DynProgr_altivec.cc File Reference

Profile generation and alignment on IBM Altivec^TM instruction set. More...

#include "matrix.h"
#include "DynProgr_altivec.h"
#include <cstdlib>
#include <malloc.h>
#include <float.h>
#include <cstdio>
#include <string.h>
#include <altivec.h>
#include <sys/types.h>

Include dependency graph for DynProgr_altivec.cc:

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 IsInteger< u_int16_t >

struct IsInteger< u_int32_t >

struct IsInteger< u_int8_t >

struct IsSigned< T >

struct MaxValue< T >

struct MaxValue< double >

struct MaxValue< float >

struct MinValue< T >

struct MinValue< double >

struct MinValue< float >

struct Profile< T, V >

Defines

#define ALIGN16(x) (((x)+15)&(-16))

Typedefs

typedef vector float v_float_t

Saturated addition for floating point data types.

Functions

template<typename T, typename V>

static Profile< T, V > * allocateProfile (int len)

Allocates a profile data structure.

template<typename T, typename V>

static T dynProgrLocal (const char *db, int dbLen, Profile< T, V > *profile, Options *options)

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

template<typename T, typename V>

static T dynProgrLocal2 (const char *db, int dbLen, Profile< T, V > *profile, Options *options)

Unrolled version of dynProgrLocal.

template<typename T, typename V>

void freeProfile (Profile< T, V > *profile)

Releases memory occupied by a profile data structure.

template<typename T>

static T max (T a, T b)

template<typename T>

static T min (T a, T b)

template<typename T, typename V, typename X>

EXPORT Profile< T, V > * swps3_createProfileAltivec (const char *query, int queryLen, X *simi)

Template version for allocation and computation of a profile for the given data type and similarity matrix.

EXPORT void * swps3_createProfileByteAltivec (const char *query, int queryLen, SBMatrix matrix)

C version for allocation and computation of a 8-bit integer profile for the given data type and similarity matrix.

EXPORT void * swps3_createProfileFloatAltivec (const char *query, int queryLen, SBMatrix matrix)

C version for allocation and computation of a 32-bit floating point profile for the given data type and similarity matrix.

EXPORT void * swps3_createProfileShortAltivec (const char *query, int queryLen, SBMatrix matrix)

C version for allocation and computation of a 16-bit integer profile for the given data type and similarity matrix.

template<typename T, typename V>

EXPORT double swps3_dynProgrAltivec (const char *db, int dbLen, Profile< T, V > *profile, Options *options)

Template version of alignment routine for Altivec.

EXPORT double swps3_dynProgrByteAltivec (const char *db, int dbLen, void *profile, Options *options)

C version of alignment routine for Altivec for signed 8-bit integers.

EXPORT double swps3_dynProgrFloatAltivec (const char *db, int dbLen, void *profile, Options *options)

C version of alignment routine for Altivec for signed 32-bit floating point values.

EXPORT double swps3_dynProgrShortAltivec (const char *db, int dbLen, void *profile, Options *options)

C version of alignment routine for Altivec for signed 16-bit integers.

template<typename V>

static V vec_addx (V a, V b)

Saturated addition for integer data types.

template<>

static v_float_t vec_addx< v_float_t > (v_float_t a, v_float_t b)

template<typename V>

static V vec_subx (V a, V b)

Saturated subtraction for integer data types.

template<>

static v_float_t vec_subx< v_float_t > (v_float_t a, v_float_t b)

Detailed Description

Profile generation and alignment on IBM Altivec^TM instruction set.

Definition in file DynProgr_altivec.cc.

Define Documentation

#define ALIGN16 ( x ) (((x)+15)&(-16))

Definition at line 40 of file DynProgr_altivec.cc.

Referenced by alloc(), allocateProfile(), dynProgrLocal(), dynProgrLocal2(), handleCommand(), swps3_createProfileAltivec(), TcreateProfile(), and TdynProgLocal().

Typedef Documentation

typedef vector float v_float_t

Saturated addition for floating point data types.

Saturated substraction for floating point data types.

Definition at line 118 of file DynProgr_altivec.cc.

Function Documentation

template<typename T, typename V>

static Profile<T,V>* allocateProfile ( int len ) [inline, static]

Allocates a profile data structure.

Parameters:

	T	The datatype for the profile.
	V	The datatype of the corresponding packed vectors.
	len	The query length.

Returns:: A profile data structure.

Definition at line 81 of file DynProgr_altivec.cc.

References ALIGN16, Profile< T, V >::len, Profile< T, V >::loadOpt, MATRIX_DIM, Profile< T, V >::profile, profile, Profile< T, V >::rD, Profile< T, V >::storeOpt, and T.

template<typename T, typename V>

static T dynProgrLocal	(	const char *	db,
		int	dbLen,
		Profile< T, V > *	profile,
		Options *	options
	)			`[inline, static]`

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

Parameters:

	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	The profile created previously from the query sequence.
	options	Some global options.

