libpappsomspp
Library for mass spectrometry
pappso::MgfOutput Class Reference

#include <mgfoutput.h>

Public Member Functions

 MgfOutput (QIODevice *p_output_device)
 
void write (const QualifiedMassSpectrum &mass_spectrum)
 
void close ()
 
virtual ~MgfOutput ()
 

Private Attributes

QTextStream * mpa_outputStream
 

Detailed Description

Todo:
write docs

Definition at line 39 of file mgfoutput.h.

Constructor & Destructor Documentation

◆ MgfOutput()

MgfOutput::MgfOutput ( QIODevice *  p_output_device)

Default constructor

Definition at line 5 of file mgfoutput.cpp.

6{
7
8 mpa_outputStream = new QTextStream(p_output_device);
9}
QTextStream * mpa_outputStream
Definition: mgfoutput.h:55

References mpa_outputStream.

◆ ~MgfOutput()

MgfOutput::~MgfOutput ( )
virtual

Destructor

Definition at line 11 of file mgfoutput.cpp.

12{
13}

Member Function Documentation

◆ close()

void MgfOutput::close ( )

Definition at line 61 of file mgfoutput.cpp.

62{
63 mpa_outputStream->flush();
64}

References mpa_outputStream.

◆ write()

void MgfOutput::write ( const QualifiedMassSpectrum mass_spectrum)

Definition at line 16 of file mgfoutput.cpp.

17{
18 /*
19 * BEGIN IONS
20TITLE=20120906_balliau_extract_1_A01_urnb-1.15968.15968.2
21RTINSECONDS=2843.58
22PEPMASS=638.36934732588 270659.09375
23CHARGE=2+
2489.01705933 1255.7088623047
2589.06031799 258758.140625
2690.06361389 12425.6162109375
27*/
28 *mpa_outputStream << "BEGIN IONS" << Qt::endl;
29 *mpa_outputStream << "TITLE="
30 << mass_spectrum.getMassSpectrumId()
32 .get()
33 ->getSampleName()
34 << "."
35 << mass_spectrum.getMassSpectrumId().getSpectrumIndex()
36 << Qt::endl;
37 *mpa_outputStream << "RTINSECONDS="
38 << QString::number(mass_spectrum.getRtInSeconds(), 'f', 2)
39 << Qt::endl;
40 *mpa_outputStream << "PEPMASS="
41 << QString::number(mass_spectrum.getPrecursorMz(), 'g', 15)
42 << " "
43 << QString::number(
44 mass_spectrum.getPrecursorIntensity(), 'f', 5)
45 << Qt::endl;
46 *mpa_outputStream << "CHARGE=" << mass_spectrum.getPrecursorCharge() << "+"
47 << Qt::endl;
48
49 if(mass_spectrum.getMassSpectrumCstSPtr() != nullptr)
50 {
51 for(auto &&peak : *(mass_spectrum.getMassSpectrumCstSPtr().get()))
52 {
53 *mpa_outputStream << QString::number(peak.x, 'g', 15) << " "
54 << QString::number(peak.y, 'g', 15) << Qt::endl;
55 }
56 }
57 *mpa_outputStream << "END IONS" << Qt::endl;
58}
std::size_t getSpectrumIndex() const
const MsRunIdCstSPtr & getMsRunIdCstSPtr() const
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
uint getPrecursorCharge(bool *ok=nullptr) const
Get the precursor charge.
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
pappso_double getPrecursorMz(bool *ok=nullptr) const
Get the precursor m/z ratio.
pappso_double getRtInSeconds() const
Get the retention time in seconds.

References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getMsRunIdCstSPtr(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getPrecursorMz(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MassSpectrumId::getSpectrumIndex(), and mpa_outputStream.

Member Data Documentation

◆ mpa_outputStream

QTextStream* pappso::MgfOutput::mpa_outputStream
private

Definition at line 55 of file mgfoutput.h.

Referenced by MgfOutput(), close(), and write().


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