BitMagic-C++
Data Structures | Public Types | Protected Types | Protected Member Functions | Friends
bm::rsc_sparse_vector< Val, SV > Class Template Reference

Rank-Select compressed sparse vector. More...

#include <bmsparsevec_compr.h>

Inheritance diagram for bm::rsc_sparse_vector< Val, SV >:
Inheritance graph
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Data Structures

class  back_insert_iterator
 Back insert iterator implements buffered insert, faster than generic access assignment. More...
 
class  const_iterator
 Const iterator to traverse the rsc sparse vector. More...
 
struct  is_remap_support
 
struct  is_rsc_support
 
class  reference
 Reference class to access elements via common [] operator. More...
 
struct  statistics
 

Public Types

enum  bit_plains { sv_plains = (sizeof(Val) * 8 + 1), sv_value_plains = (sizeof(Val) * 8) }
 
enum  vector_capacity { max_vector_size = 1 }
 
typedef Val value_type
 
typedef const value_typeconst_reference
 
typedef SV::size_type size_type
 
typedef SV sparse_vector_type
 
typedef SV::const_iterator sparse_vector_const_iterator
 
typedef SV::bvector_type bvector_type
 
typedef bvector_typebvector_type_ptr
 
typedef const bvector_typebvector_type_const_ptr
 
typedef bvector_type::allocator_type allocator_type
 
typedef bvector_type::allocation_policy allocation_policy_type
 
typedef bvector_type::rs_index_type rs_index_type
 
typedef bvector_type::enumerator bvector_enumerator_type
 
typedef SV::bmatrix_type bmatrix_type
 

Public Member Functions

Construction and assignment
 rsc_sparse_vector (bm::null_support null_able=bm::use_null, allocation_policy_type ap=allocation_policy_type(), size_type bv_max_size=bm::id_max, const allocator_type &alloc=allocator_type())
 
 rsc_sparse_vector (const bvector_type &bv_null)
 Contructor to pre-initialize the list of assigned (not NULL) elements. More...
 
 ~rsc_sparse_vector ()
 
 rsc_sparse_vector (const rsc_sparse_vector< Val, SV > &csv)
 
rsc_sparse_vector< Val, SV > & operator= (const rsc_sparse_vector< Val, SV > &csv)
 
 rsc_sparse_vector (rsc_sparse_vector< Val, SV > &&csv) BMNOEXCEPT
 
rsc_sparse_vector< Val, SV > & operator= (rsc_sparse_vector< Val, SV > &&csv) BMNOEXCEPT
 
Size, etc
size_type size () const BMNOEXCEPT
 return size of the vector More...
 
bool empty () const
 return true if vector is empty More...
 
void sync_size () BMNOEXCEPT
 recalculate size to exclude tail NULL elements After this call size() will return the true size of the vector More...
 
Element access
value_type operator[] (size_type idx) const
 get specified element without bounds checking More...
 
value_type at (size_type idx) const
 access specified element with bounds checking More...
 
value_type get (size_type idx) const BMNOEXCEPT
 get specified element without bounds checking More...
 
void push_back (size_type idx, value_type v)
 set specified element with bounds checking and automatic resize More...
 
void set (size_type idx, value_type v)
 set specified element with bounds checking and automatic resize More...
 
void inc (size_type idx)
 increment specified element by one More...
 
void inc (size_type idx, value_type v)
 increment specified element by one More...
 
void inc_not_null (size_type idx, value_type v)
 increment specified element by one, element MUST be NOT NULL Faster than just inc() if element is NULL - behavior is undefined More...
 
void set_null (size_type idx)
 set specified element to NULL RSC vector actually erases element when it is set to NULL (expensive). More...
 
bool is_null (size_type idx) const BMNOEXCEPT
 test if specified element is NULL More...
 
const bvector_typeget_null_bvector () const BMNOEXCEPT
 Get bit-vector of assigned values (or NULL) More...
 
bool find_rank (size_type rank, size_type &idx) const BMNOEXCEPT
 find position of compressed element by its rank More...
 
