1 #ifndef ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP
2 #define ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP
70 virtual void SetDefaults();
79 m_Opts->SetLookupTableType(
type);
88 m_Opts->SetWordSize(ws);
94 return m_Opts->GetStrandOption();
99 m_Opts->SetStrandOption(strand);
148 return m_Opts->GetWindowMaskerDatabase();
155 m_Opts->SetWindowMaskerDatabase(db);
213 void SetTraditionalBlastnDefaults();
215 void SetTraditionalMegablastDefaults();
217 void SetVecScreenDefaults();
223 m_Opts->SetRemoteProgramAndService_Blast3(
"blastn",
"megablast");
227 virtual void SetLookupTableDefaults();
229 virtual void SetMBLookupTableDefaults();
231 virtual void SetQueryOptionDefaults();
233 virtual void SetInitialWordOptionsDefaults();
235 virtual void SetMBInitialWordOptionsDefaults();
237 virtual void SetGappedExtensionDefaults();
239 virtual void SetMBGappedExtensionDefaults();
241 virtual void SetScoringOptionsDefaults();
243 virtual void SetMBScoringOptionsDefaults();
245 virtual void SetHitSavingOptionsDefaults();
247 virtual void SetMBHitSavingOptionsDefaults();
249 virtual void SetEffectiveLengthsOptionsDefaults();
251 virtual void SetSubjectSequenceOptionsDefaults();
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
EBlastPrelimGapExt
The algorithm to be used for preliminary gapped extensions.
EBlastTbackExt
The algorithm to be used for final gapped extensions with traceback.
ELookupTableType
Types of the lookup table.
Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.
Handle to the nucleotide-nucleotide options to the BLAST algorithm.
Handle to the options to the BLAST algorithm.
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
@ eLocal
To be used for running BLAST locally.
int GetDustFilteringLinker() const
Get linker parameter for dust.
void SetLookupTableType(ELookupTableType type)
Sets LookupTableType.
int GetGapExtensionCost() const
Returns GapExtensionCost.
EBlastPrelimGapExt GetGapExtnAlgorithm() const
Returns GapExtnAlgorithm.
void SetDustFilteringWindow(int window)
Set window parameter for dust.
EBlastTbackExt GetGapTracebackAlgorithm() const
Returns GapTracebackAlgorithm.
bool GetDustFiltering() const
Is dust filtering enabled?
int GetWordSize() const
Returns WordSize.
void SetMatchReward(int r)
Sets MatchReward.
int GetMatchReward() const
Returns MatchReward.
void SetGapExtnAlgorithm(EBlastPrelimGapExt algo)
Sets GapExtnAlgorithm.
void SetWindowMaskerTaxId(int taxid)
Enable window masker and select a taxid (or 0 to disable).
void SetDustFilteringLinker(int linker)
Set linker parameter for dust.
const char * GetMatrixName() const
Returns MatrixName.
double GetXDropoff() const
Returns XDropoff.
int GetDustFilteringLevel() const
Get level parameter for dust.
void SetGapTracebackAlgorithm(EBlastTbackExt algo)
Sets GapTracebackAlgorithm.
const char * GetWindowMaskerDatabase() const
Get the window masker database name (or NULL if not set).
CBlastNucleotideOptionsHandle(const CBlastNucleotideOptionsHandle &rhs)
Disallow copy constructor.
virtual void SetRemoteProgramAndService_Blast3()
Set the program and service name for remote blast.
void SetMismatchPenalty(int p)
Sets MismatchPenalty.
void SetMatrixName(const char *matrix)
Sets MatrixName.
void SetRepeatFilteringDB(const char *db)
Enable repeat filtering.
void SetXDropoff(double x)
Sets XDropoff.
void SetRepeatFiltering(bool val)
Enable repeat filtering.
bool GetRepeatFiltering() const
Is repeat filtering enabled?
int GetDustFilteringWindow() const
Get window parameter for dust.
void SetGapExtensionCost(int e)
Sets GapExtensionCost.
int GetGapOpeningCost() const
Returns GapOpeningCost.
objects::ENa_strand GetStrandOption() const
Returns StrandOption.
int GetWindowMaskerTaxId() const
Get the window masker taxid (or 0 if not set).
const char * GetRepeatFilteringDB() const
Get the repeat filtering database.
ELookupTableType GetLookupTableType() const
Returns LookupTableType.
void SetWordSize(int ws)
Sets WordSize.
CBlastNucleotideOptionsHandle & operator=(const CBlastNucleotideOptionsHandle &rhs)
Disallow assignment operator.
void SetDustFiltering(bool val)
Enable dust filtering.
int GetMismatchPenalty() const
Returns MismatchPenalty.
void SetWindowMaskerDatabase(const char *db)
Enable window masker and select a database (or NULL to disable).
void SetDustFilteringLevel(int level)
Set level parameter for dust.
void SetGapOpeningCost(int g)
Sets GapOpeningCost.
void SetStrandOption(objects::ENa_strand strand)
Sets StrandOption.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
ENa_strand
strand of nucleic acid
double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)
int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)