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

Represents ASN.1 type Spliced-exon defined in file seqalign.asn

Search Toolkit Book for CSpliced_exon_Base

complete or partial exon two consecutive Spliced-exons may belong to one exon More...

#include <objects/seqalign/Spliced_exon_.hpp>

+ Inheritance diagram for CSpliced_exon_Base:
+ Collaboration diagram for CSpliced_exon_Base:

Public Types

enum class  E_memberIndex {
  e__allMandatory = 0 , e_product_start , e_product_end , e_genomic_start ,
  e_genomic_end , e_product_id , e_genomic_id , e_product_strand ,
  e_genomic_strand , e_parts , e_scores , e_acceptor_before_exon ,
  e_donor_after_exon , e_partial , e_ext
}
 
typedef CProduct_pos TProduct_start
 
typedef CProduct_pos TProduct_end
 
typedef TSeqPos TGenomic_start
 
typedef TSeqPos TGenomic_end
 
typedef CSeq_id TProduct_id
 
typedef CSeq_id TGenomic_id
 
typedef ENa_strand TProduct_strand
 
typedef ENa_strand TGenomic_strand
 
typedef list< CRef< CSpliced_exon_chunk > > TParts
 
typedef CScore_set TScores
 
typedef CSplice_site TAcceptor_before_exon
 
typedef CSplice_site TDonor_after_exon
 
typedef bool TPartial
 
typedef list< CRef< CUser_object > > TExt
 
typedef Tparent::CMemberIndex< E_memberIndex, 15 > 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...
 

Public Member Functions

 CSpliced_exon_Base (void)
 
virtual ~CSpliced_exon_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetProduct_start (void) const
 product-end >= product-start Check if a value has been assigned to Product_start data member. More...
 
bool CanGetProduct_start (void) const
 Check if it is safe to call GetProduct_start method. More...
 
void ResetProduct_start (void)
 Reset Product_start data member. More...
 
const TProduct_startGetProduct_start (void) const
 Get the Product_start member data. More...
 
void SetProduct_start (TProduct_start &value)
 Assign a value to Product_start data member. More...
 
TProduct_startSetProduct_start (void)
 Assign a value to Product_start data member. More...
 
bool IsSetProduct_end (void) const
 Check if a value has been assigned to Product_end data member. More...
 
bool CanGetProduct_end (void) const
 Check if it is safe to call GetProduct_end method. More...
 
void ResetProduct_end (void)
 Reset Product_end data member. More...
 
const TProduct_endGetProduct_end (void) const
 Get the Product_end member data. More...
 
void SetProduct_end (TProduct_end &value)
 Assign a value to Product_end data member. More...
 
TProduct_endSetProduct_end (void)
 Assign a value to Product_end data member. More...
 
bool IsSetGenomic_start (void) const
 genomic-end >= genomic-start Check if a value has been assigned to Genomic_start data member. More...
 
bool CanGetGenomic_start (void) const
 Check if it is safe to call GetGenomic_start method. More...
 
void ResetGenomic_start (void)
 Reset Genomic_start data member. More...
 
TGenomic_start GetGenomic_start (void) const
 Get the Genomic_start member data. More...
 
void SetGenomic_start (TGenomic_start value)
 Assign a value to Genomic_start data member. More...
 
TGenomic_startSetGenomic_start (void)
 Assign a value to Genomic_start data member. More...
 
bool IsSetGenomic_end (void) const
 Check if a value has been assigned to Genomic_end data member. More...
 
bool CanGetGenomic_end (void) const
 Check if it is safe to call GetGenomic_end method. More...
 
void ResetGenomic_end (void)
 Reset Genomic_end data member. More...
 
TGenomic_end GetGenomic_end (void) const
 Get the Genomic_end member data. More...
 
void SetGenomic_end (TGenomic_end value)
 Assign a value to Genomic_end data member. More...
 
TGenomic_endSetGenomic_end (void)
 Assign a value to Genomic_end data member. More...
 
bool IsSetProduct_id (void) const
 product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
 
bool CanGetProduct_id (void) const
 Check if it is safe to call GetProduct_id method. More...
 
void ResetProduct_id (void)
 Reset Product_id data member. More...
 
const TProduct_idGetProduct_id (void) const
 Get the Product_id member data. More...
 
void SetProduct_id (TProduct_id &value)
 Assign a value to Product_id data member. More...
 
TProduct_idSetProduct_id (void)
 Assign a value to Product_id data member. More...
 
bool IsSetGenomic_id (void) const
 Check if a value has been assigned to Genomic_id data member. More...
 
bool CanGetGenomic_id (void) const
 Check if it is safe to call GetGenomic_id method. More...
 
void ResetGenomic_id (void)
 Reset Genomic_id data member. More...
 
const TGenomic_idGetGenomic_id (void) const
 Get the Genomic_id member data. More...
 
void SetGenomic_id (TGenomic_id &value)
 Assign a value to Genomic_id data member. More...
 
