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

Represents ASN.1 type PDB-seq-id defined in file seqloc.asn

Search Toolkit Book for CPDB_seq_id_Base

must set either chain or chain_id, but not both More...

#include <objects/seqloc/PDB_seq_id_.hpp>

+ Inheritance diagram for CPDB_seq_id_Base:
+ Collaboration diagram for CPDB_seq_id_Base:

Public Types

typedef CPDB_mol_id TMol
 
typedef int TChain
 
typedef CDate TRel
 
typedef string TChain_id
 
- 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

 CPDB_seq_id_Base (void)
 
virtual ~CPDB_seq_id_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetMol (void) const
 the molecule name Check if a value has been assigned to Mol data member. More...
 
bool CanGetMol (void) const
 Check if it is safe to call GetMol method. More...
 
void ResetMol (void)
 Reset Mol data member. More...
 
const TMolGetMol (void) const
 Get the Mol member data. More...
 
void SetMol (const TMol &value)
 Assign a value to Mol data member. More...
 
TMolSetMol (void)
 Assign a value to Mol data member. More...
 
bool IsSetChain (void) const
 Deprecated : For single ASCII character chain identifiers of pre-2015 PDB structures Check if a value has been assigned to Chain data member. More...
 
bool CanGetChain (void) const
 Check if it is safe to call GetChain method. More...
 
void ResetChain (void)
 Reset Chain data member. More...
 
void SetDefaultChain (void)
 Assign default value to Chain data member. More...
 
TChain GetChain (void) const
 Get the Chain member data. More...
 
void SetChain (TChain value)
 Assign a value to Chain data member. More...
 
TChainSetChain (void)
 Assign a value to Chain data member. More...
 
bool IsSetRel (void) const
 release date, month and year Check if a value has been assigned to Rel data member. More...
 
bool CanGetRel (void) const
 Check if it is safe to call GetRel method. More...
 
void ResetRel (void)
 Reset Rel data member. More...
 
const TRelGetRel (void) const
 Get the Rel member data. More...
 
void SetRel (TRel &value)
 Assign a value to Rel data member. More...
 
TRelSetRel (void)
 Assign a value to Rel data member. More...
 
bool IsSetChain_id (void) const
 chain identifier Check if a value has been assigned to Chain_id data member. More...
 
bool CanGetChain_id (void) const
 Check if it is safe to call GetChain_id method. More...
 
void ResetChain_id (void)
 Reset Chain_id data member. More...
 
const TChain_idGetChain_id (void) const
 Get the Chain_id member data. More...
 
void SetChain_id (const TChain_id &value)
 Assign a value to Chain_id data member. More...
 
TChain_idSetChain_id (void)
 Assign a value to Chain_id 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

 CPDB_seq_id_Base (const CPDB_seq_id_Base &)
 
CPDB_seq_id_Baseoperator= (const CPDB_seq_id_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
CPDB_mol_id m_Mol
 
int m_Chain
 
CRef< TRelm_Rel
 
string m_Chain_id
 

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

must set either chain or chain_id, but not both

CPDB_seq_id_Base

Definition at line 78 of file PDB_seq_id_.hpp.

Member Typedef Documentation

Definition at line 92 of file PDB_seq_id_.hpp.

Definition at line 94 of file PDB_seq_id_.hpp.

Definition at line 91 of file PDB_seq_id_.hpp.

Definition at line 80 of file PDB_seq_id_.hpp.

Definition at line 93 of file PDB_seq_id_.hpp.

Constructor & Destructor Documentation

END_CLASS_INFO CPDB_seq_id_Base::CPDB_seq_id_Base ( void  )

Definition at line 101 of file PDB_seq_id_.cpp.

References m_set_State.

CPDB_seq_id_Base::~CPDB_seq_id_Base ( void  )
virtual

Definition at line 108 of file PDB_seq_id_.cpp.

CPDB_seq_id_Base::CPDB_seq_id_Base ( const CPDB_seq_id_Base )
private

Member Function Documentation

bool CPDB_seq_id_Base::CanGetChain ( void  ) const
inline

Check if it is safe to call GetChain method.

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

Definition at line 323 of file PDB_seq_id_.hpp.

Referenced by CGencollIdMapper::x_FixImperfectId().

bool CPDB_seq_id_Base::CanGetChain_id ( void  ) const
inline

Check if it is safe to call GetChain_id method.

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

Definition at line 394 of file PDB_seq_id_.hpp.

References IsSetChain_id().

Referenced by GetChain_id().

bool CPDB_seq_id_Base::CanGetMol ( void  ) const
inline

Check if it is safe to call GetMol method.

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

Definition at line 288 of file PDB_seq_id_.hpp.

References IsSetMol().

Referenced by GetMol(), CWriteDB_IsamIndex::x_AddPdb(), and CGencollIdMapper::x_FixImperfectId().

bool CPDB_seq_id_Base::CanGetRel ( void  ) const
inline

Check if it is safe to call GetRel method.

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

Definition at line 373 of file PDB_seq_id_.hpp.

References IsSetRel().

Referenced by GetRel(), and CDBSourceItem::x_FormatDBSourceID().

CPDB_seq_id_Base::DECLARE_INTERNAL_TYPE_INFO ( )
CPDB_seq_id_Base::TChain CPDB_seq_id_Base::GetChain ( void  ) const
inline
const CPDB_seq_id_Base::TChain_id & CPDB_seq_id_Base::GetChain_id ( void  ) const
inline

Get the Chain_id member data.

Returns
Reference to the member data.

Definition at line 400 of file PDB_seq_id_.hpp.

References CanGetChain_id(), m_Chain_id, and CSerialObject::ThrowUnassigned().

const CPDB_seq_id_Base::TMol & CPDB_seq_id_Base::GetMol ( void  ) const
inline
const CPDB_seq_id_Base::TRel & CPDB_seq_id_Base::GetRel ( void  ) const
inline

Get the Rel member data.

Returns
Reference to the member data.

Definition at line 379 of file PDB_seq_id_.hpp.

References CanGetRel(), m_Rel, and CSerialObject::ThrowUnassigned().

Referenced by CopySeqId(), CSeq_id_PDB_Tree::FindMatch(), x_Assign(), and CDBSourceItem::x_FormatDBSourceID().

bool CPDB_seq_id_Base::IsSetChain ( void  ) const
inline

Deprecated : For single ASCII character chain identifiers of pre-2015 PDB structures Check if a value has been assigned to Chain data member.

Data member Chain is optional with default 32; its type is defined as 'typedef int TChain'

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

Definition at line 317 of file PDB_seq_id_.hpp.

References m_set_State.

Referenced by CopySeqId(), ExtractPdbMolChain(), SetChain(), CValidError_bioseq::ValidateSeqId(), x_Assign(), and CDeflineGenerator::x_SetFlags().

bool CPDB_seq_id_Base::IsSetChain_id ( void  ) const
inline

chain identifier Check if a value has been assigned to Chain_id data member.

Data member Chain_id is optional; its type is defined as 'typedef string TChain_id'

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

Definition at line 388 of file PDB_seq_id_.hpp.

References m_set_State.

Referenced by CanGetChain_id(), SetChain_id(), and CValidError_bioseq::ValidateSeqId().

bool CPDB_seq_id_Base::IsSetMol ( void  ) const
inline

the molecule name Check if a value has been assigned to Mol data member.

Data member Mol is mandatory; its type is defined as 'typedef CPDB_mol_id TMol'

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

Definition at line 282 of file PDB_seq_id_.hpp.

References m_set_State.

Referenced by CanGetMol().

bool CPDB_seq_id_Base::IsSetRel ( void  ) const
inline

release date, month and year Check if a value has been assigned to Rel data member.

Data member Rel is optional; its type is defined as 'typedef CDate TRel'

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

Definition at line 367 of file PDB_seq_id_.hpp.

References m_Rel.

Referenced by CanGetRel(), CopySeqId(), CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Tree::FindReverseMatch(), x_Assign(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_ETC().

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

Reset the whole object.

Definition at line 80 of file PDB_seq_id_.cpp.

References ResetChain(), ResetChain_id(), ResetMol(), and ResetRel().

void CPDB_seq_id_Base::ResetChain ( void  )
inline

Reset Chain data member.

Definition at line 329 of file PDB_seq_id_.hpp.

References m_Chain, and m_set_State.

Referenced by Reset(), CSeq_id::Set(), SetDefaultChain(), and x_Assign().

void CPDB_seq_id_Base::ResetChain_id ( void  )

Reset Chain_id data member.

Definition at line 74 of file PDB_seq_id_.cpp.

References m_Chain_id, and m_set_State.

