NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
CLocationEditPolicy Class Reference

Search Toolkit Book for CLocationEditPolicy

#include <objtools/edit/loc_edit.hpp>

+ Inheritance diagram for CLocationEditPolicy:
+ Collaboration diagram for CLocationEditPolicy:

Public Types

enum  EPartialPolicy {
  ePartialPolicy_eNoChange = 0 , ePartialPolicy_eSet , ePartialPolicy_eSetAtEnd , ePartialPolicy_eSetForBadEnd ,
  ePartialPolicy_eSetForFrame , ePartialPolicy_eClear , ePartialPolicy_eClearNotAtEnd , ePartialPolicy_eClearForGoodEnd
}
 
enum  EMergePolicy { eMergePolicy_NoChange = 0 , eMergePolicy_Join , eMergePolicy_Order , eMergePolicy_SingleInterval }
 
- 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...
 

Public Member Functions

 CLocationEditPolicy (EPartialPolicy partial5=ePartialPolicy_eNoChange, EPartialPolicy partial3=ePartialPolicy_eNoChange, bool extend_5=true, bool extend_3=true, EMergePolicy merge=eMergePolicy_NoChange)
 
 ~CLocationEditPolicy ()
 
EPartialPolicy GetPartial5Policy ()
 
EPartialPolicy GetPartial3Policy ()
 
void SetPartial5Policy (EPartialPolicy policy)
 
void SetPartial3Policy (EPartialPolicy policy)
 
EMergePolicy GetMergePolicy ()
 
void SetMergePolicy (EMergePolicy policy)
 
bool GetExtend5 ()
 
bool GetExtend3 ()
 
void SetExtend5 (bool policy)
 
void SetExtend3 (bool policy)
 
bool ApplyPolicyToFeature (CSeq_feat &feat, CScope &scope) const
 
bool Interpret5Policy (const CSeq_feat &orig_feat, CScope &scope, bool &do_set_5_partial, bool &do_clear_5_partial) const
 
bool Interpret3Policy (const CSeq_feat &orig_feat, CScope &scope, bool &do_set_3_partial, bool &do_clear_3_partial) const
 
- 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
 

Static Public Member Functions

static CRef< CSeq_locConvertToJoin (const CSeq_loc &orig_loc, bool &changed)
 
static CRef< CSeq_locConvertToOrder (const CSeq_loc &orig_loc, bool &changed)
 
static bool Extend5 (CSeq_feat &feat, CScope &scope)
 
static bool Extend3 (CSeq_feat &feat, CScope &scope)
 
static bool HasNulls (const CSeq_loc &orig_loc)
 
static bool Is5AtEndOfSeq (const CSeq_loc &loc, CBioseq_Handle bsh)
 
static bool Is3AtEndOfSeq (const CSeq_loc &loc, CBioseq_Handle bsh)
 
static bool Is5AtEndOfSeq (const CSeq_loc &loc, CScope &scope, bool &confident)
 
static bool Is3AtEndOfSeq (const CSeq_loc &loc, CScope &scope, bool &confident)
 
- 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 Attributes

EPartialPolicy m_PartialPolicy5
 
EPartialPolicy m_PartialPolicy3
 
bool m_Extend5
 
bool m_Extend3
 
EMergePolicy m_MergePolicy
 

Additional Inherited Members

- 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

Definition at line 51 of file loc_edit.hpp.

Member Enumeration Documentation

◆ EMergePolicy

Enumerator
eMergePolicy_NoChange 
eMergePolicy_Join 
eMergePolicy_Order 
eMergePolicy_SingleInterval 

Definition at line 64 of file loc_edit.hpp.

◆ EPartialPolicy

Enumerator
ePartialPolicy_eNoChange 
ePartialPolicy_eSet 
ePartialPolicy_eSetAtEnd 
ePartialPolicy_eSetForBadEnd 
ePartialPolicy_eSetForFrame 
ePartialPolicy_eClear 
ePartialPolicy_eClearNotAtEnd 
ePartialPolicy_eClearForGoodEnd 

Definition at line 54 of file loc_edit.hpp.

Constructor & Destructor Documentation

◆ CLocationEditPolicy()

CLocationEditPolicy::CLocationEditPolicy ( EPartialPolicy  partial5 = ePartialPolicy_eNoChange,
EPartialPolicy  partial3 = ePartialPolicy_eNoChange,
bool  extend_5 = true,
bool  extend_3 = true,
EMergePolicy  merge = eMergePolicy_NoChange 
)
inline

Definition at line 70 of file loc_edit.hpp.

◆ ~CLocationEditPolicy()

CLocationEditPolicy::~CLocationEditPolicy ( )
inline

Definition at line 83 of file loc_edit.hpp.

