CSearch_hit_Base::C_Attlist Class Reference

Search Toolkit Book for CSearch_hit_Base::C_Attlist

C_Attlist –. More...

#include <algo/ms/formats/pepxml/Search_hit_.hpp>

Inheritance diagram for CSearch_hit_Base::C_Attlist:

Collaboration diagram for CSearch_hit_Base::C_Attlist:

Public Types
enum	EAttlist_is_rejected { eAttlist_is_rejected_0 = 1 , eAttlist_is_rejected_1 = 2 }
enum class	E_memberIndex {   e__allMandatory = 0 , e_hit_rank , e_peptide , e_peptide_prev_aa ,   e_peptide_next_aa , e_protein , e_num_tot_proteins , e_num_matched_ions ,   e_tot_num_ions , e_calc_neutral_pep_mass , e_massdiff , e_num_tol_term ,   e_num_missed_cleavages , e_is_rejected , e_protein_descr , e_calc_pI ,   e_protein_mw }
typedef int	THit_rank
typedef string	TPeptide
typedef string	TPeptide_prev_aa
typedef string	TPeptide_next_aa
typedef string	TProtein
typedef int	TNum_tot_proteins
typedef int	TNum_matched_ions
typedef int	TTot_num_ions
typedef double	TCalc_neutral_pep_mass
typedef string	TMassdiff
typedef int	TNum_tol_term
typedef int	TNum_missed_cleavages
typedef EAttlist_is_rejected	TIs_rejected
typedef string	TProtein_descr
typedef string	TCalc_pI
typedef double	TProtein_mw
typedef Tparent::CMemberIndex< E_memberIndex, 17 >	TmemberIndex
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	C_Attlist (void)
	~C_Attlist (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetHit_rank (void) const
	Check if a value has been assigned to Hit_rank data member. More...
bool	CanGetHit_rank (void) const
	Check if it is safe to call GetHit_rank method. More...
void	ResetHit_rank (void)
	Reset Hit_rank data member. More...
THit_rank	GetHit_rank (void) const
	Get the Hit_rank member data. More...
void	SetHit_rank (THit_rank value)
	Assign a value to Hit_rank data member. More...
THit_rank &	SetHit_rank (void)
	Assign a value to Hit_rank data member. More...
bool	IsSetPeptide (void) const
	Check if a value has been assigned to Peptide data member. More...
bool	CanGetPeptide (void) const
	Check if it is safe to call GetPeptide method. More...
void	ResetPeptide (void)
	Reset Peptide data member. More...
const TPeptide &	GetPeptide (void) const
	Get the Peptide member data. More...
void	SetPeptide (const TPeptide &value)
	Assign a value to Peptide data member. More...
void	SetPeptide (TPeptide &&value)
TPeptide &	SetPeptide (void)
	Assign a value to Peptide data member. More...
bool	IsSetPeptide_prev_aa (void) const
	Check if a value has been assigned to Peptide_prev_aa data member. More...
bool	CanGetPeptide_prev_aa (void) const
	Check if it is safe to call GetPeptide_prev_aa method. More...
void	ResetPeptide_prev_aa (void)
	Reset Peptide_prev_aa data member. More...
const TPeptide_prev_aa &	GetPeptide_prev_aa (void) const
	Get the Peptide_prev_aa member data. More...
void	SetPeptide_prev_aa (const TPeptide_prev_aa &value)
	Assign a value to Peptide_prev_aa data member. More...
void	SetPeptide_prev_aa (TPeptide_prev_aa &&value)
TPeptide_prev_aa &	SetPeptide_prev_aa (void)
	Assign a value to Peptide_prev_aa data member. More...
bool	IsSetPeptide_next_aa (void) const
	Check if a value has been assigned to Peptide_next_aa data member. More...
bool	CanGetPeptide_next_aa (void) const
	Check if it is safe to call GetPeptide_next_aa method. More...
void	ResetPeptide_next_aa (void)
	Reset Peptide_next_aa data member. More...
const TPeptide_next_aa &	GetPeptide_next_aa (void) const
	Get the Peptide_next_aa member data. More...
void	SetPeptide_next_aa (const TPeptide_next_aa &value)
	Assign a value to Peptide_next_aa data member. More...
void	SetPeptide_next_aa (TPeptide_next_aa &&value)
TPeptide_next_aa &	SetPeptide_next_aa (void)
	Assign a value to Peptide_next_aa data member. More...
bool	IsSetProtein (void) const
	Check if a value has been assigned to Protein data member. More...
bool	CanGetProtein (void) const
	Check if it is safe to call GetProtein method. More...
void	ResetProtein (void)
	Reset Protein data member. More...
const TProtein &	GetProtein (void) const
	Get the Protein member data. More...
void	SetProtein (const TProtein &value)
	Assign a value to Protein data member. More...
void	SetProtein (TProtein &&value)
TProtein &	SetProtein (void)
	Assign a value to Protein data member. More...
bool	IsSetNum_tot_proteins (void) const
