swps3: DynProgr_SPE_functions.cc File Reference

#include "DynProgr_SPE_functions.h"
#include "DynProgr_SPE.h"
#include "matrix.h"
#include <cstdlib>
#include <malloc.h>
#include <float.h>
#include <cstdio>
#include <string.h>
#include <spu_intrinsics.h>
#include <sys/types.h>

Go to the source code of this file.


Classes
struct	IsInteger< T >
struct	IsInteger< int16_t >
struct	IsInteger< int32_t >
struct	IsInteger< int8_t >
struct	MaxValue< T >
struct	MaxValue< double >
struct	MaxValue< float >
struct	MinValue< T >
struct	MinValue< double >
struct	MinValue< float >
Functions
template<class T, class V>
static void	doCreateProfile (int blockStart, int currentBlockSize, const T simi, V currentBlock)
	Computes a profile and writes it to the specified memory location.
template<class T, class V>
static T	dynProgrLocalBlock (int currentBlockSize, T zero, T goal, T maxS, T delS, const V profile, V loadOpt, V storeOpt, V rD)
	Performs an local alignment using the given profile segment and database sequence.
template<typename T>
static T	max (T a, T b)
template<typename T>
static T	min (T a, T b)
template<class V>
static V	spu_max (V a, V b)
	Emulates a packed maximum operation.
template<class V>
static V	spu_min (V a, V b)
	Emulates a packed minimum operation.
template<class T, class V>
static void	TcreateProfile (void)
	Template for creating a profile using global variables as parameters.
template<class T, class V>
static double	TdynProgLocal (void)
	Template for computing a local alignment score using global variables as parameters.
Variables
int	blockSize
	length of current profile segment
int	blockStart
	start position of current profile block
vvf_t	createProfile []
	A structure for accessing different flavors of the profile creation routine.
void *	delS
	storage for intermediate column deletion scores
dvf_t	dynProgLocal []
	A structure for accessing different flavors of the local alignment routine.
double	fixedDel
	gap initiation penalty
double	incDel
	gap extension penalty
void *	loadOpt
	temporary storage for score column
int	ls1
	query sequence length
int	ls2
	database sequence length
int	maxDbLen
	maximal database sequence length
void *	maxS
	storage for intermediate score row
double	mn
	minimum score
double	mx
	maximum score
void *	profile
	current profile segment
void *	rD
	temporary storage for row delection scores
ppu_addr_t	remote_profile
	64-bit pointer to profile location in main memory
char *	s1
	query sequence
char *	s2
	database sequence
void *	simi
	similarity matrix
void *	storeOpt
	temporary storage for score column

Detailed Description

Function Documentation

template<class T, class V>

static void doCreateProfile	(	int	blockStart,
		int	currentBlockSize,
		const T *	simi,
		V *	currentBlock
	)			`[inline, static]`

Computes a profile and writes it to the specified memory location.

Parameters:

	blockStart	Current position in the query sequence.
	currentBlockSize	Length of current profile segment.
	simi	The similarity matrix.
	currentBlock	Memory location to write the profile to.

Definition at line 558 of file DynProgr_SPE_functions.cc.

References ls1, MATRIX_DIM, s1, and T.

Referenced by TcreateProfile().

template<class T, class V>

static T dynProgrLocalBlock	(	int	currentBlockSize,
		T	zero,
		T	goal,
		T *	maxS,
		T *	delS,
		const V *	profile,
		V *	loadOpt,
		V *	storeOpt,
		V *	rD
	)			`[inline, static]`

Performs an local alignment using the given profile segment and database sequence.

Parameters:

	currentBlockSize	Length of the current profile segment in terms of query sequence characters.
	zero	Defines a value for the zero score.
	goal	Defines a maximum value for the score.
	maxS	Intermediate row with maximum scores.
	delS	Intermediate row with column deletion scores.
	profile	A segment of the profile created previously from the query sequence.
	loadOpt	Temporary storage for a column.
	storeOpt	Temporary storage for a column.
	rD	Temporary storage for a column of row deletion scores.

Returns:: The local alignment score or a maximum value if result exceeds threshold.

Definition at line 97 of file DynProgr_SPE_functions.cc.

References fixedDel, incDel, LIKELY, ls1, ls2, s2, spu_max(), spu_min(), T, and UNLIKELY.

template<typename T>

static T max	(	T	a,
		T	b
	)			`[inline, static]`

Definition at line 42 of file DynProgr_SPE_functions.cc.

template<typename T>

static T min	(	T	a,
		T	b
	)			`[inline, static]`

Definition at line 41 of file DynProgr_SPE_functions.cc.

template<class V>

static V spu_max	(	V	a,
		V	b
	)			`[inline, static]`

Emulates a packed maximum operation.

Definition at line 68 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock().

template<class V>

static V spu_min	(	V	a,
		V	b
	)			`[inline, static]`

Emulates a packed minimum operation.

Definition at line 74 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock().

template<class T, class V>

static void TcreateProfile ( void ) [inline, static]

Template for creating a profile using global variables as parameters.

Parameters:

	T	The data type for the alignment scores.
	V	The corresponding packed vector data type.

Definition at line 582 of file DynProgr_SPE_functions.cc.

References ALIGN16, blockSize, blockStart, doCreateProfile(), ls1, min, simi, and T.

template<class T, class V>

static double TdynProgLocal ( void ) [inline, static]

Template for computing a local alignment score using global variables as parameters.

Parameters:

	T	The data type for the alignment scores.
	V	The corresponding packed vector data type.

Definition at line 594 of file DynProgr_SPE_functions.cc.

References ALIGN16, blockSize, blockStart, ls1, ls2, MATRIX_DIM, MAX_TRANSFER, min, mn, mx, remote_profile, simi, and T.

Variable Documentation

int blockSize

length of current profile segment

Definition at line 59 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), TcreateProfile(), and TdynProgLocal().

int blockStart

start position of current profile block

Definition at line 59 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), TcreateProfile(), and TdynProgLocal().

vvf_t createProfile[]

Initial value:

 {
        TcreateProfile<int8_t, vector int8_t>,
        TcreateProfile<int16_t, vector int16_t>,
        TcreateProfile<int32_t, vector int32_t>,
        TcreateProfile<float, vector float>,
        TcreateProfile<double, vector double>
}

A structure for accessing different flavors of the profile creation routine.

Definition at line 676 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand().

void * delS

storage for intermediate column deletion scores

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand().

dvf_t dynProgLocal[]

Initial value:

 {
        TdynProgLocal<int8_t, vector int8_t>,
        TdynProgLocal<int16_t, vector int16_t>,
        TdynProgLocal<int32_t, vector int32_t>,
        TdynProgLocal<float, vector float>,
        TdynProgLocal<double, vector double>
}

A structure for accessing different flavors of the local alignment routine.

Definition at line 665 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand().

double fixedDel

gap initiation penalty

Definition at line 61 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock(), and handleCommand().

double incDel

gap extension penalty

Definition at line 61 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock(), and handleCommand().

void * loadOpt