NCBI C++ ToolKit
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SBlastScoreMatrix Struct Reference

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Scoring matrix used in BLAST. More...

#include <algo/blast/core/blast_stat.h>

+ Collaboration diagram for SBlastScoreMatrix:

Public Attributes

int ** data
 actual scoring matrix data, stored in row-major form More...
 
size_t ncols
 number of columns More...
 
size_t nrows
 number of rows More...
 
double * freqs
 array of assumed matrix background frequencies -RMH- More...
 
double lambda
 derived value of the matrix lambda -RMH- More...
 

Detailed Description

Scoring matrix used in BLAST.

Definition at line 139 of file blast_stat.h.

Member Data Documentation

◆ data

int** SBlastScoreMatrix::data

actual scoring matrix data, stored in row-major form

Definition at line 140 of file blast_stat.h.

Referenced by _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIConvertFreqRatiosToPSSM(), ALIGN_EX(), BLAST_GetGappedScore(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_RedoAlignmentCore_MT(), Blast_SemiGappedAlign(), BLAST_SmithWatermanGetGappedScore(), BlastCompressedAaLookupTableNew(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignment(), BlastScoreBlkMaxScoreSet(), BlastScoreBlkNucleotideMatrixRead(), BlastScoreBlkNuclMatrixCreate(), BlastScoreBlkProteinMatrixLoad(), BlastScoreBlkProteinMatrixRead(), BlastScoreFreqCalc(), BOOST_AUTO_TEST_CASE(), CScoreBuilder::GetBlastScoreDenseg(), CScoreBuilder::GetBlastScoreProtToNucl(), Kappa_compactSearchItemsNew(), LookupTableWrapInit_MT(), RPSPsiMatrixAttach(), RPSPsiMatrixDetach(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastAlignPackedNucl(), s_BlastScoreBlk_Copy(), s_BlastSearchEngineOneContext(), s_BuildCompressedScoreMatrix(), s_GetTraceback(), s_NuclSmithWaterman(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_PHIBlastAlignPatterns(), s_RecordInitialSearch(), s_RestoreSearch(), s_RestrictedGappedAlign(), s_RPSComputeTraceback(), s_SmithWatermanScoreOnly(), SBlastScoreMatrixFree(), SBlastScoreMatrixNew(), CRedoAlignmentTestFixture::setupPositionBasedBlastScoreBlk(), TestFixture::SkipMaskedRangesCore(), and SmithWatermanScoreWithTraceback().

◆ freqs

double* SBlastScoreMatrix::freqs

array of assumed matrix background frequencies -RMH-

Definition at line 144 of file blast_stat.h.

Referenced by Blast_TracebackFromHSPList(), BlastScoreBlkNucleotideMatrixRead(), s_BlastScoreBlk_Copy(), SBlastScoreMatrixFree(), and SBlastScoreMatrixNew().

◆ lambda

double SBlastScoreMatrix::lambda

derived value of the matrix lambda -RMH-

Definition at line 145 of file blast_stat.h.

Referenced by Blast_TracebackFromHSPList(), BlastScoreBlkNucleotideMatrixRead(), s_BlastScoreBlk_Copy(), and SBlastScoreMatrixNew().

◆ ncols

size_t SBlastScoreMatrix::ncols

◆ nrows

size_t SBlastScoreMatrix::nrows

The documentation for this struct was generated from the following file:
Modified on Wed Feb 28 07:15:15 2024 by modify_doxy.py rev. 669887