	Check if a value has been assigned to Num_tot_proteins data member. More...
bool	CanGetNum_tot_proteins (void) const
	Check if it is safe to call GetNum_tot_proteins method. More...
void	ResetNum_tot_proteins (void)
	Reset Num_tot_proteins data member. More...
TNum_tot_proteins	GetNum_tot_proteins (void) const
	Get the Num_tot_proteins member data. More...
void	SetNum_tot_proteins (TNum_tot_proteins value)
	Assign a value to Num_tot_proteins data member. More...
TNum_tot_proteins &	SetNum_tot_proteins (void)
	Assign a value to Num_tot_proteins data member. More...
bool	IsSetNum_matched_ions (void) const
	Check if a value has been assigned to Num_matched_ions data member. More...
bool	CanGetNum_matched_ions (void) const
	Check if it is safe to call GetNum_matched_ions method. More...
void	ResetNum_matched_ions (void)
	Reset Num_matched_ions data member. More...
TNum_matched_ions	GetNum_matched_ions (void) const
	Get the Num_matched_ions member data. More...
void	SetNum_matched_ions (TNum_matched_ions value)
	Assign a value to Num_matched_ions data member. More...
TNum_matched_ions &	SetNum_matched_ions (void)
	Assign a value to Num_matched_ions data member. More...
bool	IsSetTot_num_ions (void) const
	Check if a value has been assigned to Tot_num_ions data member. More...
bool	CanGetTot_num_ions (void) const
	Check if it is safe to call GetTot_num_ions method. More...
void	ResetTot_num_ions (void)
	Reset Tot_num_ions data member. More...
TTot_num_ions	GetTot_num_ions (void) const
	Get the Tot_num_ions member data. More...
void	SetTot_num_ions (TTot_num_ions value)
	Assign a value to Tot_num_ions data member. More...
TTot_num_ions &	SetTot_num_ions (void)
	Assign a value to Tot_num_ions data member. More...
bool	IsSetCalc_neutral_pep_mass (void) const
	Check if a value has been assigned to Calc_neutral_pep_mass data member. More...
bool	CanGetCalc_neutral_pep_mass (void) const
	Check if it is safe to call GetCalc_neutral_pep_mass method. More...
void	ResetCalc_neutral_pep_mass (void)
	Reset Calc_neutral_pep_mass data member. More...
TCalc_neutral_pep_mass	GetCalc_neutral_pep_mass (void) const
	Get the Calc_neutral_pep_mass member data. More...
void	SetCalc_neutral_pep_mass (TCalc_neutral_pep_mass value)
	Assign a value to Calc_neutral_pep_mass data member. More...
TCalc_neutral_pep_mass &	SetCalc_neutral_pep_mass (void)
	Assign a value to Calc_neutral_pep_mass data member. More...
bool	IsSetMassdiff (void) const
	Mass(precursor ion) - Mass(peptide) Check if a value has been assigned to Massdiff data member. More...
bool	CanGetMassdiff (void) const
	Check if it is safe to call GetMassdiff method. More...
void	ResetMassdiff (void)
	Reset Massdiff data member. More...
const TMassdiff &	GetMassdiff (void) const
	Get the Massdiff member data. More...
void	SetMassdiff (const TMassdiff &value)
	Assign a value to Massdiff data member. More...
void	SetMassdiff (TMassdiff &&value)
TMassdiff &	SetMassdiff (void)
	Assign a value to Massdiff data member. More...
bool	IsSetNum_tol_term (void) const
	Check if a value has been assigned to Num_tol_term data member. More...
bool	CanGetNum_tol_term (void) const
	Check if it is safe to call GetNum_tol_term method. More...
void	ResetNum_tol_term (void)
	Reset Num_tol_term data member. More...
TNum_tol_term	GetNum_tol_term (void) const
	Get the Num_tol_term member data. More...
void	SetNum_tol_term (TNum_tol_term value)
	Assign a value to Num_tol_term data member. More...
TNum_tol_term &	SetNum_tol_term (void)
	Assign a value to Num_tol_term data member. More...
bool	IsSetNum_missed_cleavages (void) const
	Check if a value has been assigned to Num_missed_cleavages data member. More...
bool	CanGetNum_missed_cleavages (void) const
	Check if it is safe to call GetNum_missed_cleavages method. More...
void	ResetNum_missed_cleavages (void)
	Reset Num_missed_cleavages data member. More...
TNum_missed_cleavages	GetNum_missed_cleavages (void) const
	Get the Num_missed_cleavages member data. More...
void	SetNum_missed_cleavages (TNum_missed_cleavages value)
	Assign a value to Num_missed_cleavages data member. More...
TNum_missed_cleavages &	SetNum_missed_cleavages (void)
	Assign a value to Num_missed_cleavages data member. More...
bool	IsSetIs_rejected (void) const
	Potential use in future for user manual validation (0 or 1) Check if a value has been assigned to Is_rejected data member. More...
