NCBI C++ ToolKit
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Search Toolkit Book for CRs_Base
defines the docsum structure for refSNP clusters, where a refSNP cluster (rs) is a grouping of individual dbSNP submissions that all refer to the same variation. More...
#include <objects/docsum/Rs_.hpp>
Classes | |
class | C_Attlist |
C_Attlist –. More... | |
class | C_Create |
date the refsnp cluster was instantiated date the refsnp cluster was instantiated More... | |
class | C_E_AlleleOrigin |
C_E_AlleleOrigin –. More... | |
class | C_E_BioSource |
C_E_BioSource –. More... | |
class | C_E_Frequency |
C_E_Frequency –. More... | |
class | C_E_MergeHistory |
C_E_MergeHistory –. More... | |
class | C_E_Phenotype |
C_E_Phenotype –. More... | |
class | C_Het |
C_Het –. More... | |
class | C_Sequence |
C_Sequence –. More... | |
class | C_Update |
most recent date the cluster was updated (member added or deleted) most recent date the cluster was updated (member added or deleted) More... | |
class | C_Validation |
C_Validation –. More... | |
Public Member Functions | |
CRs_Base (void) | |
virtual | ~CRs_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
bool | IsSetAttlist (void) const |
Check if a value has been assigned to Attlist data member. More... | |
bool | CanGetAttlist (void) const |
Check if it is safe to call GetAttlist method. More... | |
void | ResetAttlist (void) |
Reset Attlist data member. More... | |
const TAttlist & | GetAttlist (void) const |
Get the Attlist member data. More... | |
void | SetAttlist (TAttlist &value) |
Assign a value to Attlist data member. More... | |
TAttlist & | SetAttlist (void) |
Assign a value to Attlist data member. More... | |
bool | IsSetHet (void) const |
Check if a value has been assigned to Het data member. More... | |
bool | CanGetHet (void) const |
Check if it is safe to call GetHet method. More... | |
void | ResetHet (void) |
Reset Het data member. More... | |
const THet & | GetHet (void) const |
Get the Het member data. More... | |
void | SetHet (THet &value) |
Assign a value to Het data member. More... | |
THet & | SetHet (void) |
Assign a value to Het data member. More... | |
bool | IsSetValidation (void) const |
Check if a value has been assigned to Validation data member. More... | |
bool | CanGetValidation (void) const |
Check if it is safe to call GetValidation method. More... | |
void | ResetValidation (void) |
Reset Validation data member. More... | |
const TValidation & | GetValidation (void) const |
Get the Validation member data. More... | |
void | SetValidation (TValidation &value) |
Assign a value to Validation data member. More... | |
TValidation & | SetValidation (void) |
Assign a value to Validation data member. More... | |
bool | IsSetCreate (void) const |
Check if a value has been assigned to Create data member. More... | |
bool | CanGetCreate (void) const |
Check if it is safe to call GetCreate method. More... | |
void | ResetCreate (void) |
Reset Create data member. More... | |
const TCreate & | GetCreate (void) const |
Get the Create member data. More... | |
void | SetCreate (TCreate &value) |
Assign a value to Create data member. More... | |
TCreate & | SetCreate (void) |
Assign a value to Create data member. More... | |
bool | IsSetUpdate (void) const |
Check if a value has been assigned to Update data member. More... | |
bool | CanGetUpdate (void) const |
Check if it is safe to call GetUpdate method. More... | |
void | ResetUpdate (void) |
Reset Update data member. More... | |
const TUpdate & | GetUpdate (void) const |
Get the Update member data. More... | |
void | SetUpdate (TUpdate &value) |
Assign a value to Update data member. More... | |
TUpdate & | SetUpdate (void) |
Assign a value to Update data member. More... | |
bool | IsSetSequence (void) const |
Check if a value has been assigned to Sequence data member. More... | |
bool | CanGetSequence (void) const |
Check if it is safe to call GetSequence method. More... | |
void | ResetSequence (void) |
Reset Sequence data member. More... | |
const TSequence & | GetSequence (void) const |
Get the Sequence member data. More... | |
void | SetSequence (TSequence &value) |
Assign a value to Sequence data member. More... | |
TSequence & | SetSequence (void) |
Assign a value to Sequence data member. More... | |
bool | IsSetSs (void) const |
Check if a value has been assigned to Ss data member. More... | |
bool | CanGetSs (void) const |
Check if it is safe to call GetSs method. More... | |
void | ResetSs (void) |
Reset Ss data member. More... | |
const TSs & | GetSs (void) const |
Get the Ss member data. More... | |
TSs & | SetSs (void) |
Assign a value to Ss data member. More... | |
bool | IsSetAssembly (void) const |
Check if a value has been assigned to Assembly data member. More... | |
bool | CanGetAssembly (void) const |
Check if it is safe to call GetAssembly method. More... | |
void | ResetAssembly (void) |
Reset Assembly data member. More... | |
const TAssembly & | GetAssembly (void) const |
Get the Assembly member data. More... | |
TAssembly & | SetAssembly (void) |
Assign a value to Assembly data member. More... | |
bool | IsSetPrimarySequence (void) const |
Check if a value has been assigned to PrimarySequence data member. More... | |
