Search Toolkit Book for CHGVS_Coordinate
#include <objects/coords/HGVS_Coordinate.hpp>
Inheritance diagram for CHGVS_Coordinate:
Collaboration diagram for CHGVS_Coordinate:
Public Member Functions | |
| CHGVS_Coordinate (void) | |
| ~CHGVS_Coordinate (void) | |
| Public Member Functions inherited from CHGVS_Coordinate_Base | |
| CHGVS_Coordinate_Base (void) | |
| virtual | ~CHGVS_Coordinate_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetMarker_pos (void) const |
| actual marker position this is supplied because this is the position of the marker in the main sequence's coordinate space; this is different than the mapped coordinate space. More... | |
| bool | CanGetMarker_pos (void) const |
| Check if it is safe to call GetMarker_pos method. More... | |
| void | ResetMarker_pos (void) |
| Reset Marker_pos data member. More... | |
| TMarker_pos | GetMarker_pos (void) const |
| Get the Marker_pos member data. More... | |
| void | SetMarker_pos (TMarker_pos value) |
| Assign a value to Marker_pos data member. More... | |
| TMarker_pos & | SetMarker_pos (void) |
| Assign a value to Marker_pos data member. More... | |
| bool | IsSetTitle (void) const |
| pretty-printed name for the object in general, this should be the "best" seq-id for the product of a feature represented at a position Check if a value has been assigned to Title data member. More... | |
| bool | CanGetTitle (void) const |
| Check if it is safe to call GetTitle method. More... | |
| void | ResetTitle (void) |
| Reset Title data member. More... | |
| const TTitle & | GetTitle (void) const |
| Get the Title member data. More... | |
| void | SetTitle (const TTitle &value) |
| Assign a value to Title data member. More... | |
| void | SetTitle (TTitle &&value) |
| TTitle & | SetTitle (void) |
| Assign a value to Title data member. More... | |
| bool | IsSetObject_id (void) const |
| the fingerprint of the object in question this is a complex reversible hash Check if a value has been assigned to Object_id data member. More... | |
| bool | CanGetObject_id (void) const |
| Check if it is safe to call GetObject_id method. More... | |
| void | ResetObject_id (void) |
| Reset Object_id data member. More... | |
| const TObject_id & | GetObject_id (void) const |
| Get the Object_id member data. More... | |
| void | SetObject_id (const TObject_id &value) |
| Assign a value to Object_id data member. More... | |
| void | SetObject_id (TObject_id &&value) |
| TObject_id & | SetObject_id (void) |
| Assign a value to Object_id data member. More... | |
| bool | IsSetPos_mapped (void) const |
| the mapped position in the object's coordinate space it's not valid for DNA coordinate in UTR and intergenic region, while hgvs-position can be meaningful, that is why OPTIONAL. More... | |
| bool | CanGetPos_mapped (void) const |
| Check if it is safe to call GetPos_mapped method. More... | |
| void | ResetPos_mapped (void) |
| Reset Pos_mapped data member. More... | |
| TPos_mapped | GetPos_mapped (void) const |
| Get the Pos_mapped member data. More... | |
| void | SetPos_mapped (TPos_mapped value) |
| Assign a value to Pos_mapped data member. More... | |
| TPos_mapped & | SetPos_mapped (void) |
| Assign a value to Pos_mapped data member. More... | |
| bool | IsSetHgvs_position (void) const |
| a label for this position this shall always be in HGVS nomenclature Check if a value has been assigned to Hgvs_position data member. More... | |
| bool | CanGetHgvs_position (void) const |
| Check if it is safe to call GetHgvs_position method. More... | |
| void | ResetHgvs_position (void) |
| Reset Hgvs_position data member. More... | |
| const THgvs_position & | GetHgvs_position (void) const |
| Get the Hgvs_position member data. More... | |
| void | SetHgvs_position (const THgvs_position &value) |
| Assign a value to Hgvs_position data member. More... | |
| void | SetHgvs_position (THgvs_position &&value) |
| THgvs_position & | SetHgvs_position (void) |
| Assign a value to Hgvs_position data member. More... | |
| bool | IsSetSequence (void) const |
| a sequence for this position 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 (const TSequence &value) |
| Assign a value to Sequence data member. More... | |
| void | SetSequence (TSequence &&value) |
| TSequence & | SetSequence (void) |
| Assign a value to Sequence 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 CHGVS_Coordinate_Base | Tparent |
Private Member Functions | |
| CHGVS_Coordinate (const CHGVS_Coordinate &value) | |
| CHGVS_Coordinate & | operator= (const CHGVS_Coordinate &value) |
Additional Inherited Members | |
| Public Types inherited from CHGVS_Coordinate_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_marker_pos , e_title , e_object_id , e_pos_mapped , e_hgvs_position , e_sequence } |
| typedef int | TMarker_pos |
| typedef string | TTitle |
| typedef string | TObject_id |
| typedef int | TPos_mapped |
| typedef string | THgvs_position |
| typedef string | TSequence |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | 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... | |
| 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
Definition at line 65 of file HGVS_Coordinate.hpp.
The documentation for this class was generated from the following files:
- include/objects/coords/HGVS_Coordinate.hpp
- src/objects/coords/HGVS_Coordinate.cpp
