Search Toolkit Book for CINSDReference_Base
INSDReference_position contains a string value indicating the basepair span(s) to which a reference applies. More...
#include <objects/insdseq/INSDReference_.hpp>
Inheritance diagram for CINSDReference_Base:
Collaboration diagram for CINSDReference_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_reference , e_position , e_authors , e_consortium , e_title , e_journal , e_xref , e_pubmed , e_remark } |
| typedef string | TReference |
| typedef string | TPosition |
| typedef list< CINSDAuthor > | TAuthors |
| typedef string | TConsortium |
| typedef string | TTitle |
| typedef string | TJournal |
| typedef list< CRef< CINSDXref > > | TXref |
| typedef int | TPubmed |
| typedef string | TRemark |
| typedef Tparent::CMemberIndex< E_memberIndex, 10 > | 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 | |
| CINSDReference_Base (void) | |
| virtual | ~CINSDReference_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetReference (void) const |
| Check if a value has been assigned to Reference data member. More... | |
| bool | CanGetReference (void) const |
| Check if it is safe to call GetReference method. More... | |
| void | ResetReference (void) |
| Reset Reference data member. More... | |
| const TReference & | GetReference (void) const |
| Get the Reference member data. More... | |
| void | SetReference (const TReference &value) |
| Assign a value to Reference data member. More... | |
| void | SetReference (TReference &&value) |
| TReference & | SetReference (void) |
| Assign a value to Reference data member. More... | |
| bool | IsSetPosition (void) const |
| Check if a value has been assigned to Position data member. More... | |
| bool | CanGetPosition (void) const |
| Check if it is safe to call GetPosition method. More... | |
| void | ResetPosition (void) |
| Reset Position data member. More... | |
| const TPosition & | GetPosition (void) const |
| Get the Position member data. More... | |
| void | SetPosition (const TPosition &value) |
| Assign a value to Position data member. More... | |
| void | SetPosition (TPosition &&value) |
| TPosition & | SetPosition (void) |
| Assign a value to Position data member. More... | |
| bool | IsSetAuthors (void) const |
| Check if a value has been assigned to Authors data member. More... | |
| bool | CanGetAuthors (void) const |
| Check if it is safe to call GetAuthors method. More... | |
| void | ResetAuthors (void) |
| Reset Authors data member. More... | |
| const TAuthors & | GetAuthors (void) const |
| Get the Authors member data. More... | |
| TAuthors & | SetAuthors (void) |
| Assign a value to Authors data member. More... | |
| bool | IsSetConsortium (void) const |
| Check if a value has been assigned to Consortium data member. More... | |
| bool | CanGetConsortium (void) const |
| Check if it is safe to call GetConsortium method. More... | |
| void | ResetConsortium (void) |
| Reset Consortium data member. More... | |
| const TConsortium & | GetConsortium (void) const |
| Get the Consortium member data. More... | |
| void | SetConsortium (const TConsortium &value) |
| Assign a value to Consortium data member. More... | |
| void | SetConsortium (TConsortium &&value) |
| TConsortium & | SetConsortium (void) |
| Assign a value to Consortium data member. More... | |
| bool | IsSetTitle (void) const |
| 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 | IsSetJournal (void) const |
| Check if a value has been assigned to Journal data member. More... | |
| bool | CanGetJournal (void) const |
| Check if it is safe to call GetJournal method. More... | |
| void | ResetJournal (void) |
| Reset Journal data member. More... | |
| const TJournal & | GetJournal (void) const |
| Get the Journal member data. More... | |
| void | SetJournal (const TJournal &value) |
| Assign a value to Journal data member. More... | |
| void | SetJournal (TJournal &&value) |
| TJournal & | SetJournal (void) |
| Assign a value to Journal data member. More... | |
| bool | IsSetXref (void) const |
| Check if a value has been assigned to Xref data member. More... | |
| bool | CanGetXref (void) const |
| Check if it is safe to call GetXref method. More... | |
| void | ResetXref (void) |
| Reset Xref data member. More... | |
| const TXref & | GetXref (void) const |
| Get the Xref member data. More... | |
| TXref & | SetXref (void) |
| Assign a value to Xref data member. More... | |
| bool | IsSetPubmed (void) const |
| Check if a value has been assigned to Pubmed data member. More... | |
| bool | CanGetPubmed (void) const |
| Check if it is safe to call GetPubmed method. More... | |
| void | ResetPubmed (void) |
| Reset Pubmed data member. More... | |
| TPubmed | GetPubmed (void) const |
| Get the Pubmed member data. More... | |
| void | SetPubmed (TPubmed value) |
| Assign a value to Pubmed data member. More... | |
| TPubmed & | SetPubmed (void) |
| Assign a value to Pubmed data member. More... | |
| bool | IsSetRemark (void) const |
| Check if a value has been assigned to Remark data member. More... | |
| bool | CanGetRemark (void) const |
| Check if it is safe to call GetRemark method. More... | |
| void | ResetRemark (void) |
| Reset Remark data member. More... | |
| const TRemark & | GetRemark (void) const |
| Get the Remark member data. More... | |
| void | SetRemark (const TRemark &value) |
| Assign a value to Remark data member. More... | |
| void | SetRemark (TRemark &&value) |
| TRemark & | SetRemark (void) |
| Assign a value to Remark 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 | |
| CINSDReference_Base (const CINSDReference_Base &) | |
| CINSDReference_Base & | operator= (const CINSDReference_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| string | m_Reference |
| string | m_Position |
| list< CINSDAuthor > | m_Authors |
| string | m_Consortium |
| string | m_Title |
| string | m_Journal |
| list< CRef< CINSDXref > > | m_Xref |
| int | m_Pubmed |
| string | m_Remark |
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
INSDReference_position contains a string value indicating the basepair span(s) to which a reference applies.
The allowable formats are:
X..Y : Where X and Y are integers separated by two periods, X >= 1 , Y <= sequence length, and X <= Y
Multiple basepair spans can exist, separated by a semi-colon and a space. For example : 10..20; 100..500
sites : The string literal 'sites', indicating that a reference provides sequence annotation information, but the specific basepair spans are either not captured, or were too numerous to record.
The 'sites' literal string is singly occuring, and cannot be used in conjunction with any X..Y basepair spans.
'sites' is a convention utilized by GenBank, and might not be presented in XML provided by EMBL and DDBJ.
References that lack an INSDReference_position element are not attributed to any particular region of the sequence.
Definition at line 101 of file INSDReference_.hpp.
The documentation for this class was generated from the following files:
- include/objects/insdseq/INSDReference_.hpp
- src/objects/insdseq/INSDReference_.cpp
