swps3
DynProgr_altivec.h File Reference

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

#include "swps3.h"
Include dependency graph for DynProgr_altivec.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions

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.
 
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.
 
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.
 
double swps3_dynProgrByteAltivec (const char *db, int dbLen, void *profile, Options *options)
 C version of alignment routine for Altivec for signed 8-bit integers.
 
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.
 
double swps3_dynProgrShortAltivec (const char *db, int dbLen, void *profile, Options *options)
 C version of alignment routine for Altivec for signed 16-bit integers.
 

Detailed Description

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

Definition in file DynProgr_altivec.h.

Function Documentation

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
queryThe query sequence.
queryLenThe length of the query sequence.
matrixThe similarity matrix.
Returns
An initialized profile data structure.

Definition at line 774 of file DynProgr_altivec.cc.

Referenced by main().

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
queryThe query sequence.
queryLenThe length of the query sequence.
matrixThe similarity matrix.
Returns
An initialized profile data structure.

Definition at line 804 of file DynProgr_altivec.cc.

Referenced by main().

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
queryThe query sequence.
queryLenThe length of the query sequence.
matrixThe similarity matrix.
Returns
An initialized profile data structure.

Definition at line 789 of file DynProgr_altivec.cc.

Referenced by main().

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
dbThe database sequence.
dbLenThe length of the database sequence.
profileA profile data structure previously computed from the query sequence.
optionsSome 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().

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
dbThe database sequence.
dbLenThe length of the database sequence.
profileA profile data structure previously computed from the query sequence.
optionsSome 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().

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
dbThe database sequence.
dbLenThe length of the database sequence.
profileA profile data structure previously computed from the query sequence.
optionsSome 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().