pappso::specglob Namespace Reference

Classes
struct	AminoAcidModel
class	ExperimentalSpectrum
struct	ExperimentalSpectrumDataPoint
class	PeptideModel
class	PeptideSpectrum
struct	PeptideSpectrumDataPoint
class	PostTreatment
class	ScoreValues
class	SpectralAlignment
struct	SpectralAlignmentDataPoint
struct	TheoreticalPeakDataPoint

Typedefs
typedef std::shared_ptr< const ExperimentalSpectrum >	ExperimentalSpectrumCsp
typedef std::shared_ptr< const PeptideSpectrum >	PeptideSpectraCsp

Enumerations
enum class	SpectralAlignmentType : std::uint8_t { nonAlign , reAlign = 1 , align = 2 }
enum class	ScoreValueType : std::uint8_t {   scoreNonAlign = 0 , scoreReAlignNative = 1 , scoreReAlignSym = 2 , scoreReAlignBoth = 3 ,   scoreAlignNative = 4 , scoreAlignSym = 5 , scoreAlignBoth = 6 , scoreReAlignNativeNO ,   scoreReAlignSymNO , scoreReAlignBothNO = 9 }
enum class	ExperimentalSpectrumDataPointType : std::uint8_t { native = 0 , symmetric , both , synthetic }

Typedef Documentation

ExperimentalSpectrumCsp

typedef std::shared_ptr<const ExperimentalSpectrum> pappso::specglob::ExperimentalSpectrumCsp

Definition at line 59 of file experimentalspectrum.h.

PeptideSpectraCsp

typedef std::shared_ptr<const PeptideSpectrum> pappso::specglob::PeptideSpectraCsp

Definition at line 58 of file peptidespectrum.h.

Enumeration Type Documentation

ExperimentalSpectrumDataPointType

enum class pappso::specglob::ExperimentalSpectrumDataPointType : std::uint8_t

strong

Enumerator
native	native peak, but has no mz counterpart (the complement ion), we had to compute the symmetric mass
symmetric	new peak : computed symmetric mass from a corresponding native peak
both	both, the ion and the complement exists in the original spectrum
synthetic	does not correspond to existing peak, for computational purpose

Definition at line 77 of file types.h.

{
  native = 0, ///< native peak, but has no mz counterpart (the complement ion),
              ///< we had to compute the symmetric mass
  symmetric =
    1, ///< new peak : computed symmetric mass from a corresponding native peak
  both =
    2, ///< both, the ion and the complement exists in the original spectrum
  synthetic =
    3, ///< does not correspond to existing peak, for computational purpose
};

ScoreValueType

enum class pappso::specglob::ScoreValueType : std::uint8_t

strong

Enumerator
scoreNonAlign	Score for non alignment (int)
scoreReAlignNative
scoreReAlignSym	Score for re-alignment symmetric (int)
scoreReAlignBoth	Score for re-alignment both (int)
scoreAlignNative	Score for good alignment native (int)
scoreAlignSym	Score for good alignment symmetric (int)
scoreAlignBoth	Score for good alignment both (int)
scoreReAlignNativeNO	Score for re-alignment without offset native (int)
scoreReAlignSymNO	Score for re-alignment without offset symmetric (int)
scoreReAlignBothNO	Score for re-alignment without offset both (int)

Definition at line 56 of file types.h.

{
  scoreNonAlign = 0, ///< Score for non alignment (int)
 
  scoreReAlignNative = 1, ////algorithm< Score for re-alignment native  (int)
  scoreReAlignSym    = 2, ///< Score for re-alignment symmetric  (int)
  scoreReAlignBoth   = 3, ///< Score for re-alignment both  (int)
 
 
  scoreAlignNative = 4, ///< Score for good alignment native (int)
  scoreAlignSym    = 5, ///< Score for good alignment symmetric (int)
  scoreAlignBoth   = 6, ///< Score for good alignment both (int)
 
  scoreReAlignNativeNO =
    7, ///< Score for re-alignment without offset native (int)
  scoreReAlignSymNO =
    8, ///< Score for re-alignment without offset symmetric (int)
  scoreReAlignBothNO = 9, ///< Score for re-alignment without offset both (int)
};

SpectralAlignmentType

enum class pappso::specglob::SpectralAlignmentType : std::uint8_t

strong

Enumerator
nonAlign	the type of alignment to put in origin matrix NON Alignment (0 - NA)
reAlign	Re Alignment (1 - RE)
align	Alignment (2 - AL)

Definition at line 47 of file types.h.

{
  nonAlign =
    0, ///< the type of alignment to put in origin matrix NON Alignment (0 - NA)
  reAlign = 1, ///< Re Alignment (1 - RE)
  align   = 2, ///< Alignment (2 - AL)
};