Search Toolkit Book for CRs_Base::C_Validation
#include <objects/docsum/Rs_.hpp>
Inheritance diagram for CRs_Base::C_Validation:
Collaboration diagram for CRs_Base::C_Validation:
Classes | |
| class | C_Attlist |
| C_Attlist –. More... | |
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_attlist , e_otherPopBatchId , e_twoHit2AlleleBatchId , e_frequencyClass , e_hapMapPhase , e_tGPPhase , e_suspectEvidence } |
| typedef C_Attlist | TAttlist |
| typedef list< int > | TOtherPopBatchId |
| typedef list< int > | TTwoHit2AlleleBatchId |
| typedef list< int > | TFrequencyClass |
| typedef list< int > | THapMapPhase |
| typedef list< int > | TTGPPhase |
| typedef list< string > | TSuspectEvidence |
| typedef Tparent::CMemberIndex< E_memberIndex, 8 > | 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< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
Public Member Functions | |
| C_Validation (void) | |
| ~C_Validation (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 | IsSetOtherPopBatchId (void) const |
| dbSNP batch-id's for other pop snp validation data. More... | |
| bool | CanGetOtherPopBatchId (void) const |
| Check if it is safe to call GetOtherPopBatchId method. More... | |
| void | ResetOtherPopBatchId (void) |
| Reset OtherPopBatchId data member. More... | |
| const TOtherPopBatchId & | GetOtherPopBatchId (void) const |
| Get the OtherPopBatchId member data. More... | |
| TOtherPopBatchId & | SetOtherPopBatchId (void) |
| Assign a value to OtherPopBatchId data member. More... | |
| bool | IsSetTwoHit2AlleleBatchId (void) const |
| dbSNP batch-id's for double-hit snp validation data. More... | |
| bool | CanGetTwoHit2AlleleBatchId (void) const |
| Check if it is safe to call GetTwoHit2AlleleBatchId method. More... | |
| void | ResetTwoHit2AlleleBatchId (void) |
| Reset TwoHit2AlleleBatchId data member. More... | |
| const TTwoHit2AlleleBatchId & | GetTwoHit2AlleleBatchId (void) const |
| Get the TwoHit2AlleleBatchId member data. More... | |
| TTwoHit2AlleleBatchId & | SetTwoHit2AlleleBatchId (void) |
| Assign a value to TwoHit2AlleleBatchId data member. More... | |
| bool | IsSetFrequencyClass (void) const |
| Frequency validation class (1) low frequency variation that is cited in journal and other reputable sources (2) greater than 5 percent minor allele freq in each and all populations (4) greater than 5 percent minor allele freq in 1+ populations (8) if the variant has 2+ minor allele count based on freq or genotype data (16) less than 1 percent minor allele freq in each and all populations (32) less than 1 percent minor freq in 1+ populations Check if a value has been assigned to FrequencyClass data member. More... | |
| bool | CanGetFrequencyClass (void) const |
| Check if it is safe to call GetFrequencyClass method. More... | |
| void | ResetFrequencyClass (void) |
| Reset FrequencyClass data member. More... | |
| const TFrequencyClass & | GetFrequencyClass (void) const |
| Get the FrequencyClass member data. More... | |
| TFrequencyClass & | SetFrequencyClass (void) |
| Assign a value to FrequencyClass data member. More... | |
| bool | IsSetHapMapPhase (void) const |
| alidated by HapMap Project phase1-genotyped (1), Phase 1 genotyped; filtered, non-redundant phase2-genotyped (2), Phase 2 genotyped; filtered, non-redundant phase3-genotyped (4) Phase 3 genotyped; filtered, non-redundant Check if a value has been assigned to HapMapPhase data member. More... | |
| bool | CanGetHapMapPhase (void) const |
| Check if it is safe to call GetHapMapPhase method. More... | |
| void | ResetHapMapPhase (void) |
| Reset HapMapPhase data member. More... | |
| const THapMapPhase & | GetHapMapPhase (void) const |
| Get the HapMapPhase member data. More... | |
| THapMapPhase & | SetHapMapPhase (void) |
| Assign a value to HapMapPhase data member. More... | |
| bool | IsSetTGPPhase (void) const |
| Validated by 1000 Genomes Project (TGP) pilot 1 (1), pilot 2 (2), pilot 3 (4) Check if a value has been assigned to TGPPhase data member. More... | |
| bool | CanGetTGPPhase (void) const |
| Check if it is safe to call GetTGPPhase method. More... | |
| void | ResetTGPPhase (void) |
| Reset TGPPhase data member. More... | |
| const TTGPPhase & | GetTGPPhase (void) const |
| Get the TGPPhase member data. More... | |
| TTGPPhase & | SetTGPPhase (void) |
| Assign a value to TGPPhase data member. More... | |
| bool | IsSetSuspectEvidence (void) const |
| Suspected to be false SNP evidence Single Nucleotide Difference - paralogous genes (1), Genotype or base calling errors (2), Submission evidence or errors (4), Others (8) Check if a value has been assigned to SuspectEvidence data member. More... | |
| bool | CanGetSuspectEvidence (void) const |
| Check if it is safe to call GetSuspectEvidence method. More... | |
| void | ResetSuspectEvidence (void) |
| Reset SuspectEvidence data member. More... | |
| const TSuspectEvidence & | GetSuspectEvidence (void) const |
| Get the SuspectEvidence member data. More... | |
| TSuspectEvidence & | SetSuspectEvidence (void) |
| Assign a value to SuspectEvidence data member. More... | |
| 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 | |
| C_Validation (const C_Validation &) | |
| C_Validation & | operator= (const C_Validation &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| CRef< TAttlist > | m_Attlist |
| list< int > | m_OtherPopBatchId |
| list< int > | m_TwoHit2AlleleBatchId |
| list< int > | m_FrequencyClass |
| list< int > | m_HapMapPhase |
| list< int > | m_TGPPhase |
| list< string > | m_SuspectEvidence |
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
C_Validation –.
The documentation for this class was generated from the following files:
