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 More... | |
virtual bool | empty () const |
returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More... | |
virtual const SpectrumIdentity & | spectrumIdentity (size_t index) const =0 |
access to a spectrum index More... | |
virtual size_t | find (const std::string &id) const |
find id in the spectrum index (returns size() on failure) More... | |
virtual size_t | findAbbreviated (const std::string &abbreviatedId, char delimiter='.') const |
find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure) More... | |
virtual IndexList | findNameValue (const std::string &name, const std::string &value) const |
find all spectrum indexes with specified name/value pair More... | |
virtual IndexList | findSpotID (const std::string &spotID) const |
find all spectrum indexes with spotID (returns empty vector on failure) More... | |
virtual SpectrumPtr | spectrum (size_t index, bool getBinaryData=false) const =0 |
retrieve a spectrum by index More... | |
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 More... | |
virtual SpectrumPtr | spectrum (size_t index, DetailLevel detailLevel) const |
retrieve a spectrum by index More... | |
virtual const boost::shared_ptr< const DataProcessing > | dataProcessingPtr () const |
returns the data processing affecting spectra retrieved through this interface More... | |
virtual void | warn_once (const char *msg) const |
issues a warning once per SpectrumList instance (based on string hash) More... | |
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 656 of file MSData.hpp.
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inlinevirtual |
Definition at line 703 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::analysis::SpectrumList_ScanSummer, pwiz::msdata::detail::SpectrumList_UIMF, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::msdata::SpectrumListWrapper, 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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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::analysis::SpectrumList_ScanSummer, pwiz::msdata::detail::SpectrumList_UIMF, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, 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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find id in the spectrum index (returns size() on failure)
Reimplemented in pwiz::msdata::detail::SpectrumList_UIMF, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, 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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find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure)
Referenced by testSpectrumListSimple().
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find all spectrum indexes with specified name/value pair
Referenced by testSpectrumListSimple().
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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_ChargeFromIsotope, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::analysis::SpectrumList_MZRefiner, pwiz::analysis::SpectrumList_ScanSummer, pwiz::analysis::SpectrumList_TitleMaker, pwiz::msdata::detail::SpectrumList_UIMF, pwiz::analysis::SpectrumList_PrecursorRefine, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::analysis::SpectrumList_ChargeStateCalculator, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_ZeroSamplesFilter, pwiz::msdata::detail::SpectrumList_Waters, pwiz::msdata::SpectrumListCache, pwiz::analysis::SpectrumList_Smoother, pwiz::msdata::detail::SpectrumList_ABI, pwiz::analysis::SpectrumList_PrecursorRecalculator, pwiz::analysis::SpectrumList_3D, pwiz::analysis::SpectrumList_LockmassRefiner, pwiz::analysis::SpectrumList_PeakFilter, pwiz::analysis::SpectrumList_MetadataFixer, pwiz::analysis::SpectrumList_MZWindow, pwiz::msdata::detail::SpectrumList_ABI_T2D, pwiz::analysis::SpectrumList_IonMobility, and MyBase.
Referenced by pwiz::msdata::TextWriter::operator()(), printSpectrumList(), test(), testSpectrumListSimple(), validateMmgfMzxmlRoundTrip(), and verifySpectrumSize().
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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
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retrieve a spectrum by index
Reimplemented in pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_ScanSummer, pwiz::msdata::detail::SpectrumList_UIMF, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::msdata::detail::SpectrumList_Waters, pwiz::analysis::SpectrumList_PeakPicker, pwiz::msdata::detail::SpectrumList_ABI, pwiz::analysis::SpectrumList_PeakFilter, and pwiz::analysis::SpectrumList_LockmassRefiner.
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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().
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issues a warning once per SpectrumList instance (based on string hash)
Reimplemented in pwiz::msdata::SpectrumListBase.