An class that uses on-disk caching to read and write spectra and chromatograms. More...
#include <OpenMS/ANALYSIS/OPENSWATH/CachedmzML.h>
Public Types | |
typedef MSExperiment< Peak1D > | MapType |
typedef MSSpectrum< Peak1D > | SpectrumType |
typedef MSChromatogram < ChromatogramPeak > | ChromatogramType |
typedef double | DatumSingleton |
typedef std::vector < DatumSingleton > | Datavector |
![]() | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Public Member Functions | |
void | createMemdumpIndex (String filename) |
Create an index on the location of all the spectra and chromatograms. More... | |
void | writeMetadata (MapType exp, String out_meta) |
Write only the meta data of an MSExperiment. More... | |
Constructors and Destructor | |
CachedmzML () | |
Default constructor. More... | |
~CachedmzML () | |
Default destructor. More... | |
CachedmzML & | operator= (const CachedmzML &rhs) |
Assignment operator. More... | |
Read / Write an MSExperiment | |
void | writeMemdump (MapType &exp, String out) |
Write complete spectra as a dump to the disk. More... | |
void | readMemdump (MapType &exp_reading, String filename) const |
Read all spectra from a dump from the disk. More... | |
Read a single MSSpectrum | |
void | readSingleSpectrum (MSSpectrum< Peak1D > &spectrum, const String &filename, const Size &idx) const |
Read a single spectrum from the given filename. More... | |
void | readSingleSpectrum (MSSpectrum< Peak1D > &spectrum, std::ifstream &ifs, const Size &idx) const |
Access to the binary indices | |
const std::vector< Size > & | getSpectraIndex () const |
const std::vector< Size > & | getChromatogramIndex () const |
![]() | |
ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
Static Public Member Functions | |
static void | readSpectrumFast (OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs, int ms_level, double rt) |
fast access without copying More... | |
static void | readChromatogramFast (OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs) |
fast access without copying More... | |
Protected Member Functions | |
void | readSpectrum_ (Datavector &data1, Datavector &data2, std::ifstream &ifs, int &ms_level, double &rt) const |
void | readChromatogram_ (Datavector &data1, Datavector &data2, std::ifstream &ifs) const |
void | readSpectrum_ (SpectrumType &spectrum, std::ifstream &ifs) const |
void | readChromatogram_ (ChromatogramType &chromatogram, std::ifstream &ifs) const |
void | writeSpectrum_ (const SpectrumType &spectrum, std::ofstream &ofs) |
void | writeChromatogram_ (const ChromatogramType &chromatogram, std::ofstream &ofs) |
Protected Attributes | |
std::vector< Size > | spectra_index_ |
std::vector< Size > | chrom_index_ |
![]() | |
LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
Private Attributes | |
int | int_field_ |
double | dbl_field_ |
Additional Inherited Members | |
![]() | |
static int | recursion_depth_ |
An class that uses on-disk caching to read and write spectra and chromatograms.
This class implements the OpenSWATH Spectrum Access interface (ISpectrumAccess) using the CachedmzML class which is able to read and write a cached mzML file.
typedef std::vector<DatumSingleton> Datavector |
typedef double DatumSingleton |
typedef MSExperiment<Peak1D> MapType |
typedef MSSpectrum<Peak1D> SpectrumType |
|
inline |
Default constructor.
|
inline |
Default destructor.
|
inline |
Create an index on the location of all the spectra and chromatograms.
References MAGIC_NUMBER.
|
inline |
|
inline |
|
inline |
Assignment operator.
References CachedmzML::chrom_index_, and CachedmzML::spectra_index_.
|
inlineprotected |
|
inlineprotected |
References ChromatogramPeak::setIntensity(), and ChromatogramPeak::setRT().
|
inlinestatic |
fast access without copying
Read all spectra from a dump from the disk.
References MSExperiment< PeakT, ChromatogramPeakT >::addSpectrum(), MAGIC_NUMBER, MSExperiment< PeakT, ChromatogramPeakT >::reserve(), and MSExperiment< PeakT, ChromatogramPeakT >::setChromatograms().
|
inline |
Read a single spectrum from the given filename.
|
inline |
|
inlineprotected |
|
inlineprotected |
|
inlinestatic |
fast access without copying
|
inlineprotected |
Write complete spectra as a dump to the disk.
Write only the meta data of an MSExperiment.
References MSExperiment< PeakT, ChromatogramPeakT >::clear(), MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::setChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::size(), and MzMLFile::store().
|
inlineprotected |
References MSSpectrum< PeakT >::getMSLevel(), and MSSpectrum< PeakT >::getRT().
|
protected |
Referenced by CachedmzML::operator=().
|
private |
|
private |
|
protected |
Referenced by CachedmzML::operator=().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |