libpappsomspp
Library for mass spectrometry
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mgfoutput.cpp
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1#include "mgfoutput.h"
2
3using namespace pappso;
4
5MgfOutput::MgfOutput(QIODevice *p_output_device)
6{
7
8 mpa_outputStream = new QTextStream(p_output_device);
9}
10
14
15void
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()
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
60void
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
const QString & getSampleName() const
Definition msrunid.cpp:86
Class representing a fully specified mass spectrum.
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
uint getPrecursorCharge(bool *ok=nullptr) const
get precursor charge
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
get precursor intensity
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
pappso_double getPrecursorMz(bool *ok=nullptr) const
get precursor mz
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