Export content to C-stype array
size_type decode (value_type *arr, size_type idx_from, size_type size, bool zero_mem=true) const
 C-style decode. More...
 
size_type decode_buf (value_type *arr, value_type *arr_buf_tmp, size_type idx_from, size_type size, bool zero_mem=true) const BMNOEXCEPT
 C-style decode (variant with external memory) Analog of decode, but requires two arrays. More...
 
Comparison
bool equal (const rsc_sparse_vector< Val, SV > &csv) const BMNOEXCEPT
 check if another vector has the same content More...
 
Load-Export compressed vector with data
void load_from (const sparse_vector_type &sv_src)
 Load compressed vector from a sparse vector (with NULLs) More...
 
void load_to (sparse_vector_type &sv) const
 Exort compressed vector to a sparse vector (with NULLs) More...
 
Iterator access
const_iterator begin () const BMNOEXCEPT
 Provide const iterator access to container content. More...
 
const_iterator end () const BMNOEXCEPT
 Provide const iterator access to the end. More...
 
const_iterator get_const_iterator (size_type idx) const BMNOEXCEPT
 Get const_itertor re-positioned to specific element. More...
 
back_insert_iterator get_back_inserter ()
 
Memory optimization
void optimize (bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, statistics *stat=0)
 run memory optimization for all vector plains More...
 
void clear_all (bool free_mem) BMNOEXCEPT
 resize to zero, free memory More...
 
void clear () BMNOEXCEPT
 resize to zero, free memory More...
 
void calc_stat (struct rsc_sparse_vector< Val, SV >::statistics *st) const BMNOEXCEPT
 Calculates memory statistics. More...
 
Merge, split, partition data
void copy_range (const rsc_sparse_vector< Val, SV > &csv, size_type left, size_type right)
 copy range of values from another sparse vector More...
 
void merge_not_null (rsc_sparse_vector< Val, SV > &csv)
 merge two vectors (argument gets destroyed) It is important that both vectors have the same NULL vectors More...
 
Fast access structues sync
void sync (bool force)
 Re-calculate rank-select index for faster access to vector. More...
 
void sync ()
 Re-calculate prefix sum table used for rank search (if necessary) More...
 
bool in_sync () const BMNOEXCEPT
 returns true if prefix sum table is in sync with the vector More...
 
void unsync () BMNOEXCEPT
 Unsync the prefix sum table. More...
 

Protected Types

enum  octet_plains { sv_octet_plains = sizeof(value_type) }
 
typedef bm::heap_matrix< unsigned char, 1, 1, typename bvector_type::allocator_typeremap_matrix_type
 unused remap matrix type for compatibility with the sparse serializer More...
 

Protected Member Functions

bool resolve (size_type idx, size_type *idx_to) const BMNOEXCEPT
 Resolve logical address to access via rank compressed address. More...
 
bool resolve_range (size_type from, size_type to, size_type *idx_from, size_type *idx_to) const BMNOEXCEPT
 
void resize_internal (size_type sz)
 
size_type size_internal () const BMNOEXCEPT
 
bool is_remap () const BMNOEXCEPT
 
size_t remap_size () const BMNOEXCEPT
 
const unsigned char * get_remap_buffer () const BMNOEXCEPT
 
unsigned char * init_remap_buffer () BMNOEXCEPT
 
void set_remap () BMNOEXCEPT
 
const remap_matrix_typeget_remap_matrix () const
 
remap_matrix_typeget_remap_matrix ()
 
void push_back_no_check (size_type idx, value_type v)
 

Friends

template<class SVect >
class sparse_vector_scanner
 
template<class SVect >
class sparse_vector_serializer
 
template<class SVect >
class sparse_vector_deserializer
 

Various traits

bool is_nullable () const
 if container supports NULL(unassigned) values (true) More...
 
static bool is_compressed ()
 trait if sparse vector is "compressed" (true) More...
 