Referenced by Reset().

void CPDB_seq_id_Base::ResetMol ( void  )

Reset Mol data member.

Definition at line 51 of file PDB_seq_id_.cpp.

References m_Mol, m_set_State, and CAliasBase< TPrim >::Set().

Referenced by Reset().

void CPDB_seq_id_Base::ResetRel ( void  )

Reset Rel data member.

Definition at line 57 of file PDB_seq_id_.cpp.

References m_Rel.

Referenced by CSeq_id::GetMatchingIds(), Reset(), CSeq_id::Set(), and x_Assign().

void CPDB_seq_id_Base::SetChain ( CPDB_seq_id_Base::TChain  value)
inline

Assign a value to Chain data member.

Parameters
valueValue to assign

Definition at line 348 of file PDB_seq_id_.hpp.

References m_Chain, m_set_State, and value.

Referenced by CopySeqId(), CSeq_id::Set(), sscanSeqId(), and x_Assign().

CPDB_seq_id_Base::TChain & CPDB_seq_id_Base::SetChain ( void  )
inline

Assign a value to Chain data member.

Returns
Reference to the data value.

Definition at line 355 of file PDB_seq_id_.hpp.

References IsSetChain(), m_Chain, m_set_State, and CSerialObject::UnassignedByte().

void CPDB_seq_id_Base::SetChain_id ( const TChain_id value)
inline

Assign a value to Chain_id data member.

Parameters
valueValue to assign

Definition at line 409 of file PDB_seq_id_.hpp.

References m_Chain_id, m_set_State, and value.

CPDB_seq_id_Base::TChain_id & CPDB_seq_id_Base::SetChain_id ( void  )
inline

Assign a value to Chain_id data member.

Returns
Reference to the data value.

Definition at line 416 of file PDB_seq_id_.hpp.

References IsSetChain_id(), m_Chain_id, m_set_State, and CSerialObject::UnassignedString().

void CPDB_seq_id_Base::SetDefaultChain ( void  )
inline

Assign default value to Chain data member.

Definition at line 336 of file PDB_seq_id_.hpp.

References ResetChain().

void CPDB_seq_id_Base::SetMol ( const TMol value)
inline

Assign a value to Mol data member.

Parameters
valueValue to assign

Definition at line 303 of file PDB_seq_id_.hpp.

References m_Mol, m_set_State, and value.

Referenced by BOOST_AUTO_TEST_CASE(), CopySeqId(), CSeq_id::Set(), sscanSeqId(), and x_Assign().

CPDB_seq_id_Base::TMol & CPDB_seq_id_Base::SetMol ( void  )
inline

Assign a value to Mol data member.

Returns
Reference to the data value.

Definition at line 310 of file PDB_seq_id_.hpp.

References m_Mol, and m_set_State.

void CPDB_seq_id_Base::SetRel ( CPDB_seq_id_Base::TRel value)

Assign a value to Rel data member.

Parameters
valueReference to value.

Definition at line 62 of file PDB_seq_id_.cpp.

References m_Rel.

Referenced by CopySeqId(), x_Assign(), and CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_identification_identification_pdb_pdb_ETC().

CPDB_seq_id_Base::TRel & CPDB_seq_id_Base::SetRel ( void  )

Assign a value to Rel data member.

Returns
Reference to the data value.

Definition at line 67 of file PDB_seq_id_.cpp.

References m_Rel.

Member Data Documentation

int CPDB_seq_id_Base::m_Chain
private

Definition at line 267 of file PDB_seq_id_.hpp.

Referenced by GetChain(), ResetChain(), and SetChain().

string CPDB_seq_id_Base::m_Chain_id
private

Definition at line 269 of file PDB_seq_id_.hpp.

Referenced by GetChain_id(), ResetChain_id(), and SetChain_id().

CPDB_mol_id CPDB_seq_id_Base::m_Mol
private

Definition at line 266 of file PDB_seq_id_.hpp.

Referenced by GetMol(), ResetMol(), and SetMol().

CRef< TRel > CPDB_seq_id_Base::m_Rel
private

Definition at line 268 of file PDB_seq_id_.hpp.

Referenced by GetRel(), IsSetRel(), ResetRel(), and SetRel().

Uint4 CPDB_seq_id_Base::m_set_State[1]
private

The documentation for this class was generated from the following files:
Modified on Sat Apr 22 17:06:05 2017 by modify_doxy.py rev. 533848