Member Function Documentation

◆ ApplyPolicyToFeature()

bool CLocationEditPolicy::ApplyPolicyToFeature ( CSeq_feat feat,
CScope scope 
) const

◆ ConvertToJoin()

CRef< CSeq_loc > CLocationEditPolicy::ConvertToJoin ( const CSeq_loc orig_loc,
bool changed 
)
static

◆ ConvertToOrder()

CRef< CSeq_loc > CLocationEditPolicy::ConvertToOrder ( const CSeq_loc orig_loc,
bool changed 
)
static

◆ Extend3()

bool CLocationEditPolicy::Extend3 ( CSeq_feat feat,
CScope scope 
)
static

◆ Extend5()

bool CLocationEditPolicy::Extend5 ( CSeq_feat feat,
CScope scope 
)
static

◆ GetExtend3()

bool CLocationEditPolicy::GetExtend3 ( )
inline

Definition at line 92 of file loc_edit.hpp.

References m_Extend3.

◆ GetExtend5()

bool CLocationEditPolicy::GetExtend5 ( )
inline

Definition at line 91 of file loc_edit.hpp.

References m_Extend5.

◆ GetMergePolicy()

EMergePolicy CLocationEditPolicy::GetMergePolicy ( )
inline

Definition at line 89 of file loc_edit.hpp.

References m_MergePolicy.

◆ GetPartial3Policy()

EPartialPolicy CLocationEditPolicy::GetPartial3Policy ( )
inline

Definition at line 86 of file loc_edit.hpp.

References m_PartialPolicy3.

◆ GetPartial5Policy()

EPartialPolicy CLocationEditPolicy::GetPartial5Policy ( )
inline

Definition at line 85 of file loc_edit.hpp.

References m_PartialPolicy5.

◆ HasNulls()

bool CLocationEditPolicy::HasNulls ( const CSeq_loc orig_loc)
static

◆ Interpret3Policy()

bool CLocationEditPolicy::Interpret3Policy ( const CSeq_feat orig_feat,
CScope scope,
bool do_set_3_partial,
bool do_clear_3_partial 
) const

◆ Interpret5Policy()

bool CLocationEditPolicy::Interpret5Policy ( const CSeq_feat orig_feat,
CScope scope,
bool do_set_5_partial,
bool do_clear_5_partial 
) const

◆ Is3AtEndOfSeq() [1/2]

bool CLocationEditPolicy::Is3AtEndOfSeq ( const CSeq_loc loc,
CBioseq_Handle  bsh 
)
static

◆ Is3AtEndOfSeq() [2/2]

bool CLocationEditPolicy::Is3AtEndOfSeq ( const CSeq_loc loc,
CScope scope,
bool confident 
)
static

◆ Is5AtEndOfSeq() [1/2]

bool CLocationEditPolicy::Is5AtEndOfSeq ( const CSeq_loc loc,
CBioseq_Handle  bsh 
)
static

◆ Is5AtEndOfSeq() [2/2]

bool CLocationEditPolicy::Is5AtEndOfSeq ( const CSeq_loc loc,
CScope scope,
bool confident 
)
static

◆ SetExtend3()

void CLocationEditPolicy::SetExtend3 ( bool  policy)
inline

Definition at line 94 of file loc_edit.hpp.

References m_Extend3.

◆ SetExtend5()

void CLocationEditPolicy::SetExtend5 ( bool  policy)
inline

Definition at line 93 of file loc_edit.hpp.

References m_Extend5.

◆ SetMergePolicy()

void CLocationEditPolicy::SetMergePolicy ( EMergePolicy  policy)
inline

Definition at line 90 of file loc_edit.hpp.

References m_MergePolicy.

◆ SetPartial3Policy()

void CLocationEditPolicy::SetPartial3Policy ( EPartialPolicy  policy)
inline

Definition at line 88 of file loc_edit.hpp.

References m_PartialPolicy3.

◆ SetPartial5Policy()

void CLocationEditPolicy::SetPartial5Policy ( EPartialPolicy  policy)
inline

Definition at line 87 of file loc_edit.hpp.

References m_PartialPolicy5.

Member Data Documentation

◆ m_Extend3

bool CLocationEditPolicy::m_Extend3
private

Definition at line 120 of file loc_edit.hpp.

Referenced by ApplyPolicyToFeature(), GetExtend3(), Interpret3Policy(), and SetExtend3().

◆ m_Extend5

bool CLocationEditPolicy::m_Extend5
private

Definition at line 119 of file loc_edit.hpp.

Referenced by ApplyPolicyToFeature(), GetExtend5(), Interpret5Policy(), and SetExtend5().

◆ m_MergePolicy

EMergePolicy CLocationEditPolicy::m_MergePolicy
private

Definition at line 121 of file loc_edit.hpp.

Referenced by ApplyPolicyToFeature(), GetMergePolicy(), and SetMergePolicy().

◆ m_PartialPolicy3

EPartialPolicy CLocationEditPolicy::m_PartialPolicy3
private

◆ m_PartialPolicy5

EPartialPolicy CLocationEditPolicy::m_PartialPolicy5
private

The documentation for this class was generated from the following files:
Modified on Wed Jul 17 13:22:29 2024 by modify_doxy.py rev. 669887