Access to internals

bvector_type_const_ptr get_plain (unsigned i) const BMNOEXCEPT
 get access to bit-plain, function checks and creates a plain More...
 
bvector_type_ptr get_plain (unsigned i) BMNOEXCEPT
 
unsigned effective_plains () const BMNOEXCEPT
 
const sparse_vector_typeget_sv () const BMNOEXCEPT
 access dense vector More...
 
size_type effective_size () const BMNOEXCEPT
 size of internal dense vector More...
 
size_type effective_vector_max () const BMNOEXCEPT
 Always 1 (non-matrix type) More...
 
const bmatrix_typeget_bmatrix () const BMNOEXCEPT
 
static unsigned plains () BMNOEXCEPT
 get total number of bit-plains in the vector More...
 
static unsigned stored_plains ()
 Number of stored bit-plains (value plains + extra. More...
 

Detailed Description

template<class Val, class SV>
class bm::rsc_sparse_vector< Val, SV >

Rank-Select compressed sparse vector.

Container uses Rank-Select method of compression, where all NULL columns gets dropped, effective address of columns is computed using address bit-vector.

Use for cases, where memory efficiency is preferable over single element access latency.

Examples:
xsample08.cpp.

Definition at line 58 of file bmsparsevec_compr.h.

Member Typedef Documentation

◆ allocation_policy_type

template<class Val, class SV>
typedef bvector_type::allocation_policy bm::rsc_sparse_vector< Val, SV >::allocation_policy_type

Definition at line 76 of file bmsparsevec_compr.h.

◆ allocator_type

template<class Val, class SV>
typedef bvector_type::allocator_type bm::rsc_sparse_vector< Val, SV >::allocator_type

Definition at line 75 of file bmsparsevec_compr.h.

◆ bmatrix_type

template<class Val, class SV>
typedef SV::bmatrix_type bm::rsc_sparse_vector< Val, SV >::bmatrix_type

Definition at line 79 of file bmsparsevec_compr.h.

◆ bvector_enumerator_type

template<class Val, class SV>
typedef bvector_type::enumerator bm::rsc_sparse_vector< Val, SV >::bvector_enumerator_type

Definition at line 78 of file bmsparsevec_compr.h.

◆ bvector_type

template<class Val, class SV>
typedef SV::bvector_type bm::rsc_sparse_vector< Val, SV >::bvector_type

Definition at line 72 of file bmsparsevec_compr.h.

◆ bvector_type_const_ptr

template<class Val, class SV>
typedef const bvector_type* bm::rsc_sparse_vector< Val, SV >::bvector_type_const_ptr

Definition at line 74 of file bmsparsevec_compr.h.

◆ bvector_type_ptr

template<class Val, class SV>
typedef bvector_type* bm::rsc_sparse_vector< Val, SV >::bvector_type_ptr

Definition at line 73 of file bmsparsevec_compr.h.

◆ const_reference

template<class Val, class SV>
typedef const value_type& bm::rsc_sparse_vector< Val, SV >::const_reference

Definition at line 68 of file bmsparsevec_compr.h.

◆ remap_matrix_type

template<class Val, class SV>
typedef bm::heap_matrix<unsigned char, 1, 1, typename bvector_type::allocator_type> bm::rsc_sparse_vector< Val, SV >::remap_matrix_type
protected

unused remap matrix type for compatibility with the sparse serializer

Definition at line 772 of file bmsparsevec_compr.h.

◆ rs_index_type

template<class Val, class SV>
typedef bvector_type::rs_index_type bm::rsc_sparse_vector< Val, SV >::rs_index_type

Definition at line 77 of file bmsparsevec_compr.h.

◆ size_type

template<class Val, class SV>
typedef SV::size_type bm::rsc_sparse_vector< Val, SV >::size_type

Definition at line 69 of file bmsparsevec_compr.h.

◆ sparse_vector_const_iterator

template<class Val, class SV>
typedef SV::const_iterator bm::rsc_sparse_vector< Val, SV >::sparse_vector_const_iterator

Definition at line 71 of file bmsparsevec_compr.h.

