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 57 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 }

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
20 TITLE=20120906_balliau_extract_1_A01_urnb-1.15968.15968.2
21 RTINSECONDS=2843.58
22 PEPMASS=638.36934732588 270659.09375
23 CHARGE=2+
24 89.01705933 1255.7088623047
25 89.06031799 258758.140625
26 90.06361389 12425.6162109375
27 */
28  *mpa_outputStream << "BEGIN IONS" << endl;
29  *mpa_outputStream << "TITLE="
30  << mass_spectrum.getMassSpectrumId()
32  .get()
33  ->getSampleName()
34  << "."
35  << mass_spectrum.getMassSpectrumId().getSpectrumIndex()
36  << endl;
37  *mpa_outputStream << "RTINSECONDS="
38  << QString::number(mass_spectrum.getRtInSeconds(), 'f', 2)
39  << endl;
40  *mpa_outputStream << "PEPMASS="
41  << QString::number(mass_spectrum.getPrecursorMz(), 'g', 15)
42  << " "
43  << QString::number(
44  mass_spectrum.getPrecursorIntensity(), 'f', 5)
45  << endl;
46  *mpa_outputStream << "CHARGE=" << mass_spectrum.getPrecursorCharge() << "+"
47  << 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) << endl;
55  }
56  }
57  *mpa_outputStream << "END IONS" << endl;
58 }

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 91 of file mgfoutput.h.

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


The documentation for this class was generated from the following files:
pappso::MgfOutput::mpa_outputStream
QTextStream * mpa_outputStream
Definition: mgfoutput.h:91
pappso::QualifiedMassSpectrum::getPrecursorIntensity
pappso_double getPrecursorIntensity() const
Get the intensity of the precursor ion.
Definition: qualifiedmassspectrum.cpp:319
pappso::QualifiedMassSpectrum::getPrecursorCharge
uint getPrecursorCharge() const
Get the precursor charge.
Definition: qualifiedmassspectrum.cpp:200
pappso::MassSpectrumId::getSpectrumIndex
std::size_t getSpectrumIndex() const
Definition: massspectrumid.cpp:131
pappso::QualifiedMassSpectrum::getMassSpectrumId
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
Definition: qualifiedmassspectrum.cpp:146
pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
Definition: qualifiedmassspectrum.cpp:170
pappso::MassSpectrumId::getMsRunIdCstSPtr
const MsRunIdCstSPtr & getMsRunIdCstSPtr() const
Definition: massspectrumid.cpp:103
pappso::QualifiedMassSpectrum::getPrecursorMz
pappso_double getPrecursorMz() const
Get the precursor m/z ratio.
Definition: qualifiedmassspectrum.cpp:216
pappso::QualifiedMassSpectrum::getRtInSeconds
pappso_double getRtInSeconds() const
Get the retention time in seconds.
Definition: qualifiedmassspectrum.cpp:248