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NCBI C++ ToolKit: CBlastInputSourceConfig Class Reference

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Class that centralizes the configuration data for sequences to be converted. More...

#include <algo/blast/blastinput/blast_input.hpp>

static const unsigned int kSeqLenThreshold2Guess = 25 This value and the seqlen_thresh2guess argument to this class' constructor are related as follows: if the default parameter value is used, then no sequence type guessing will occurs, instead the sequence type specified in CBlastInputSourceConfig::SDataLoader::m_IsLoadingProteins is assumed correct. More...

Class that centralizes the configuration data for sequences to be converted.

Definition at line 48 of file blast_input.hpp.

◆ CBlastInputSourceConfig()

Constructor.

Parameters: dlconfig Configuration object for the data loaders used in CBlastScopeSource [in] strand All SeqLoc types will have this strand assigned; If set to 'other', the strand will be set to 'unknown' for protein sequences and 'both' for nucleotide [in] lowercase If true, lowercase mask locations are generated for all input sequences [in] believe_defline If true, all sequences ID's are parsed; otherwise all sequences receive a local ID set to a monotonically increasing count value [in] retrieve_seq_data When gis/accessions are provided in the input, should the sequence data be fetched by this library? range Range restriction for all sequences (default means no restriction). To support the specification of a single coordinate (start or stop), use the SetRange() method, the missing coordinate will be set the default value (e.g.: 0 for starting coordinate, sequence length for ending coordinate) [in] seqlen_thresh2guess sequence length threshold for molecule type guessing (see kSeqLenThreshold2Guess) [in] local_id_counter counter used to create the CSeqidGenerator to create local identifiers for sequences read [in] skip_seq_check When set this will avoid the sequence validation step when using the CFastaReader. -RMH-

Definition at line 48 of file blast_input.cpp.

References eNa_strand_both, eNa_strand_other, and eNa_strand_unknown.

◆ ~CBlastInputSourceConfig() CBlastInputSourceConfig::~CBlastInputSourceConfig ( ) inline ◆ GetBelieveDeflines() bool CBlastInputSourceConfig::GetBelieveDeflines ( ) const inline ◆ GetConvertGapsToNs() bool CBlastInputSourceConfig::GetConvertGapsToNs ( void ) const inline

Retrieve gaps to Ns converstion option value.

Definition at line 203 of file blast_input.hpp.

◆ GetDataLoaderConfig() ◆ GetLocalIdCounterInitValue() int CBlastInputSourceConfig::GetLocalIdCounterInitValue ( ) const inline ◆ GetLocalIdPrefix() const string& CBlastInputSourceConfig::GetLocalIdPrefix ( ) const inline ◆ GetLowercaseMask() bool CBlastInputSourceConfig::GetLowercaseMask ( ) const inline ◆ GetRange() TSeqRange CBlastInputSourceConfig::GetRange ( ) const inline ◆ GetSeqLenThreshold2Guess() unsigned int CBlastInputSourceConfig::GetSeqLenThreshold2Guess ( ) const inline ◆ GetSkipSeqCheck() bool CBlastInputSourceConfig::GetSkipSeqCheck ( ) const inline ◆ GetStrand() ◆ IsProteinInput() bool CBlastInputSourceConfig::IsProteinInput ( ) const inline

Determine if this object is for configuring reading protein sequences.

Definition at line 171 of file blast_input.hpp.

◆ RetrieveSeqData() bool CBlastInputSourceConfig::RetrieveSeqData ( ) const inline ◆ SetBelieveDeflines() void CBlastInputSourceConfig::SetBelieveDeflines ( bool believe ) inline ◆ SetConvertGapsToNs() void CBlastInputSourceConfig::SetConvertGapsToNs ( bool val ) inline ◆ SetDataLoaderConfig() ◆ SetLocalIdCounterInitValue() void CBlastInputSourceConfig::SetLocalIdCounterInitValue ( int val ) inline ◆ SetLocalIdPrefix() void CBlastInputSourceConfig::SetLocalIdPrefix ( const string & prefix ) inline

Set the custom prefix string used for generating local ids.

Definition at line 187 of file blast_input.hpp.

◆ SetLowercaseMask() void CBlastInputSourceConfig::SetLowercaseMask ( bool mask ) inline ◆ SetQueryLocalIdMode() void CBlastInputSourceConfig::SetQueryLocalIdMode ( ) inline ◆ SetRange() [1/2] ◆ SetRange() [2/2] TSeqRange& CBlastInputSourceConfig::SetRange ( void ) inline

Set range for all sequences.

Returns: range to modify

Definition at line 159 of file blast_input.hpp.

◆ SetRetrieveSeqData() void CBlastInputSourceConfig::SetRetrieveSeqData ( bool value ) inline ◆ SetSeqLenThreshold2Guess() void CBlastInputSourceConfig::SetSeqLenThreshold2Guess ( unsigned int val ) inline ◆ SetSkipSeqCheck() void CBlastInputSourceConfig::SetSkipSeqCheck ( bool skip ) inline

Turn validation of sequence on/off.

Parameters: skip boolean to toggle validation of sequence -RMH-

Definition at line 152 of file blast_input.hpp.

◆ SetStrand() ◆ SetSubjectLocalIdMode() void CBlastInputSourceConfig::SetSubjectLocalIdMode ( ) inline ◆ kSeqLenThreshold2Guess const unsigned int CBlastInputSourceConfig::kSeqLenThreshold2Guess = 25 static

This value and the seqlen_thresh2guess argument to this class' constructor are related as follows: if the default parameter value is used, then no sequence type guessing will occurs, instead the sequence type specified in CBlastInputSourceConfig::SDataLoader::m_IsLoadingProteins is assumed correct.

If an alternate value is specified, then any sequences shorter than that length will be treated as described above, otherwise those sequences will have their sequence type guessed (and be subject to validation between what is guessed by CFastaReader and what is expected by CBlastInputSource).

By design, the default setting should be fine for command line BLAST search binaries, but on the BLAST web pages we use kSeqLenThreshold2Guess to validate sequences longer than that length, and to accept sequences shorter than that length.

See also: Implementation in CCustomizedFastaReader; TestSmallDubiousSequences unit test

Definition at line 71 of file blast_input.hpp.

◆ m_BelieveDeflines bool CBlastInputSourceConfig::m_BelieveDeflines private ◆ m_DLConfig ◆ m_GapsToNs bool CBlastInputSourceConfig::m_GapsToNs private ◆ m_LocalIdCounter int CBlastInputSourceConfig::m_LocalIdCounter private

Initialization parameter to CSeqidGenerator.

Definition at line 228 of file blast_input.hpp.

◆ m_LocalIdPrefix string CBlastInputSourceConfig::m_LocalIdPrefix private

Custom prefix string passed to CSeqidGenerator.

Definition at line 232 of file blast_input.hpp.

◆ m_LowerCaseMask bool CBlastInputSourceConfig::m_LowerCaseMask private ◆ m_Range ◆ m_RetrieveSeqData bool CBlastInputSourceConfig::m_RetrieveSeqData private ◆ m_SeqLenThreshold2Guess unsigned int CBlastInputSourceConfig::m_SeqLenThreshold2Guess private

The sequence length threshold to guess molecule type.

Definition at line 230 of file blast_input.hpp.

◆ m_SkipSeqCheck bool CBlastInputSourceConfig::m_SkipSeqCheck private ◆ m_Strand

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

include/algo/blast/blastinput/blast_input.hpp
src/algo/blast/blastinput/blast_input.cpp

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