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CBlast4Field Class Reference

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Field properties for options in a Blast4 parameter list. More...

#include <objects/blast/names.hpp>

+ Collaboration diagram for CBlast4Field:

Public Member Functions

 CBlast4Field ()
 Default constructor (for STL) More...
 
 CBlast4Field (const std::string &nm, CBlast4_value::E_Choice ch)
 Construct field with name and type. More...
 
const string & GetName () const
 Get field name (key). More...
 
bool Match (const CBlast4_parameter &p) const
 Match field name and type to parameter. More...
 
CBlast4_value::E_Choice GetType () const
 Get field type. More...
 
bool GetBoolean (const CBlast4_parameter &p) const
 Verify parameter name and type, and get boolean value. More...
 
Int8 GetBig_integer (const CBlast4_parameter &p) const
 Verify parameter name and type, and get big integer value. More...
 
CConstRef< CBlast4_cutoff > GetCutoff (const CBlast4_parameter &p) const
 Verify parameter name and type, and get cutoff value. More...
 
int GetInteger (const CBlast4_parameter &p) const
 Verify parameter name and type, and get integer value. More...
 
list< int > GetIntegerList (const CBlast4_parameter &p) const
 Verify parameter name and type, and get integer list value. More...
 
CConstRef< CPssmWithParameters > GetMatrix (const CBlast4_parameter &p) const
 Verify parameter name and type, and get matrix (pssm) value. More...
 
CConstRef< CBlast4_mask > GetQueryMask (const CBlast4_parameter &p) const
 Verify parameter name and type, and get query mask value. More...
 
double GetReal (const CBlast4_parameter &p) const
 Verify parameter name and type, and get real value. More...
 
EBlast4_strand_type GetStrandType (const CBlast4_parameter &p) const
 Verify parameter name and type, and get strand_type value. More...
 
string GetString (const CBlast4_parameter &p) const
 Verify parameter name and type, and get string value. More...
 

Static Public Member Functions

static CBlast4Field & Get (EBlastOptIdx opt)
 
static const string & GetName (EBlastOptIdx opt)
 

Private Types

typedef map< EBlastOptIdx, CBlast4Field > TFieldMap
 Type for map of all blast4 field objects. More...
 

Private Attributes

string m_Name
 Field name string as used in Blast4_parameter objects. More...
 
CBlast4_value::E_Choice m_Type
 Field value type as used in Blast4_parameter objects. More...
 

Static Private Attributes

static CSafeStatic< TFieldMap > m_Fields
 Map of all blast4 field objects. More...
 

Detailed Description

Field properties for options in a Blast4 parameter list.

Definition at line 166 of file names.hpp.

Member Typedef Documentation

◆ TFieldMap

typedef map<EBlastOptIdx, CBlast4Field> CBlast4Field::TFieldMap
private

Type for map of all blast4 field objects.

Definition at line 226 of file names.hpp.

Constructor & Destructor Documentation

◆ CBlast4Field() [1/2]

CBlast4Field::CBlast4Field ( )
inline

Default constructor (for STL)

Definition at line 169 of file names.hpp.

Referenced by Get().

◆ CBlast4Field() [2/2]

CBlast4Field::CBlast4Field ( const std::string &  nm,
CBlast4_value::E_Choice  ch 
)
inline

Construct field with name and type.

Definition at line 172 of file names.hpp.

Member Function Documentation

◆ Get()

CBlast4Field & CBlast4Field::Get ( EBlastOptIdx  opt)
static

Definition at line 45 of file names.cpp.