TGenomic_idSetGenomic_id (void)
 Assign a value to Genomic_id data member. More...
 
bool IsSetProduct_strand (void) const
 should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
 
bool CanGetProduct_strand (void) const
 Check if it is safe to call GetProduct_strand method. More...
 
void ResetProduct_strand (void)
 Reset Product_strand data member. More...
 
TProduct_strand GetProduct_strand (void) const
 Get the Product_strand member data. More...
 
void SetProduct_strand (TProduct_strand value)
 Assign a value to Product_strand data member. More...
 
TProduct_strandSetProduct_strand (void)
 Assign a value to Product_strand data member. More...
 
bool IsSetGenomic_strand (void) const
 genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_strand data member. More...
 
bool CanGetGenomic_strand (void) const
 Check if it is safe to call GetGenomic_strand method. More...
 
void ResetGenomic_strand (void)
 Reset Genomic_strand data member. More...
 
TGenomic_strand GetGenomic_strand (void) const
 Get the Genomic_strand member data. More...
 
void SetGenomic_strand (TGenomic_strand value)
 Assign a value to Genomic_strand data member. More...
 
TGenomic_strandSetGenomic_strand (void)
 Assign a value to Genomic_strand data member. More...
 
bool IsSetParts (void) const
 basic seqments always are in biologic order Check if a value has been assigned to Parts data member. More...
 
bool CanGetParts (void) const
 Check if it is safe to call GetParts method. More...
 
void ResetParts (void)
 Reset Parts data member. More...
 
const TPartsGetParts (void) const
 Get the Parts member data. More...
 
TPartsSetParts (void)
 Assign a value to Parts data member. More...
 
bool IsSetScores (void) const
 scores for this exon 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...
 
void SetScores (TScores &value)
 Assign a value to Scores data member. More...
 
TScoresSetScores (void)
 Assign a value to Scores data member. More...
 
bool IsSetAcceptor_before_exon (void) const
 splice sites Check if a value has been assigned to Acceptor_before_exon data member. More...
 
bool CanGetAcceptor_before_exon (void) const
 Check if it is safe to call GetAcceptor_before_exon method. More...
 
void ResetAcceptor_before_exon (void)
 Reset Acceptor_before_exon data member. More...
 
const TAcceptor_before_exonGetAcceptor_before_exon (void) const
 Get the Acceptor_before_exon member data. More...
 
void SetAcceptor_before_exon (TAcceptor_before_exon &value)
 Assign a value to Acceptor_before_exon data member. More...
 
TAcceptor_before_exonSetAcceptor_before_exon (void)
 Assign a value to Acceptor_before_exon data member. More...
 
bool IsSetDonor_after_exon (void) const
 Check if a value has been assigned to Donor_after_exon data member. More...
 
bool CanGetDonor_after_exon (void) const
 Check if it is safe to call GetDonor_after_exon method. More...
 
void ResetDonor_after_exon (void)
 Reset Donor_after_exon data member. More...
 
const TDonor_after_exonGetDonor_after_exon (void) const
 Get the Donor_after_exon member data. More...
 
void SetDonor_after_exon (TDonor_after_exon &value)
 Assign a value to Donor_after_exon data member. More...
 
TDonor_after_exonSetDonor_after_exon (void)
 Assign a value to Donor_after_exon data member. More...
 
bool IsSetPartial (void) const
 flag: is this exon complete or partial? Check if a value has been assigned to Partial data member. More...
 
bool CanGetPartial (void) const
 Check if it is safe to call GetPartial method. More...
 
void ResetPartial (void)
 Reset Partial data member. More...
 
TPartial GetPartial (void) const
 Get the Partial member data. More...
 
void SetPartial (TPartial value)
 Assign a value to Partial data member. More...
 
TPartialSetPartial (void)
 Assign a value to Partial data member. More...
 
bool IsSetExt (void) const
 extra info 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...
 
TExtSetExt (void)
 Assign a value to Ext 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

 CSpliced_exon_Base (const CSpliced_exon_Base &)
 
CSpliced_exon_Baseoperator= (const CSpliced_exon_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
CRef< TProduct_startm_Product_start
 
CRef< TProduct_endm_Product_end
 
TSeqPos m_Genomic_start
 
TSeqPos m_Genomic_end
 
CRef< TProduct_idm_Product_id
 
CRef< TGenomic_idm_Genomic_id
 
ENa_strand m_Product_strand
 
ENa_strand m_Genomic_strand
 
list< CRef< CSpliced_exon_chunk > > m_Parts
 
CRef< TScoresm_Scores
 
CRef< TAcceptor_before_exonm_Acceptor_before_exon
 
CRef< TDonor_after_exonm_Donor_after_exon
 
bool m_Partial
 
list< CRef< CUser_object > > m_Ext
 

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

complete or partial exon two consecutive Spliced-exons may belong to one exon

CSpliced_exon_Base

Definition at line 84 of file Spliced_exon_.hpp.


The documentation for this class was generated from the following files:
Modified on Mon May 20 05:05:10 2024 by modify_doxy.py rev. 669887