Definitions of auxiliary functions/classes for PSI-BLAST. More...
#include <ncbi_pch.hpp>#include "psiblast_aux_priv.hpp"#include <algo/blast/core/blast_stat.h>#include <algo/blast/core/blast_options.h>#include <algo/blast/core/blast_encoding.h>#include <algo/blast/api/pssm_engine.hpp>#include <algo/blast/api/psi_pssm_input.hpp>#include <algo/blast/api/blast_exception.hpp>#include <algo/blast/api/blast_options_handle.hpp>#include <algo/blast/api/objmgrfree_query_data.hpp>#include "blast_aux_priv.hpp"#include "../core/blast_psi_priv.h"#include <util/format_guess.hpp>#include <util/math/matrix.hpp>#include <objects/seqset/Seq_entry.hpp>#include <objects/seqloc/Seq_id.hpp>#include <objects/scoremat/Pssm.hpp>#include <objects/scoremat/PssmFinalData.hpp>#include <objects/scoremat/PssmParameters.hpp>#include <objects/scoremat/FormatRpsDbParameters.hpp>#include <objects/scoremat/PssmIntermediateData.hpp>#include <objects/scoremat/PssmWithParameters.hpp>#include <objects/seqalign/Seq_align.hpp>#include <objects/seqalign/Seq_align_set.hpp>#include <objects/general/Object_id.hpp>#include <objects/seqalign/Score.hpp>#include <objects/seqalign/Dense_seg.hpp>#include <sstream>
Include dependency graph for psiblast_aux_priv.cpp:
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Functions | |
| USING_SCOPE (objects) | |
| void | PsiBlastSetupScoreBlock (BlastScoreBlk *score_blk, CConstRef< objects::CPssmWithParameters > pssm, TSearchMessages &messages, CConstRef< CBlastOptions > options) |
| Setup CORE BLAST score block structure with data from the scoremat PSSM. More... | |
| template<class T > | |
| void | Convert2Matrix (const list< T > &source, CNcbiMatrix< T > &dest, bool by_row, SIZE_TYPE num_rows, SIZE_TYPE num_columns) |
| Convert a list of values into a CNcbiMatrix. More... | |
| void | PsiBlastAddAncillaryPssmData (objects::CPssmWithParameters &pssm, int gap_open, int gap_extend) |
| Even though the query sequence and the matrix gap costs are not a product of the PSSM engine, set them as they are required for the PSI-BLAST (query sequence) and RPS-BLAST/formatrpsdb (gap costs) More... | |
| static void | s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix (objects::CPssmWithParameters &pssm) |
| After creating the PSSM from frequency ratios, adjust the frequency ratios matrix to match the dimensions of the score matrix. More... | |
| void | PsiBlastComputePssmScores (CRef< objects::CPssmWithParameters > pssm, const CBlastOptions &opts) |
| Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores. More... | |
| static double | s_GetEvalue (const CScore &score) |
| Returns the evalue from this score object. More... | |
| static double | s_GetBitScore (const CScore &score) |
| Returns the bit_score from this score object. More... | |
| double | GetLowestEvalue (const objects::CDense_seg::TScores &scores, double *bit_score=NULL) |
| Returns the lowest score from the list of scores in CDense_seg::TScores. More... | |
Detailed Description
Definitions of auxiliary functions/classes for PSI-BLAST.
Definition in file psiblast_aux_priv.cpp.
