Auxiliary classes/functions for BLAST input library. More...

#include <algo/blast/api/sseqloc.hpp>
#include <corelib/ncbiargs.hpp>
#include <objects/seqset/Bioseq_set.hpp>

Include dependency graph for blast_input_aux.hpp:

This graph shows which files directly or indirectly include this file:

Classes
class	CAutoOutputFileReset
	Auxiliary class to store the name of an output file, which is reset every time its GetStream method is invoked. More...

class	CArgAllowMaximumFileNameLength
	Class to constrain the length of the file name passed to a given CArgDescriptions key. More...

class	CArgAllowValuesGreaterThanOrEqual
	Class to constrain the values of an argument to those greater than or equal to the value specified in the constructor. More...

class	CArgAllowValuesLessThanOrEqual
	Class to constrain the values of an argument to those less than or equal to the value specified in the constructor. More...

class	CArgAllowValuesBetween
	Class to constrain the values of an argument to those in between the values specified in the constructor. More...

class	CArgAllowIntegerSet

class	CArgAllowStringSet

Macros
#define	DEFINE_CARGALLOW_SET_CLASS(ClassName, DataType, String2DataTypeFn)
	Macro to create a subclass of CArgAllow that allows the specification of sets of data. More...

Functions
TSeqRange	ParseSequenceRange (const string &range_str, const char *error_prefix=NULL)
	Parse and extract a sequence range from argument provided to this function. More...

TSeqRange	ParseSequenceRangeOpenEnd (const string &range_str, const char *error_prefix=NULL)
	Parse and extract a sequence range from argument provided to this function. More...

int	GetQueryBatchSize (EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)
	Retrieve the appropriate batch size for the specified task. More...

CRef< objects::CScope >	ReadSequencesToBlast (CNcbiIstream &in, bool read_proteins, const TSeqRange &range, bool parse_deflines, bool use_lcase_masking, CRef< CBlastQueryVector > &sequences, bool gaps_to_Ns=false)
	Read sequence input for BLAST. More...

string	CalculateFormattingParams (TSeqPos max_target_seqs, TSeqPos num_descriptions, TSeqPos num_alignments, TSeqPos *num_overview=NULL)
	Calculates the formatting parameters based on the maximum number of target sequences selected (a.k.a. More...

bool	HasRawSequenceData (const objects::CBioseq &bioseq)
	Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field. More...

void	CheckForEmptySequences (const TSeqLocVector &sequences, string &warnings)
	Inspect the sequences parameter for empty sequences. More...

void	CheckForEmptySequences (CRef< CBlastQueryVector > sequences, string &warnings)
	Inspect the sequences parameter for empty sequences. More...

void	CheckForEmptySequences (CRef< objects::CBioseq_set > sequences, string &warnings)
	Inspect the sequences parameter for empty sequences. More...

Detailed Description

Auxiliary classes/functions for BLAST input library.

Definition in file blast_input_aux.hpp.

Macro Definition Documentation

◆ DEFINE_CARGALLOW_SET_CLASS

#define DEFINE_CARGALLOW_SET_CLASS	(	ClassName,
		DataType,
		String2DataTypeFn
	)

Macro to create a subclass of CArgAllow that allows the specification of sets of data.

Parameters

ClassName	Name of the class to be created [in]
DataType	data type of the allowed arguments [in]
String2DataTypeFn	Conversion function from a string to DataType [in]

Definition at line 201 of file blast_input_aux.hpp.

Function Documentation

◆ CalculateFormattingParams()

string CalculateFormattingParams	(	TSeqPos	max_target_seqs,
		TSeqPos *	num_descriptions,
		TSeqPos *	num_alignments,
		TSeqPos *	num_overview = `NULL`
	)

Calculates the formatting parameters based on the maximum number of target sequences selected (a.k.a.

: hitlist size).

Parameters

max_target_seqs	the hitlist size [in]
num_descriptions	the number of one-line descriptions to show [out]
num_alignments	the number of alignments to show [out]
num_overview	the number of sequences to show in the overview image displayed in the BLAST report on the web [out]

Returns: string containing warnings (if any)

Definition at line 250 of file blast_input_aux.cpp.

References _ASSERT, NStr::IntToString(), kDfltArgMaxTargetSequences, and min().

◆ CheckForEmptySequences() [1/3]

void CheckForEmptySequences	(	const TSeqLocVector &	sequences,
		string &	warnings
	)

Inspect the sequences parameter for empty sequences.

Returns a non-empty string in the warnings parameter if there are empty sequence(s) in its first parameter.

Parameters

sequences	sequence set to inspect [in]
warnings	populated if empty sequence(s) are found among non-empty sequences [in\|out]

Exceptions

CInputException if there is only 1 empty sequence

Definition at line 368 of file blast_input_aux.cpp.

References GetLength(), i, ITERATE, NCBI_THROW, and query.

Referenced by BOOST_AUTO_TEST_CASE().

◆ CheckForEmptySequences() [2/3]

void CheckForEmptySequences	(	CRef< CBlastQueryVector >	sequences,
		string &	warnings
	)

Inspect the sequences parameter for empty sequences.

Returns a non-empty string in the warnings parameter if there are empty sequence(s) in its first parameter.

Parameters

sequences	sequence set to inspect [in]
warnings	populated if empty sequence(s) are found among non-empty sequences [in\|out]

Exceptions

CInputException if there is only 1 empty sequence

Definition at line 332 of file blast_input_aux.cpp.

References CBlastQueryVector::Empty(), CRef< C, Locker >::Empty(), i, ITERATE, NCBI_THROW, and query.

◆ CheckForEmptySequences() [3/3]

void CheckForEmptySequences	(	CRef< objects::CBioseq_set >	sequences,
		string &	warnings
	)

Inspect the sequences parameter for empty sequences.

Returns a non-empty string in the warnings parameter if there are empty sequence(s) in its first parameter.

Parameters

sequences	sequence set to inspect [in]
warnings	populated if empty sequence(s) are found among non-empty sequences [in\|out]

Exceptions

CInputException if there is only 1 empty sequence

◆ GetQueryBatchSize()

int GetQueryBatchSize	(	EProgram	program,
		bool	is_ungapped = `false`,
		bool	remote = `false`,
		bool	use_default = `true`,
		string	task = `""`,
		bool	mt_mode = `false`
	)

Retrieve the appropriate batch size for the specified task.

Parameters

program	BLAST task [in]
is_ungapped	true if ungapped BLAST search is requested [in]
remote	true if remote BLAST search is requested [in]
use_default	true if a defaut value should be returned [in]
task	task (e.g., blastx-fast). Auto-set if empty [in]
mt_mode	thread by queries (true) or by database (false) [in]

Definition at line 70 of file blast_input_aux.cpp.

References _TRACE, eBlastn, eBlastp, eBlastx, eDiscMegablast, eMapper, eMegablast, EProgramToTaskName(), eTblastn, eTblastx, and NStr::StringToInt().

◆ HasRawSequenceData()

bool HasRawSequenceData ( const objects::CBioseq & bioseq )

Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field.

Parameters

bioseq Bioseq to examine [in]

Definition at line 302 of file blast_input_aux.cpp.

References CDelta_seq_Base::e_Loc, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_virtual, CBlastBioseqMaker::IsEmptyBioseq(), and ITERATE.

Referenced by CBlastFastaInputSource::x_FastaToSeqLoc(), CBlastFormatterApp::x_QueryBioseqToSSeqLoc(), and CBlastFormatterVdbApp::x_QueryBioseqToSSeqLoc().

◆ ParseSequenceRange()

TSeqRange ParseSequenceRange	(	const string &	range_str,
		const char *	error_prefix = `NULL`
	)

Parse and extract a sequence range from argument provided to this function.

The format is N-M, where N and M are positive integers in 1-based offsets and N < M.

Parameters

range_str	string to extract the range from [in]
error_prefix	error message prefix which will be encoded in the exception thrown in case of error (if NULL a default message will be used) [in]

Returns: properly constructed range if parsing succeeded in 0-based offsets.

Exceptions

CStringException or CBlastException with error code eInvalidArgument if parsing fails or the range is invalid (i.e.: empty, negative, N>M, in 0-based offsets)

Definition at line 146 of file blast_input_aux.cpp.

References NCBI_THROW, CRange_Base::SetFrom(), CRange_Base::SetTo(), NStr::Split(), and NStr::StringToInt().

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), and CQueryOptionsArgs::ExtractAlgorithmOptions().

◆ ParseSequenceRangeOpenEnd()

TSeqRange ParseSequenceRangeOpenEnd	(	const string &	range_str,
		const char *	error_prefix = `NULL`
	)

Parse and extract a sequence range from argument provided to this function.

The format is N-M, where N and M are positive integers in 1-based offsets and N < M. Open end range N- and single range N-N formats are supported.

Parameters

range_str	string to extract the range from [in]
error_prefix	error message prefix which will be encoded in the exception thrown in case of error (if NULL a default message will be used) [in]

Returns: properly constructed range if parsing succeeded in 0-based offsets.

Exceptions

CStringException or CBlastException with error code eInvalidArgument if parsing fails or the range is invalid (i.e.: empty, negative, N>M, in 0-based offsets)

Definition at line 182 of file blast_input_aux.cpp.

References NCBI_THROW, CRange_Base::SetFrom(), CRange_Base::SetTo(), NStr::Split(), and NStr::StringToInt().

Referenced by CBlastDBCmdApp::x_InitSearchRequest(), and CBlastDBCmdApp::x_ModifyConfigForBatchEntry().

◆ ReadSequencesToBlast()

CRef<objects::CScope> ReadSequencesToBlast	(	CNcbiIstream &	in,
		bool	read_proteins,
		const TSeqRange &	range,
		bool	parse_deflines,
		bool	use_lcase_masking,
		CRef< CBlastQueryVector > &	sequences,
		bool	gaps_to_Ns = `false`
	)

Read sequence input for BLAST.

Parameters

in	input stream from which to read [in]
read_proteins	expect proteins or nucleotides as input [in]
range	range restriction to apply to sequences read [in]
parse_deflines	true if the subject deflines should be parsed [in]
use_lcase_masking	true if the subject lowercase sequence characters should be interpreted as masked regions [in]
sequences	output will be placed here [in\|out] @praram gaps_to_Ns convert all gaps in the sequences to Ns (only for nucleotide sequences) [in]

Returns: CScope object which contains all the sequences read

Definition at line 222 of file blast_input_aux.cpp.

References CObjectManager::GetInstance(), in(), input(), SDataLoaderConfig::OptimizeForWholeLargeSequenceRetrieval(), compile_time_bits::range(), CBlastInputSourceConfig::SetBelieveDeflines(), CBlastInputSourceConfig::SetConvertGapsToNs(), CBlastInputSourceConfig::SetLowercaseMask(), CBlastInputSourceConfig::SetRange(), and CBlastInputSourceConfig::SetSubjectLocalIdMode().

Referenced by CBlastDatabaseArgs::ExtractAlgorithmOptions(), and CIgBlastArgs::ExtractAlgorithmOptions().

Classes

Macros

Functions

Detailed Description

Macro Definition Documentation

◆ DEFINE_CARGALLOW_SET_CLASS

Function Documentation

◆ CalculateFormattingParams()

◆ CheckForEmptySequences() [1/3]

◆ CheckForEmptySequences() [2/3]

◆ CheckForEmptySequences() [3/3]

◆ GetQueryBatchSize()

◆ HasRawSequenceData()

◆ ParseSequenceRange()

◆ ParseSequenceRangeOpenEnd()

◆ ReadSequencesToBlast()