap)
 does the container have a PeptideIdentification in its members or as unassignedPepID ? More...
 
- Static Public Attributes inherited from QCBase
static const std::string names_of_requires []
 strings corresponding to enum Requires More...
 
static const std::string names_of_toleranceUnit []
 strings corresponding to enum ToleranceUnit More...
 

Constructor & Destructor Documentation

◆ TIC()

TIC ( )
default

Constructor.

◆ ~TIC()

virtual ~TIC ( )
virtualdefault

Destructor.

Member Function Documentation

◆ addMetaDataMetricsToMzTab()

void addMetaDataMetricsToMzTab ( MzTabMetaData meta,
std::vector< Result > &  tics 
)

append QC data for given metrics to mzTab's MTD section

◆ compute()

Result compute ( const MSExperiment exp,
float  bin_size = 0,
UInt  ms_level = 1 
)

Compute Total Ion Count and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given.

All MS1 TICs within a bin are summed up.

Parameters
expPeak map to compute the MS1 tick from
bin_sizeRT bin size in seconds
ms_levelMS level of spectra for calculation
Returns
result struct with with computed QC metrics: intensities, RTs (in seconds), area under TIC, 10x MS1 signal fall, 10x MS1 signal jump

◆ getName()

const String& getName ( ) const
overridevirtual

Returns the name of the metric.

Implements QCBase.

◆ getResults()

const std::vector<MSChromatogram>& getResults ( ) const

◆ requires()

QCBase::Status requires ( ) const
overridevirtual

Returns the input data requirements of the compute(...) function.

Implements QCBase.

Member Data Documentation

◆ name_

const String name_ = "TIC"
private