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| MSDataCachedConsumer (const String &filename, bool clearData=true) |
| Constructor. More...
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| ~MSDataCachedConsumer () override |
| Destructor. More...
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void | consumeSpectrum (SpectrumType &s) override |
| Write a spectrum to the output file. More...
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void | consumeChromatogram (ChromatogramType &c) override |
| Write a chromatogram to the output file. More...
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void | setExpectedSize (Size, Size) override |
| Set expected size of spectra and chromatograms to be consumed. More...
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void | setExperimentalSettings (const ExperimentalSettings &) override |
| Set experimental settings (meta-data) of the data to be consumed. More...
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Public Member Functions inherited from CachedMzMLHandler |
| CachedMzMLHandler () |
| Default constructor. More...
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| ~CachedMzMLHandler () |
| Default destructor. More...
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CachedMzMLHandler & | operator= (const CachedMzMLHandler &rhs) |
| Assignment operator. More...
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void | writeMemdump (const MapType &exp, const String &out) const |
| Write complete spectra as a dump to the disk. More...
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void | writeMetadata (MapType exp, String out_meta, bool addCacheMetaValue=false) |
| Write only the meta data of an MSExperiment. More...
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void | writeMetadata_x (const MapType &exp, const String &out_meta, bool addCacheMetaValue=false) |
| Write only the meta data of an MSExperiment. More...
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void | readMemdump (MapType &exp_reading, String filename) const |
| Read all spectra from a dump from the disk. More...
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void | createMemdumpIndex (String filename) |
| Create an index on the location of all the spectra and chromatograms. More...
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const std::vector< std::streampos > & | getSpectraIndex () const |
| Access to a constant copy of the binary spectra index. More...
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const std::vector< std::streampos > & | getChromatogramIndex () const |
| Access to a constant copy of the binary chromatogram index. More...
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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More...
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virtual | ~IMSDataConsumer () |
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Public Types inherited from CachedMzMLHandler |
typedef PeakMap | MapType |
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typedef MSSpectrum | SpectrumType |
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typedef MSChromatogram | ChromatogramType |
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typedef double | DatumSingleton |
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typedef std::vector< DatumSingleton > | Datavector |
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enum | LogType { CMD,
GUI,
NONE
} |
| Possible log types. More...
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typedef MSSpectrum | SpectrumType |
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typedef MSChromatogram | ChromatogramType |
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Static Public Member Functions inherited from CachedMzMLHandler |
static void | readSpectrumFast (OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs, int &ms_level, double &rt) |
| fast access to a spectrum (a direct copy of the data into the provided arrays) More...
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static std::vector< OpenSwath::BinaryDataArrayPtr > | readSpectrumFast (std::ifstream &ifs, int &ms_level, double &rt) |
| Fast access to a spectrum. More...
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static void | readChromatogramFast (OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs) |
| Fast access to a chromatogram. More...
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static std::vector< OpenSwath::BinaryDataArrayPtr > | readChromatogramFast (std::ifstream &ifs) |
| Fast access to a chromatogram. More...
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static void | readSpectrum (SpectrumType &spectrum, std::ifstream &ifs) |
| Read a single spectrum directly into an OpenMS MSSpectrum (assuming file is already at the correct position) More...
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static void | readChromatogram (ChromatogramType &chromatogram, std::ifstream &ifs) |
| Read a single chromatogram directly into an OpenMS MSChromatogram (assuming file is already at the correct position) More...
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Protected Member Functions inherited from CachedMzMLHandler |
void | writeSpectrum_ (const SpectrumType &spectrum, std::ofstream &ofs) const |
| write a single spectrum to filestream More...
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void | writeChromatogram_ (const ChromatogramType &chromatogram, std::ofstream &ofs) const |
| write a single chromatogram to filestream More...
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Static Protected Member Functions inherited from CachedMzMLHandler |
static void | readDataFast_ (std::ifstream &ifs, std::vector< OpenSwath::BinaryDataArrayPtr > &data, const Size &data_size, const Size &nr_float_arrays) |
| helper method for fast reading of spectra and chromatograms More...
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static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More...
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static int | recursion_depth_ |
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Transforming and cached writing consumer of MS data.
Is able to transform a spectrum on the fly while it is read using a function pointer that can be set on the object. The spectra is then cached to disk using the functions provided in CachedMzMLHandler.