libpappsomspp
Library for mass spectrometry
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pappso::cbor::psm::PsmIonSeries Class Reference

computes spectrum isotope match for each PSM and stores ion series in "props" More...

#include <psmionseries.h>

Inheritance diagram for pappso::cbor::psm::PsmIonSeries:
pappso::cbor::psm::PsmFileScanProcessAndCopy pappso::cbor::psm::PsmFileScanProcess pappso::cbor::psm::PsmFileReaderBase pappso::cbor::CborStreamReaderInterface

Public Member Functions

 PsmIonSeries (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QJsonObject &parameters)
virtual ~PsmIonSeries ()
void filterMassSpectrum (pappso::MassSpectrum &mass_spectrum) const
Public Member Functions inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
 PsmFileScanProcessAndCopy (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &operation)
virtual ~PsmFileScanProcessAndCopy ()
void close () override
 convenient function to clean pointer before leaving
Public Member Functions inherited from pappso::cbor::psm::PsmFileScanProcess
 PsmFileScanProcess (std::size_t buffer_scan_size)
virtual ~PsmFileScanProcess ()
Public Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
 PsmFileReaderBase ()
virtual ~PsmFileReaderBase () override
void readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
void readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
 CborStreamReaderInterface ()
virtual ~CborStreamReaderInterface ()

Protected Member Functions

CborScanMapBase * newCborScanMap () override
void parameterMapReady (pappso::UiMonitorInterface &monitor) override
Protected Member Functions inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
void delayProteinMapInMemory ()
void informationsReady (pappso::UiMonitorInterface &monitor) override
void logReady (pappso::UiMonitorInterface &monitor) override
void fastaFilesReady (pappso::UiMonitorInterface &monitor) override
virtual void proteinMapReady (pappso::UiMonitorInterface &monitor) override
virtual void processBufferScanDone (pappso::UiMonitorInterface &monitor) override
void sampleStarted (pappso::UiMonitorInterface &monitor) override
void sampleFinished (pappso::UiMonitorInterface &monitor) override
void sampleListStarted (pappso::UiMonitorInterface &monitor) override
void sampleListFinished (pappso::UiMonitorInterface &monitor) override
Protected Member Functions inherited from pappso::cbor::psm::PsmFileScanProcess
void readScan (pappso::UiMonitorInterface &monitor) override
void scanFinished (pappso::UiMonitorInterface &monitor) override
virtual void processBufferScan (pappso::UiMonitorInterface &monitor)
void clearScanBuffer ()
Protected Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
void readRoot (pappso::UiMonitorInterface &monitor)
virtual void readInformations (pappso::UiMonitorInterface &monitor)
virtual void readLog (pappso::UiMonitorInterface &monitor)
virtual void readParameterMap (pappso::UiMonitorInterface &monitor)
virtual void readProteinMap (pappso::UiMonitorInterface &monitor)
virtual void readSample (pappso::UiMonitorInterface &monitor)
virtual void readPsm (pappso::UiMonitorInterface &monitor)
virtual void psmReady (pappso::UiMonitorInterface &monitor)
virtual void scanStarted (pappso::UiMonitorInterface &monitor)
PsmFile readPsmFile (bool &is_ok)
void writePsmFile (CborStreamWriter &writer, const PsmFile &psm_file)
void writePsmFileList (CborStreamWriter &writer, const std::vector< PsmFile > &file_list)
PsmProteinRef readPsmProteinRef (bool &is_ok)
pappso::PeptideSp getCurrentPsmPeptideSp () const
pappso::QualifiedMassSpectrumSPtr getCurrentQualifiedMassSpectrumSPtr () const
 get the qualified Spectrum for the current PSM
bool currentProteinRefListContainsDecoy () const
 tells if the current PSM has a decoy accession
bool currentProteinRefListContainsTarget () const
 tells if the current PSM has a target accession
double getPrecursorMass (double mz_prec, uint charge) const
 convenient function do compute precusor ion mass
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool getExpectedString ()
void initCborReader (QFile *pcborfile)
void initCborReader (QIODevice *pcborfile)

Protected Attributes

QJsonObject m_psmIonSeriesParameters
pappso::PrecisionPtr m_fragmentTolerance
Protected Attributes inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
CborStreamWriter * mp_cborOutput
CborStreamWriter * mp_copyCborOutput = nullptr
QString m_operation
pappso::cbor::psm::PsmProteinMap m_psmNewProteinMap
QBuffer * mpa_bufferAfterProteinMap = nullptr
pappso::cbor::CborStreamWriter * mpa_bufferWriterAfterProteinMap = nullptr
Protected Attributes inherited from pappso::cbor::psm::PsmFileScanProcess
std::size_t m_bufferScanSize = 1000
std::vector< CborScanMapBase * > m_cborScanList
Protected Attributes inherited from pappso::cbor::psm::PsmFileReaderBase
QStringList m_targetFastaFiles
QStringList m_decoyFastaFiles
PsmProteinMap m_proteinMap
QString m_currentSampleName
PsmFile m_currentPeaklistFile
std::vector< PsmFile > m_currentIdentificationFileList
QCborMap m_cborInformations
QCborArray m_cborLog
QCborMap m_cborParameterMap
QCborMap m_cborScanId
QCborMap m_cborScanPrecursor
QCborMap m_cborScanMs2
QCborMap m_cborScanProps
QCborMap m_cborScanPsmEval
QCborMap m_cborScanPsmProps
QString m_currentPsmProforma
std::vector< PsmProteinRef > m_currentPsmProteinRefList
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader * mpa_cborReader = nullptr
QString m_expectedString
QByteArray m_data

Detailed Description

computes spectrum isotope match for each PSM and stores ion series in "props"

Definition at line 45 of file psmionseries.h.

