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CSeq_inst Class Reference

Represents ASN.1 type Seq-inst defined in file seq.asn

Search Toolkit Book for CSeq_inst

#include <objects/seq/Seq_inst.hpp>

+ Inheritance diagram for CSeq_inst:
+ Collaboration diagram for CSeq_inst:

Public Member Functions

 CSeq_inst (void)
 
 ~CSeq_inst (void)
 
bool IsNa (void) const
 
bool IsAa (void) const
 
bool ConvertDeltaToRaw ()
 
- Public Member Functions inherited from CSeq_inst_Base
 CSeq_inst_Base (void)
 
virtual ~CSeq_inst_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetRepr (void) const
 Check if a value has been assigned to Repr data member. More...
 
bool CanGetRepr (void) const
 Check if it is safe to call GetRepr method. More...
 
void ResetRepr (void)
 Reset Repr data member. More...
 
TRepr GetRepr (void) const
 Get the Repr member data. More...
 
void SetRepr (TRepr value)
 Assign a value to Repr data member. More...
 
TReprSetRepr (void)
 Assign a value to Repr data member. More...
 
bool IsSetMol (void) const
 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...
 
TMol GetMol (void) const
 Get the Mol member data. More...
 
void SetMol (TMol value)
 Assign a value to Mol data member. More...
 
TMolSetMol (void)
 Assign a value to Mol data member. More...
 
bool IsSetLength (void) const
 length of sequence in residues Check if a value has been assigned to Length data member. More...
 
bool CanGetLength (void) const
 Check if it is safe to call GetLength method. More...
 
void ResetLength (void)
 Reset Length data member. More...
 
TLength GetLength (void) const
 Get the Length member data. More...
 
void SetLength (TLength value)
 Assign a value to Length data member. More...
 
TLengthSetLength (void)
 Assign a value to Length data member. More...
 
bool IsSetFuzz (void) const
 length uncertainty Check if a value has been assigned to Fuzz data member. More...
 
bool CanGetFuzz (void) const
 Check if it is safe to call GetFuzz method. More...
 
void ResetFuzz (void)
 Reset Fuzz data member. More...
 
const TFuzzGetFuzz (void) const
 Get the Fuzz member data. More...
 
void SetFuzz (TFuzz &value)
 Assign a value to Fuzz data member. More...
 
TFuzzSetFuzz (void)
 Assign a value to Fuzz data member. More...
 
bool IsSetTopology (void) const
 Check if a value has been assigned to Topology data member. More...
 
bool CanGetTopology (void) const
 Check if it is safe to call GetTopology method. More...
 
void ResetTopology (void)
 Reset Topology data member. More...
 
void SetDefaultTopology (void)
 Assign default value to Topology data member. More...
 
TTopology GetTopology (void) const
 Get the Topology member data. More...
 
void SetTopology (TTopology value)
 Assign a value to Topology data member. More...
 
TTopologySetTopology (void)
 Assign a value to Topology data member. More...
 
bool IsSetStrand (void) const
 Check if a value has been assigned to Strand data member. More...
 
bool CanGetStrand (void) const
 Check if it is safe to call GetStrand method. More...
 
void ResetStrand (void)
 Reset Strand data member. More...
 
TStrand GetStrand (void) const
 Get the Strand member data. More...
 
void SetStrand (TStrand value)
 Assign a value to Strand data member. More...
 
TStrandSetStrand (void)
 Assign a value to Strand data member. More...
 
bool IsSetSeq_data (void) const
 the sequence Check if a value has been assigned to Seq_data data member. More...
 
bool CanGetSeq_data (void) const
 Check if it is safe to call GetSeq_data method. More...
 
void ResetSeq_data (void)
 Reset Seq_data data member. More...
 
const TSeq_dataGetSeq_data (void) const
 Get the Seq_data member data. More...
 
void SetSeq_data (TSeq_data &value)
 Assign a value to Seq_data data member. More...
 
TSeq_dataSetSeq_data (void)
 Assign a value to Seq_data data member. More...
 
bool IsSetExt (void) const
 extensions for special types Check if a value has been assigned to Ext data member. More...
 
bool CanGetExt (void) const
 Check if it is safe to call GetExt method. More...
 
void ResetExt (void)
 Reset Ext data member. More...
 
const TExtGetExt (void) const
 Get the Ext member data. More...
 
void SetExt (TExt &value)
 Assign a value to Ext data member. More...
 
