NCBI C++ ToolKit
Public Types | Public Member Functions | Protected Attributes | Friends | List of all members
COffsetData_Base Class Reference

Search Toolkit Book for COffsetData_Base

Class representing index hash table and offset list database. More...

#include <algo/blast/dbindex/dbindex.hpp>

+ Inheritance diagram for COffsetData_Base:
+ Collaboration diagram for COffsetData_Base:

Public Types

typedef CDbIndex::TWord TWord
 Index word type (public to support Solaris). More...
 
typedef CDbIndex::SOffsetValue TOffsetValue
 
typedef CVectorWrap< TWordTHashTable
 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
 

Detailed Description

Class representing index hash table and offset list database.

Definition at line 957 of file dbindex.hpp.

Member Typedef Documentation

◆ 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.

◆ TOffsetValue

Definition at line 966 of file dbindex.hpp.

◆ TWord

Index word type (public to support Solaris).

Definition at line 964 of file dbindex.hpp.

Constructor & Destructor Documentation

◆ COffsetData_Base()

COffsetData_Base::COffsetData_Base ( TWord **  map,
unsigned long  hkey_width,
unsigned long  stride,
unsigned long  ws_hint 
)

Object constructor.

Creates the object by mapping data from a memory segment.

Parameters
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_.

Member Function Documentation

◆ getMinOffset()

unsigned long COffsetData_Base::getMinOffset ( ) const
inline

Accessor for minimum offset value.

Returns
the minimum offset value

Definition at line 994 of file dbindex.hpp.

References min_offset_.

Referenced by CPreOrderedOffsetIterator::Reset().

◆ getStride()

unsigned long COffsetData_Base::getStride ( ) const
inline

Accessor for stride value.

Returns
the stride value

Definition at line 1000 of file dbindex.hpp.

References stride_.

Referenced by CPreOrderedOffsetIterator::Reset().

◆ getWSHint()

unsigned long COffsetData_Base::getWSHint ( ) const
inline

Accessor for ws_hint value.

Returns
the ws_hint value

Definition at line 1006 of file dbindex.hpp.

References ws_hint_.

Referenced by CPreOrderedOffsetIterator::Reset().

◆ hkey_width()

unsigned long COffsetData_Base::hkey_width ( ) const
inline

Get the width of the hash key in base pairs.

Returns
hash key width

Definition at line 988 of file dbindex.hpp.

References hkey_width_.

Referenced by CDbIndex_Impl< LEGACY >::hkey_width(), and CPreOrderedOffsetIterator::Reset().

Friends And Related Function Documentation

◆ CPreOrderedOffsetIterator

friend class CPreOrderedOffsetIterator
friend

Definition at line 959 of file dbindex.hpp.

Member Data Documentation

◆ hash_table_

THashTable COffsetData_Base::hash_table_
protected

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().

◆ hkey_width_

unsigned long COffsetData_Base::hkey_width_
protected

Hash key width in bp.

Definition at line 1015 of file dbindex.hpp.

Referenced by COffsetData_Base(), and hkey_width().

◆ min_offset_

unsigned long COffsetData_Base::min_offset_
protected

Minimum offset value used by the index.

Definition at line 1018 of file dbindex.hpp.

Referenced by getMinOffset().

◆ stride_

unsigned long COffsetData_Base::stride_
protected

Stride value used by the index.

Definition at line 1016 of file dbindex.hpp.

Referenced by getStride().

◆ total_

TWord COffsetData_Base::total_
protected

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().

◆ ws_hint_

unsigned long COffsetData_Base::ws_hint_
protected

ws_hint values used by the index.

Definition at line 1017 of file dbindex.hpp.

Referenced by getWSHint().


The documentation for this class was generated from the following files:
Modified on Thu Apr 11 15:21:33 2024 by modify_doxy.py rev. 669887