NCBI C++ ToolKit
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Search Toolkit Book for CSrcTablePrimerColumn
#include <gui/packages/pkg_sequence_edit/srcedit_util.hpp>
Public Types | |
enum | EPrimerColType { eFwdSeq = 0 , eFwdName , eRevSeq , eRevName , eNotPrimerCol } |
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enum | ESourceType { eNotSet = 0 , eDescriptor , eFeature } |
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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... | |
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< string > | GetValsFromBioSource (const CBioSource &src) const |
virtual void | SetConstraint (const string &field_name, CConstRef< edit::CStringConstraint > string_constraint) |
virtual bool | AllowMultipleValues () |
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virtual vector< string > | GetValsFromBioSource (const objects::CBioSource &src) const |
virtual string | GetLabel () const |
virtual vector< string > | IsValid (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< string > | GetVals (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 |
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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... | |
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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) |
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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... | |
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static void | EnableDebugDump (bool on) |
Protected Attributes | |
EPrimerColType | m_ColType |
EPrimerColType | m_ConstraintCol |
CRef< edit::CStringConstraint > | m_StringConstraint |
Additional Inherited Members | |
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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... | |
Definition at line 427 of file srcedit_util.hpp.
Enumerator | |
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eFwdSeq | |
eFwdName | |
eRevSeq | |
eRevName | |
eNotPrimerCol |
Definition at line 430 of file srcedit_util.hpp.
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Definition at line 438 of file srcedit_util.hpp.
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Reimplemented from CSrcTableColumnBase.
Definition at line 2322 of file srcedit_util.cpp.
References eNotPrimerCol, i, m_ConstraintCol, m_StringConstraint, NON_CONST_ITERATE, CBioSource_Base::SetPcr_primers(), NStr::Split(), rapidjson::value, and x_ApplyStringToReaction().
Referenced by ClearInBioSource().
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Reimplemented from CSrcTableColumnBase.
Reimplemented in CSrcTableAllPrimersColumn.
Definition at line 454 of file srcedit_util.hpp.
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Reimplemented from CSrcTableColumnBase.
Reimplemented in CSrcTableRevPrimerNameColumn, CSrcTableFwdPrimerNameColumn, CSrcTableRevPrimerSeqColumn, CSrcTableFwdPrimerSeqColumn, and CSrcTableAllPrimersColumn.
Definition at line 2377 of file srcedit_util.cpp.
References AddToBioSource(), eExistingText_replace_old, and x_RemoveEmptyValues().
Implements CSrcTableColumnBase.
Reimplemented in CSrcTableAllPrimersColumn, CSrcTableRevPrimerNameColumn, CSrcTableFwdPrimerNameColumn, CSrcTableRevPrimerSeqColumn, and CSrcTableFwdPrimerSeqColumn.
Definition at line 2349 of file srcedit_util.cpp.
References m_ColType, and x_GetValues().
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Definition at line 1934 of file srcedit_util.cpp.
References eFwdName, eFwdSeq, eNotPrimerCol, eRevName, eRevSeq, IsFwdPrimerName(), IsFwdPrimerSeq(), IsRevPrimerName(), and IsRevPrimerSeq().
Referenced by SetConstraint().
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Definition at line 2360 of file srcedit_util.cpp.
References CPCRReactionSet_Base::Get(), CBioSource_Base::GetPcr_primers(), CBioSource_Base::IsSetPcr_primers(), ITERATE, m_ColType, x_DoesReactionMatchConstraint(), and x_GetValues().
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Reimplemented from CSrcTableColumnBase.
Definition at line 1949 of file srcedit_util.cpp.
References eNotPrimerCol, GetPrimerColumnType(), m_ConstraintCol, m_StringConstraint, NULL, and CRef< C, Locker >::Reset().
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Definition at line 2133 of file srcedit_util.cpp.
References eFwdName, eFwdSeq, eRevName, eRevSeq, m_ColType, CPCRPrimer_Base::SetName(), CPCRPrimer_Base::SetSeq(), and val.
Referenced by x_ApplyStringToPrimerSet().
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Definition at line 2178 of file srcedit_util.cpp.
References AddValueToString(), eExistingText_replace_old, eFwdName, eFwdSeq, eNotPrimerCol, eRevName, eRevSeq, i, NStr::IsBlank(), m_ColType, m_ConstraintCol, m_StringConstraint, NON_CONST_ITERATE, NStr::Split(), str(), val, and x_AddFieldToPrimerSet().
Referenced by x_ApplyStringToReaction().
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Definition at line 2103 of file srcedit_util.cpp.
References eExistingText_add_qual, eFwdName, eFwdSeq, eRevName, eRevSeq, m_ColType, CPCRReaction_Base::SetForward(), CPCRReaction_Base::SetReverse(), val, x_ApplyStringToPrimerSet(), x_DoesReactionHaveSpace(), and x_DoesReactionMatchConstraint().
Referenced by AddToBioSource().
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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().
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Definition at line 1965 of file srcedit_util.cpp.
References eFwdName, eFwdSeq, eRevName, eRevSeq, CPCRReaction_Base::GetForward(), CPCRReaction_Base::IsSetForward(), CPCRReaction_Base::IsSetReverse(), m_ColType, and x_DoesPrimerSetHaveSpace().
Referenced by x_ApplyStringToReaction().
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Definition at line 2018 of file srcedit_util.cpp.
References eNotPrimerCol, m_ConstraintCol, m_StringConstraint, and x_GetValues().
Referenced by GetValsFromBioSource(), and x_ApplyStringToReaction().
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Definition at line 2030 of file srcedit_util.cpp.
References CPCRReactionSet_Base::Get(), CBioSource_Base::GetPcr_primers(), CBioSource_Base::IsSetPcr_primers(), and ITERATE.
Referenced by GetFromBioSource(), GetValsFromBioSource(), x_DoesReactionMatchConstraint(), and x_GetValues().
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Definition at line 2045 of file srcedit_util.cpp.
References eFwdName, eFwdSeq, eRevName, eRevSeq, CPCRReaction_Base::GetForward(), CPCRReaction_Base::GetReverse(), CPCRReaction_Base::IsSetForward(), CPCRReaction_Base::IsSetReverse(), and x_GetValues().
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Definition at line 2245 of file srcedit_util.cpp.
References CPCRReactionSet_Base::Get(), CBioSource_Base::GetPcr_primers(), CPCRReactionSet_Base::IsSet(), CBioSource_Base::IsSetPcr_primers(), CBioSource_Base::ResetPcr_primers(), and CBioSource_Base::SetPcr_primers().
Referenced by ClearInBioSource(), and x_RemoveEmptyValues().
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Definition at line 2287 of file srcedit_util.cpp.
References set< Key, Compare >::begin(), set< Key, Compare >::empty(), set< Key, Compare >::end(), set< Key, Compare >::erase(), NStr::IsBlank(), and str().
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Definition at line 2269 of file srcedit_util.cpp.
References CPCRReaction_Base::GetForward(), CPCRReaction_Base::GetReverse(), CPCRPrimerSet_Base::IsSet(), CPCRReaction_Base::IsSetForward(), CPCRReaction_Base::IsSetReverse(), CPCRReaction_Base::ResetForward(), CPCRReaction_Base::ResetReverse(), CPCRReaction_Base::SetForward(), CPCRReaction_Base::SetReverse(), and x_RemoveEmptyValues().
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Definition at line 457 of file srcedit_util.hpp.
Referenced by GetFromBioSource(), GetValsFromBioSource(), x_AddFieldToPrimerSet(), x_ApplyStringToPrimerSet(), x_ApplyStringToReaction(), x_DoesPrimerSetHaveSpace(), and x_DoesReactionHaveSpace().
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Definition at line 458 of file srcedit_util.hpp.
Referenced by AddToBioSource(), SetConstraint(), x_ApplyStringToPrimerSet(), and x_DoesReactionMatchConstraint().
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Definition at line 459 of file srcedit_util.hpp.
Referenced by AddToBioSource(), SetConstraint(), x_ApplyStringToPrimerSet(), and x_DoesReactionMatchConstraint().