NCBI C++ ToolKit
Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members

Represents ASN.1 type Std-seg defined in file seqalign.asn

Search Toolkit Book for CStd_seg_Base

CStd_seg_Base –. More...

#include <objects/seqalign/Std_seg_.hpp>

+ Inheritance diagram for CStd_seg_Base:
+ Collaboration diagram for CStd_seg_Base:

Public Types

enum  E_memberIndex {
  E_memberIndex::e__allMandatory = 0, E_memberIndex::e_dim, E_memberIndex::e_ids, E_memberIndex::e_loc,
  E_memberIndex::e_scores
}
 
typedef int TDim
 
typedef vector< CRef< CSeq_id > > TIds
 
typedef vector< CRef< CSeq_loc > > TLoc
 
typedef vector< CRef< CScore > > TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CStd_seg_Base (void)
 
virtual ~CStd_seg_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void ResetDim (void)
 Reset Dim data member. More...
 
void SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim GetDim (void) const
 Get the Dim member data. More...
 
void SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimSetDim (void)
 Assign a value to Dim data member. More...
 
bool IsSetIds (void) const
 Check if a value has been assigned to Ids data member. More...
 
bool CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void ResetIds (void)
 Reset Ids data member. More...
 
const TIdsGetIds (void) const
 Get the Ids member data. More...
 
TIdsSetIds (void)
 Assign a value to Ids data member. More...
 
bool IsSetLoc (void) const
 Check if a value has been assigned to Loc data member. More...
 
bool CanGetLoc (void) const
 Check if it is safe to call GetLoc method. More...
 
void ResetLoc (void)
 Reset Loc data member. More...
 
const TLocGetLoc (void) const
 Get the Loc member data. More...
 
TLocSetLoc (void)
 Assign a value to Loc data member. More...
 
bool IsSetScores (void) const
 Check if a value has been assigned to Scores data member. More...
 
bool CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void ResetScores (void)
 Reset Scores data member. More...
 
const TScoresGetScores (void) const
 Get the Scores member data. More...
 
TScoresSetScores (void)
 Assign a value to Scores 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 CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (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...
 
CObjectoperator= (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 CSerialObject Tparent
 

Private Member Functions

 CStd_seg_Base (const CStd_seg_Base &)
 
CStd_seg_Baseoperator= (const CStd_seg_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
int m_Dim
 
vector< CRef< CSeq_id > > m_Ids
 
vector< CRef< CSeq_loc > > m_Loc
 
vector< CRef< CScore > > m_Scores
 

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_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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

CStd_seg_Base –.

Definition at line 78 of file Std_seg_.hpp.

Member Typedef Documentation

Definition at line 91 of file Std_seg_.hpp.

typedef vector< CRef< CSeq_id > > CStd_seg_Base::TIds

Definition at line 92 of file Std_seg_.hpp.

typedef vector< CRef< CSeq_loc > > CStd_seg_Base::TLoc

Definition at line 93 of file Std_seg_.hpp.

Definition at line 104 of file Std_seg_.hpp.

Definition at line 80 of file Std_seg_.hpp.

typedef vector< CRef< CScore > > CStd_seg_Base::TScores

Definition at line 94 of file Std_seg_.hpp.

Constructor & Destructor Documentation

END_CLASS_INFO CStd_seg_Base::CStd_seg_Base ( void  )

Definition at line 93 of file Std_seg_.cpp.

References m_set_State.

CStd_seg_Base::~CStd_seg_Base ( void  )
virtual

Definition at line 100 of file Std_seg_.cpp.

CStd_seg_Base::CStd_seg_Base ( const CStd_seg_Base )
private

Member Function Documentation

bool CStd_seg_Base::CanGetDim ( void  ) const
inline

Check if it is safe to call GetDim method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 276 of file Std_seg_.hpp.

bool CStd_seg_Base::CanGetIds ( void  ) const
inline

Check if it is safe to call GetIds method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 326 of file Std_seg_.hpp.

bool CStd_seg_Base::CanGetLoc ( void  ) const
inline

Check if it is safe to call GetLoc method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 351 of file Std_seg_.hpp.

bool CStd_seg_Base::CanGetScores ( void  ) const
inline

Check if it is safe to call GetScores method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 376 of file Std_seg_.hpp.

CStd_seg_Base::DECLARE_INTERNAL_TYPE_INFO ( )
CStd_seg_Base::TDim CStd_seg_Base::GetDim ( void  ) const
inline
const CStd_seg_Base::TIds & CStd_seg_Base::GetIds ( void  ) const
inline
const CStd_seg_Base::TLoc & CStd_seg_Base::GetLoc ( void  ) const
inline
const CStd_seg_Base::TScores & CStd_seg_Base::GetScores ( void  ) const
inline

Get the Scores member data.

Returns
Reference to the member data.

Definition at line 382 of file Std_seg_.hpp.

References m_Scores.

Referenced by CSeq_align_Mapper_Base::x_Init().

bool CStd_seg_Base::IsSetDim ( void  ) const
inline

dimensionality Check if a value has been assigned to Dim data member.

