CBlastNucleotideOptionsHandle Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CBlastNucleotideOptionsHandle

#include <blast_nucl_options.hpp>

Inheritance diagram for CBlastNucleotideOptionsHandle:

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Collaboration diagram for CBlastNucleotideOptionsHandle:

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List of all members.

Detailed Description

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

Adapter class for nucleotide-nucleotide BLAST comparisons. Exposes an interface to allow manipulation the options that are relevant to this type of search.

NB: By default, traditional megablast defaults are used. If blastn defaults are desired, please call the appropriate member function:

void SetTraditionalBlastnDefaults(); void SetTraditionalMegablastDefaults();

Definition at line 58 of file blast_nucl_options.hpp.

Public Member Functions

 CBlastNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set.
virtual void SetDefaults ()
 Sets Defaults.
ELookupTableType GetLookupTableType () const
 Returns LookupTableType.
void SetLookupTableType (ELookupTableType type)
 Sets LookupTableType.
int GetWordSize () const
 Returns WordSize.
void SetWordSize (int ws)
 Sets WordSize.
objects::ENa_strand GetStrandOption () const
 Returns StrandOption.
void SetStrandOption (objects::ENa_strand strand)
 Sets StrandOption.
bool GetDustFiltering () const
 Is dust filtering enabled?
void SetDustFiltering (bool val)
 Enable dust filtering.
int GetDustFilteringLevel () const
 Get level parameter for dust.
void SetDustFilteringLevel (int level)
 Set level parameter for dust.
int GetDustFilteringWindow () const
 Get window parameter for dust.
void SetDustFilteringWindow (int window)
 Set window parameter for dust.
int GetDustFilteringLinker () const
 Get linker parameter for dust.
void SetDustFilteringLinker (int linker)
 Set linker parameter for dust.
bool GetRepeatFiltering () const
 Is repeat filtering enabled?
void SetRepeatFiltering (bool val)
 Enable repeat filtering.
const char * GetRepeatFilteringDB () const
 Get the repeat filtering database.
void SetRepeatFilteringDB (const char *db)
 Enable repeat filtering.
int GetWindowMaskerTaxId () const
 Get the window masker taxid (or 0 if not set).
void SetWindowMaskerTaxId (int taxid)
 Enable window masker and select a taxid (or 0 to disable).
const char * GetWindowMaskerDatabase () const
 Get the window masker database name (or NULL if not set).
void SetWindowMaskerDatabase (const char *db)
 Enable window masker and select a database (or NULL to disable).
double GetXDropoff () const
 Returns XDropoff.
void SetXDropoff (double x)
 Sets XDropoff.
EBlastPrelimGapExt GetGapExtnAlgorithm () const
 Returns GapExtnAlgorithm.
void SetGapExtnAlgorithm (EBlastPrelimGapExt algo)
 Sets GapExtnAlgorithm.
EBlastTbackExt GetGapTracebackAlgorithm () const
 Returns GapTracebackAlgorithm.
void SetGapTracebackAlgorithm (EBlastTbackExt algo)
 Sets GapTracebackAlgorithm.
int GetMatchReward () const
 Returns MatchReward.
void SetMatchReward (int r)
 Sets MatchReward.
int GetMismatchPenalty () const
 Returns MismatchPenalty.
void SetMismatchPenalty (int p)
 Sets MismatchPenalty.
const char * GetMatrixName () const
 Returns MatrixName.
void SetMatrixName (const char *matrix)
 Sets MatrixName.
int GetGapOpeningCost () const
 Returns GapOpeningCost.
void SetGapOpeningCost (int g)
 Sets GapOpeningCost.
int GetGapExtensionCost () const
 Returns GapExtensionCost.
void SetGapExtensionCost (int e)
 Sets GapExtensionCost.
void SetTraditionalBlastnDefaults ()
 Sets TraditionalBlastnDefaults.
void SetTraditionalMegablastDefaults ()
 Sets TraditionalMegablastDefaults.

