#include <objects/omssa/MSResponse.hpp>

Inheritance diagram for CMSResponse:

Collaboration diagram for CMSResponse:

Public Types
typedef set< int >	TOidSet
	typdef for set of blast oids More...

Public Types inherited from CMSResponse_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_hitsets , e_scale , e_rid , e_error , e_version , e_email , e_dbversion , e_bioseqs }

typedef vector< CRef< CMSHitSet > >	THitsets

typedef int	TScale

typedef string	TRid

typedef int	TError

typedef string	TVersion

typedef string	TEmail

typedef int	TDbversion

typedef CMSBioseqSet	TBioseqs

typedef Tparent::CMemberIndex< E_memberIndex, 9 >	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
	CMSResponse (void)

	~CMSResponse (void)

string	CSVString (const string &in)

void	PrintCSV (ostream &os, CRef< CMSModSpecSet > ModSet)

void	GetOidsBelowThreshold (TOidSet &OidSet, const double Threshold) const
	insert oids into oidset if hit is below threhold More...

CRef< CMSHitSet >	FindHitSet (const int Number) const
	Find hitset with given number. More...

Public Member Functions inherited from CMSResponse_Base
	CMSResponse_Base (void)

virtual	~CMSResponse_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetHitsets (void) const
	hits grouped by spectrum Check if a value has been assigned to Hitsets data member. More...

bool	CanGetHitsets (void) const
	Check if it is safe to call GetHitsets method. More...

void	ResetHitsets (void)
	Reset Hitsets data member. More...

const THitsets &	GetHitsets (void) const
	Get the Hitsets member data. More...

THitsets &	SetHitsets (void)
	Assign a value to Hitsets data member. More...

bool	IsSetScale (void) const
	scale to change m/z float to integer Check if a value has been assigned to Scale data member. More...

bool	CanGetScale (void) const
	Check if it is safe to call GetScale method. More...

void	ResetScale (void)
	Reset Scale data member. More...

void	SetDefaultScale (void)
	Assign default value to Scale data member. More...

TScale	GetScale (void) const
	Get the Scale member data. More...

void	SetScale (TScale value)
	Assign a value to Scale data member. More...

TScale &	SetScale (void)
	Assign a value to Scale data member. More...

bool	IsSetRid (void) const
	request id Check if a value has been assigned to Rid data member. More...

bool	CanGetRid (void) const
	Check if it is safe to call GetRid method. More...

void	ResetRid (void)
	Reset Rid data member. More...

const TRid &	GetRid (void) const
	Get the Rid member data. More...

void	SetRid (const TRid &value)
	Assign a value to Rid data member. More...

void	SetRid (TRid &&value)

TRid &	SetRid (void)
	Assign a value to Rid data member. More...

bool	IsSetError (void) const
	error response Check if a value has been assigned to Error data member. More...

bool	CanGetError (void) const
	Check if it is safe to call GetError method. More...

void	ResetError (void)
	Reset Error data member. More...

TError	GetError (void) const
	Get the Error member data. More...

void	SetError (TError value)
	Assign a value to Error data member. More...

TError &	SetError (void)
	Assign a value to Error data member. More...

bool	IsSetVersion (void) const
	version of OMSSA Check if a value has been assigned to Version data member. More...

bool	CanGetVersion (void) const
	Check if it is safe to call GetVersion method. More...

void	ResetVersion (void)
	Reset Version data member. More...

const TVersion &	GetVersion (void) const
	Get the Version member data. More...

void	SetVersion (const TVersion &value)
	Assign a value to Version data member. More...

void	SetVersion (TVersion &&value)

TVersion &	SetVersion (void)
	Assign a value to Version data member. More...

bool	IsSetEmail (void) const
	email address for notification Check if a value has been assigned to Email data member. More...

bool	CanGetEmail (void) const
	Check if it is safe to call GetEmail method. More...

void	ResetEmail (void)
	Reset Email data member. More...

const TEmail &	GetEmail (void) const
	Get the Email member data. More...

void	SetEmail (const TEmail &value)
	Assign a value to Email data member. More...

void	SetEmail (TEmail &&value)

TEmail &	SetEmail (void)
	Assign a value to Email data member. More...

bool	IsSetDbversion (void) const
	version of db searched (usually size) Check if a value has been assigned to Dbversion data member. More...

bool	CanGetDbversion (void) const
	Check if it is safe to call GetDbversion method. More...

void	ResetDbversion (void)
	Reset Dbversion data member. More...

