Search Toolkit Book for CConvertCDSToProt
#include <gui/objutils/convert_feat.hpp>
Inheritance diagram for CConvertCDSToProt:
Collaboration diagram for CConvertCDSToProt:
Public Member Functions | |
| CConvertCDSToProt (objects::CSeqFeatData::ESubtype feat_to) | |
| virtual string | GetDescription () |
| virtual bool | CanConvertTo (objects::CSeqFeatData::ESubtype subtype) |
| virtual CRef< CCmdComposite > | Convert (const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope) |
| Public Member Functions inherited from CConvertFeatureBase | |
| CConvertFeatureBase (objects::CSeqFeatData::ESubtype feat_to=objects::CSeqFeatData::eSubtype_bad, objects::CSeqFeatData::ESubtype feat_from=objects::CSeqFeatData::eSubtype_bad) | |
| ~CConvertFeatureBase () | |
| virtual bool | CanConvertFrom (objects::CSeqFeatData::ESubtype subtype) |
| TOptions & | SetOptions () |
| const TOptions & | GetOptions () const |
| CRef< CConversionOption > | FindRemoveTranscriptId () |
| string | x_GetCDSProduct (const objects::CSeq_feat &orig, objects::CScope &scope) |
| void | SetCreateGeneralOnly (bool flag) |
| void | SetOffset (int *offset) |
| 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... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. 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 |
Additional Inherited Members | |
| Public Types inherited from CConvertFeatureBase | |
| typedef vector< CRef< CConversionOption > > | TOptions |
| 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 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 CConvertFeatureBase | |
| static const string | s_RemovemRNA |
| static const string | s_RemoveGene |
| static const string | s_RemoveTranscriptID |
| static const string | s_NcrnaClass |
| static const string | s_SiteType |
| static const string | s_BondType |
| static const string | s_PlaceOnProt |
| static const string | s_IsPseudo |
| 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 CConvertFeatureBase | |
| CRef< CCmdComposite > | x_SimpleConversion (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope) |
| CRef< CCmdComposite > | x_ConvertToCDS (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope, vector< string > product) |
| bool | x_MoveFeatureToProtein (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope) |
| vector< string > | x_ExtractQuals (CRef< objects::CSeq_feat > new_feat, string qual_name) |
| vector< string > | x_ExtractProductQuals (CRef< objects::CSeq_feat > new_feat) |
| void | x_AddToComment (string comment, CRef< objects::CSeq_feat > new_feat, objects::edit::EExistingText existing_text=objects::edit::eExistingText_prefix_semi) |
| void | x_ClearGenericFields (CRef< objects::CSeq_feat > new_feat) |
| void | x_AddCDSSourceConversionOptions () |
| void | x_AddCDSDestinationConversionOptions () |
| void | x_AddRnaDestinationConversionOptions () |
| void | x_AddSiteDestinationConversionOptions () |
| void | x_AddBondDestinationConversionOptions () |
| void | x_AddRegionDestionationConversionOptions () |
| CRef< CConversionOption > | x_FindOption (const string &label) |
| CRef< CConversionOption > | x_FindRemoveGene () |
| CRef< CConversionOption > | x_FindRemovemRNA () |
| CRef< CConversionOption > | x_FindNcrnaClass () |
| CRef< CConversionOption > | x_FindSiteType () |
| CRef< CConversionOption > | x_FindBondType () |
| CRef< CConversionOption > | x_FindPlaceOnProt () |
| CRef< CConversionOption > | x_FindPseudo () |
| bool | x_IsImportSubtype (objects::CSeqFeatData::ESubtype subtype) |
| bool | x_IsProtSubtype (objects::CSeqFeatData::ESubtype subtype) |
| bool | x_IsRnaSubtype (objects::CSeqFeatData::ESubtype subtype) |
| string | GetSiteName (objects::CSeqFeatData::TSite site_type) |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Protected Attributes inherited from CConvertFeatureBase | |
| objects::CSeqFeatData::ESubtype | m_To |
| objects::CSeqFeatData::ESubtype | m_From |
| TOptions | m_Options |
| objects::CSiteList | m_SiteList |
| objects::CBondList | m_BondList |
| bool | m_create_general_only = false |
| int * | m_offset = nullptr |
Detailed Description
Definition at line 462 of file convert_feat.hpp.
Constructor & Destructor Documentation
◆ CConvertCDSToProt()
|
inline |
Definition at line 465 of file convert_feat.hpp.
Member Function Documentation
◆ CanConvertTo()
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inlinevirtual |
Reimplemented from CConvertFeatureBase.
Definition at line 467 of file convert_feat.hpp.
References CConvertFeatureBase::x_IsProtSubtype().
◆ Convert()
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virtual |
Reimplemented from CConvertFeatureBase.
Definition at line 1386 of file convert_feat.cpp.
References CSerialObject::Assign(), cmd, CSeqFeatData_Base::e_Prot, CSeqFeatData::eSubtype_mat_peptide, CSeqFeatData::eSubtype_mat_peptide_aa, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CProt_ref_Base::GetDesc(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::GetProt(), CSeqFeatData_Base::IsProt(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CProt_ref_Base::IsSetDesc(), CConvertFeatureBase::m_To, NULL, orig, CSeq_feat_Base::ResetProduct(), CSeq_feat_Base::SetData(), CConvertFeatureBase::x_GetCDSProduct(), CConvertFeatureBase::x_MoveFeatureToProtein(), and CConvertFeatureBase::x_SimpleConversion().
◆ GetDescription()
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virtual |
Reimplemented from CConvertFeatureBase.
Definition at line 1375 of file convert_feat.cpp.
References CConvertFeatureBase::m_To, and CSeqFeatData::SubtypeValueToName().
The documentation for this class was generated from the following files:
- include/gui/objutils/convert_feat.hpp
- src/gui/objutils/convert_feat.cpp
