pappso::specpeptidoms Namespace Reference

Classes
struct	AaPosition
struct	Alignment
class	CorrectionTree
struct	KeyCell
struct	Location
class	LocationSaver
class	Scenario
struct	ScenarioCell
class	ScoreValues
class	SemiGlobalAlignment
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)

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 65 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_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().