Protected Member Functions

virtual void SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast.
virtual void SetLookupTableDefaults ()
 Overrides LookupTableDefaults for nucleotide options.
virtual void SetMBLookupTableDefaults ()
 Overrides MBLookupTableDefaults for nucleotide options.
virtual void SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for nucleotide options.
virtual void SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for nucleotide options.
virtual void SetMBInitialWordOptionsDefaults ()
 Overrides MBInitialWordOptionsDefaults for nucleotide options.
virtual void SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for nucleotide options.
virtual void SetMBGappedExtensionDefaults ()
 Overrides MBGappedExtensionDefaults for nucleotide options.
virtual void SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for nucleotide options.
virtual void SetMBScoringOptionsDefaults ()
 Overrides MBScoringOptionsDefaults for nucleotide options.
virtual void SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for nucleotide options.
virtual void SetMBHitSavingOptionsDefaults ()
 Overrides MBHitSavingOptionsDefaults for nucleotide options.
virtual void SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for nucleotide options.
virtual void SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for nucleotide options.

Private Member Functions

 CBlastNucleotideOptionsHandle (const CBlastNucleotideOptionsHandle &rhs)
 Disallow copy constructor.
CBlastNucleotideOptionsHandle & operator= (const CBlastNucleotideOptionsHandle &rhs)
 Disallow assignment operator.

Constructor & Destructor Documentation

CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (  const CBlastNucleotideOptionsHandle &  rhs  )  [private]
 

Disallow copy constructor.

Member Function Documentation

bool CBlastNucleotideOptionsHandle::GetDustFiltering (   )  const [inline]
 

Is dust filtering enabled?

Definition at line 100 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

int CBlastNucleotideOptionsHandle::GetDustFilteringLevel (   )  const [inline]
 

Get level parameter for dust.

Definition at line 106 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetDustFilteringLinker (   )  const [inline]
 

Get linker parameter for dust.

Definition at line 118 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetDustFilteringWindow (   )  const [inline]
 

Get window parameter for dust.

Definition at line 112 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetGapExtensionCost (   )  const [inline]
 

Returns GapExtensionCost.

Definition at line 204 of file blast_nucl_options.hpp.

EBlastPrelimGapExt CBlastNucleotideOptionsHandle::GetGapExtnAlgorithm (   )  const [inline]
 

Returns GapExtnAlgorithm.

Definition at line 165 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetGapOpeningCost (   )  const [inline]
 

Returns GapOpeningCost.

Definition at line 198 of file blast_nucl_options.hpp.

EBlastTbackExt CBlastNucleotideOptionsHandle::GetGapTracebackAlgorithm (   )  const [inline]
 

Returns GapTracebackAlgorithm.

Definition at line 172 of file blast_nucl_options.hpp.

ELookupTableType CBlastNucleotideOptionsHandle::GetLookupTableType (   )  const [inline]
 

Returns LookupTableType.

Definition at line 71 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetMatchReward (   )  const [inline]
 

Returns MatchReward.

Definition at line 180 of file blast_nucl_options.hpp.

const char* CBlastNucleotideOptionsHandle::GetMatrixName (   )  const [inline]
 

Returns MatrixName.

Definition at line 192 of file blast_nucl_options.hpp.

int CBlastNucleotideOptionsHandle::GetMismatchPenalty (   )  const [inline]
 

Returns MismatchPenalty.

Definition at line 186 of file blast_nucl_options.hpp.

bool CBlastNucleotideOptionsHandle::GetRepeatFiltering (   )  const [inline]
 

Is repeat filtering enabled?

Definition at line 124 of file blast_nucl_options.hpp.

Referenced by Blast_FindRepeatFilterLoc(), and BOOST_AUTO_TEST_CASE().

const char* CBlastNucleotideOptionsHandle::GetRepeatFilteringDB (   )  const [inline]
 

Get the repeat filtering database.

Definition at line 130 of file blast_nucl_options.hpp.

