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" << 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 }
59 
60 void
62 {
63  mpa_outputStream->flush();
64 }
std::size_t getSpectrumIndex() const
const MsRunIdCstSPtr & getMsRunIdCstSPtr() const
QTextStream * mpa_outputStream
Definition: mgfoutput.h:55
virtual ~MgfOutput()
Definition: mgfoutput.cpp:11
MgfOutput(QIODevice *p_output_device)
Definition: mgfoutput.cpp:5
void write(const QualifiedMassSpectrum &mass_spectrum)
Definition: mgfoutput.cpp:16
Class representing a fully specified mass spectrum.
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.
write msrun peaks into MGF output stream
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39