Data member Dim is optional with default 2; its type is defined as 'typedef int TDim'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 270 of file Std_seg_.hpp.

References m_set_State.

Referenced by SetDim().

bool CStd_seg_Base::IsSetIds ( void  ) const
inline

Check if a value has been assigned to Ids data member.

Data member Ids is optional; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 320 of file Std_seg_.hpp.

References m_set_State.

Referenced by CStd_seg::CheckNumRows(), CStd_seg::RemapToLoc(), CStd_seg::SwapRows(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_std_E_E_ETC(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStd().

bool CStd_seg_Base::IsSetLoc ( void  ) const
inline

Check if a value has been assigned to Loc data member.

Data member Loc is mandatory; its type is defined as 'typedef vector< CRef< CSeq_loc > > TLoc'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 345 of file Std_seg_.hpp.

References m_set_State.

Referenced by CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_std_E_E_ETC().

bool CStd_seg_Base::IsSetScores ( void  ) const
inline

Check if a value has been assigned to Scores data member.

Data member Scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TScores'

Returns
  • true, if a value has been assigned.
  • false, otherwise.

Definition at line 370 of file Std_seg_.hpp.

References m_set_State.

Referenced by CSeq_align_Mapper_Base::x_Init().

CStd_seg_Base& CStd_seg_Base::operator= ( const CStd_seg_Base )
private
void CStd_seg_Base::Reset ( void  )
virtual

Reset the whole object.

Definition at line 71 of file Std_seg_.cpp.

References ResetDim(), ResetIds(), ResetLoc(), and ResetScores().

void CStd_seg_Base::ResetDim ( void  )
inline

Reset Dim data member.

Definition at line 282 of file Std_seg_.hpp.

References m_Dim, and m_set_State.

Referenced by Reset(), and SetDefaultDim().

void CStd_seg_Base::ResetIds ( void  )

Reset Ids data member.

Definition at line 53 of file Std_seg_.cpp.

References m_Ids, and m_set_State.

Referenced by Reset().

void CStd_seg_Base::ResetLoc ( void  )

Reset Loc data member.

Definition at line 59 of file Std_seg_.cpp.

References m_Loc, and m_set_State.

Referenced by Reset().

void CStd_seg_Base::ResetScores ( void  )

Reset Scores data member.

Definition at line 65 of file Std_seg_.cpp.

References m_Scores, and m_set_State.

Referenced by Reset().

void CStd_seg_Base::SetDefaultDim ( void  )
inline

Assign default value to Dim data member.

Definition at line 289 of file Std_seg_.hpp.

References ResetDim().

void CStd_seg_Base::SetDim ( CStd_seg_Base::TDim  value)
inline

Assign a value to Dim data member.

Parameters
valueValue to assign

Definition at line 301 of file Std_seg_.hpp.

References m_Dim, m_set_State, and rapidjson::value.

Referenced by CCompartmentAccessor< THit >::AsSeqAlignSet(), s_CreateStdSegs(), s_OOFBlastHSP2SeqAlign(), CSeq_align_Mapper_Base::x_GetDstStd(), x_NonTranslatedHSPToStdSeg(), and x_UngappedHSPToStdSeg().

CStd_seg_Base::TDim & CStd_seg_Base::SetDim ( void  )
inline

Assign a value to Dim data member.

Returns
Reference to the data value.

Definition at line 308 of file Std_seg_.hpp.

References IsSetDim(), m_Dim, m_set_State, and CSerialObject::UnassignedByte().

CStd_seg_Base::TIds & CStd_seg_Base::SetIds ( void  )
inline
CStd_seg_Base::TLoc & CStd_seg_Base::SetLoc ( void  )
inline
CStd_seg_Base::TScores & CStd_seg_Base::SetScores ( void  )
inline

Assign a value to Scores data member.

Returns
Reference to the data value.

Definition at line 388 of file Std_seg_.hpp.

References m_Scores, and m_set_State.

Referenced by MakeCompartment(), CSeq_align_Mapper_Base::x_GetDstStd(), x_NonTranslatedHSPToStdSeg(), and x_UngappedHSPToStdSeg().

Member Data Documentation

int CStd_seg_Base::m_Dim
private

Definition at line 254 of file Std_seg_.hpp.

Referenced by GetDim(), ResetDim(), and SetDim().

vector< CRef< CSeq_id > > CStd_seg_Base::m_Ids
private

Definition at line 255 of file Std_seg_.hpp.

Referenced by GetIds(), ResetIds(), and SetIds().

vector< CRef< CSeq_loc > > CStd_seg_Base::m_Loc
private

Definition at line 256 of file Std_seg_.hpp.

Referenced by GetLoc(), ResetLoc(), and SetLoc().

vector< CRef< CScore > > CStd_seg_Base::m_Scores
private

Definition at line 257 of file Std_seg_.hpp.

Referenced by GetScores(), ResetScores(), and SetScores().

Uint4 CStd_seg_Base::m_set_State[1]
private

The documentation for this class was generated from the following files:
Modified on Tue May 22 12:44:07 2018 by modify_doxy.py rev. 546573