Search Toolkit Book for CCdd_descr_Base
The description of CDD's refers to the specific set of aligned sequences, the region that is being aligned and the information contained in the alignment. More...
#include <objects/cdd/Cdd_descr_.hpp>
Inheritance diagram for CCdd_descr_Base:
Collaboration diagram for CCdd_descr_Base:
Public Member Functions | |
| CCdd_descr_Base (void) | |
| virtual | ~CCdd_descr_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| virtual void | ResetSelection (void) |
| Reset the selection (set it to e_not_set). More... | |
| E_Choice | Which (void) const |
| Which variant is currently selected. More... | |
| void | CheckSelected (E_Choice index) const |
| Verify selection, throw exception if it differs from the expected. More... | |
| void | ThrowInvalidSelection (E_Choice index) const |
| Throw 'InvalidSelection' exception. More... | |
| void | Select (E_Choice index, EResetVariant reset=eDoResetVariant) |
| Select the requested variant if needed. More... | |
| void | Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool) |
| Select the requested variant if needed, allocating CObject variants from memory pool. More... | |
| bool | IsOthername (void) const |
| Check if variant Othername is selected. More... | |
| const TOthername & | GetOthername (void) const |
| Get the variant data. More... | |
| TOthername & | SetOthername (void) |
| Select the variant. More... | |
| void | SetOthername (const TOthername &value) |
| Select the variant and set its data. More... | |
| bool | IsCategory (void) const |
| Check if variant Category is selected. More... | |
| const TCategory & | GetCategory (void) const |
| Get the variant data. More... | |
| TCategory & | SetCategory (void) |
| Select the variant. More... | |
| void | SetCategory (const TCategory &value) |
| Select the variant and set its data. More... | |
| bool | IsComment (void) const |
| Check if variant Comment is selected. More... | |
| const TComment & | GetComment (void) const |
| Get the variant data. More... | |
| TComment & | SetComment (void) |
| Select the variant. More... | |
| void | SetComment (const TComment &value) |
| Select the variant and set its data. More... | |
| bool | IsReference (void) const |
| Check if variant Reference is selected. More... | |
| const TReference & | GetReference (void) const |
| Get the variant data. More... | |
| TReference & | SetReference (void) |
| Select the variant. More... | |
| void | SetReference (TReference &value) |
| Select the variant and set its data. More... | |
| bool | IsCreate_date (void) const |
| Check if variant Create_date is selected. More... | |
| const TCreate_date & | GetCreate_date (void) const |
| Get the variant data. More... | |
| TCreate_date & | SetCreate_date (void) |
| Select the variant. More... | |
| void | SetCreate_date (TCreate_date &value) |
| Select the variant and set its data. More... | |
| bool | IsTax_source (void) const |
| Check if variant Tax_source is selected. More... | |
| const TTax_source & | GetTax_source (void) const |
| Get the variant data. More... | |
| TTax_source & | SetTax_source (void) |
| Select the variant. More... | |
| void | SetTax_source (TTax_source &value) |
| Select the variant and set its data. More... | |
| bool | IsSource (void) const |
| Check if variant Source is selected. More... | |
| const TSource & | GetSource (void) const |
| Get the variant data. More... | |
| TSource & | SetSource (void) |
| Select the variant. More... | |
| void | SetSource (const TSource &value) |
| Select the variant and set its data. More... | |
| bool | IsStatus (void) const |
| Check if variant Status is selected. More... | |
| TStatus | GetStatus (void) const |
| Get the variant data. More... | |
| TStatus & | SetStatus (void) |
| Select the variant. More... | |
| void | SetStatus (TStatus value) |
| Select the variant and set its data. More... | |
| bool | IsUpdate_date (void) const |
| Check if variant Update_date is selected. More... | |
| const TUpdate_date & | GetUpdate_date (void) const |
| Get the variant data. More... | |
| TUpdate_date & | SetUpdate_date (void) |
| Select the variant. More... | |
| void | SetUpdate_date (TUpdate_date &value) |
| Select the variant and set its data. More... | |
| bool | IsScrapbook (void) const |
| Check if variant Scrapbook is selected. More... | |
| const TScrapbook & | GetScrapbook (void) const |
| Get the variant data. More... | |
| TScrapbook & | SetScrapbook (void) |
| Select the variant. More... | |
| bool | IsSource_id (void) const |
| Check if variant Source_id is selected. More... | |
| const TSource_id & | GetSource_id (void) const |
| Get the variant data. More... | |
| TSource_id & | SetSource_id (void) |
