NCBI C++ ToolKit
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Search Toolkit Book for CConvertBioSrcToRptRegion
#include <gui/objutils/convert_feat.hpp>
Public Member Functions | |
CConvertBioSrcToRptRegion () | |
virtual string | GetDescription () |
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) |
virtual bool | CanConvertTo (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 |
Definition at line 238 of file convert_feat.hpp.
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inline |
Definition at line 241 of file convert_feat.hpp.
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virtual |
Reimplemented from CConvertFeatureBase.
Definition at line 756 of file convert_feat.cpp.
References CSerialObject::Assign(), cmd, CSubSource_Base::eSubtype_insertion_seq_name, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_transposon_name, NStr::IsBlank(), ITERATE, orig, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetQual(), and CConvertFeatureBase::x_SimpleConversion().
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inlinevirtual |
Reimplemented from CConvertFeatureBase.
Definition at line 242 of file convert_feat.hpp.