◆ sparse_vector_type

template<class Val, class SV>
typedef SV bm::rsc_sparse_vector< Val, SV >::sparse_vector_type

Definition at line 70 of file bmsparsevec_compr.h.

◆ value_type

template<class Val, class SV>
typedef Val bm::rsc_sparse_vector< Val, SV >::value_type

Definition at line 67 of file bmsparsevec_compr.h.

Member Enumeration Documentation

◆ bit_plains

template<class Val, class SV>
enum bm::rsc_sparse_vector::bit_plains
Enumerator
sv_plains 
sv_value_plains 

Definition at line 61 of file bmsparsevec_compr.h.

◆ octet_plains

template<class Val, class SV>
enum bm::rsc_sparse_vector::octet_plains
protected
Enumerator
sv_octet_plains 

Definition at line 739 of file bmsparsevec_compr.h.

◆ vector_capacity

template<class Val, class SV>
enum bm::rsc_sparse_vector::vector_capacity
Enumerator
max_vector_size 

Definition at line 81 of file bmsparsevec_compr.h.

Constructor & Destructor Documentation

◆ rsc_sparse_vector() [1/4]

template<class Val , class SV >
bm::rsc_sparse_vector< Val, SV >::rsc_sparse_vector ( bm::null_support  null_able = bm::use_null,
allocation_policy_type  ap = allocation_policy_type(),
size_type  bv_max_size = bm::id_max,
const allocator_type alloc = allocator_type() 
)

◆ rsc_sparse_vector() [2/4]

template<class Val , class SV >
bm::rsc_sparse_vector< Val, SV >::rsc_sparse_vector ( const bvector_type bv_null)

Contructor to pre-initialize the list of assigned (not NULL) elements.

If the list of not NULL elements is known upfront it can help to pre-declare it, enable rank-select index and then use set function. This scenario gives significant speed boost, comparing random assignment

Parameters
bv_null- not NULL vector for the container

Definition at line 821 of file bmsparsevec_compr.h.

◆ ~rsc_sparse_vector()

template<class Val , class SV >
bm::rsc_sparse_vector< Val, SV >::~rsc_sparse_vector ( )

Definition at line 846 of file bmsparsevec_compr.h.

◆ rsc_sparse_vector() [3/4]

template<class Val, class SV>
bm::rsc_sparse_vector< Val, SV >::rsc_sparse_vector ( const rsc_sparse_vector< Val, SV > &  csv)

copy-ctor

Definition at line 854 of file bmsparsevec_compr.h.

◆ rsc_sparse_vector() [4/4]

template<class Val, class SV>
bm::rsc_sparse_vector< Val, SV >::rsc_sparse_vector ( rsc_sparse_vector< Val, SV > &&  csv)

move-ctor

Definition at line 868 of file bmsparsevec_compr.h.

Member Function Documentation

◆ at()

template<class Val , class SV >
rsc_sparse_vector< Val, SV >::value_type bm::rsc_sparse_vector< Val, SV >::at ( size_type  idx) const

access specified element with bounds checking

Parameters
idx- element index
Returns
value of the element

Definition at line 1231 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ begin()

template<class Val, class SV>
const_iterator bm::rsc_sparse_vector< Val, SV >::begin ( ) const
inline

Provide const iterator access to container content.

Definition at line 575 of file bmsparsevec_compr.h.

◆ calc_stat()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::calc_stat ( struct rsc_sparse_vector< Val, SV >::statistics st) const

Calculates memory statistics.

Function fills statistics structure containing information about how this vector uses memory and estimation of max. amount of memory bvector needs to serialize itself.

Parameters
st- pointer on statistics structure to be filled in.
See also
statistics

Definition at line 1298 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::clear().

◆ clear()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::clear ( )
inline

resize to zero, free memory

Parameters
free_mem- free bit vector planes if true

Definition at line 614 of file bmsparsevec_compr.h.

