NCBI C++ ToolKit
Classes | Macros | Functions | Variables
block_align.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbidiag.hpp>
#include <vector>
#include <list>
#include <algorithm>
#include <algo/structure/struct_dp/struct_dp.h>
+ Include dependency graph for block_align.cpp:

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Classes

class  Cell
 
class  Matrix< T >
 
struct  Traceback
 

Macros

#define ERROR_MESSAGE(s)   ERR_POST(Error << "block_align: " << s << '!')
 
#define WARNING_MESSAGE(s)   ERR_POST(Warning << "block_align: " << s)
 
#define INFO_MESSAGE(s)   ERR_POST(Info << "block_align: " << s)
 
#define NO_TRACEBACK   kMax_UInt
 

Functions

int ValidateFrozenBlockPositions (const DP_BlockInfo *blocks, unsigned int queryFrom, unsigned int queryTo, bool checkGapSum)
 
int CalculateGlobalMatrix (Matrix &matrix, const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo)
 
int CalculateGlobalMatrixGeneric (Matrix &matrix, const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo)
 
int CalculateLocalMatrix (Matrix &matrix, const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo)
 
int CalculateLocalMatrixGeneric (Matrix &matrix, const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo)
 
int TracebackAlignment (const Matrix &matrix, unsigned int lastBlock, unsigned int lastBlockPos, unsigned int queryFrom, DP_AlignmentResult *alignment)
 
int TracebackGlobalAlignment (const Matrix &matrix, const DP_BlockInfo *blocks, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int TracebackLocalAlignment (const Matrix &matrix, const DP_BlockInfo *blocks, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int TracebackMultipleLocalAlignments (const Matrix &matrix, const DP_BlockInfo *blocks, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)
 
 USING_SCOPE (struct_dp)
 
int DP_GlobalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int DP_GlobalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, 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)
 
int DP_LocalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
 
int DP_MultipleLocalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)
 
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)
 
DP_BlockInfoDP_CreateBlockInfo (unsigned int nBlocks)
 
void DP_DestroyBlockInfo (DP_BlockInfo *blocks)
 
void DP_DestroyAlignmentResult (DP_AlignmentResult *alignment)
 
void DP_DestroyMultipleAlignmentResults (DP_MultipleAlignmentResults *alignments)
 
unsigned int DP_CalculateMaxLoopLength (unsigned int nLoops, const unsigned int *loops, double percentile, unsigned int extension, unsigned int cutoff)
 

Variables

 USING_NCBI_SCOPE
 

Macro Definition Documentation

◆ ERROR_MESSAGE

#define ERROR_MESSAGE (   s)    ERR_POST(Error << "block_align: " << s << '!')

Definition at line 49 of file block_align.cpp.

◆ INFO_MESSAGE

#define INFO_MESSAGE (   s)    ERR_POST(Info << "block_align: " << s)

Definition at line 51 of file block_align.cpp.

◆ NO_TRACEBACK

#define NO_TRACEBACK   kMax_UInt

Definition at line 53 of file block_align.cpp.

◆ WARNING_MESSAGE

#define WARNING_MESSAGE (   s)    ERR_POST(Warning << "block_align: " << s)

Definition at line 50 of file block_align.cpp.

Function Documentation

◆ CalculateGlobalMatrix()

int CalculateGlobalMatrix ( Matrix matrix,
const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
unsigned int  queryFrom,
unsigned int  queryTo 
)

◆ CalculateGlobalMatrixGeneric()

int CalculateGlobalMatrixGeneric ( Matrix matrix,
const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
DP_LoopPenaltyFunction  LoopScore,
unsigned int  queryFrom,
unsigned int  queryTo 
)

◆ CalculateLocalMatrix()

int CalculateLocalMatrix ( Matrix matrix,
const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
unsigned int  queryFrom,
unsigned int  queryTo 
)

◆ CalculateLocalMatrixGeneric()

int CalculateLocalMatrixGeneric ( Matrix matrix,
const DP_BlockInfo blocks,
DP_BlockScoreFunction  BlockScore,
DP_LoopPenaltyFunction  LoopScore,
unsigned int  queryFrom,
unsigned int  queryTo 
)

◆ DP_CalculateMaxLoopLength()

unsigned int DP_CalculateMaxLoopLength ( unsigned int  nLoops,
const unsigned int loops,
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 
)

◆ TracebackAlignment()

int TracebackAlignment ( const Matrix matrix,
unsigned int  lastBlock,
unsigned int  lastBlockPos,
unsigned int  queryFrom,
DP_AlignmentResult alignment 
)

◆ TracebackGlobalAlignment()

int TracebackGlobalAlignment ( const Matrix matrix,
const DP_BlockInfo blocks,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ TracebackLocalAlignment()

int TracebackLocalAlignment ( const Matrix matrix,
const DP_BlockInfo blocks,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_AlignmentResult **  alignment 
)

◆ TracebackMultipleLocalAlignments()

int TracebackMultipleLocalAlignments ( const Matrix matrix,
const DP_BlockInfo blocks,
unsigned int  queryFrom,
unsigned int  queryTo,
DP_MultipleAlignmentResults **  alignments,
unsigned int  maxAlignments 
)

◆ USING_SCOPE()

USING_SCOPE ( struct_dp  )

◆ ValidateFrozenBlockPositions()

int ValidateFrozenBlockPositions ( const DP_BlockInfo blocks,
unsigned int  queryFrom,
unsigned int  queryTo,
bool  checkGapSum 
)

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 44 of file block_align.cpp.

Modified on Sat May 18 11:35:53 2024 by modify_doxy.py rev. 669887