Constructor & Destructor Documentation

◆ PsmIonSeries()

pappso::cbor::psm::PsmIonSeries::PsmIonSeries ( std::size_t buffer_scan_size,
CborStreamWriter * cbor_output_p,
const QJsonObject & parameters )

Default constructor

Definition at line 35 of file psmionseries.cpp.

38 : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, "IonSeries")
39{
40 m_psmIonSeriesParameters = parameters;
41
42 if(parameters.value("fragment_tolerance_unit").toString() == "dalton")
43 {
44 m_fragmentTolerance = pappso::PrecisionFactory::getDaltonInstance(
45 parameters.value("fragment_tolerance").toDouble());
46 }
47 else if(parameters.value("fragment_tolerance_unit").toString() == "ppm")
48 {
49 m_fragmentTolerance =
50 pappso::PrecisionFactory::getPpmInstance(parameters.value("fragment_tolerance").toDouble());
51 }
52}
pappso::PrecisionFactory::getPpmInstance
static PrecisionPtr getPpmInstance(pappso_double value)
get a ppm precision pointer
Definition precision.cpp:155
pappso::PrecisionFactory::getDaltonInstance
static PrecisionPtr getDaltonInstance(pappso_double value)
get a Dalton precision pointer
Definition precision.cpp:136
pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy
PsmFileScanProcessAndCopy(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &operation)
Definition psmfilescanprocessandcopy.cpp:41
pappso::cbor::psm::PsmIonSeries::m_fragmentTolerance
pappso::PrecisionPtr m_fragmentTolerance
Definition psmionseries.h:69

References pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy(), and m_psmIonSeriesParameters.

◆ ~PsmIonSeries()

pappso::cbor::psm::PsmIonSeries::~PsmIonSeries ( )
virtual

Destructor

Definition at line 54 of file psmionseries.cpp.

55{
56}

Member Function Documentation

◆ filterMassSpectrum()

void pappso::cbor::psm::PsmIonSeries::filterMassSpectrum ( pappso::MassSpectrum & mass_spectrum) const

References newCborScanMap(), and parameterMapReady().

◆ newCborScanMap()

pappso::cbor::psm::CborScanMapBase * pappso::cbor::psm::PsmIonSeries::newCborScanMap ( )
overrideprotectedvirtual

Implements pappso::cbor::psm::PsmFileScanProcess.

Definition at line 78 of file psmionseries.cpp.

79{
80 return new PsmIonSeriesScan(*this, m_fragmentTolerance);
81}

References m_fragmentTolerance.

Referenced by filterMassSpectrum().

◆ parameterMapReady()

void pappso::cbor::psm::PsmIonSeries::parameterMapReady ( pappso::UiMonitorInterface & monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 59 of file psmionseries.cpp.

61{
62 QCborMap cbor_features_parameters;
63
64 cbor_features_parameters.insert(QString("fragment_tolerance_unit"),
65 Utils::toString(m_fragmentTolerance->unit()));
66 cbor_features_parameters.insert(QString("fragment_tolerance"), m_fragmentTolerance->getNominal());
67 cbor_features_parameters.insert(QString("ion_list"), "y b");
68
69
70 m_cborParameterMap.insert(QString("ion-series"), cbor_features_parameters);
71
72 mp_cborOutput->append("parameter_map");
73 mp_cborOutput->writeCborMap(m_cborParameterMap);
74}
pappso::Utils::toString
static QString toString(specglob::SpectralAlignmentType type)
Convenience function to return a string describing the specglob alingment type.
Definition utils.cpp:544

References pappso::cbor::psm::PsmFileReaderBase::m_cborParameterMap, m_fragmentTolerance, pappso::cbor::psm::PsmFileScanProcessAndCopy::mp_cborOutput, and pappso::Utils::toString().

Referenced by filterMassSpectrum().

Member Data Documentation

◆ m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmIonSeries::m_fragmentTolerance
protected

Definition at line 69 of file psmionseries.h.

Referenced by newCborScanMap(), and parameterMapReady().

◆ m_psmIonSeriesParameters

QJsonObject pappso::cbor::psm::PsmIonSeries::m_psmIonSeriesParameters
protected

Definition at line 68 of file psmionseries.h.

Referenced by PsmIonSeries().

The documentation for this class was generated from the following files: