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

Search Toolkit Book for CSeqTableInfo

#include <objmgr/impl/seq_table_info.hpp>

+ Inheritance diagram for CSeqTableInfo:
+ Collaboration diagram for CSeqTableInfo:

Public Member Functions

 CSeqTableInfo (const CSeq_table &feat_table, bool is_feat)
 
 CSeqTableInfo (const CSeq_table &feat_table)
 
 ~CSeqTableInfo ()
 
bool IsFeatTable (void) const
 
size_t GetNumRows (void) const
 
void UpdateSeq_feat (size_t row, CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const
 
CConstRef< CSeq_locGetTableLocation (void) const
 
TSeqPos GetSortedMaxLength (void) const
 
bool IsSorted (void) const
 
SAnnotTypeSelector GetType (void) const
 
const CSeqTableLocColumnsGetLocation (void) const
 
const CSeqTableLocColumnsGetProduct (void) const
 
bool RowIsDisabled (size_t row) const
 
bool IsPartial (size_t row) const
 
CConstRef< CSeq_idGetLocationId (size_t row) const
 
TSeqPos GetLocationFrom (size_t row) const
 
CRange< TSeqPosGetLocationRange (size_t row) const
 
ENa_strand GetLocationStrand (size_t row) const
 
bool HasLabel (size_t row) const
 
string GetLabel (size_t row) const
 
bool MatchBitFilter (const SAnnotSelector &sel, size_t row) const
 
const CSeqTableColumnInfoFindColumn (int field_id) const
 
const CSeqTableColumnInfoFindColumn (const string &field_name) const
 
const CSeqTableColumnInfoGetColumn (int field_id) const
 
const CSeqTableColumnInfoGetColumn (const string &field_name) 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 bool IsGoodFeatTable (const CSeq_table &table)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 Types

typedef CSeqTableSetFeatField TSetter
 
typedef pair< CSeqTableColumnInfo, CConstRef< TSetter > > TColumnInfo
 
typedef vector< TColumnInfoTExtraColumns
 
typedef map< int, CSeqTableColumnInfoTColumnsById
 
typedef map< string, CSeqTableColumnInfoTColumnsByName
 

Private Member Functions

void x_Initialize (const CSeq_table &table)
 
bool x_IsSorted (void) const
 
 CSeqTableInfo (const CSeqTableInfo &)
 
void operator= (const CSeqTableInfo &)
 

Private Attributes

CConstRef< CSeq_tablem_Seq_table
 
bool m_IsFeatTable
 
bool m_IsSorted
 
CSeqTableColumnInfo m_Disabled
 
CSeqTableLocColumns m_Location
 
CSeqTableLocColumns m_Product
 
CSeqTableColumnInfo m_Partial
 
TExtraColumns m_ExtraColumns
 
CConstRef< CSeq_locm_TableLocation
 
TSeqPos m_SortedMaxLength
 
TColumnsById m_ColumnsById
 
TColumnsByName m_ColumnsByName
 

Additional Inherited Members

- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- 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 206 of file seq_table_info.hpp.

Member Typedef Documentation

Definition at line 277 of file seq_table_info.hpp.

Definition at line 295 of file seq_table_info.hpp.

Definition at line 296 of file seq_table_info.hpp.

typedef vector<TColumnInfo> CSeqTableInfo::TExtraColumns
private

Definition at line 278 of file seq_table_info.hpp.

Definition at line 276 of file seq_table_info.hpp.

Constructor & Destructor Documentation

CSeqTableInfo::CSeqTableInfo ( const CSeq_table feat_table,
bool  is_feat 
)
explicit

Definition at line 766 of file seq_table_info.cpp.

References x_Initialize().

CSeqTableInfo::CSeqTableInfo ( const CSeq_table feat_table)
explicit

Definition at line 775 of file seq_table_info.cpp.

References x_Initialize().

CSeqTableInfo::~CSeqTableInfo ( )

Definition at line 949 of file seq_table_info.cpp.

CSeqTableInfo::CSeqTableInfo ( const CSeqTableInfo )
private

Member Function Documentation

const CSeqTableColumnInfo * CSeqTableInfo::FindColumn ( int  field_id) const
const CSeqTableColumnInfo * CSeqTableInfo::FindColumn ( const string field_name) const
const CSeqTableColumnInfo & CSeqTableInfo::GetColumn ( int  field_id) const

Definition at line 1137 of file seq_table_info.cpp.

References column, FindColumn(), and NCBI_THROW_FMT.

const CSeqTableColumnInfo & CSeqTableInfo::GetColumn ( const string field_name) const

Definition at line 1150 of file seq_table_info.cpp.

References column, FindColumn(), and NCBI_THROW_FMT.

string CSeqTableInfo::GetLabel ( size_t  row) const
const CSeqTableLocColumns& CSeqTableInfo::GetLocation ( void  ) const
inline
TSeqPos CSeqTableInfo::GetLocationFrom ( size_t  row) const
inline
CConstRef<CSeq_id> CSeqTableInfo::GetLocationId ( size_t  row) const
inline

Definition at line 248 of file seq_table_info.hpp.

