SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.
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| SpectrumList_ChargeStateCalculator (const msdata::SpectrumListPtr &inner, bool overrideExistingChargeState=true, int maxMultipleCharge=3, int minMultipleCharge=2, double intensityFractionBelowPrecursorForSinglyCharged=0.9, int maxKnownCharge=0, bool makeMS2=false) |
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virtual msdata::SpectrumPtr | spectrum (size_t index, bool getBinaryData=true) const |
| charge calculation requires binary data to function, so returned spectra will always provide the binary data More...
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| SpectrumListWrapper (const SpectrumListPtr &inner) |
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virtual size_t | size () const |
| returns the number of spectra More...
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virtual bool | empty () const |
| returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
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virtual const SpectrumIdentity & | spectrumIdentity (size_t index) const |
| access to a spectrum index More...
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virtual SpectrumPtr | spectrum (size_t index, DetailLevel detailLevel) const |
| retrieve a spectrum by index More...
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virtual const boost::shared_ptr< const DataProcessing > | dataProcessingPtr () const |
| returns the data processing affecting spectra retrieved through this interface More...
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SpectrumListPtr | inner () const |
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SpectrumListPtr | innermost () const |
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virtual size_t | find (const std::string &id) const |
| find id in the spectrum index (returns size() on failure) More...
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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...
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virtual IndexList | findNameValue (const std::string &name, const std::string &value) const |
| find all spectrum indexes with specified name/value pair More...
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virtual IndexList | findSpotID (const std::string &spotID) const |
| find all spectrum indexes with spotID (returns empty vector on failure) More...
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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...
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virtual void | warn_once (const char *msg) const |
| issues a warning once per SpectrumList instance (based on string hash) More...
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virtual | ~SpectrumList () |
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SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.
Definition at line 37 of file SpectrumList_ChargeStateCalculator.hpp.