References _ASSERT, CBlast4Field(), DEFINE_STATIC_MUTEX, CBlast4_value_Base::e_Big_integer, CBlast4_value_Base::e_Boolean, CBlast4_value_Base::e_Cutoff, CBlast4_value_Base::e_Integer, CBlast4_value_Base::e_Integer_list, CBlast4_value_Base::e_Matrix, CBlast4_value_Base::e_not_set, CBlast4_value_Base::e_Query_mask, CBlast4_value_Base::e_Real, CBlast4_value_Base::e_Strand_type, CBlast4_value_Base::e_String, eBlastOpt_BestHitOverhang, eBlastOpt_BestHitScoreEdge, eBlastOpt_ComplexityAdjMode, eBlastOpt_CompositionBasedStats, eBlastOpt_Culling, eBlastOpt_CullingLimit, eBlastOpt_CutoffScore, eBlastOpt_DbFilteringAlgorithmId, eBlastOpt_DbFilteringAlgorithmKey, eBlastOpt_DbGeneticCode, eBlastOpt_DbLength, eBlastOpt_DomainInclusionThreshold, eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringLinker, eBlastOpt_DustFilteringWindow, eBlastOpt_EffectiveSearchSpace, eBlastOpt_EntrezQuery, eBlastOpt_EvalueThreshold, eBlastOpt_FilterString, eBlastOpt_FinalDbSeq, eBlastOpt_FirstDbSeq, eBlastOpt_ForceMbIndex, eBlastOpt_GapExtensionCost, eBlastOpt_GapExtnAlgorithm, eBlastOpt_GapOpeningCost, eBlastOpt_GappedMode, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_GapTrigger, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_GiList, eBlastOpt_HitlistSize, eBlastOpt_HspRangeMax, eBlastOpt_IgnoreMsaMaster, eBlastOpt_InclusionThreshold, eBlastOpt_LCaseMask, eBlastOpt_LongestIntronLength, eBlastOpt_MaskAtHash, eBlastOpt_MaskLevel, eBlastOpt_MatchReward, eBlastOpt_MatrixName, eBlastOpt_MatrixTable, eBlastOpt_MaxHspsPerSubject, eBlastOpt_MbIndexName, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_MismatchPenalty, eBlastOpt_NegativeGiList, eBlastOpt_NegativeTaxidList, eBlastOpt_OutOfFrameMode, eBlastOpt_PercentIdentity, eBlastOpt_PHIPattern, eBlastOpt_PseudoCount, eBlastOpt_QueryCovHspPerc, eBlastOpt_QueryGeneticCode, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_RequiredEnd, eBlastOpt_RequiredStart, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringHicut, eBlastOpt_SegFilteringLocut, eBlastOpt_SegFilteringWindow, eBlastOpt_SmithWatermanMode, eBlastOpt_StrandOption, eBlastOpt_SubjectBestHit, eBlastOpt_SubjectMaskingType, eBlastOpt_SumStatisticsMode, eBlastOpt_TaxidList, eBlastOpt_UnifiedP, eBlastOpt_UseRealDbSize, eBlastOpt_Web_BlastSpecialPage, eBlastOpt_Web_DBGroup, eBlastOpt_Web_DBInput, eBlastOpt_Web_DBSubgroup, eBlastOpt_Web_DBSubgroupName, eBlastOpt_Web_EntrezQuery, eBlastOpt_Web_ExclModels, eBlastOpt_Web_ExclSeqUncult, eBlastOpt_Web_JobTitle, eBlastOpt_Web_NewWindow, eBlastOpt_Web_OrganismName, eBlastOpt_Web_RunPsiBlast, eBlastOpt_Web_ShortQueryAdjust, eBlastOpt_Web_StepNumber, eBlastOpt_WindowMaskerDatabase, eBlastOpt_WindowMaskerTaxId, eBlastOpt_WindowSize, eBlastOpt_WordSize, eBlastOpt_WordThreshold, ERR_POST, m_Fields, and Warning().

Referenced by CBlastOptionsBuilder::AdjustProgram(), BOOST_AUTO_TEST_CASE(), GetName(), CRemoteBlast::SetDbFilteringAlgorithmId(), CRemoteBlast::SetDbFilteringAlgorithmKey(), CRemoteBlast::SetEntrezQuery(), CBlastOptions::SetFilterString(), CRemoteBlast::SetGIList(), CRemoteBlast::SetNegativeGIList(), CBlastOptionsRemote::SetValue(), CBlastOptions::SetWindowMaskerDatabase(), CBlastOptions::SetWindowMaskerTaxId(), CRemoteBlast::x_InitQueries(), CExportStrategy::x_Process_Query(), CExportStrategy::x_Process_SearchDb(), CBlastOptionsBuilder::x_ProcessOneOption(), and CRemoteBlast::x_QueryMaskingLocationsToNetwork().