References CSeqTableLocColumns::GetId(), and GetLocation().

Referenced by CAnnotObject_Ref::CAnnotObject_Ref().

CRange<TSeqPos> CSeqTableInfo::GetLocationRange ( size_t  row) const
inline

Definition at line 254 of file seq_table_info.hpp.

References GetLocation(), and CSeqTableLocColumns::GetRange().

Referenced by CSeq_annot_SortedIter::x_Valid().

ENa_strand CSeqTableInfo::GetLocationStrand ( size_t  row) const
inline
size_t CSeqTableInfo::GetNumRows ( void  ) const
inline
const CSeqTableLocColumns& CSeqTableInfo::GetProduct ( void  ) const
inline
TSeqPos CSeqTableInfo::GetSortedMaxLength ( void  ) const

Definition at line 972 of file seq_table_info.cpp.

References m_SortedMaxLength.

Referenced by CSeq_annot_Info::StartSortedIterator().

CConstRef< CSeq_loc > CSeqTableInfo::GetTableLocation ( void  ) const
SAnnotTypeSelector CSeqTableInfo::GetType ( void  ) const
bool CSeqTableInfo::HasLabel ( size_t  row) const
bool CSeqTableInfo::IsFeatTable ( void  ) const
inline
bool CSeqTableInfo::IsGoodFeatTable ( const CSeq_table table)
static
bool CSeqTableInfo::IsPartial ( size_t  row) const
inline
bool CSeqTableInfo::IsSorted ( void  ) const
inline

Definition at line 229 of file seq_table_info.hpp.

References m_IsSorted.

Referenced by CSeq_annot_Info::IsSortedTable().

bool CSeqTableInfo::MatchBitFilter ( const SAnnotSelector sel,
size_t  row 
) const
void CSeqTableInfo::operator= ( const CSeqTableInfo )
private
bool CSeqTableInfo::RowIsDisabled ( size_t  row) const
inline
void CSeqTableInfo::UpdateSeq_feat ( size_t  row,
CRef< CSeq_feat > &  seq_feat,
CRef< CSeq_point > &  seq_pnt,
CRef< CSeq_interval > &  seq_int 
) const
void CSeqTableInfo::x_Initialize ( const CSeq_table table)
private
bool CSeqTableInfo::x_IsSorted ( void  ) const
private

Member Data Documentation

TColumnsById CSeqTableInfo::m_ColumnsById
private

Definition at line 297 of file seq_table_info.hpp.

Referenced by FindColumn(), and x_Initialize().

TColumnsByName CSeqTableInfo::m_ColumnsByName
private

Definition at line 298 of file seq_table_info.hpp.

Referenced by FindColumn(), and x_Initialize().

CSeqTableColumnInfo CSeqTableInfo::m_Disabled
private

Definition at line 286 of file seq_table_info.hpp.

Referenced by RowIsDisabled(), and x_Initialize().

TExtraColumns CSeqTableInfo::m_ExtraColumns
private

Definition at line 290 of file seq_table_info.hpp.

Referenced by GetLabel(), HasLabel(), MatchBitFilter(), UpdateSeq_feat(), and x_Initialize().

bool CSeqTableInfo::m_IsFeatTable
private

Definition at line 284 of file seq_table_info.hpp.

Referenced by IsFeatTable().

bool CSeqTableInfo::m_IsSorted
private

Definition at line 285 of file seq_table_info.hpp.

Referenced by IsSorted(), and x_Initialize().

CSeqTableLocColumns CSeqTableInfo::m_Location
private

Definition at line 287 of file seq_table_info.hpp.

Referenced by GetLocation(), UpdateSeq_feat(), x_Initialize(), and x_IsSorted().

CSeqTableColumnInfo CSeqTableInfo::m_Partial
private

Definition at line 289 of file seq_table_info.hpp.

Referenced by IsPartial(), UpdateSeq_feat(), and x_Initialize().

CSeqTableLocColumns CSeqTableInfo::m_Product
private

Definition at line 288 of file seq_table_info.hpp.

Referenced by GetProduct(), UpdateSeq_feat(), x_Initialize(), and x_IsSorted().

CConstRef<CSeq_table> CSeqTableInfo::m_Seq_table
private

Definition at line 283 of file seq_table_info.hpp.

Referenced by GetNumRows(), GetType(), and x_Initialize().

TSeqPos CSeqTableInfo::m_SortedMaxLength
private

Definition at line 293 of file seq_table_info.hpp.

Referenced by GetSortedMaxLength(), x_Initialize(), and x_IsSorted().

CConstRef<CSeq_loc> CSeqTableInfo::m_TableLocation
private

Definition at line 292 of file seq_table_info.hpp.

Referenced by GetTableLocation(), x_Initialize(), and x_IsSorted().


The documentation for this class was generated from the following files:
Modified on Sat Apr 22 17:06:37 2017 by modify_doxy.py rev. 533848