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struct_dp.h File Reference

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#include <corelib/ncbi_limits.h>
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Classes

struct  DP_BlockInfo
 
struct  DP_AlignmentResult
 
struct  DP_MultipleAlignmentResults
 

Macros

#define STRUCT_DP_FOUND_ALIGNMENT   1 /* found an alignment */
 
#define STRUCT_DP_NO_ALIGNMENT   2 /* algorithm successful, but no significant alignment found */
 
#define STRUCT_DP_PARAMETER_ERROR   3 /* error/inconsistency in function parameters */
 
#define STRUCT_DP_ALGORITHM_ERROR   4 /* error encountered during algorithm execution */
 
#define STRUCT_DP_OKAY   5 /* generic ok status */
 

Typedefs

typedef int(* DP_BlockScoreFunction) (unsigned int block, unsigned int queryPos)
 
typedef unsigned int(* DP_LoopPenaltyFunction) (unsigned int loopNumber, unsigned int loopLength)
 

Functions

DP_BlockInfoDP_CreateBlockInfo (unsigned int nBlocks)
 
void DP_DestroyBlockInfo (DP_BlockInfo *blocks)
 
unsigned int DP_CalculateMaxLoopLength (unsigned int nLoops, const unsigned int *loopLengths, double percentile, unsigned int extension, unsigned int cutoff)
 
void DP_DestroyAlignmentResult (DP_AlignmentResult *alignment)
 
int DP_GlobalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int DP_LocalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
void DP_DestroyMultipleAlignmentResults (DP_MultipleAlignmentResults *alignments)
 
int DP_MultipleLocalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)
 
int DP_GlobalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int DP_LocalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int DP_MultipleLocalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)
 

Variables

static const int DP_NEGATIVE_INFINITY = kMin_Int
 
static const unsigned int DP_POSITIVE_INFINITY = kMax_UInt
 
static const unsigned int DP_UNFROZEN_BLOCK = kMax_UInt
 

Macro Definition Documentation

◆ STRUCT_DP_ALGORITHM_ERROR

#define STRUCT_DP_ALGORITHM_ERROR   4 /* error encountered during algorithm execution */

Definition at line 47 of file struct_dp.h.

◆ STRUCT_DP_FOUND_ALIGNMENT

#define STRUCT_DP_FOUND_ALIGNMENT   1 /* found an alignment */

Definition at line 44 of file struct_dp.h.

◆ STRUCT_DP_NO_ALIGNMENT

#define STRUCT_DP_NO_ALIGNMENT   2 /* algorithm successful, but no significant alignment found */

Definition at line 45 of file struct_dp.h.

◆ STRUCT_DP_OKAY

#define STRUCT_DP_OKAY   5 /* generic ok status */

Definition at line 48 of file struct_dp.h.

◆ STRUCT_DP_PARAMETER_ERROR

#define STRUCT_DP_PARAMETER_ERROR   3 /* error/inconsistency in function parameters */

Definition at line 46 of file struct_dp.h.

Typedef Documentation

◆ DP_BlockScoreFunction

typedef int(* DP_BlockScoreFunction) (unsigned int block, unsigned int queryPos)

Definition at line 98 of file struct_dp.h.

◆ DP_LoopPenaltyFunction

typedef unsigned int(* DP_LoopPenaltyFunction) (unsigned int loopNumber, unsigned int loopLength)

Definition at line 157 of file struct_dp.h.

Function Documentation

◆ DP_CalculateMaxLoopLength()

unsigned int DP_CalculateMaxLoopLength ( unsigned int  nLoops,
const unsigned int loopLengths,
double  percentile,
unsigned int  extension,
unsigned int  cutoff 
)

◆ DP_CreateBlockInfo()

DP_BlockInfo* DP_CreateBlockInfo ( unsigned int  nBlocks)

◆ DP_DestroyAlignmentResult()

void DP_DestroyAlignmentResult ( DP_AlignmentResult alignment)

◆ DP_DestroyBlockInfo()

void DP_DestroyBlockInfo ( DP_BlockInfo blocks)

◆ DP_DestroyMultipleAlignmentResults()

void DP_DestroyMultipleAlignmentResults ( DP_MultipleAlignmentResults alignments)

◆ DP_GlobalBlockAlign()

int DP_GlobalBlockAlign ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ DP_GlobalBlockAlignGeneric()

int DP_GlobalBlockAlignGeneric ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
DP_LoopPenaltyFunction  LoopScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ DP_LocalBlockAlign()

int DP_LocalBlockAlign ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ DP_LocalBlockAlignGeneric()

int DP_LocalBlockAlignGeneric ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
DP_LoopPenaltyFunction  LoopScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ DP_MultipleLocalBlockAlign()

int DP_MultipleLocalBlockAlign ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_MultipleAlignmentResults **  alignments,
unsigned int  maxAlignments 
)

◆ DP_MultipleLocalBlockAlignGeneric()

int DP_MultipleLocalBlockAlignGeneric ( const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
DP_LoopPenaltyFunction  LoopScore,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_MultipleAlignmentResults **  alignments,
unsigned int  maxAlignments 
)

Variable Documentation

◆ DP_NEGATIVE_INFINITY

const int DP_NEGATIVE_INFINITY = kMin_Int
static

◆ DP_POSITIVE_INFINITY

const unsigned int DP_POSITIVE_INFINITY = kMax_UInt
static

Definition at line 54 of file struct_dp.h.

Referenced by CalculateGlobalMatrixGeneric(), and CalculateLocalMatrixGeneric().

◆ DP_UNFROZEN_BLOCK

const unsigned int DP_UNFROZEN_BLOCK = kMax_UInt
static
Modified on Sat Feb 24 07:48:07 2024 by modify_doxy.py rev. 669887