NCBI C++ ToolKit
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CConvertProtToProt Class Reference

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#include <gui/objutils/convert_feat.hpp>

+ Inheritance diagram for CConvertProtToProt:
+ Collaboration diagram for CConvertProtToProt:

Public Member Functions

 CConvertProtToProt (objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)
 
virtual string GetDescription ()
 
virtual bool CanConvertTo (objects::CSeqFeatData::ESubtype subtype)
 
virtual bool CanConvertFrom (objects::CSeqFeatData::ESubtype subtype)
 
- 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 CRef< CCmdCompositeConvert (const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)
 
TOptionsSetOptions ()
 
const TOptionsGetOptions () const
 
CRef< CConversionOptionFindRemoveTranscriptId ()
 
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...
 
CObjectoperator= (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< Uint8TCounter
 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< CCmdCompositex_SimpleConversion (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope)
 
CRef< CCmdCompositex_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< stringx_ExtractQuals (CRef< objects::CSeq_feat > new_feat, string qual_name)
 
vector< stringx_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< CConversionOptionx_FindOption (const string &label)
 
CRef< CConversionOptionx_FindRemoveGene ()
 
CRef< CConversionOptionx_FindRemovemRNA ()
 
CRef< CConversionOptionx_FindNcrnaClass ()
 
CRef< CConversionOptionx_FindSiteType ()
 
CRef< CConversionOptionx_FindBondType ()
 
CRef< CConversionOptionx_FindPlaceOnProt ()
 
CRef< CConversionOptionx_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
 
intm_offset = nullptr
 

Detailed Description

Definition at line 452 of file convert_feat.hpp.

Constructor & Destructor Documentation

◆ CConvertProtToProt()

CConvertProtToProt::CConvertProtToProt ( objects::CSeqFeatData::ESubtype  feat_to,
objects::CSeqFeatData::ESubtype  feat_from 
)
inline

Definition at line 455 of file convert_feat.hpp.

Member Function Documentation

◆ CanConvertFrom()

virtual bool CConvertProtToProt::CanConvertFrom ( objects::CSeqFeatData::ESubtype  subtype)
inlinevirtual

Reimplemented from CConvertFeatureBase.

Definition at line 458 of file convert_feat.hpp.

References CConvertFeatureBase::x_IsProtSubtype().

◆ CanConvertTo()

virtual bool CConvertProtToProt::CanConvertTo ( objects::CSeqFeatData::ESubtype  subtype)
inlinevirtual

Reimplemented from CConvertFeatureBase.

Definition at line 457 of file convert_feat.hpp.

References CConvertFeatureBase::x_IsProtSubtype().

◆ GetDescription()

virtual string CConvertProtToProt::GetDescription ( void  )
inlinevirtual

Reimplemented from CConvertFeatureBase.

Definition at line 456 of file convert_feat.hpp.


The documentation for this class was generated from the following file:
Modified on Sun Jul 21 04:14:35 2024 by modify_doxy.py rev. 669887