Search Toolkit Book for CSite_annot
#include <objects/scoremat/Site_annot.hpp>
Inheritance diagram for CSite_annot:
Collaboration diagram for CSite_annot:
Public Member Functions | |
| CSite_annot (void) | |
| ~CSite_annot (void) | |
| Public Member Functions inherited from CSite_annot_Base | |
| CSite_annot_Base (void) | |
| virtual | ~CSite_annot_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetStartPosition (void) const |
| location of the annotation, Check if a value has been assigned to StartPosition data member. More... | |
| bool | CanGetStartPosition (void) const |
| Check if it is safe to call GetStartPosition method. More... | |
| void | ResetStartPosition (void) |
| Reset StartPosition data member. More... | |
| TStartPosition | GetStartPosition (void) const |
| Get the StartPosition member data. More... | |
| void | SetStartPosition (TStartPosition value) |
| Assign a value to StartPosition data member. More... | |
| TStartPosition & | SetStartPosition (void) |
| Assign a value to StartPosition data member. More... | |
| bool | IsSetStopPosition (void) const |
| start and stop position in the PSSM Check if a value has been assigned to StopPosition data member. More... | |
| bool | CanGetStopPosition (void) const |
| Check if it is safe to call GetStopPosition method. More... | |
| void | ResetStopPosition (void) |
| Reset StopPosition data member. More... | |
| TStopPosition | GetStopPosition (void) const |
| Get the StopPosition member data. More... | |
| void | SetStopPosition (TStopPosition value) |
| Assign a value to StopPosition data member. More... | |
| TStopPosition & | SetStopPosition (void) |
| Assign a value to StopPosition data member. More... | |
| bool | IsSetDescription (void) const |
| holds description or names, that can be used for labels in visualization Check if a value has been assigned to Description data member. More... | |
| bool | CanGetDescription (void) const |
| Check if it is safe to call GetDescription method. More... | |
| void | ResetDescription (void) |
| Reset Description data member. More... | |
| const TDescription & | GetDescription (void) const |
| Get the Description member data. More... | |
| void | SetDescription (const TDescription &value) |
| Assign a value to Description data member. More... | |
| void | SetDescription (TDescription &&value) |
| TDescription & | SetDescription (void) |
| Assign a value to Description data member. More... | |
| bool | IsSetType (void) const |
| type of the annotated feature, similarly to Align-annot in NCBI-Cdd Check if a value has been assigned to Type data member. More... | |
| bool | CanGetType (void) const |
| Check if it is safe to call GetType method. More... | |
| void | ResetType (void) |
| Reset Type data member. More... | |
| TType | GetType (void) const |
| Get the Type member data. More... | |
| void | SetType (TType value) |
| Assign a value to Type data member. More... | |
| TType & | SetType (void) |
| Assign a value to Type data member. More... | |
| bool | IsSetAliases (void) const |
| additional names for the annotation Check if a value has been assigned to Aliases data member. More... | |
| bool | CanGetAliases (void) const |
| Check if it is safe to call GetAliases method. More... | |
| void | ResetAliases (void) |
| Reset Aliases data member. More... | |
| const TAliases & | GetAliases (void) const |
| Get the Aliases member data. More... | |
| TAliases & | SetAliases (void) |
| Assign a value to Aliases data member. More... | |
| bool | IsSetMotif (void) const |
| motif to validate mapping of sites Check if a value has been assigned to Motif data member. More... | |
| bool | CanGetMotif (void) const |
| Check if it is safe to call GetMotif method. More... | |
| void | ResetMotif (void) |
| Reset Motif data member. More... | |
| const TMotif & | GetMotif (void) const |
| Get the Motif member data. More... | |
| void | SetMotif (const TMotif &value) |
| Assign a value to Motif data member. More... | |
| void | SetMotif (TMotif &&value) |
| TMotif & | SetMotif (void) |
| Assign a value to Motif data member. More... | |
| bool | IsSetMotifuse (void) const |
| 0 for validation 1 for motif in seqloc 2 for multiple motifs in seqloc Check if a value has been assigned to Motifuse data member. More... | |
| bool | CanGetMotifuse (void) const |
| Check if it is safe to call GetMotifuse method. More... | |
| void | ResetMotifuse (void) |
| Reset Motifuse data member. More... | |
| TMotifuse | GetMotifuse (void) const |
| Get the Motifuse member data. More... | |
| void | SetMotifuse (TMotifuse value) |
| Assign a value to Motifuse data member. More... | |
| TMotifuse & | SetMotifuse (void) |
| Assign a value to Motifuse 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 CSite_annot_Base | Tparent |
Private Member Functions | |
| CSite_annot (const CSite_annot &value) | |
| CSite_annot & | operator= (const CSite_annot &value) |
Additional Inherited Members | |
| Public Types inherited from CSite_annot_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_startPosition , e_stopPosition , e_description , e_type , e_aliases , e_motif , e_motifuse } |
| typedef int | TStartPosition |
| typedef int | TStopPosition |
| typedef string | TDescription |
| typedef int | TType |
| typedef list< string > | TAliases |
| typedef string | TMotif |
| typedef int | TMotifuse |
| 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... | |
| 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
CSite_annot –.
Definition at line 65 of file Site_annot.hpp.
The documentation for this class was generated from the following files:
- include/objects/scoremat/Site_annot.hpp
- src/objects/scoremat/Site_annot.cpp
