NCBI C++ ToolKit
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Search Toolkit Book for COffsetData_Base
Class representing index hash table and offset list database. More...
#include <algo/blast/dbindex/dbindex.hpp>
Public Types | |
typedef CDbIndex::TWord | TWord |
Index word type (public to support Solaris). More... | |
typedef CDbIndex::SOffsetValue | TOffsetValue |
typedef CVectorWrap< TWord > | THashTable |
The type of the hash table. More... | |
Public Member Functions | |
COffsetData_Base (TWord **map, unsigned long hkey_width, unsigned long stride, unsigned long ws_hint) | |
Object constructor. More... | |
unsigned long | hkey_width () const |
Get the width of the hash key in base pairs. More... | |
unsigned long | getMinOffset () const |
Accessor for minimum offset value. More... | |
unsigned long | getStride () const |
Accessor for stride value. More... | |
unsigned long | getWSHint () const |
Accessor for ws_hint value. More... | |
Protected Attributes | |
TWord | total_ |
Auxiliary data member used for importing the offset list data. More... | |
unsigned long | hkey_width_ |
Hash key width in bp. More... | |
unsigned long | stride_ |
Stride value used by the index. More... | |
unsigned long | ws_hint_ |
ws_hint values used by the index. More... | |
unsigned long | min_offset_ |
Minimum offset value used by the index. More... | |
THashTable | hash_table_ |
The hash table (mapping from Nmer values to the lists of offsets. More... | |
Friends | |
class | CPreOrderedOffsetIterator |
Class representing index hash table and offset list database.
Definition at line 957 of file dbindex.hpp.
typedef CVectorWrap< TWord > COffsetData_Base::THashTable |
The type of the hash table.
The hash table implements the mapping from Nmer values to the corresponding offset lists.
Definition at line 972 of file dbindex.hpp.
Definition at line 966 of file dbindex.hpp.
Index word type (public to support Solaris).
Definition at line 964 of file dbindex.hpp.
COffsetData_Base::COffsetData_Base | ( | TWord ** | map, |
unsigned long | hkey_width, | ||
unsigned long | stride, | ||
unsigned long | ws_hint | ||
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Object constructor.
Creates the object by mapping data from a memory segment.
map | [I/O] pointer to the memory segment |
hkey_width | [I] width in bp of the hash key |
stride | [I] stride of the index |
ws_hint | [I] ws_hint value of the index |
Definition at line 550 of file dbindex.cpp.
References hash_table_, hkey_width_, CVectorWrap< T >::SetPtr(), and total_.
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Accessor for minimum offset value.
Definition at line 994 of file dbindex.hpp.
References min_offset_.
Referenced by CPreOrderedOffsetIterator::Reset().
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Accessor for stride value.
Definition at line 1000 of file dbindex.hpp.
References stride_.
Referenced by CPreOrderedOffsetIterator::Reset().
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Accessor for ws_hint value.
Definition at line 1006 of file dbindex.hpp.
References ws_hint_.
Referenced by CPreOrderedOffsetIterator::Reset().
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Get the width of the hash key in base pairs.
Definition at line 988 of file dbindex.hpp.
References hkey_width_.
Referenced by CDbIndex_Impl< LEGACY >::hkey_width(), and CPreOrderedOffsetIterator::Reset().
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Definition at line 959 of file dbindex.hpp.
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The hash table (mapping from Nmer values to the lists of offsets.
Definition at line 1020 of file dbindex.hpp.
Referenced by COffsetData_Base(), and CPreOrderedOffsetIterator::Reset().
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Hash key width in bp.
Definition at line 1015 of file dbindex.hpp.
Referenced by COffsetData_Base(), and hkey_width().
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Minimum offset value used by the index.
Definition at line 1018 of file dbindex.hpp.
Referenced by getMinOffset().
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Stride value used by the index.
Definition at line 1016 of file dbindex.hpp.
Referenced by getStride().
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Auxiliary data member used for importing the offset list data.
Definition at line 1013 of file dbindex.hpp.
Referenced by COffsetData< iterator_t >::COffsetData(), and COffsetData_Base().
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ws_hint values used by the index.
Definition at line 1017 of file dbindex.hpp.
Referenced by getWSHint().