NCBI C++ ToolKit
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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>
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_start & | GetProduct_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_start & | SetProduct_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_end & | GetProduct_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_end & | SetProduct_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_start & | SetGenomic_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_end & | SetGenomic_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_id & | GetProduct_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_id & | SetProduct_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_id & | GetGenomic_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_id & | SetGenomic_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_strand & | SetProduct_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_strand & | SetGenomic_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 TParts & | GetParts (void) const |
Get the Parts member data. More... | |
TParts & | SetParts (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 TScores & | GetScores (void) const |
Get the Scores member data. More... | |
void | SetScores (TScores &value) |
Assign a value to Scores data member. More... | |
TScores & | SetScores (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_exon & | GetAcceptor_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_exon & | SetAcceptor_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_exon & | GetDonor_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_exon & | SetDonor_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... | |
TPartial & | SetPartial (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 TExt & | GetExt (void) const |
Get the Ext member data. More... | |
TExt & | SetExt (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 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 CSerialObject | Tparent |
Private Member Functions | |
CSpliced_exon_Base (const CSpliced_exon_Base &) | |
CSpliced_exon_Base & | operator= (const CSpliced_exon_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
CRef< TProduct_start > | m_Product_start |
CRef< TProduct_end > | m_Product_end |
TSeqPos | m_Genomic_start |
TSeqPos | m_Genomic_end |
CRef< TProduct_id > | m_Product_id |
CRef< TGenomic_id > | m_Genomic_id |
ENa_strand | m_Product_strand |
ENa_strand | m_Genomic_strand |
list< CRef< CSpliced_exon_chunk > > | m_Parts |
CRef< TScores > | m_Scores |
CRef< TAcceptor_before_exon > | m_Acceptor_before_exon |
CRef< TDonor_after_exon > | m_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... | |
complete or partial exon two consecutive Spliced-exons may belong to one exon
Definition at line 84 of file Spliced_exon_.hpp.