◆ clear_all()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::clear_all ( bool  free_mem)

◆ copy_range()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::copy_range ( const rsc_sparse_vector< Val, SV > &  csv,
size_type  left,
size_type  right 
)

copy range of values from another sparse vector

Copy [left..right] values from the source vector, clear everything outside the range.

Parameters
csv- source vector
left- index from in losed diapason of [left..right]
right- index to in losed diapason of [left..right]

Definition at line 1483 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::clear().

◆ decode()

template<class Val , class SV >
rsc_sparse_vector< Val, SV >::size_type bm::rsc_sparse_vector< Val, SV >::decode ( value_type arr,
size_type  idx_from,
size_type  size,
bool  zero_mem = true 
) const

C-style decode.

Parameters
arr- decode target array (must be properly sized)
idx_from- start address to decode
size- number of elements to decode
zero_mem- flag if array needs to beset to zeros first
Returns
actual decoded size
See also
decode_buf

Definition at line 1343 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ decode_buf()

template<class Val , class SV >
rsc_sparse_vector< Val, SV >::size_type bm::rsc_sparse_vector< Val, SV >::decode_buf ( value_type arr,
value_type arr_buf_tmp,
size_type  idx_from,
size_type  size,
bool  zero_mem = true 
) const

C-style decode (variant with external memory) Analog of decode, but requires two arrays.

Faster than decode in many cases.

Parameters
arr- decode target array (must be properly sized)
arr_buf_tmp- decode temp bufer (must be same size of arr)
idx_from- start address to decode
size- number of elements to decode
zero_mem- flag if array needs to beset to zeros first
Returns
actual decoded size
See also
decode

Definition at line 1402 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ effective_plains()

template<class Val, class SV>
unsigned bm::rsc_sparse_vector< Val, SV >::effective_plains ( ) const
inline

Number of effective bit-plains in the value type

Definition at line 702 of file bmsparsevec_compr.h.

◆ effective_size()

template<class Val, class SV>
size_type bm::rsc_sparse_vector< Val, SV >::effective_size ( ) const
inline

size of internal dense vector

Definition at line 723 of file bmsparsevec_compr.h.

◆ effective_vector_max()

template<class Val, class SV>
size_type bm::rsc_sparse_vector< Val, SV >::effective_vector_max ( ) const
inline

Always 1 (non-matrix type)

Definition at line 728 of file bmsparsevec_compr.h.

◆ empty()

template<class Val, class SV>
bool bm::rsc_sparse_vector< Val, SV >::empty ( ) const
inline

return true if vector is empty

Returns
true if empty

Definition at line 374 of file bmsparsevec_compr.h.

Referenced by main(), and run_benchmark().

◆ end()

template<class Val, class SV>
const_iterator bm::rsc_sparse_vector< Val, SV >::end ( ) const
inline

Provide const iterator access to the end.

Definition at line 579 of file bmsparsevec_compr.h.

◆ equal()

template<class Val, class SV>
bool bm::rsc_sparse_vector< Val, SV >::equal ( const rsc_sparse_vector< Val, SV > &  csv) const

check if another vector has the same content

Returns
true, if it is the same

Definition at line 1058 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::is_compressed(), and main().

◆ find_rank()

template<class Val , class SV >
bool bm::rsc_sparse_vector< Val, SV >::find_rank ( size_type  rank,
size_type idx 
) const

find position of compressed element by its rank

Parameters
rank- rank (virtual index in sparse vector)
idx- index (true position)

Definition at line 1325 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ get()

template<class Val , class SV >
rsc_sparse_vector< Val, SV >::value_type bm::rsc_sparse_vector< Val, SV >::get ( size_type  idx) const

get specified element without bounds checking

Parameters
idx- element index
Returns
value of the element
Examples:
xsample08.cpp.

Definition at line 1249 of file bmsparsevec_compr.h.

Referenced by compute_frequent_kmers(), compute_kmer_histogram(), main(), print_model(), raw_data_size(), and test_data().