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

Definition at line 152 of file DynProgr_altivec.cc.

References ALIGN16, Profile< T, V >::bias, Options::gapExt, Options::gapOpen, Profile< T, V >::len, LIKELY, Profile< T, V >::loadOpt, Profile< T, V >::profile, Profile< T, V >::rD, Profile< T, V >::storeOpt, T, UNLIKELY, vec_addx(), and vec_subx().

template<typename T, typename V>

static T dynProgrLocal2	(	const char *	db,
		int	dbLen,
		Profile< T, V > *	profile,
		Options *	options
	)			`[inline, static]`

Unrolled version of dynProgrLocal.

Parameters:

	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	The profile created previously from the query sequence.
	options	Some global options.

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

See also:: dynProgrLocal()
swps3_createProfileAltivec()

Definition at line 365 of file DynProgr_altivec.cc.

template<typename T, typename V>

void freeProfile ( Profile< T, V > * profile ) [inline]

Releases memory occupied by a profile data structure.

Definition at line 98 of file DynProgr_altivec.cc.

References Profile< T, V >::loadOpt, Profile< T, V >::profile, Profile< T, V >::rD, and Profile< T, V >::storeOpt.

template<typename T>

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

Definition at line 44 of file DynProgr_altivec.cc.

template<typename T>

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

Definition at line 43 of file DynProgr_altivec.cc.

template<typename T, typename V, typename X>

EXPORT Profile<T,V>* swps3_createProfileAltivec	(	const char *	query,
		int	queryLen,
		X *	simi
	)			`[inline]`

Template version for allocation and computation of a profile for the given data type and similarity matrix.

Parameters:

	T	The data type for the alignment scores.
	V	The corresponding packed vector data type.
	X	The data type of the similarity matrix.
	query	The query sequence.
	queryLen	The length of the query sequence.
	simi	The similarity matrix.

Returns:: An initialized profile data structure.

Definition at line 629 of file DynProgr_altivec.cc.

References ALIGN16, MATRIX_DIM, Profile< T, V >::profile, profile, and T.

EXPORT void* swps3_createProfileByteAltivec	(	const char *	query,
		int	queryLen,
		SBMatrix	matrix
	)

C version for allocation and computation of a 8-bit integer profile for the given data type and similarity matrix.

Parameters:

	query	The query sequence.
	queryLen	The length of the query sequence.
	matrix	The similarity matrix.

Returns:: An initialized profile data structure.

Definition at line 774 of file DynProgr_altivec.cc.

Referenced by main().

EXPORT void* swps3_createProfileFloatAltivec	(	const char *	query,
		int	queryLen,
		SBMatrix	matrix
	)

C version for allocation and computation of a 32-bit floating point profile for the given data type and similarity matrix.

Parameters:

	query	The query sequence.
	queryLen	The length of the query sequence.
	matrix	The similarity matrix.

Returns:: An initialized profile data structure.

Definition at line 804 of file DynProgr_altivec.cc.

Referenced by main().

EXPORT void* swps3_createProfileShortAltivec	(	const char *	query,
		int	queryLen,
		SBMatrix	matrix
	)

C version for allocation and computation of a 16-bit integer profile for the given data type and similarity matrix.

Parameters:

	query	The query sequence.
	queryLen	The length of the query sequence.
	matrix	The similarity matrix.

Returns:: An initialized profile data structure.

Definition at line 789 of file DynProgr_altivec.cc.

Referenced by main().

template<typename T, typename V>

EXPORT double swps3_dynProgrAltivec	(	const char *	db,
		int	dbLen,
		Profile< T, V > *	profile,
		Options *	options
	)			`[inline]`

Template version of alignment routine for Altivec.

To be called from C++ code.

Parameters:

	T	The data type for the alignment scores.
	V	The corresponding packed vector data type.
	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	A profile data structure previously computed from the query sequence.
	options	Some global options.

Returns:: The local alignment score or DBL_MAX if score exceeds threshold.

See also:: swps3_createProfileAltivec()

Definition at line 669 of file DynProgr_altivec.cc.

References T.

EXPORT double swps3_dynProgrByteAltivec	(	const char *	db,
		int	dbLen,
		void *	profile,
		Options *	options
	)

C version of alignment routine for Altivec for signed 8-bit integers.

Parameters:

	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	A profile data structure previously computed from the query sequence.
	options	Some global options.

Returns:: The local alignment score or DBL_MAX if score exceeds threshold.

See also:: swps3_createProfileByteAltivec()
swps3_dynProgrAltivec()

Definition at line 718 of file DynProgr_altivec.cc.

Referenced by main().

EXPORT double swps3_dynProgrFloatAltivec	(	const char *	db,
		int	dbLen,
		void *	profile,
		Options *	options
	)

C version of alignment routine for Altivec for signed 32-bit floating point values.

Parameters:

	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	A profile data structure previously computed from the query sequence.
	options	Some global options.

