libpappsomspp
Library for mass spectrometry
mgfoutput.cpp
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1 #include "mgfoutput.h"
2 
3 using namespace pappso;
4 
5 MgfOutput::MgfOutput(QIODevice *p_output_device)
6 {
7 
8  mpa_outputStream = new QTextStream(p_output_device);
9 }
10 
12 {
13 }
14 
15 void
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 }
59 
60 void
62 {
63  mpa_outputStream->flush();
64 }
pappso::MgfOutput::mpa_outputStream
QTextStream * mpa_outputStream
Definition: mgfoutput.h:55
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition: aa.cpp:39
pappso::QualifiedMassSpectrum::getPrecursorIntensity
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
Definition: qualifiedmassspectrum.cpp:381
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::QualifiedMassSpectrum::getPrecursorCharge
uint getPrecursorCharge(bool *ok=nullptr) const
Get the precursor charge.
Definition: qualifiedmassspectrum.cpp:316
pappso::MassSpectrumId::getSpectrumIndex
std::size_t getSpectrumIndex() const
Definition: massspectrumid.cpp:110
pappso::MgfOutput::~MgfOutput
virtual ~MgfOutput()
Definition: mgfoutput.cpp:11
mgfoutput.h
write msrun peaks into MGF output stream
pappso::QualifiedMassSpectrum::getMassSpectrumId
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
Definition: qualifiedmassspectrum.cpp:157
pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
Definition: qualifiedmassspectrum.cpp:141
pappso::MgfOutput::close
void close()
Definition: mgfoutput.cpp:61
pappso::MgfOutput::write
void write(const QualifiedMassSpectrum &mass_spectrum)
Definition: mgfoutput.cpp:16
pappso::MgfOutput::MgfOutput
MgfOutput(QIODevice *p_output_device)
Definition: mgfoutput.cpp:5
pappso::MassSpectrumId::getMsRunIdCstSPtr
const MsRunIdCstSPtr & getMsRunIdCstSPtr() const
Definition: massspectrumid.cpp:82
pappso::QualifiedMassSpectrum::getPrecursorMz
pappso_double getPrecursorMz(bool *ok=nullptr) const
Get the precursor m/z ratio.
Definition: qualifiedmassspectrum.cpp:238
pappso::QualifiedMassSpectrum::getRtInSeconds
pappso_double getRtInSeconds() const
Get the retention time in seconds.
Definition: qualifiedmassspectrum.cpp:203