DynProgr_SPE_functions.h File Reference

Profile generation and alignment on Cell/BE SPE. More...

#include <spu_mfcio.h>
#include "DynProgr_SPE.h"

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Defines
#define	SPU
Typedefs
typedef double(*	dvf_t )(void)
typedef void(*	vvf_t )(void)
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

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Detailed Description

Profile generation and alignment on Cell/BE SPE.

Definition in file DynProgr_SPE_functions.h.

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Define Documentation

#define SPU

Definition at line 34 of file DynProgr_SPE_functions.h.

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Typedef Documentation

typedef double(* dvf_t)(void)

Definition at line 62 of file DynProgr_SPE_functions.h.

typedef void(* vvf_t)(void)

Definition at line 63 of file DynProgr_SPE_functions.h.

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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[]

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[]

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

temporary storage for score column

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), swps3_alignmentByteSSE(), swps3_alignmentShort2SSE(), and swps3_alignmentShortSSE().

int ls1

query sequence length

Definition at line 58 of file DynProgr_SPE_functions.cc.

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

int ls2

database sequence length

Definition at line 58 of file DynProgr_SPE_functions.cc.

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

int maxDbLen

maximal database sequence length

Definition at line 60 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand().

void * maxS

storage for intermediate score row

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand().

double mn

minimum score

Definition at line 61 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), and TdynProgLocal().

double mx

maximum score

Definition at line 61 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), and TdynProgLocal().

void * profile

current profile segment

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by allocateProfile(), handleCommand(), swps3_createProfileAltivec(), swps3_createProfileByteSSE(), and swps3_createProfileShortSSE().

void * rD

temporary storage for row delection scores

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), swps3_alignmentByteSSE(), swps3_alignmentShort2SSE(), and swps3_alignmentShortSSE().

ppu_addr_t remote_profile

64-bit pointer to profile location in main memory

Definition at line 63 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), and TdynProgLocal().

char* s1

query sequence

Definition at line 57 of file DynProgr_SPE_functions.cc.

Referenced by doCreateProfile(), and handleCommand().

char * s2

database sequence

Definition at line 57 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock(), and handleCommand().

void* simi

similarity matrix

Definition at line 62 of file DynProgr_SPE_functions.cc.

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

void * storeOpt

temporary storage for score column

Definition at line 62 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), swps3_alignmentByteSSE(), swps3_alignmentShort2SSE(), and swps3_alignmentShortSSE().

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