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 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... | |
void | warn_once (const char *msg) const |
makes it easy to issue simple warnings without repeats (based on string hash) More... | |
virtual | ~SpectrumList () |
Private Attributes | |
std::set< size_t > | warn_msg_hashes |
Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML).
Implementation notes:
Definition at line 652 of file MSData.hpp.
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inlinevirtual |
Definition at line 705 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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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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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_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::msdata::detail::SpectrumList_ABI, pwiz::analysis::SpectrumList_PeakFilter, 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 682 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_Bruker, pwiz::msdata::detail::SpectrumList_Waters, and pwiz::msdata::detail::SpectrumList_ABI.
Definition at line 689 of file MSData.hpp.
References pwiz::msdata::DetailLevel_FastMetadata, pwiz::msdata::DetailLevel_FullData, and pwiz::msdata::DetailLevel_InstantMetadata.
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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().
void pwiz::msdata::SpectrumList::warn_once | ( | const char * | msg | ) | const |
makes it easy to issue simple warnings without repeats (based on string hash)
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mutableprivate |
Definition at line 708 of file MSData.hpp.