pappso::specpeptidoms Namespace Reference

Classes
class	CorrectionTree
struct	Location
class	LocationSaver
struct	AminoAcidModel
class	PeptideModel
	modelize peptide sequence to facilitate rendering in bracket or proforma More...
struct	ScenarioCell
class	Scenario
class	ScoreValues
struct	KeyCell
struct	Alignment
class	SemiGlobalAlignment
struct	SpOMSAa
class	SpOMSProtein
struct	AaPosition
class	SpOMSSpectrum

Typedefs
typedef std::shared_ptr< CorrectionTree >	CorrectionTreeSp
typedef std::shared_ptr< const SpOMSSpectrum >	SpOMSSpectrumCsp

Enumerations
enum class	ScoreType : std::uint8_t {   foundDouble = 0 , found = 1 , foundShiftDouble = 2 , foundShift = 3 ,   notFound = 4 , init = 5 }
enum class	AlignType {   found , shift , perfectShift , notFound ,   init }

Functions
const uint	MAX_SAVED_ALIGNMENTS (5)
const uint	ALIGNMENT_SURPLUS (5)
const int	MIN_ALIGNMENT_SCORE (15)
const uint	MAX_RETURNED_RESULTS (2)
const uint	TOL_PEAKS_MISSING (4)
const uint	TOL_PEAKS_MISSING_FIRST_COLUMN (5)
const float	ALIGNMENT_FILTER (0.9)

Typedef Documentation

CorrectionTreeSp

typedef std::shared_ptr<CorrectionTree> pappso::specpeptidoms::CorrectionTreeSp

Definition at line 42 of file correctiontree.h.

SpOMSSpectrumCsp

typedef std::shared_ptr<const SpOMSSpectrum> pappso::specpeptidoms::SpOMSSpectrumCsp

Definition at line 66 of file spomsspectrum.h.

Enumeration Type Documentation

AlignType

enum class pappso::specpeptidoms::AlignType

strong

Enumerator
found
shift
perfectShift
notFound
init

Definition at line 50 of file types.h.

{
  found,
  shift,
  perfectShift,
  notFound,
  init
};

ScoreType

enum class pappso::specpeptidoms::ScoreType : std::uint8_t

strong

Enumerator
foundDouble
found
foundShiftDouble
foundShift
notFound
init

Definition at line 40 of file types.h.

{
  foundDouble      = 0,
  found            = 1,
  foundShiftDouble = 2,
  foundShift       = 3,
  notFound         = 4,
  init             = 5,
};

Function Documentation

ALIGNMENT_FILTER()

const float pappso::specpeptidoms::ALIGNMENT_FILTER

(

0.

9

)

Referenced by pappso::specpeptidoms::LocationSaver::getMinScore().

ALIGNMENT_SURPLUS()

const uint pappso::specpeptidoms::ALIGNMENT_SURPLUS

(

5

)

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().

MAX_RETURNED_RESULTS()

const uint pappso::specpeptidoms::MAX_RETURNED_RESULTS

(

2

)

MAX_SAVED_ALIGNMENTS()

const uint pappso::specpeptidoms::MAX_SAVED_ALIGNMENTS

(

5

)

Referenced by pappso::specpeptidoms::LocationSaver::LocationSaver().

MIN_ALIGNMENT_SCORE()

const int pappso::specpeptidoms::MIN_ALIGNMENT_SCORE

(

15

)

Referenced by pappso::specpeptidoms::LocationSaver::LocationSaver(), pappso::specpeptidoms::SemiGlobalAlignment::correctAlign(), pappso::specpeptidoms::LocationSaver::getNextTree(), pappso::specpeptidoms::SemiGlobalAlignment::preciseAlign(), and pappso::specpeptidoms::LocationSaver::resetLocationSaver().

TOL_PEAKS_MISSING()

const uint pappso::specpeptidoms::TOL_PEAKS_MISSING

(

4

)

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().

TOL_PEAKS_MISSING_FIRST_COLUMN()

const uint pappso::specpeptidoms::TOL_PEAKS_MISSING_FIRST_COLUMN

(

5

)

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().