swps3
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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Macros

#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
 

Detailed Description

Profile generation and alignment on Cell/BE SPE.

Definition in file DynProgr_SPE_functions.h.

Macro Definition Documentation

#define SPU

Definition at line 34 of file DynProgr_SPE_functions.h.

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.

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 doCreateProfile(), handleCommand(), TcreateProfile(), and TdynProgLocal().

vvf_t createProfile[]

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

Definition at line 677 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(), and TdynProgLocal().

dvf_t dynProgLocal[]

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

Definition at line 666 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().

int ls1
int ls2

database sequence length

Definition at line 58 of file DynProgr_SPE_functions.cc.

Referenced by dynProgrLocalBlock(), handleCommand(), swps3_alignScalar(), and TdynProgLocal().

int maxDbLen

maximal database sequence length

Definition at line 60 of file DynProgr_SPE_functions.cc.

Referenced by handleCommand(), and SPEInit().

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 * rD

temporary storage for row delection scores

Definition at line 62 of file DynProgr_SPE_functions.cc.

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

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