TExtSetExt (void)
 Assign a value to Ext data member. More...
 
bool IsSetHist (void) const
 sequence history Check if a value has been assigned to Hist data member. More...
 
bool CanGetHist (void) const
 Check if it is safe to call GetHist method. More...
 
void ResetHist (void)
 Reset Hist data member. More...
 
const THistGetHist (void) const
 Get the Hist member data. More...
 
void SetHist (THist &value)
 Assign a value to Hist data member. More...
 
THistSetHist (void)
 Assign a value to Hist 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
 

Static Public Member Functions

static bool IsNa (EMol mol)
 
static bool IsAa (EMol mol)
 
static string GetMoleculeClass (EMol mol)
 
- Static Public Member Functions inherited from CSeq_inst_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() ERepr (void)
 Access to ERepr's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EMol (void)
 Access to EMol's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() ETopology (void)
 Access to ETopology's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EStrand (void)
 Access to EStrand'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 CSeq_inst_Base Tparent
 

Private Member Functions

 CSeq_inst (const CSeq_inst &value)
 
CSeq_instoperator= (const CSeq_inst &value)
 

Additional Inherited Members

- Public Types inherited from CSeq_inst_Base
enum  ERepr {
  eRepr_not_set = 0 , eRepr_virtual = 1 , eRepr_raw = 2 , eRepr_seg = 3 ,
  eRepr_const = 4 , eRepr_ref = 5 , eRepr_consen = 6 , eRepr_map = 7 ,
  eRepr_delta = 8 , eRepr_other = 255
}
 representation class More...
 
enum  EMol {
  eMol_not_set = 0 , eMol_dna = 1 , eMol_rna = 2 , eMol_aa = 3 ,
  eMol_na = 4 , eMol_other = 255
}
 molecule class in living organism More...
 
enum  ETopology {
  eTopology_not_set = 0 , eTopology_linear = 1 , eTopology_circular = 2 , eTopology_tandem = 3 ,
  eTopology_other = 255
}
 topology of molecule More...
 
enum  EStrand {
  eStrand_not_set = 0 , eStrand_ss = 1 , eStrand_ds = 2 , eStrand_mixed = 3 ,
  eStrand_other = 255
}
 strandedness in living organism More...
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_repr , e_mol , e_length ,
  e_fuzz , e_topology , e_strand , e_seq_data ,
  e_ext , e_hist
}
 
typedef ERepr TRepr
 
typedef EMol TMol
 
typedef TSeqPos TLength
 
typedef CInt_fuzz TFuzz
 
typedef ETopology TTopology
 
typedef EStrand TStrand
 
typedef CSeq_data TSeq_data
 
typedef CSeq_ext TExt
 
typedef CSeq_hist THist
 
typedef Tparent::CMemberIndex< E_memberIndex, 10 > 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- 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 50 of file Seq_inst.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 52 of file Seq_inst.hpp.

Constructor & Destructor Documentation

◆ CSeq_inst() [1/2]

CSeq_inst::CSeq_inst ( void  )
inline

Definition at line 84 of file Seq_inst.hpp.

◆ ~CSeq_inst()

CSeq_inst::~CSeq_inst ( void  )

Definition at line 50 of file Seq_inst.cpp.

◆ CSeq_inst() [2/2]

CSeq_inst::CSeq_inst ( const CSeq_inst value)
private

Member Function Documentation

◆ ConvertDeltaToRaw()

bool CSeq_inst::ConvertDeltaToRaw ( )

◆ GetMoleculeClass()

string CSeq_inst::GetMoleculeClass ( CSeq_inst::EMol  mol)
static

Definition at line 72 of file Seq_inst.cpp.

References kEmptyStr.

Referenced by CValidError_bioseq::x_ReportLineageConflictWithMol().

◆ IsAa() [1/2]

bool CSeq_inst::IsAa ( EMol  mol)
inlinestatic

◆ IsAa() [2/2]

bool CSeq_inst::IsAa ( void  ) const
inline

◆ IsNa() [1/2]

bool CSeq_inst::IsNa ( EMol  mol)
inlinestatic

◆ IsNa() [2/2]

bool CSeq_inst::IsNa ( void  ) const
inline

◆ operator=()

CSeq_inst& CSeq_inst::operator= ( const CSeq_inst value)
private

The documentation for this class was generated from the following files:
Modified on Mon May 27 04:39:21 2024 by modify_doxy.py rev. 669887