ProteoWizard
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Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
#include <MSData.hpp>
Public Member Functions | |
virtual size_t | size () const =0 |
returns the number of spectra | |
virtual bool | empty () const |
returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) | |
virtual const SpectrumIdentity & | spectrumIdentity (size_t index) const =0 |
access to a spectrum index | |
virtual size_t | find (const std::string &id) const |
find id in the spectrum index (returns size() on failure) | |
virtual IndexList | findNameValue (const std::string &name, const std::string &value) const |
find all spectrum indexes with specified name/value pair | |
virtual IndexList | findSpotID (const std::string &spotID) const |
find all spectrum indexes with spotID (returns empty vector on failure) | |
virtual SpectrumPtr | spectrum (size_t index, bool getBinaryData=false) const =0 |
retrieve a spectrum by index | |
virtual SpectrumPtr | spectrum (const SpectrumPtr &seed, bool getBinaryData) const |
get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data | |
virtual SpectrumPtr | spectrum (size_t index, DetailLevel detailLevel) const |
retrieve a spectrum by index | |
virtual const boost::shared_ptr< const DataProcessing > | dataProcessingPtr () const |
returns the data processing affecting spectra retrieved through this interface | |
virtual | ~SpectrumList () |
Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML).
Implementation notes:
Definition at line 651 of file MSData.hpp.
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inlinevirtual |
Definition at line 701 of file MSData.hpp.
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pure virtual |
returns the number of spectra
Implemented in pwiz::msdata::SpectrumListSimple, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::msdata::detail::SpectrumList_Waters, pwiz::msdata::detail::SpectrumList_ABI, pwiz::msdata::detail::SpectrumList_ABI_T2D, MyBase, and MyBase.
Referenced by pwiz::msdata::TextWriter::operator()(), printSpectrumList(), test(), and testSpectrumListSimple().
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virtual |
returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
Reimplemented in pwiz::msdata::SpectrumListSimple, and pwiz::msdata::SpectrumListWrapper.
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pure virtual |
access to a spectrum index
Implemented in pwiz::msdata::SpectrumListSimple, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::msdata::detail::SpectrumList_Waters, pwiz::msdata::detail::SpectrumList_ABI, pwiz::msdata::detail::SpectrumList_ABI_T2D, and MyBase.
Referenced by test(), and testSpectrumListSimple().
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virtual |
find id in the spectrum index (returns size() on failure)
Reimplemented in pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::msdata::detail::SpectrumList_Waters, pwiz::msdata::detail::SpectrumList_ABI, and pwiz::msdata::detail::SpectrumList_ABI_T2D.
Referenced by testSpectrumListSimple().
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virtual |
find all spectrum indexes with specified name/value pair
Referenced by testSpectrumListSimple().
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virtual |
find all spectrum indexes with spotID (returns empty vector on failure)
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pure virtual |
retrieve a spectrum by index
Implemented in pwiz::msdata::SpectrumListSimple, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::analysis::SpectrumList_TitleMaker, pwiz::analysis::SpectrumList_PrecursorRefine, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::SpectrumListWrapper, pwiz::analysis::SpectrumList_ZeroSamplesFilter, pwiz::msdata::SpectrumListCache, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::analysis::SpectrumList_ChargeStateCalculator, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_Smoother, pwiz::msdata::detail::SpectrumList_Waters, pwiz::analysis::SpectrumList_PrecursorRecalculator, pwiz::analysis::SpectrumList_PeakFilter, pwiz::msdata::detail::SpectrumList_ABI, pwiz::analysis::SpectrumList_MetadataFixer, pwiz::analysis::SpectrumList_MZWindow, pwiz::msdata::detail::SpectrumList_ABI_T2D, and MyBase.
Referenced by pwiz::msdata::TextWriter::operator()(), printSpectrumList(), test(), testSpectrumListSimple(), and verifySpectrumSize().
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inlinevirtual |
get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data
Definition at line 681 of file MSData.hpp.
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inlinevirtual |
retrieve a spectrum by index
Reimplemented in pwiz::analysis::SpectrumList_Filter, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Waters, and pwiz::msdata::detail::SpectrumList_ABI.
Definition at line 688 of file MSData.hpp.
References pwiz::msdata::DetailLevel_FastMetadata, pwiz::msdata::DetailLevel_FullData, and pwiz::msdata::DetailLevel_InstantMetadata.
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virtual |
returns the data processing affecting spectra retrieved through this interface
Reimplemented in pwiz::msdata::SpectrumListSimple, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::SpectrumListBase, and MyBase.
Referenced by pwiz::msdata::TextWriter::operator()(), and testSpectrumListSimple().