◆ get_back_inserter()

template<class Val, class SV>
back_insert_iterator bm::rsc_sparse_vector< Val, SV >::get_back_inserter ( )
inline

Definition at line 588 of file bmsparsevec_compr.h.

Referenced by main().

◆ get_bmatrix()

template<class Val, class SV>
const bmatrix_type& bm::rsc_sparse_vector< Val, SV >::get_bmatrix ( ) const
inline

get read-only access to inetrnal bit-matrix

Definition at line 733 of file bmsparsevec_compr.h.

Referenced by deserialize_df2().

◆ get_const_iterator()

template<class Val, class SV>
const_iterator bm::rsc_sparse_vector< Val, SV >::get_const_iterator ( size_type  idx) const
inline

Get const_itertor re-positioned to specific element.

Parameters
idx- position in the sparse vector

Definition at line 585 of file bmsparsevec_compr.h.

Referenced by main().

◆ get_null_bvector()

template<class Val , class SV >
const rsc_sparse_vector< Val, SV >::bvector_type * bm::rsc_sparse_vector< Val, SV >::get_null_bvector ( ) const

◆ get_plain() [1/2]

template<class Val, class SV>
bvector_type_const_ptr bm::rsc_sparse_vector< Val, SV >::get_plain ( unsigned  i) const
inline

get access to bit-plain, function checks and creates a plain

Returns
bit-vector for the bit plain

Definition at line 693 of file bmsparsevec_compr.h.

◆ get_plain() [2/2]

template<class Val, class SV>
bvector_type_ptr bm::rsc_sparse_vector< Val, SV >::get_plain ( unsigned  i)
inline

Definition at line 696 of file bmsparsevec_compr.h.

◆ get_remap_buffer()

template<class Val, class SV>
const unsigned char* bm::rsc_sparse_vector< Val, SV >::get_remap_buffer ( ) const
inlineprotected

Definition at line 765 of file bmsparsevec_compr.h.

◆ get_remap_matrix() [1/2]

template<class Val, class SV>
const remap_matrix_type* bm::rsc_sparse_vector< Val, SV >::get_remap_matrix ( ) const
inlineprotected

Definition at line 774 of file bmsparsevec_compr.h.

◆ get_remap_matrix() [2/2]

template<class Val, class SV>
remap_matrix_type* bm::rsc_sparse_vector< Val, SV >::get_remap_matrix ( )
inlineprotected

Definition at line 775 of file bmsparsevec_compr.h.

◆ get_sv()

template<class Val, class SV>
const sparse_vector_type& bm::rsc_sparse_vector< Val, SV >::get_sv ( ) const
inline

access dense vector

Definition at line 718 of file bmsparsevec_compr.h.

◆ in_sync()

template<class Val, class SV>
bool bm::rsc_sparse_vector< Val, SV >::in_sync ( ) const
inline

returns true if prefix sum table is in sync with the vector

Definition at line 677 of file bmsparsevec_compr.h.

Referenced by main().

◆ inc() [1/2]

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::inc ( size_type  idx)

increment specified element by one

Parameters
idx- element index

Definition at line 943 of file bmsparsevec_compr.h.

Referenced by main(), and bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ inc() [2/2]

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::inc ( size_type  idx,
value_type  v 
)

increment specified element by one

Parameters
idx- element index
v- increment value

Definition at line 975 of file bmsparsevec_compr.h.

◆ inc_not_null()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::inc_not_null ( size_type  idx,
value_type  v 
)

increment specified element by one, element MUST be NOT NULL Faster than just inc() if element is NULL - behavior is undefined

Parameters
idx- element index
v- increment value
See also
inc

Definition at line 1007 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ init_remap_buffer()

template<class Val, class SV>
unsigned char* bm::rsc_sparse_vector< Val, SV >::init_remap_buffer ( )
inlineprotected

Definition at line 766 of file bmsparsevec_compr.h.