bool	CanGetIs_rejected (void) const
	Check if it is safe to call GetIs_rejected method. More...
void	ResetIs_rejected (void)
	Reset Is_rejected data member. More...
void	SetDefaultIs_rejected (void)
	Assign default value to Is_rejected data member. More...
TIs_rejected	GetIs_rejected (void) const
	Get the Is_rejected member data. More...
void	SetIs_rejected (TIs_rejected value)
	Assign a value to Is_rejected data member. More...
TIs_rejected &	SetIs_rejected (void)
	Assign a value to Is_rejected data member. More...
bool	IsSetProtein_descr (void) const
	Check if a value has been assigned to Protein_descr data member. More...
bool	CanGetProtein_descr (void) const
	Check if it is safe to call GetProtein_descr method. More...
void	ResetProtein_descr (void)
	Reset Protein_descr data member. More...
const TProtein_descr &	GetProtein_descr (void) const
	Get the Protein_descr member data. More...
void	SetProtein_descr (const TProtein_descr &value)
	Assign a value to Protein_descr data member. More...
void	SetProtein_descr (TProtein_descr &&value)
TProtein_descr &	SetProtein_descr (void)
	Assign a value to Protein_descr data member. More...
bool	IsSetCalc_pI (void) const
	Check if a value has been assigned to Calc_pI data member. More...
bool	CanGetCalc_pI (void) const
	Check if it is safe to call GetCalc_pI method. More...
void	ResetCalc_pI (void)
	Reset Calc_pI data member. More...
const TCalc_pI &	GetCalc_pI (void) const
	Get the Calc_pI member data. More...
void	SetCalc_pI (const TCalc_pI &value)
	Assign a value to Calc_pI data member. More...
void	SetCalc_pI (TCalc_pI &&value)
TCalc_pI &	SetCalc_pI (void)
	Assign a value to Calc_pI data member. More...
bool	IsSetProtein_mw (void) const
	Check if a value has been assigned to Protein_mw data member. More...
bool	CanGetProtein_mw (void) const
	Check if it is safe to call GetProtein_mw method. More...
void	ResetProtein_mw (void)
	Reset Protein_mw data member. More...
TProtein_mw	GetProtein_mw (void) const
	Get the Protein_mw member data. More...
void	SetProtein_mw (TProtein_mw value)
	Assign a value to Protein_mw data member. More...
TProtein_mw &	SetProtein_mw (void)
	Assign a value to Protein_mw data member. More...
void	Reset (void)
	Reset the whole object. More...
Public Member Functions inherited from CSerialObject
	CSerialObject (void)
virtual	~CSerialObject (void)
virtual const CTypeInfo *	GetThisTypeInfo (void) const =0
virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...
virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
void	ThrowUnassigned (TMemberIndex index) const
void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...
const string &	GetNamespaceName (void) const
	Get namespace name. More...
bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...
const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Static Public Member Functions
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EAttlist_is_rejected (void)
	Access to EAttlist_is_rejected's attributes (values, names) as defined in spec. More...
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)
static void	SetVerifyDataGlobal (ESerialVerifyData verify)
static string	UnassignedString (void)
static CStringUTF8	UnassignedStringUTF8 (void)
static char	UnassignedByte (void)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Private Types
typedef CSerialObject	Tparent

Private Member Functions
	C_Attlist (const C_Attlist &)
C_Attlist &	operator= (const C_Attlist &)

Private Attributes
Uint4	m_set_State [1]
int	m_Hit_rank
string	m_Peptide
string	m_Peptide_prev_aa
string	m_Peptide_next_aa
string	m_Protein
int	m_Num_tot_proteins
int	m_Num_matched_ions
int	m_Tot_num_ions
double	m_Calc_neutral_pep_mass
string	m_Massdiff
int	m_Num_tol_term
int	m_Num_missed_cleavages
EAttlist_is_rejected	m_Is_rejected
string	m_Protein_descr
string	m_Calc_pI
double	m_Protein_mw

Additional Inherited Members
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<*unassigned*>"
static const char	ms_UnassignedByte = char(0xcd)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

C_Attlist –.

Definition at line 99 of file Search_hit_.hpp.

---

The documentation for this class was generated from the following files:

• include/algo/ms/formats/pepxml/Search_hit_.hpp
• src/algo/ms/formats/pepxml/Search_hit_.cpp