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CSrcTablePrimerColumn Class Reference

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#include <gui/packages/pkg_sequence_edit/srcedit_util.hpp>

+ Inheritance diagram for CSrcTablePrimerColumn:
+ Collaboration diagram for CSrcTablePrimerColumn:

Public Types

enum  EPrimerColType {
  eFwdSeq = 0 , eFwdName , eRevSeq , eRevName ,
  eNotPrimerCol
}
 
- Public Types inherited from CSrcTableColumnBase
enum  ESourceType { eNotSet = 0 , eDescriptor , eFeature }
 
- 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

 CSrcTablePrimerColumn (EPrimerColType col_type)
 
virtual bool AddToBioSource (objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)
 
virtual void ClearInBioSource (objects::CBioSource &src)
 
virtual string GetFromBioSource (const objects::CBioSource &src) const
 
virtual vector< stringGetValsFromBioSource (const CBioSource &src) const
 
virtual void SetConstraint (const string &field_name, CConstRef< edit::CStringConstraint > string_constraint)
 
virtual bool AllowMultipleValues ()
 
- Public Member Functions inherited from CSrcTableColumnBase
virtual vector< stringGetValsFromBioSource (const objects::CBioSource &src) const
 
virtual string GetLabel () const
 
virtual vector< stringIsValid (const vector< string > &values)
 
vector< CRef< objects::edit::CApplyObject > > GetApplyObjects (CBioseq_Handle bsh)
 
vector< CConstRef< CObject > > GetObjects (CBioseq_Handle bsh)
 
string GetVal (const CObject &object)
 
vector< stringGetVals (const CObject &object)
 
void ClearVal (CObject &object)
 
void SetSourceType (ESourceType type)
 
virtual void AddToBioSource (objects::CBioSource &in_out_bioSource, const string &newValue)
 
virtual string GetLabel () 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 EPrimerColType GetPrimerColumnType (const string &field_name)
 
- 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)
 

Protected Member Functions

bool x_DoesReactionHaveSpace (const CPCRReaction &reaction)
 
bool x_DoesPrimerSetHaveSpace (const CPCRPrimerSet &set)
 
bool x_DoesReactionMatchConstraint (const CPCRReaction &reaction) const
 
vector< stringx_GetValues (EPrimerColType col, const CBioSource &src) const
 
vector< stringx_GetValues (EPrimerColType col, const CPCRReaction &reaction) const
 
vector< stringx_GetValues (EPrimerColType col, const CPCRPrimerSet &set) const
 
bool x_ApplyStringToReaction (const string &val, CPCRReaction &reaction, objects::edit::EExistingText existing_text)
 
bool x_ApplyStringToPrimerSet (const string &val, CPCRPrimerSet &set, objects::edit::EExistingText existing_text)
 
bool x_AddFieldToPrimerSet (const string &val, CPCRPrimerSet &set)
 
bool x_ApplyStringToSrc (const string &val, CBioSource &src, objects::edit::EExistingText existing_text)
 
void x_RemoveEmptyValues (CBioSource &src)
 
void x_RemoveEmptyValues (CPCRReaction &reaction)
 
void x_RemoveEmptyValues (CPCRPrimerSet &set)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

EPrimerColType m_ColType
 
EPrimerColType m_ConstraintCol
 
CRef< edit::CStringConstraint > m_StringConstraint
 

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...
 

Detailed Description

Definition at line 427 of file srcedit_util.hpp.

Member Enumeration Documentation

◆ EPrimerColType

Enumerator
eFwdSeq 
eFwdName 
eRevSeq 
eRevName 
eNotPrimerCol 

Definition at line 430 of file srcedit_util.hpp.

Constructor & Destructor Documentation

◆ CSrcTablePrimerColumn()

CSrcTablePrimerColumn::CSrcTablePrimerColumn ( EPrimerColType  col_type)
inline

Definition at line 438 of file srcedit_util.hpp.

Member Function Documentation

◆ AddToBioSource()

bool CSrcTablePrimerColumn::AddToBioSource ( objects::CBioSource &  src,
const string newValue,
objects::edit::EExistingText  existing_text 
)
virtual

◆ AllowMultipleValues()

virtual bool CSrcTablePrimerColumn::AllowMultipleValues ( )
inlinevirtual

Reimplemented from CSrcTableColumnBase.

Reimplemented in CSrcTableAllPrimersColumn.

Definition at line 454 of file srcedit_util.hpp.

◆ ClearInBioSource()

void CSrcTablePrimerColumn::ClearInBioSource ( objects::CBioSource &  src)
virtual

◆ GetFromBioSource()

string CSrcTablePrimerColumn::GetFromBioSource ( const objects::CBioSource &  src) const
virtual

◆ GetPrimerColumnType()

CSrcTablePrimerColumn::EPrimerColType CSrcTablePrimerColumn::GetPrimerColumnType ( const string field_name)
static

◆ GetValsFromBioSource()

vector< string > CSrcTablePrimerColumn::GetValsFromBioSource ( const CBioSource src) const
virtual

◆ SetConstraint()

void CSrcTablePrimerColumn::SetConstraint ( const string field_name,
CConstRef< edit::CStringConstraint >  string_constraint 
)
virtual

◆ x_AddFieldToPrimerSet()

bool CSrcTablePrimerColumn::x_AddFieldToPrimerSet ( const string val,
CPCRPrimerSet set 
)
protected

◆ x_ApplyStringToPrimerSet()

bool CSrcTablePrimerColumn::x_ApplyStringToPrimerSet ( const string val,
CPCRPrimerSet set,
objects::edit::EExistingText  existing_text 
)
protected

◆ x_ApplyStringToReaction()

bool CSrcTablePrimerColumn::x_ApplyStringToReaction ( const string val,
CPCRReaction reaction,
objects::edit::EExistingText  existing_text 
)
protected

◆ x_ApplyStringToSrc()

bool CSrcTablePrimerColumn::x_ApplyStringToSrc ( const string val,
CBioSource src,
objects::edit::EExistingText  existing_text 
)
protected

◆ x_DoesPrimerSetHaveSpace()

bool CSrcTablePrimerColumn::x_DoesPrimerSetHaveSpace ( const CPCRPrimerSet set)
protected

Definition at line 1992 of file srcedit_util.cpp.

References eFwdName, eFwdSeq, eRevName, eRevSeq, m_ColType, and set< Key, Compare >::size().

Referenced by x_DoesReactionHaveSpace().

◆ x_DoesReactionHaveSpace()

bool CSrcTablePrimerColumn::x_DoesReactionHaveSpace ( const CPCRReaction reaction)
protected

◆ x_DoesReactionMatchConstraint()

bool CSrcTablePrimerColumn::x_DoesReactionMatchConstraint ( const CPCRReaction reaction) const
protected

◆ x_GetValues() [1/3]

vector< string > CSrcTablePrimerColumn::x_GetValues ( EPrimerColType  col,
const CBioSource src 
) const
protected

◆ x_GetValues() [2/3]

vector< string > CSrcTablePrimerColumn::x_GetValues ( EPrimerColType  col,
const CPCRPrimerSet set 
) const
protected

Definition at line 2074 of file srcedit_util.cpp.

References eFwdName, eFwdSeq, eRevName, eRevSeq, and ITERATE.

◆ x_GetValues() [3/3]

vector< string > CSrcTablePrimerColumn::x_GetValues ( EPrimerColType  col,
const CPCRReaction reaction 
) const
protected

◆ x_RemoveEmptyValues() [1/3]

void CSrcTablePrimerColumn::x_RemoveEmptyValues ( CBioSource src)
protected

◆ x_RemoveEmptyValues() [2/3]

void CSrcTablePrimerColumn::x_RemoveEmptyValues ( CPCRPrimerSet set)
protected

◆ x_RemoveEmptyValues() [3/3]

void CSrcTablePrimerColumn::x_RemoveEmptyValues ( CPCRReaction reaction)
protected

Member Data Documentation

◆ m_ColType

EPrimerColType CSrcTablePrimerColumn::m_ColType
protected

◆ m_ConstraintCol

EPrimerColType CSrcTablePrimerColumn::m_ConstraintCol
protected

◆ m_StringConstraint

CRef<edit::CStringConstraint> CSrcTablePrimerColumn::m_StringConstraint
protected

The documentation for this class was generated from the following files:
Modified on Wed May 22 11:34:55 2024 by modify_doxy.py rev. 669887