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NCBI C++ ToolKit: src/algo/structure/struct_dp/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>

Go to the source code of this file.

Go to the SVN repository for this file.

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_BlockInfo * DP_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) ◆ ERROR_MESSAGE ◆ INFO_MESSAGE ◆ NO_TRACEBACK ◆ WARNING_MESSAGE ◆ CalculateGlobalMatrix() ◆ CalculateGlobalMatrixGeneric() ◆ CalculateLocalMatrix() ◆ CalculateLocalMatrixGeneric() ◆ DP_CalculateMaxLoopLength() unsigned int DP_CalculateMaxLoopLength ( unsigned int nLoops, const unsigned int * loops, double percentile, unsigned int extension, unsigned int cutoff ) ◆ DP_CreateBlockInfo()

Definition at line 839 of file block_align.cpp.

References DP_BlockInfo::blockPositions, blocks, DP_BlockInfo::blockSizes, DP_UNFROZEN_BLOCK, DP_BlockInfo::freezeBlocks, i, DP_BlockInfo::maxLoops, and DP_BlockInfo::nBlocks.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), and DPApp::Run().

◆ DP_DestroyAlignmentResult() ◆ DP_DestroyBlockInfo() ◆ DP_DestroyMultipleAlignmentResults() ◆ DP_GlobalBlockAlign()

Definition at line 659 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateGlobalMatrix(), ERROR_MESSAGE, i, if(), DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackGlobalAlignment(), and ValidateFrozenBlockPositions().

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), and AlignmentUtility::DoLeaveOneOut().

◆ DP_GlobalBlockAlignGeneric()

Definition at line 694 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateGlobalMatrixGeneric(), ERROR_MESSAGE, i, if(), DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackGlobalAlignment(), and ValidateFrozenBlockPositions().

◆ DP_LocalBlockAlign()

Definition at line 731 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrix(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackLocalAlignment(), and WARNING_MESSAGE.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), and DPApp::Run().

◆ DP_LocalBlockAlignGeneric()

Definition at line 758 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrixGeneric(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackLocalAlignment(), and WARNING_MESSAGE.

◆ DP_MultipleLocalBlockAlign()

Definition at line 785 of file block_align.cpp.

◆ DP_MultipleLocalBlockAlignGeneric()

Definition at line 812 of file block_align.cpp.

◆ TracebackAlignment() ◆ TracebackGlobalAlignment() ◆ TracebackLocalAlignment() ◆ TracebackMultipleLocalAlignments()

Definition at line 560 of file block_align.cpp.

References a, blocks, DP_NEGATIVE_INFINITY, ERROR_MESSAGE, DP_MultipleAlignmentResults::nAlignments, DP_BlockInfo::nBlocks, NO_TRACEBACK, NULL, pythonpp::resize(), STRUCT_DP_ALGORITHM_ERROR, STRUCT_DP_FOUND_ALIGNMENT, STRUCT_DP_NO_ALIGNMENT, STRUCT_DP_PARAMETER_ERROR, t, and TracebackAlignment().

Referenced by DP_MultipleLocalBlockAlign(), and DP_MultipleLocalBlockAlignGeneric().

◆ USING_SCOPE() USING_SCOPE ( struct_dp ) ◆ ValidateFrozenBlockPositions()

Definition at line 76 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, kMax_UInt, DP_BlockInfo::maxLoops, DP_BlockInfo::nBlocks, NONE, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, and WARNING_MESSAGE.

Referenced by DP_GlobalBlockAlign(), and DP_GlobalBlockAlignGeneric().

◆ USING_NCBI_SCOPE

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