Referenced by Blast_FindRepeatFilterLoc().

objects::ENa_strand CBlastNucleotideOptionsHandle::GetStrandOption (   )  const [inline]
 

Returns StrandOption.

Definition at line 90 of file blast_nucl_options.hpp.

const char* CBlastNucleotideOptionsHandle::GetWindowMaskerDatabase (   )  const [inline]
 

Get the window masker database name (or NULL if not set).

Definition at line 143 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

int CBlastNucleotideOptionsHandle::GetWindowMaskerTaxId (   )  const [inline]
 

Get the window masker taxid (or 0 if not set).

Definition at line 136 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

int CBlastNucleotideOptionsHandle::GetWordSize (   )  const [inline]
 

Returns WordSize.

Definition at line 80 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

double CBlastNucleotideOptionsHandle::GetXDropoff (   )  const [inline]
 

Returns XDropoff.

Definition at line 158 of file blast_nucl_options.hpp.

CBlastNucleotideOptionsHandle& CBlastNucleotideOptionsHandle::operator= (  const CBlastNucleotideOptionsHandle &  rhs  )  [private]
 

Disallow assignment operator.

void CBlastNucleotideOptionsHandle::SetDustFiltering (  bool  val  )  [inline]
 

Enable dust filtering.

Parameters:
val enable dust filtering [in]

Definition at line 103 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_AUTO_UNIT_TEST(), DoSearchWordSize4(), s_CreateRepeatsSearchOptions(), and SetQueryOptionDefaults().

void CBlastNucleotideOptionsHandle::SetDustFilteringLevel (  int  level  )  [inline]
 

Set level parameter for dust.

Acceptable values: 2 < level < 64

Parameters:
level dust filtering parameter level [in]

Definition at line 109 of file blast_nucl_options.hpp.

void CBlastNucleotideOptionsHandle::SetDustFilteringLinker (  int  linker  )  [inline]
 

Set linker parameter for dust.

Acceptable values: 1 < linker < 32

Parameters:
linker dust filtering parameter linker [in]

Definition at line 121 of file blast_nucl_options.hpp.

void CBlastNucleotideOptionsHandle::SetDustFilteringWindow (  int  window  )  [inline]
 

Set window parameter for dust.

Acceptable values: 8 < windowsize < 64

Parameters:
window dust filtering parameter window [in]

Definition at line 115 of file blast_nucl_options.hpp.

void CBlastNucleotideOptionsHandle::SetGapExtensionCost (  int  e  )  [inline]
 

Sets GapExtensionCost.

Parameters:
e GapExtensionCost [in]

Definition at line 207 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), s_CreateRepeatsSearchOptions(), SetMBScoringOptionsDefaults(), and SetScoringOptionsDefaults().

void CBlastNucleotideOptionsHandle::SetGapExtnAlgorithm (  EBlastPrelimGapExt  algo  )  [inline]
 

Sets GapExtnAlgorithm.

Parameters:
algo GapExtnAlgorithm [in]

Definition at line 169 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), SetGappedExtensionDefaults(), CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and SetMBGappedExtensionDefaults().

void CBlastNucleotideOptionsHandle::SetGapOpeningCost (  int  g  )  [inline]
 

Sets GapOpeningCost.

Parameters:
g GapOpeningCost [in]

Definition at line 201 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), s_CreateRepeatsSearchOptions(), SetMBScoringOptionsDefaults(), and SetScoringOptionsDefaults().

void CBlastNucleotideOptionsHandle::SetGapTracebackAlgorithm (  EBlastTbackExt  algo  )  [inline]
 

Sets GapTracebackAlgorithm.

Parameters:
algo GapTracebackAlgorithm [in]

Definition at line 176 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), SetGappedExtensionDefaults(), CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and SetMBGappedExtensionDefaults().

void CBlastNucleotideOptionsHandle::SetLookupTableType (  ELookupTableType  type  )  [inline]
 

Sets LookupTableType.