TDbversion	GetDbversion (void) const
	Get the Dbversion member data. More...

void	SetDbversion (TDbversion value)
	Assign a value to Dbversion data member. More...

TDbversion &	SetDbversion (void)
	Assign a value to Dbversion data member. More...

bool	IsSetBioseqs (void) const
	sequences found in search Check if a value has been assigned to Bioseqs data member. More...

bool	CanGetBioseqs (void) const
	Check if it is safe to call GetBioseqs method. More...

void	ResetBioseqs (void)
	Reset Bioseqs data member. More...

const TBioseqs &	GetBioseqs (void) const
	Get the Bioseqs member data. More...

void	SetBioseqs (TBioseqs &value)
	Assign a value to Bioseqs data member. More...

TBioseqs &	SetBioseqs (void)
	Assign a value to Bioseqs data member. More...

virtual 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

Private Types
typedef CMSResponse_Base	Tparent

Private Member Functions
	CMSResponse (const CMSResponse &value)

CMSResponse &	operator= (const CMSResponse &value)

Additional Inherited Members
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)

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

Definition at line 57 of file MSResponse.hpp.

Member Typedef Documentation

◆ TOidSet

typedef set<int> CMSResponse::TOidSet

typdef for set of blast oids

Definition at line 73 of file MSResponse.hpp.

◆ Tparent

typedef CMSResponse_Base CMSResponse::Tparent

private

Definition at line 59 of file MSResponse.hpp.

Constructor & Destructor Documentation

◆ CMSResponse() [1/2]

CMSResponse::CMSResponse ( void )

inline

Definition at line 104 of file MSResponse.hpp.

◆ ~CMSResponse()

CMSResponse::~CMSResponse ( void )

Definition at line 50 of file MSResponse.cpp.

◆ CMSResponse() [2/2]

CMSResponse::CMSResponse ( const CMSResponse & value )

private

Member Function Documentation

◆ CSVString()

string CMSResponse::CSVString ( const string & in )

Definition at line 57 of file MSResponse.cpp.

References in(), and NStr::Replace().

Referenced by PrintCSV().

◆ FindHitSet()

CRef< CMSHitSet > CMSResponse::FindHitSet ( const int Number ) const

Find hitset with given number.

Parameters

Number the number of the hitset

Returns: hitset or null

Definition at line 148 of file MSResponse.cpp.

References CMSResponse_Base::GetHitsets(), and ITERATE.

Referenced by CSearch< LEGACY, NHITS >::SetResult().

◆ GetOidsBelowThreshold()

void CMSResponse::GetOidsBelowThreshold	(	TOidSet &	OidSet,
		const double	Threshold
	)		const

insert oids into oidset if hit is below threhold

Parameters

OidSet	the set of oids
Threshold	the evalue threshold

Definition at line 132 of file MSResponse.cpp.

References CMSResponse_Base::GetHitsets(), set< Key, Compare >::insert(), and ITERATE.

◆ operator=()

CMSResponse& CMSResponse::operator= ( const CMSResponse & value )

private

◆ PrintCSV()

void CMSResponse::PrintCSV	(	ostream &	os,
		CRef< CMSModSpecSet >	ModSet
	)

Definition at line 66 of file MSResponse.cpp.

References CMSResponse_Base::CanGetError(), CMSResponse_Base::CanGetHitsets(), CMSResponse_Base::CanGetScale(), CSVString(), eMSHitError_notenuffpeaks, CMSResponse_Base::GetHitsets(), CMSResponse_Base::GetScale(), ITERATE, and ZERO_GI.

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

include/objects/omssa/MSResponse.hpp
src/objects/omssa/MSResponse.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TOidSet

◆ Tparent

Constructor & Destructor Documentation

◆ CMSResponse() [1/2]

◆ ~CMSResponse()

◆ CMSResponse() [2/2]

Member Function Documentation

◆ CSVString()

◆ FindHitSet()

◆ GetOidsBelowThreshold()

◆ operator=()

◆ PrintCSV()