src/algo/blast/api/blast_options_cxx.cpp File Reference

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Detailed Description

Implements the CBlastOptions class, which encapsulates options structures from algo/blast/core.

Definition in file blast_options_cxx.cpp.

#include <ncbi_pch.hpp>
#include <algo/blast/api/blast_options.hpp>
#include "blast_setup.hpp"
#include "blast_options_local_priv.hpp"
#include "blast_memento_priv.hpp"
#include <algo/blast/core/blast_extend.h>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/blast/Blast4_cutoff.hpp>
#include <objects/blast/names.hpp>

Include dependency graph for blast_options_cxx.cpp:

Go to the source code of this file.

Classes
class	CBlastOptionsRemote
	Encapsulates all blast input parameters. More...
Enumerations
enum	EBlastOptIdx {   eBlastOpt_Program = 100, eBlastOpt_WordThreshold, eBlastOpt_LookupTableType, eBlastOpt_WordSize,   eBlastOpt_AlphabetSize, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_FilterString,   eBlastOpt_MaskAtHash, eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringWindow,   eBlastOpt_DustFilteringLinker, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringWindow, eBlastOpt_SegFilteringLocut,   eBlastOpt_SegFilteringHicut, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_StrandOption,   eBlastOpt_QueryGeneticCode, eBlastOpt_WindowSize, eBlastOpt_SeedContainerType, eBlastOpt_SeedExtensionMethod,   eBlastOpt_XDropoff, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_GapTrigger,   eBlastOpt_GapExtnAlgorithm, eBlastOpt_HitlistSize, eBlastOpt_MaxNumHspPerSequence, eBlastOpt_CullingLimit,   eBlastOpt_EvalueThreshold, eBlastOpt_CutoffScore, eBlastOpt_PercentIdentity, eBlastOpt_SumStatisticsMode,   eBlastOpt_LongestIntronLength, eBlastOpt_GappedMode, eBlastOpt_MatrixName, eBlastOpt_MatrixPath,   eBlastOpt_MatchReward, eBlastOpt_MismatchPenalty, eBlastOpt_GapOpeningCost, eBlastOpt_GapExtensionCost,   eBlastOpt_FrameShiftPenalty, eBlastOpt_OutOfFrameMode, eBlastOpt_DbLength, eBlastOpt_DbSeqNum,   eBlastOpt_EffectiveSearchSpace, eBlastOpt_DbGeneticCode, eBlastOpt_PHIPattern, eBlastOpt_InclusionThreshold,   eBlastOpt_PseudoCount, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_CompositionBasedStats, eBlastOpt_SmithWatermanMode,   eBlastOpt_UnifiedP, eBlastOpt_WindowMaskerDatabase, eBlastOpt_WindowMaskerTaxId, eBlastOpt_ForceMbIndex,   eBlastOpt_MbIndexName, eBlastOpt_BestHitScoreEdge, eBlastOpt_BestHitOverhang }
	Index of remote BLAST options. More...
Functions
	USING_SCOPE (objects)
Variables
static char const	rcsid []

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Variable Documentation

char const rcsid[] [static]

Initial value: "$Id: blast_options_cxx.cpp 170780 2009-09-16 18:25:06Z camacho $" Definition at line 2 of file blast_options_cxx.cpp.

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