bool | CanGetPrimarySequence (void) const |
Check if it is safe to call GetPrimarySequence method. More... | |
void | ResetPrimarySequence (void) |
Reset PrimarySequence data member. More... | |
const TPrimarySequence & | GetPrimarySequence (void) const |
Get the PrimarySequence member data. More... | |
TPrimarySequence & | SetPrimarySequence (void) |
Assign a value to PrimarySequence data member. More... | |
bool | IsSetRsStruct (void) const |
Check if a value has been assigned to RsStruct data member. More... | |
bool | CanGetRsStruct (void) const |
Check if it is safe to call GetRsStruct method. More... | |
void | ResetRsStruct (void) |
Reset RsStruct data member. More... | |
const TRsStruct & | GetRsStruct (void) const |
Get the RsStruct member data. More... | |
TRsStruct & | SetRsStruct (void) |
Assign a value to RsStruct data member. More... | |
bool | IsSetRsLinkout (void) const |
Check if a value has been assigned to RsLinkout data member. More... | |
bool | CanGetRsLinkout (void) const |
Check if it is safe to call GetRsLinkout method. More... | |
void | ResetRsLinkout (void) |
Reset RsLinkout data member. More... | |
const TRsLinkout & | GetRsLinkout (void) const |
Get the RsLinkout member data. More... | |
TRsLinkout & | SetRsLinkout (void) |
Assign a value to RsLinkout data member. More... | |
bool | IsSetMergeHistory (void) const |
Check if a value has been assigned to MergeHistory data member. More... | |
bool | CanGetMergeHistory (void) const |
Check if it is safe to call GetMergeHistory method. More... | |
void | ResetMergeHistory (void) |
Reset MergeHistory data member. More... | |
const TMergeHistory & | GetMergeHistory (void) const |
Get the MergeHistory member data. More... | |
TMergeHistory & | SetMergeHistory (void) |
Assign a value to MergeHistory data member. More... | |
bool | IsSetHgvs (void) const |
HGVS name list Check if a value has been assigned to Hgvs data member. More... | |
bool | CanGetHgvs (void) const |
Check if it is safe to call GetHgvs method. More... | |
void | ResetHgvs (void) |
Reset Hgvs data member. More... | |
const THgvs & | GetHgvs (void) const |
Get the Hgvs member data. More... | |
THgvs & | SetHgvs (void) |
Assign a value to Hgvs data member. More... | |
bool | IsSetAlleleOrigin (void) const |
Check if a value has been assigned to AlleleOrigin data member. More... | |
bool | CanGetAlleleOrigin (void) const |
Check if it is safe to call GetAlleleOrigin method. More... | |
void | ResetAlleleOrigin (void) |
Reset AlleleOrigin data member. More... | |
const TAlleleOrigin & | GetAlleleOrigin (void) const |
Get the AlleleOrigin member data. More... | |
TAlleleOrigin & | SetAlleleOrigin (void) |
Assign a value to AlleleOrigin data member. More... | |
bool | IsSetPhenotype (void) const |
Check if a value has been assigned to Phenotype data member. More... | |
bool | CanGetPhenotype (void) const |
Check if it is safe to call GetPhenotype method. More... | |
void | ResetPhenotype (void) |
Reset Phenotype data member. More... | |
const TPhenotype & | GetPhenotype (void) const |
Get the Phenotype member data. More... | |
TPhenotype & | SetPhenotype (void) |
Assign a value to Phenotype data member. More... | |
bool | IsSetBioSource (void) const |
Check if a value has been assigned to BioSource data member. More... | |
bool | CanGetBioSource (void) const |
Check if it is safe to call GetBioSource method. More... | |
void | ResetBioSource (void) |
Reset BioSource data member. More... | |
const TBioSource & | GetBioSource (void) const |
Get the BioSource member data. More... | |
TBioSource & | SetBioSource (void) |
Assign a value to BioSource data member. More... | |
bool | IsSetFrequency (void) const |
Check if a value has been assigned to Frequency data member. More... | |
bool | CanGetFrequency (void) const |
Check if it is safe to call GetFrequency method. More... | |
void | ResetFrequency (void) |
Reset Frequency data member. More... | |
const TFrequency & | GetFrequency (void) const |
Get the Frequency member data. More... | |
TFrequency & | SetFrequency (void) |
Assign a value to Frequency 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 | |
CRs_Base (const CRs_Base &) | |
CRs_Base & | operator= (const CRs_Base &) |
Private Attributes | |
Uint4 | m_set_State [2] |
CRef< TAttlist > | m_Attlist |
CRef< THet > | m_Het |
CRef< TValidation > | m_Validation |
CRef< TCreate > | m_Create |
CRef< TUpdate > | m_Update |
CRef< TSequence > | m_Sequence |
list< CRef< CSs > > | m_Ss |
list< CRef< CAssembly > > | m_Assembly |
list< CRef< CPrimarySequence > > | m_PrimarySequence |
list< CRef< CRsStruct > > | m_RsStruct |
list< CRef< CRsLinkout > > | m_RsLinkout |
list< CRef< C_E_MergeHistory > > | m_MergeHistory |
list< string > | m_Hgvs |
list< CRef< C_E_AlleleOrigin > > | m_AlleleOrigin |
list< CRef< C_E_Phenotype > > | m_Phenotype |
list< CRef< C_E_BioSource > > | m_BioSource |
list< CRef< C_E_Frequency > > | m_Frequency |
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... | |
defines the docsum structure for refSNP clusters, where a refSNP cluster (rs) is a grouping of individual dbSNP submissions that all refer to the same variation.
The refsnp provides a single unified record for annotation of NCBI resources such as reference genome sequence.
CRs_Base –