◆ is_compressed()

template<class Val, class SV>
static bool bm::rsc_sparse_vector< Val, SV >::is_compressed ( )
inlinestatic

trait if sparse vector is "compressed" (true)

Definition at line 533 of file bmsparsevec_compr.h.

◆ is_null()

template<class Val , class SV >
bool bm::rsc_sparse_vector< Val, SV >::is_null ( size_type  idx) const

test if specified element is NULL

Parameters
idx- element index
Returns
true if it is NULL false if it was assigned or container is not configured to support assignment flags
Examples:
xsample08.cpp.

Definition at line 1262 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< Val, SV >::const_iterator::operator++(), bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[](), and set_feature_strand().

◆ is_nullable()

template<class Val, class SV>
bool bm::rsc_sparse_vector< Val, SV >::is_nullable ( ) const
inline

if container supports NULL(unassigned) values (true)

Definition at line 528 of file bmsparsevec_compr.h.

◆ is_remap()

template<class Val, class SV>
bool bm::rsc_sparse_vector< Val, SV >::is_remap ( ) const
inlineprotected

Definition at line 763 of file bmsparsevec_compr.h.

◆ load_from()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::load_from ( const sparse_vector_type sv_src)

Load compressed vector from a sparse vector (with NULLs)

Parameters
sv_src- source sparse vector

Definition at line 1072 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::is_compressed(), main(), and write_as_rsc_svector().

◆ load_to()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::load_to ( sparse_vector_type sv) const

Exort compressed vector to a sparse vector (with NULLs)

Parameters
sv- target sparse vector

Definition at line 1113 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::is_compressed(), and main().

◆ merge_not_null()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::merge_not_null ( rsc_sparse_vector< Val, SV > &  csv)

merge two vectors (argument gets destroyed) It is important that both vectors have the same NULL vectors

Parameters
csv- [in,out] argumnet vector to merge (works like move so arg should not be used after the merge)

Definition at line 1515 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::clear().

◆ operator=() [1/2]

template<class Val, class SV>
rsc_sparse_vector<Val,SV>& bm::rsc_sparse_vector< Val, SV >::operator= ( const rsc_sparse_vector< Val, SV > &  csv)
inline

copy assignmment operator

Definition at line 325 of file bmsparsevec_compr.h.

◆ operator=() [2/2]

template<class Val, class SV>
rsc_sparse_vector<Val,SV>& bm::rsc_sparse_vector< Val, SV >::operator= ( rsc_sparse_vector< Val, SV > &&  csv)
inline

move assignmment operator

Definition at line 345 of file bmsparsevec_compr.h.

◆ operator[]()

template<class Val, class SV>
value_type bm::rsc_sparse_vector< Val, SV >::operator[] ( size_type  idx) const
inline

get specified element without bounds checking

Parameters
idx- element index
Returns
value of the element

Definition at line 393 of file bmsparsevec_compr.h.

◆ optimize()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::optimize ( bm::word_t temp_block = 0,
typename bvector_type::optmode  opt_mode = bvector_type::opt_compress,
statistics stat = 0 
)

run memory optimization for all vector plains

Parameters
temp_block- pre-allocated memory block to avoid unnecessary re-allocs
opt_mode- requested compression depth
stat- memory allocation statistics after optimization

Definition at line 1272 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::get_back_inserter(), main(), bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::optimize(), and write_as_rsc_svector().

◆ plains()

template<class Val, class SV>
static unsigned bm::rsc_sparse_vector< Val, SV >::plains ( )
inlinestatic

get total number of bit-plains in the vector

Definition at line 708 of file bmsparsevec_compr.h.

◆ push_back()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::push_back ( size_type  idx,
value_type  v 
)

set specified element with bounds checking and automatic resize

Method cannot insert elements, so every new idx has to be greater or equal than what it used before. Elements must be loaded in a sorted order.

Parameters
idx- element index
v- element value

Definition at line 894 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ push_back_no_check()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::push_back_no_check ( size_type  idx,
value_type  v 
)
protected

◆ remap_size()

template<class Val, class SV>
size_t bm::rsc_sparse_vector< Val, SV >::remap_size ( ) const
inlineprotected

Definition at line 764 of file bmsparsevec_compr.h.

