libpappsomspp
Library for mass spectrometry
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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 ExperimentalSpectrumExperimentalSpectrumCsp
 
typedef std::shared_ptr< const PeptideSpectrumPeptideSpectraCsp
 

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

Definition at line 59 of file experimentalspectrum.h.

◆ PeptideSpectraCsp

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

Definition at line 56 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.

78{
79 native = 0, ///< native peak, but has no mz counterpart (the complement ion),
80 ///< we had to compute the symmetric mass
81 symmetric =
82 1, ///< new peak : computed symmetric mass from a corresponding native peak
83 both =
84 2, ///< both, the ion and the complement exists in the original spectrum
85 synthetic =
86 3, ///< does not correspond to existing peak, for computational purpose
87};
@ synthetic
does not correspond to existing peak, for computational purpose
@ both
both, the ion and the complement exists in the original spectrum
@ symmetric
new peak : computed symmetric mass from a corresponding native peak

◆ 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.

57{
58 scoreNonAlign = 0, ///< Score for non alignment (int)
59
60 scoreReAlignNative = 1, ////algorithm< Score for re-alignment native (int)
61 scoreReAlignSym = 2, ///< Score for re-alignment symmetric (int)
62 scoreReAlignBoth = 3, ///< Score for re-alignment both (int)
63
64
65 scoreAlignNative = 4, ///< Score for good alignment native (int)
66 scoreAlignSym = 5, ///< Score for good alignment symmetric (int)
67 scoreAlignBoth = 6, ///< Score for good alignment both (int)
68
70 7, ///< Score for re-alignment without offset native (int)
72 8, ///< Score for re-alignment without offset symmetric (int)
73 scoreReAlignBothNO = 9, ///< Score for re-alignment without offset both (int)
74};
@ scoreAlignNative
Score for good alignment native (int)
@ scoreReAlignSymNO
Score for re-alignment without offset symmetric (int)
@ scoreNonAlign
Score for non alignment (int)
@ scoreAlignBoth
Score for good alignment both (int)
@ scoreReAlignBoth
Score for re-alignment both (int)
@ scoreReAlignBothNO
Score for re-alignment without offset both (int)
@ scoreReAlignSym
Score for re-alignment symmetric (int)
@ scoreAlignSym
Score for good alignment symmetric (int)
@ scoreReAlignNativeNO
Score for re-alignment without offset native (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.

48{
49 nonAlign =
50 0, ///< the type of alignment to put in origin matrix NON Alignment (0 - NA)
51 reAlign = 1, ///< Re Alignment (1 - RE)
52 align = 2, ///< Alignment (2 - AL)
53};
@ nonAlign
the type of alignment to put in origin matrix NON Alignment (0 - NA)