bm::gap_transpose_engine< GT, BT, BLOCK_SIZE > Class Template Reference

Bit-plain splicing of a GAP block. More...

#include <bmtrans.h>

Collaboration diagram for bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >:

[legend]

Public Types
typedef tmatrix< GT, sizeof(GT)*8,(((BLOCK_SIZE *sizeof(unsigned))/(sizeof(GT)))/(sizeof(GT)*8))	tmatrix_type )
	cryptic calculation of equivalent size for the transpose matrix based on BLOCK_SIZE and sizeof(GT)(16)
Public Member Functions
	gap_transpose_engine ()
void	transpose (const GT *BMRESTRICT gap_buf)
	Transpose GAP block through a temp.
void	transpose (const GT *BMRESTRICT garr, unsigned garr_size)
	Transpose array of shorts.
void	compute_distance_matrix ()
void	reduce ()
void	restore ()
void	trestore (GT gap_head, GT *BMRESTRICT gap_buf)
	Restore GAP block from the transposed matrix.
Data Fields
tmatrix_type	tmatrix_
unsigned	eff_cols_
unsigned	distance_ [tmatrix_type::n_rows][tmatrix_type::n_rows]
unsigned char	pc_vector_ [tmatrix_type::n_rows]
unsigned	pc_vector_stat_ [bm::ibpc_end]
tmatrix_type::rstat	rstat_vector_ [tmatrix_type::n_rows]
GT BM_ALIGN16 tmp_gap_block_[BLOCK_SIZE *2]	BM_ALIGN16ATTR

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Detailed Description

template<typename GT, typename BT, unsigned BLOCK_SIZE>
class bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >

Bit-plain splicing of a GAP block.

GT - gap word type BT - block word type BLOCK_SIZE - bit block size in words (works as a transposition basis)

Definition at line 774 of file bmtrans.h.

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Member Typedef Documentation

template<typename GT , typename BT , unsigned BLOCK_SIZE>

typedef tmatrix<GT, sizeof(GT)*8, (((BLOCK_SIZE * sizeof(unsigned)) / (sizeof(GT))) / (sizeof(GT) * 8)) bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_type)

cryptic calculation of equivalent size for the transpose matrix based on BLOCK_SIZE and sizeof(GT)(16)

matrix[size_of_gap*8][(Size_block_in_bytes / size_of_gap) / number_of_planes)]

Definition at line 784 of file bmtrans.h.

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Constructor & Destructor Documentation

template<typename GT , typename BT , unsigned BLOCK_SIZE>

bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::gap_transpose_engine

(

)

[inline]

Definition at line 786 of file bmtrans.h.

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Member Function Documentation

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::compute_distance_matrix

(

)

[inline]

Definition at line 830 of file bmtrans.h.

References bm::bit_iblock_make_pcv(), bm::bit_iblock_pcv_stat(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::distance_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_stat_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_, and bm::tmatrix_distance().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::reduce

(

)

[inline]

Definition at line 846 of file bmtrans.h.

References bm::compute_tmatrix_rstat(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::eff_cols_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::rstat_vector_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_, and bm::tmatrix_reduce().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::restore

(

)

[inline]

Definition at line 852 of file bmtrans.h.

References bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::eff_cols_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_, and bm::tmatrix_restore().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::transpose	(	const GT *BMRESTRICT	garr,
		unsigned	garr_size
	)			[inline]

Transpose array of shorts.

Definition at line 810 of file bmtrans.h.

References bm::bit_block_set(), BM_ASSERT, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::eff_cols_, bm::find_effective_columns(), and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_.

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::transpose

(

const GT *BMRESTRICT

gap_buf

)

[inline]

Transpose GAP block through a temp.

block of aligned(!) memory

Definition at line 791 of file bmtrans.h.

References BM_ASSERT, bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::eff_cols_, bm::find_effective_columns(), bm::gap_2_bitblock(), and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_.

template<typename GT , typename BT , unsigned BLOCK_SIZE>

void bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::trestore	(	GT	gap_head,
		GT *BMRESTRICT	gap_buf
	)			[inline]

Restore GAP block from the transposed matrix.

Definition at line 860 of file bmtrans.h.

References BM_ASSERT, and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_.

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Field Documentation

template<typename GT , typename BT , unsigned BLOCK_SIZE>

GT BM_ALIGN16 tmp_gap_block_ [BLOCK_SIZE*2] bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::BM_ALIGN16ATTR

Definition at line 885 of file bmtrans.h.

template<typename GT , typename BT , unsigned BLOCK_SIZE>

unsigned bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::distance_[tmatrix_type::n_rows][tmatrix_type::n_rows]

Definition at line 880 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::compute_distance_matrix().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

unsigned bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::eff_cols_

Definition at line 879 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::reduce(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::restore(), and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::transpose().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

unsigned char bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_[tmatrix_type::n_rows]

Definition at line 881 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::compute_distance_matrix(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::reduce(), and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::restore().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

unsigned bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::pc_vector_stat_[bm::ibpc_end]

Definition at line 882 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::compute_distance_matrix().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

tmatrix_type::rstat bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::rstat_vector_[tmatrix_type::n_rows]

Definition at line 883 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::reduce().

template<typename GT , typename BT , unsigned BLOCK_SIZE>

tmatrix_type bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::tmatrix_

Definition at line 878 of file bmtrans.h.

Referenced by bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::compute_distance_matrix(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::reduce(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::restore(), bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::transpose(), and bm::gap_transpose_engine< GT, BT, BLOCK_SIZE >::trestore().

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

• bmtrans.h