Returns:: The local alignment score or DBL_MAX if score exceeds threshold.

See also:: swps3_createProfileFloatAltivec()
swps3_dynProgrAltivec()

Definition at line 759 of file DynProgr_altivec.cc.

Referenced by main().

EXPORT double swps3_dynProgrShortAltivec	(	const char *	db,
		int	dbLen,
		void *	profile,
		Options *	options
	)

C version of alignment routine for Altivec for signed 16-bit integers.

Parameters:

	db	The database sequence.
	dbLen	The length of the database sequence.
	profile	A profile data structure previously computed from the query sequence.
	options	Some global options.

Returns:: The local alignment score or DBL_MAX if score exceeds threshold.

See also:: swps3_createProfileShortAltivec()
swps3_dynProgrAltivec()

Definition at line 738 of file DynProgr_altivec.cc.

Referenced by main().

template<typename V>

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

Saturated addition for integer data types.

Definition at line 110 of file DynProgr_altivec.cc.

Referenced by dynProgrLocal(), and dynProgrLocal2().

template<>

static v_float_t vec_addx< v_float_t >	(	v_float_t	a,
		v_float_t	b
	)			`[inline, static]`

template<typename V>

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

Saturated subtraction for integer data types.

Definition at line 127 of file DynProgr_altivec.cc.

Referenced by dynProgrLocal(), and dynProgrLocal2().

template<>

static v_float_t vec_subx< v_float_t >	(	v_float_t	a,
		v_float_t	b
	)			`[inline, static]`

Generated on Thu Jun 5 12:44:39 2008 for swps3 by

1.5.4


Classes
struct	IsInteger< T >
struct	IsInteger< int16_t >
struct	IsInteger< int32_t >
struct	IsInteger< int8_t >
struct	IsInteger< u_int16_t >
struct	IsInteger< u_int32_t >
struct	IsInteger< u_int8_t >
struct	IsSigned< T >
struct	MaxValue< T >
struct	MaxValue< double >
struct	MaxValue< float >
struct	MinValue< T >
struct	MinValue< double >
struct	MinValue< float >
struct	Profile< T, V >
Defines
#define	ALIGN16(x) (((x)+15)&(-16))
Typedefs
typedef vector float	v_float_t
	Saturated addition for floating point data types.
Functions
template<typename T, typename V>
static Profile< T, V > *	allocateProfile (int len)
	Allocates a profile data structure.
template<typename T, typename V>
static T	dynProgrLocal (const char db, int dbLen, Profile< T, V > profile, Options *options)
	Performs an local alignment using the given profile and database sequence.
template<typename T, typename V>
static T	dynProgrLocal2 (const char db, int dbLen, Profile< T, V > profile, Options *options)
	Unrolled version of `dynProgrLocal`.
template<typename T, typename V>
void	freeProfile (Profile< T, V > *profile)
	Releases memory occupied by a profile data structure.
template<typename T>
static T	max (T a, T b)
template<typename T>
static T	min (T a, T b)
template<typename T, typename V, typename X>
EXPORT Profile< T, V > *	swps3_createProfileAltivec (const char query, int queryLen, X simi)
	Template version for allocation and computation of a profile for the given data type and similarity matrix.
EXPORT void *	swps3_createProfileByteAltivec (const char *query, int queryLen, SBMatrix matrix)
	C version for allocation and computation of a 8-bit integer profile for the given data type and similarity matrix.
EXPORT void *	swps3_createProfileFloatAltivec (const char *query, int queryLen, SBMatrix matrix)
	C version for allocation and computation of a 32-bit floating point profile for the given data type and similarity matrix.
EXPORT void *	swps3_createProfileShortAltivec (const char *query, int queryLen, SBMatrix matrix)
	C version for allocation and computation of a 16-bit integer profile for the given data type and similarity matrix.
template<typename T, typename V>
EXPORT double	swps3_dynProgrAltivec (const char db, int dbLen, Profile< T, V > profile, Options *options)
	Template version of alignment routine for Altivec.
EXPORT double	swps3_dynProgrByteAltivec (const char db, int dbLen, void profile, Options *options)
	C version of alignment routine for Altivec for signed 8-bit integers.
EXPORT double	swps3_dynProgrFloatAltivec (const char db, int dbLen, void profile, Options *options)
	C version of alignment routine for Altivec for signed 32-bit floating point values.
EXPORT double	swps3_dynProgrShortAltivec (const char db, int dbLen, void profile, Options *options)
	C version of alignment routine for Altivec for signed 16-bit integers.
template<typename V>
static V	vec_addx (V a, V b)
	Saturated addition for integer data types.
template<>
static v_float_t	vec_addx< v_float_t > (v_float_t a, v_float_t b)
template<typename V>
static V	vec_subx (V a, V b)
	Saturated subtraction for integer data types.
template<>
static v_float_t	vec_subx< v_float_t > (v_float_t a, v_float_t b)