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 | 
|  Public Types inherited from ProgressLogger | |
| 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 | 
|  Public Member Functions inherited from ProgressLogger | |
| 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_ | 
|  Protected Attributes inherited from ProgressLogger | |
| 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 Protected Attributes inherited from ProgressLogger | |
| 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=().
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 | 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 |