◆ GetBig_integer()

Int8 CBlast4Field::GetBig_integer ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get big integer value.

Definition at line 387 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetBig_integer(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetBoolean()

bool CBlast4Field::GetBoolean ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get boolean value.

Definition at line 381 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetBoolean(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetCutoff()

CConstRef< CBlast4_cutoff > CBlast4Field::GetCutoff ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get cutoff value.

Definition at line 394 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetCutoff(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetInteger()

int CBlast4Field::GetInteger ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get integer value.

Definition at line 400 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetInteger(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetIntegerList()

list< int > CBlast4Field::GetIntegerList ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get integer list value.

Definition at line 406 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetInteger_list(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetMatrix()

CConstRef< CPssmWithParameters > CBlast4Field::GetMatrix ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get matrix (pssm) value.

Definition at line 413 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetMatrix(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetName() [1/2]

const string & CBlast4Field::GetName ( void  ) const

Get field name (key).

Definition at line 357 of file names.cpp.

References m_Name.

Referenced by CBlastOptionsBuilder::AdjustProgram(), BOOST_AUTO_TEST_CASE(), CImportStrategy::FetchData(), CRemoteBlast::GetPsiNumberOfIterations(), CExportStrategy::x_AddPsiNumOfIterationsToFormatOptions(), CImportStrategy::x_GetProgramOptionIntegerList(), CExportStrategy::x_Process_Query(), and CExportStrategy::x_Process_SearchDb().

◆ GetName() [2/2]

const string & CBlast4Field::GetName ( EBlastOptIdx  opt)
static

Definition at line 352 of file names.cpp.

References Get(), and GetName().

Referenced by BOOST_AUTO_TEST_CASE(), GetName(), and CBlastOptionsRemote::x_SetOneParam().

◆ GetQueryMask()

CConstRef< CBlast4_mask > CBlast4Field::GetQueryMask ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get query mask value.

Definition at line 420 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetQuery_mask(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetReal()

double CBlast4Field::GetReal ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get real value.

Definition at line 426 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetReal(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetStrandType()

EBlast4_strand_type CBlast4Field::GetStrandType ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get strand_type value.

Definition at line 433 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetStrand_type(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetString()

string CBlast4Field::GetString ( const CBlast4_parameter &  p) const

Verify parameter name and type, and get string value.

Definition at line 375 of file names.cpp.

References _ASSERT, CBlast4_value_Base::GetString(), CBlast4_parameter_Base::GetValue(), and Match().

◆ GetType()

CBlast4_value::E_Choice CBlast4Field::GetType ( void  ) const

Get field type.

Definition at line 362 of file names.cpp.

References m_Type.

◆ Match()

bool CBlast4Field::Match ( const CBlast4_parameter &  p) const

Match field name and type to parameter.

Definition at line 367 of file names.cpp.

References CBlast4_parameter_Base::CanGetName(), CBlast4_parameter_Base::CanGetValue(), CBlast4_parameter_Base::GetName(), CBlast4_parameter_Base::GetValue(), m_Name, m_Type, and CBlast4_value_Base::Which().

Referenced by GetBig_integer(), GetBoolean(), GetCutoff(), GetInteger(), GetIntegerList(), GetMatrix(), GetQueryMask(), GetReal(), GetStrandType(), GetString(), SBlast4ParamFinder::operator()(), and CBlastOptionsBuilder::x_ProcessOneOption().

Member Data Documentation

◆ m_Fields

CSafeStatic< CBlast4Field::TFieldMap > CBlast4Field::m_Fields
staticprivate

Map of all blast4 field objects.

Definition at line 229 of file names.hpp.

Referenced by Get().

◆ m_Name

string CBlast4Field::m_Name
private

Field name string as used in Blast4_parameter objects.

Definition at line 220 of file names.hpp.

Referenced by GetName(), and Match().

◆ m_Type

CBlast4_value::E_Choice CBlast4Field::m_Type
private

Field value type as used in Blast4_parameter objects.

Definition at line 223 of file names.hpp.

Referenced by GetType(), and Match().

The documentation for this class was generated from the following files:
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