Parameters:
type LookupTableType [in]

Definition at line 74 of file blast_nucl_options.hpp.

Referenced by SetLookupTableDefaults(), and SetMBLookupTableDefaults().

void CBlastNucleotideOptionsHandle::SetMatchReward (  int  r  )  [inline]
 

Sets MatchReward.

Parameters:
r MatchReward [in]

Definition at line 183 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), CBlastOptionsFactory::CreateTask(), DoSearchWordSize4(), s_CreateRepeatsSearchOptions(), SetMBScoringOptionsDefaults(), and SetScoringOptionsDefaults().

void CBlastNucleotideOptionsHandle::SetMatrixName (  const char *  matrix  )  [inline]
 

Sets MatrixName.

Parameters:
matrix MatrixName [in]

Definition at line 195 of file blast_nucl_options.hpp.

Referenced by SetMBScoringOptionsDefaults(), and SetScoringOptionsDefaults().

void CBlastNucleotideOptionsHandle::SetMismatchPenalty (  int  p  )  [inline]
 

Sets MismatchPenalty.

Parameters:
p MismatchPenalty [in]

Definition at line 189 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_UNIT_TEST(), CBlastOptionsFactory::CreateTask(), DoSearchWordSize4(), s_CreateRepeatsSearchOptions(), SetMBScoringOptionsDefaults(), and SetScoringOptionsDefaults().

virtual void CBlastNucleotideOptionsHandle::SetRemoteProgramAndService_Blast3 (   )  [inline, protected, virtual]
 

Set the program and service name for remote blast.

Implements CBlastOptionsHandle.

Reimplemented in CDiscNucleotideOptionsHandle.

Definition at line 216 of file blast_nucl_options.hpp.

void CBlastNucleotideOptionsHandle::SetRepeatFiltering (  bool  val  )  [inline]
 

Enable repeat filtering.

Parameters:
val enable repeat filtering [in]

Definition at line 127 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastNucleotideOptionsHandle::SetRepeatFilteringDB (  const char *  db  )  [inline]
 

Enable repeat filtering.

Parameters:
db repeat filtering database [in]

Definition at line 133 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastNucleotideOptionsHandle::SetStrandOption (  objects::ENa_strand  strand  )  [inline]
 

Sets StrandOption.

Parameters:
strand StrandOption [in]

Definition at line 95 of file blast_nucl_options.hpp.

Referenced by SetQueryOptionDefaults().

void CBlastNucleotideOptionsHandle::SetWindowMaskerDatabase (  const char *  db  )  [inline]
 

Enable window masker and select a database (or NULL to disable).

Parameters:
taxid Select Window Masker filtering database by filename [in]

Definition at line 150 of file blast_nucl_options.hpp.

void CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId (  int  taxid  )  [inline]
 

Enable window masker and select a taxid (or 0 to disable).

Parameters:
taxid Select Window Masker filtering database for this taxid [in]

Definition at line 140 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

void CBlastNucleotideOptionsHandle::SetWordSize (  int  ws  )  [inline]
 

Sets WordSize.

Parameters:
ws WordSize [in]

Reimplemented in CDiscNucleotideOptionsHandle.

Definition at line 83 of file blast_nucl_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_AUTO_UNIT_TEST(), CBlastOptionsFactory::CreateTask(), DoSearchWordSize4(), s_CreateRepeatsSearchOptions(), SetLookupTableDefaults(), and SetMBLookupTableDefaults().

void CBlastNucleotideOptionsHandle::SetXDropoff (  double  x  )  [inline]
 

Sets XDropoff.

Parameters:
x XDropoff [in]

Definition at line 161 of file blast_nucl_options.hpp.

Referenced by s_CreateRepeatsSearchOptions(), SetInitialWordOptionsDefaults(), and CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults().

The documentation for this class was generated from the following files:
Generated on Mon Sep 29 11:59:44 2008 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Sep 29 16:08:28 2008 by modify_doxy.py rev. 117643