◆ resize_internal()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::resize_internal ( size_type  sz)
inlineprotected

Definition at line 757 of file bmsparsevec_compr.h.

◆ resolve()

template<class Val , class SV >
bool bm::rsc_sparse_vector< Val, SV >::resolve ( size_type  idx,
size_type idx_to 
) const
protected

Resolve logical address to access via rank compressed address.

Parameters
idx- input id to resolve
idx_to- output id
Returns
true if id is known and resolved successfully

Definition at line 1179 of file bmsparsevec_compr.h.

◆ resolve_range()

template<class Val , class SV >
bool bm::rsc_sparse_vector< Val, SV >::resolve_range ( size_type  from,
size_type  to,
size_type idx_from,
size_type idx_to 
) const
protected

◆ set()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::set ( size_type  idx,
value_type  v 
)

set specified element with bounds checking and automatic resize

Parameters
idx- element index
v- element value
Examples:
xsample08.cpp.

Definition at line 1026 of file bmsparsevec_compr.h.

Referenced by count_kmers(), fill_test_data(), main(), and set_feature_strand().

◆ set_null()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::set_null ( size_type  idx)

set specified element to NULL RSC vector actually erases element when it is set to NULL (expensive).

Parameters
idx- element index

Definition at line 925 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::operator[]().

◆ set_remap()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::set_remap ( )
inlineprotected

Definition at line 767 of file bmsparsevec_compr.h.

◆ size()

template<class Val , class SV >
rsc_sparse_vector< Val, SV >::size_type bm::rsc_sparse_vector< Val, SV >::size ( ) const

◆ size_internal()

template<class Val, class SV>
size_type bm::rsc_sparse_vector< Val, SV >::size_internal ( ) const
inlineprotected

Definition at line 761 of file bmsparsevec_compr.h.

◆ stored_plains()

template<class Val, class SV>
static unsigned bm::rsc_sparse_vector< Val, SV >::stored_plains ( )
inlinestatic

Number of stored bit-plains (value plains + extra.

Definition at line 712 of file bmsparsevec_compr.h.

◆ sync() [1/2]

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::sync ( bool  force)

Re-calculate rank-select index for faster access to vector.

Parameters
force- force recalculation even if it is already recalculated

Definition at line 1146 of file bmsparsevec_compr.h.

Referenced by fill_test_data(), main(), and SortCounting_JobFunctor< BV >::operator()().

◆ sync() [2/2]

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::sync ( )
inline

Re-calculate prefix sum table used for rank search (if necessary)

Definition at line 672 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::clear(), and bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::sync().

◆ sync_size()

template<class Val , class SV >
void bm::rsc_sparse_vector< Val, SV >::sync_size ( )

recalculate size to exclude tail NULL elements After this call size() will return the true size of the vector

Definition at line 1164 of file bmsparsevec_compr.h.

Referenced by bm::rsc_sparse_vector< unsigned, sparse_vector_u32 >::empty().

◆ unsync()

template<class Val, class SV>
void bm::rsc_sparse_vector< Val, SV >::unsync ( )
inline

Unsync the prefix sum table.

Definition at line 682 of file bmsparsevec_compr.h.

Friends And Related Function Documentation

◆ sparse_vector_deserializer

template<class Val, class SV>
template<class SVect >
friend class sparse_vector_deserializer
friend

Definition at line 790 of file bmsparsevec_compr.h.

◆ sparse_vector_scanner

template<class Val, class SV>
template<class SVect >
friend class sparse_vector_scanner
friend

Definition at line 788 of file bmsparsevec_compr.h.

◆ sparse_vector_serializer

template<class Val, class SV>
template<class SVect >
friend class sparse_vector_serializer
friend

Definition at line 789 of file bmsparsevec_compr.h.


The documentation for this class was generated from the following file: