#include <msrunxicextractordisk.h>
Definition at line 44 of file msrunxicextractordisk.h.
◆ MsRunXicExtractorDisk() [1/3]
pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk |
( |
MsRunReaderSPtr & |
msrun_reader | ) |
|
◆ MsRunXicExtractorDisk() [2/3]
◆ ~MsRunXicExtractorDisk()
pappso::MsRunXicExtractorDisk::~MsRunXicExtractorDisk |
( |
| ) |
|
|
virtual |
◆ MsRunXicExtractorDisk() [3/3]
pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk |
( |
MsRunReaderSPtr & |
msrun_reader, |
|
|
const QDir & |
temporary_dir |
|
) |
| |
|
protected |
◆ acquireSlices()
◆ appendSliceOnDisk()
void pappso::MsRunXicExtractorDisk::appendSliceOnDisk |
( |
unsigned int |
slice_number, |
|
|
MassSpectrum & |
spectrum, |
|
|
std::size_t |
ipos |
|
) |
| |
|
protected |
append a slice on disk (in a file)
- Parameters
-
slice_number | the slice number == dalton integer |
spectrum | the part of the mass spectrum (mz/intensity) in the range of the slice number |
ipos | the position in the retention time vector |
Definition at line 272 of file msrunxicextractordisk.cpp.
287 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__;
290 std::shared_ptr<MsRunSlice> msrun_slice_sp =
291 std::make_shared<MsRunSlice>(MsRunSlice());
295 if(!slice_file.exists())
297 msrun_slice_sp.get()->setSize(
m_rtSize);
298 msrun_slice_sp.get()->setSliceNumber(slice_number);
299 return msrun_slice_sp;
301 if(!slice_file.open(QIODevice::ReadOnly))
◆ endPwizRead()
void pappso::MsRunXicExtractorDisk::endPwizRead |
( |
| ) |
|
|
protectedvirtual |
◆ getXicCstSPtr()
get a XIC on this MsRun at the given mass range
- Parameters
-
mz_range | mz range to extract |
rt_begin | begining of the XIC in seconds |
rt_end | end of the XIC in seconds |
Reimplemented from pappso::MsRunXicExtractor.
Definition at line 122 of file msrunxicextractordisk.cpp.
127 const MassSpectrum &spectrum = msrun_slice.get()->getSpectrum(i);
128 for(
auto &&peak : spectrum)
130 if(mz_range.contains(peak.x))
134 xic_element.y += peak.y;
138 if(xic_element.y < peak.y)
140 xic_element.y = peak.y;
146 msrunxic_sp.get()->push_back(xic_element);
149 return (msrunxic_sp);
152 std::vector<XicCstSPtr>
154 const std::vector<MzRange> &mz_range_list)
157 std::vector<XicCstSPtr> xic_list_return;
158 for(
auto &range : mz_range_list)
160 xic_list_return.push_back(
getXicCstSPtr(range, 0, 40000000));
162 return xic_list_return;
168 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__;
References pappso::MsRunXicExtractorInterface::m_xicExtractMethod, and pappso::sum.
◆ getXicCstSPtrList()
std::vector< XicCstSPtr > pappso::MsRunXicExtractorDisk::getXicCstSPtrList |
( |
const std::vector< MzRange > & |
mz_range_list | ) |
|
|
overridevirtual |
◆ prepareExtractor()
void pappso::MsRunXicExtractorDisk::prepareExtractor |
( |
| ) |
|
|
protected |
Definition at line 88 of file msrunxicextractordisk.cpp.
92 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__;
94 QObject::tr(
"Error reading file (%1) using : %2")
105 std::shared_ptr<Xic> msrunxic_sp = std::make_shared<Xic>(Xic());
107 std::vector<MsRunSliceSPtr> slice_list;
110 if(slice_list.size() == 0)
113 QObject::tr(
"Error getMsRunXicSp slice_list.size() == 0"));
119 DataPoint xic_element;
◆ serializeMsRun()
void pappso::MsRunXicExtractorDisk::serializeMsRun |
( |
| ) |
|
|
protected |
Definition at line 187 of file msrunxicextractordisk.cpp.
190 spectrum_map.clear();
197 const MassSpectrum *p_spectrum = spectrum.get();
198 if(p_spectrum->size() > 0)
200 if(p_spectrum->begin()->x <
m_minMz)
202 m_minMz = p_spectrum->begin()->x;
206 if(p_spectrum->back().x >
m_maxMz)
208 m_maxMz = p_spectrum->back().x;
211 for(
auto &peak : *p_spectrum)
214 slice_number = peak.x;
216 std::pair<std::map<unsigned int, MassSpectrum>::iterator,
bool>
217 ret = spectrum_map.insert(std::pair<unsigned int, MassSpectrum>(
218 slice_number, MassSpectrum()));
220 ret.first->second.push_back(peak);
232 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__;
238 std::map<unsigned int, MassSpectrum> &spectrum_map, std::size_t ipos)
242 for(
auto &&spectrum_pair : spectrum_map)
252 MassSpectrum &spectrum,
References m_maxMz, m_minMz, m_retentionTimeList, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and storeSlices().
◆ storeSlices()
void pappso::MsRunXicExtractorDisk::storeSlices |
( |
std::map< unsigned int, MassSpectrum > & |
slice_vector, |
|
|
std::size_t |
ipos |
|
) |
| |
|
protectedvirtual |
store MassSpectrum slices (by daltons) for a given retention time
- Parameters
-
slice_vector | mass spectrum chunks (by daltons) |
ipos | the position in the retention time vector |
Reimplemented in pappso::MsRunXicExtractorDiskBuffer.
Definition at line 258 of file msrunxicextractordisk.cpp.
263 if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append))
266 QObject::tr(
"unable to open file %1").arg(slice_file.fileName()));
268 QDataStream stream(&slice_file);
Referenced by serializeMsRun().
◆ unserializeSlice()
MsRunSliceSPtr pappso::MsRunXicExtractorDisk::unserializeSlice |
( |
unsigned int |
slice_number | ) |
|
|
protected |
get one slice from disk by her slice number (dalton)
- Parameters
-
slice_number | the slice number == dalton integer |
Definition at line 306 of file msrunxicextractordisk.cpp.
318 QObject::tr(
"error unserializing slice %1:\n%2")
320 .arg(error.qwhat()));
322 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__;
325 std::vector<MsRunSliceSPtr>
329 std::vector<MsRunSliceSPtr> slice_list;
330 for(
unsigned int i = mz_range.lower(); i <= mz_range.upper(); i++)
335 return slice_sp.get()->getSliceNumber() == i;
339 slice_list.push_back(*it);
◆ m_maxMz
◆ m_minMz
◆ m_msRunSliceListCache
std::deque<MsRunSliceSPtr> pappso::MsRunXicExtractorDisk::m_msRunSliceListCache |
|
protected |
◆ m_mutex
QMutex pappso::MsRunXicExtractorDisk::m_mutex |
|
protected |
◆ m_retentionTimeList
◆ m_rtSize
std::size_t pappso::MsRunXicExtractorDisk::m_rtSize = 0 |
|
protected |
◆ m_temporaryDirectory
QString pappso::MsRunXicExtractorDisk::m_temporaryDirectory |
|
protected |
◆ mpa_temporaryDirectory
QTemporaryDir* pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory = nullptr |
|
protected |
◆ MsRunXicExtractorFactory
friend pappso::MsRunXicExtractorDisk::MsRunXicExtractorFactory |
|
private |
The documentation for this class was generated from the following files: