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NCBI C++ ToolKit: CSeqDB_BitSet Class Reference

Bit set class. More...

#include "seqdbbitset.hpp"
(Private to src/objtools/blast/seqdb_reader.)

CSeqDB_BitSet () Default constructor for zero-length empty bit array. More...
CSeqDB_BitSet (size_t start, size_t end, ESpecialCase sp=eNone) Constructor for bit array with start/end range. More...
CSeqDB_BitSet (size_t start, size_t end, const TByte *p1, const TByte *p2) Constructor. More...
void SetBit (size_t index) Set the specified bit (to true). More...
void ClearBit (size_t index) Clear the specified bit (to false). More...
void AssignBit (size_t i, bool value) Store a value at the given index. More...
void AssignBitRange (size_t start, size_t end, bool value) Store the provided value in a range of bits. More...
bool GetBit (size_t index) const Get the value of the specified bit. More...
bool CheckOrFindBit (size_t &index) const Check if a bit is true or find the next bit that is. More...
void Swap (CSeqDB_BitSet &other) Swap two bitsets. More...
void UnionWith (CSeqDB_BitSet &other, bool consume) This bitset is assigned to the union of it and another. More...
void IntersectWith (CSeqDB_BitSet &other, bool consume) This bitset is assigned to the intersection of it and another. More...
void Normalize () If this is a special case bitset, convert it to a normal one. More...
void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Allows to dump a snapshot of the object. More...
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...
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

Bit set class.

Definition at line 49 of file seqdbbitset.hpp.

◆ TByte ◆ anonymous enum

Some useful constants related to word size.

Enumerator eWordBits

Number of bits per stored word.

eWordShift

Shift to convert from bit index to vector index.

eWordMask

Mask to compute bit index within word.

Definition at line 61 of file seqdbbitset.hpp.

◆ ESpecialCase

Special edge cases (all-set and all-clear).

Enumerator eNone

Normal OID list.

eAllSet

All OIDs are set.

eAllClear

All OIDs are clear.

Definition at line 74 of file seqdbbitset.hpp.

◆ CSeqDB_BitSet() [1/4] CSeqDB_BitSet::CSeqDB_BitSet ( ) inline ◆ CSeqDB_BitSet() [2/4]

Constructor for bit array with start/end range.

This constructs a bit array with the given start and end points. If the `sp' parameter is set to `eNone', a normal bit array is constructed, with all bits set to `false'. If sp is `eAllSet' or `eAllClear', the array is not constructed, but rather an object that acts as though the given range of OIDs is all `true' or all `false' respectively. These are termed `special case' bit sets. Special cases tend to be much more efficient in terms of memory usage and in the efficiency of boolean operations.

Parameters: start Starting OID for this bit set. end Ending OID for this bit set. sp Special case (homogeneous value) arrays.

Definition at line 104 of file seqdbbitset.hpp.

References _ASSERT, eNone, and x_Alloc().

◆ CSeqDB_BitSet() [3/4]

Constructor.

This constructs a normal (eNone) bit array with the given start and end points, and populates it from the byte data in the memory found between addresses p1 and p2. This method is meant for reading data from OID mask files and follows the format of those files, but the start pointer should be to the start of the bit map data within the file, not to the start of the file (the file contains a header that should be skipped).

Parameters: start The first OID represented by this data. end The OID after the last OID represented by this data. p1 A pointer to the beginning of the byte data. p2 A pointer to past the end of the byte data.

Definition at line 37 of file seqdbbitset.cpp.

References _ASSERT, eWordBits, m_Bits, and x_Alloc().

◆ CSeqDB_BitSet() [4/4]

Prevent copy construction.

◆ AssignBit() void CSeqDB_BitSet::AssignBit ( size_t i, bool value ) ◆ AssignBitRange() void CSeqDB_BitSet::AssignBitRange ( size_t start, size_t end, bool value )

Store the provided value in a range of bits.

Parameters: start The index of the first bit to assign. end The index after the last bit to assign. value The value to store in this range.

Definition at line 376 of file seqdbbitset.cpp.

References _ASSERT, AssignBit(), eWordBits, eWordMask, eWordShift, i, m_Bits, m_End, m_Start, mask, and rapidjson::value.

Referenced by UnionWith(), CSeqDBOIDList::x_ClearBitRange(), CSeqDBOIDList::x_ComputeFilters(), x_Normalize(), and CSeqDBOIDList::x_Setup().

◆ CheckOrFindBit() bool CSeqDB_BitSet::CheckOrFindBit ( size_t & index ) const

Check if a bit is true or find the next bit that is.

If the index points to a `false' value, the index is increased until a `true' value is found (true is returned) or until the index exceeds the OID range (false is returned). If the index initially points to a `true' bit, the index will not change.

Parameters: index The start index, and the returned index [in|out].

Returns: true if the index points to a true value.

Definition at line 90 of file seqdbbitset.cpp.

References _ASSERT, eAllClear, eAllSet, eWordMask, eWordShift, m_Bits, m_End, m_Special, and m_Start.

Referenced by IntersectWith(), x_CopyBits(), and CSeqDBOIDList::x_GetOidMask().

◆ ClearBit() void CSeqDB_BitSet::ClearBit ( size_t index )

Clear the specified bit (to false).

Parameters: index The index of the bit to clear.

Definition at line 75 of file seqdbbitset.cpp.

References _ASSERT, eNone, eWordMask, eWordShift, m_Bits, m_End, m_Special, and m_Start.

Referenced by AssignBit(), IntersectWith(), CSeqDBOIDList::x_ApplyNegativeList(), and CSeqDBOIDList::x_GetOidMask().

◆ DebugDump() ◆ GetBit() bool CSeqDB_BitSet::GetBit ( size_t index ) const ◆ IntersectWith()

This bitset is assigned to the intersection of it and another.

Each bit in this bitset will be `true' if it was true in both this bitset and `other'. The `consume' flag can be specified as true if the value of the `other' bitset will not be used after this operation. Specifying `true' for consume may change the data in the other bitset but can sometimes use a more efficient algorithm.

Parameters: other The bitset to intersect with this bitset. consume Specify true if the other bitset is expendable.

Definition at line 193 of file seqdbbitset.cpp.

References CheckOrFindBit(), ClearBit(), eAllClear, eAllSet, eNone, i, int, m_Bits, m_End, m_Special, m_Start, max(), min(), result, Swap(), and x_Copy().

Referenced by CSeqDBOIDList::x_ApplyNegativeList(), CSeqDBOIDList::x_ApplyUserGiList(), CSeqDBOIDList::x_ComputeFilters(), and CSeqDBOIDList::x_Setup().

◆ Normalize() void CSeqDB_BitSet::Normalize ( void )

If this is a special case bitset, convert it to a normal one.

Operations on normal (`eNone') bitsets can be more expensive in terms of memory and CPU time than on special case (eAllSet and eAllClear) bitsets, but normal bitsets support operations such as SetBit() and ClearBit() that special bitsets don't.

This method checks if this bitset is a special case, and converts it to a normal (`eNone') bitset if so.

Definition at line 419 of file seqdbbitset.cpp.

References eNone, m_End, m_Special, m_Start, and x_Normalize().

Referenced by CSeqDBOIDList::x_ApplyNegativeList().

◆ operator=() ◆ SetBit() void CSeqDB_BitSet::SetBit ( size_t index )

Set the specified bit (to true).

Parameters: index The index of the bit to set.

Definition at line 60 of file seqdbbitset.cpp.

References _ASSERT, eNone, eWordMask, eWordShift, m_Bits, m_End, m_Special, and m_Start.

Referenced by AssignBit(), s_ProcessSeqIdFilters(), s_ProcessTaxIdFilters(), CSeqDBOIDList::x_ApplyUserGiList(), x_CopyBits(), and CSeqDBOIDList::x_IdsToBitSet().

◆ Swap() ◆ UnionWith()

This bitset is assigned to the union of it and another.

Each bit in this bitset will be `true' if it was true in either this bitset or `other'. The `consume' flag can be specified as true if the value of the `other' bitset will not be used after this operation. Specifying `true' for consume may change the data in the other bitset but can sometimes use a more efficient algorithm.

Parameters: other The bitset to union with this bitset. consume Specify true if the other bitset is expendable.

Definition at line 142 of file seqdbbitset.cpp.

References _ASSERT, AssignBitRange(), eAllClear, eAllSet, eNone, m_End, m_Special, m_Start, x_Copy(), x_CopyBits(), and x_Normalize().

Referenced by CSeqDBOIDList::x_ComputeFilters(), and CSeqDBOIDList::x_Setup().

◆ x_Alloc() void CSeqDB_BitSet::x_Alloc ( size_t bits ) inlineprivate ◆ x_Copy()

Set this bitset to the value of the provided one.

This is like a normal "copy assignment" operation, except that if `consume' is specified as true, a more efficient algorithm may be used. (Implementation: if `consume' is true, and the source is a normal (eNone) bitset, this is a `swap'.)

Parameters: other The bitset to copy. consume Specify true if the other bitset is expendable.

Definition at line 338 of file seqdbbitset.cpp.

References eNone, m_Bits, m_End, m_Special, m_Start, and Swap().

Referenced by IntersectWith(), and UnionWith().

◆ x_CopyBits() [1/2] ◆ x_CopyBits() [2/2]

Set all bits in the given range that are true in `src'.

Parameters: src The bitset to read from. begin The start of the index range to read. end The index past the end of the index range.

Definition at line 295 of file seqdbbitset.cpp.

References CheckOrFindBit(), i, and SetBit().

◆ x_Normalize() void CSeqDB_BitSet::x_Normalize ( size_t start, size_t end ) private

Replace `special' with normal bitsets, adjust the index range.

If this bitset is special, it becomes a normal bitset. If the start or end point is outside of the current one, the bitset expands (but does not contract). All bits that are `true' in the initial bitset will be true in the resulting bitset.