| Select the variant. More... | |
| void | SetSource_id (TSource_id &value) |
| Select the variant and set its data. More... | |
| bool | IsRepeats (void) const |
| Check if variant Repeats is selected. More... | |
| const TRepeats & | GetRepeats (void) const |
| Get the variant data. More... | |
| TRepeats & | SetRepeats (void) |
| Select the variant. More... | |
| void | SetRepeats (TRepeats &value) |
| Select the variant and set its data. More... | |
| bool | IsOld_root (void) const |
| Check if variant Old_root is selected. More... | |
| const TOld_root & | GetOld_root (void) const |
| Get the variant data. More... | |
| TOld_root & | SetOld_root (void) |
| Select the variant. More... | |
| void | SetOld_root (TOld_root &value) |
| Select the variant and set its data. More... | |
| bool | IsCuration_status (void) const |
| Check if variant Curation_status is selected. More... | |
| TCuration_status | GetCuration_status (void) const |
| Get the variant data. More... | |
| TCuration_status & | SetCuration_status (void) |
| Select the variant. More... | |
| void | SetCuration_status (TCuration_status value) |
| Select the variant and set its data. More... | |
| bool | IsReadonly_status (void) const |
| Check if variant Readonly_status is selected. More... | |
| TReadonly_status | GetReadonly_status (void) const |
| Get the variant data. More... | |
| TReadonly_status & | SetReadonly_status (void) |
| Select the variant. More... | |
| void | SetReadonly_status (TReadonly_status value) |
| Select the variant and set its data. More... | |
| bool | IsBook_ref (void) const |
| Check if variant Book_ref is selected. More... | |
| const TBook_ref & | GetBook_ref (void) const |
| Get the variant data. More... | |
| TBook_ref & | SetBook_ref (void) |
| Select the variant. More... | |
| void | SetBook_ref (TBook_ref &value) |
| Select the variant and set its data. More... | |
| bool | IsAttribution (void) const |
| Check if variant Attribution is selected. More... | |
| const TAttribution & | GetAttribution (void) const |
| Get the variant data. More... | |
| TAttribution & | SetAttribution (void) |
| Select the variant. More... | |
| void | SetAttribution (TAttribution &value) |
| Select the variant and set its data. More... | |
| bool | IsTitle (void) const |
| Check if variant Title is selected. More... | |
| const TTitle & | GetTitle (void) const |
| Get the variant data. More... | |
| TTitle & | SetTitle (void) |
| Select the variant. More... | |
| void | SetTitle (const TTitle &value) |
| Select the variant and set its data. 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 |
Static Public Member Functions | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EStatus (void) |
| Access to EStatus's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | ECuration_status (void) |
| Access to ECuration_status's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EReadonly_status (void) |
| Access to EReadonly_status's attributes (values, names) as defined in spec. More... | |
| static string | SelectionName (E_Choice index) |
| Retrieve selection name (for diagnostic purposes). 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) |
Private Types | |
| typedef CSerialObject | Tparent |
Private Member Functions | |
| CCdd_descr_Base (const CCdd_descr_Base &) | |
| CCdd_descr_Base & | operator= (const CCdd_descr_Base &) |
| void | DoSelect (E_Choice index, CObjectMemoryPool *pool=0) |
Private Attributes | |
| E_Choice | m_choice |
| union { | |
| TStatus CCdd_descr_Base::m_Status | |
| NCBI_NS_NCBI::CUnionBuffer< TScrapbook > CCdd_descr_Base::m_Scrapbook | |
| TCuration_status CCdd_descr_Base::m_Curation_status | |
| TReadonly_status CCdd_descr_Base::m_Readonly_status | |
| NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > CCdd_descr_Base::m_string | |
| NCBI_NS_NCBI::CSerialObject * CCdd_descr_Base::m_object | |
| }; | |
Static Private Attributes | |
| static const char *const | sm_SelectionNames [] |
Additional Inherited Members | |
| 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
The description of CDD's refers to the specific set of aligned sequences, the region that is being aligned and the information contained in the alignment.
It may contain a lengthy comment describing the function of the domain as well as its origin and all other anecdotal information that can't be pressed into a rigid scheme. Crosslinks to reference papers available in PubMed are possible as well. There can be as many of these as you want in the CDD.
Definition at line 89 of file Cdd_descr_.hpp.
The documentation for this class was generated from the following files:
- include/objects/cdd/Cdd_descr_.hpp
- src/objects/cdd/Cdd_descr_.cpp
