CBl2Seq Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CBl2Seq

#include <bl2seq.hpp>

Inheritance diagram for CBl2Seq:

[legend]Collaboration diagram for CBl2Seq:

[legend]List of all members.

Detailed Description

Runs the BLAST algorithm between 2 sequences.

Definition at line 54 of file bl2seq.hpp.

Public Member Functions

CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)

Constructor to compare 2 sequences with default options.

CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p)

Constructor to compare query against all subject sequences with default options.

CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p)

Constructor to allow query concatenation with default options.

CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)

Constructor to compare 2 sequences with specified options.

CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)

Constructor to compare query against all subject sequences with specified options.

CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)

Constructor to allow query concatenation with specified options.

virtual ~CBl2Seq ()

Destructor.

void SetQuery (const SSeqLoc &query)

Set the query.

const SSeqLoc & GetQuery () const

Retrieve the query sequence.

void SetQueries (const TSeqLocVector &queries)

Set a vector of query sequences for a concatenated search.

const TSeqLocVector & GetQueries () const

Retrieve a vector of query sequences.

void SetSubject (const SSeqLoc &subject)

Set the subject sequence.

const SSeqLoc & GetSubject () const

Retrieve the subject sequence.

void SetSubjects (const TSeqLocVector &subjects)

Set a vector of subject sequences.

const TSeqLocVector & GetSubjects () const

Retrieve a vector of subject sequences.

CBlastOptionsHandle & SetOptionsHandle ()

Set the options handle.

const CBlastOptionsHandle & GetOptionsHandle () const

Retrieve the options handle.

virtual TSeqAlignVector Run ()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, .

CRef< CSearchResultSet > RunEx ()

Performs the same functionality as Run(), but it returns a different data type.

virtual NCBI_DEPRECATED void RunWithoutSeqalignGeneration ()

Runs the search but does not produce seqalign output (useful if the raw search results are needed, rather than a set of complete Seq-aligns).

NCBI_DEPRECATED BlastHSPResults * GetResults () const

Retrieves the list of HSP results from the engine (to be used after RunWithoutSeqalignGeneration() method).

TSeqLocInfoVector GetFilteredQueryRegions () const

Retrieves regions filtered on the query/queries.

void GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const

Retrieves regions filtered on the subject sequence(s).

BlastDiagnostics * GetDiagnostics () const

Retrieves the diagnostics information returned from the engine.

void GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const

Get the ancillary results for a BLAST search (to be used with the Run() method).

void GetMessages (TSearchMessages &messages) const

Returns error messages/warnings.

TInterruptFnPtr SetInterruptCallback (TInterruptFnPtr fnptr, void *user_data=NULL)

Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.

Protected Member Functions

virtual void SetupSearch ()

Process the queries, do setup, and build the lookup table.

virtual void RunFullSearch ()

Creates a BlastHSPStream and calls the engine.

virtual TSeqAlignVector x_Results2SeqAlign ()

Return a seqalign list for each query/subject pair, even if it is empty.

void x_BuildAncillaryData (const TSeqAlignVector &alignments)

Populate the internal m_AncillaryData member.

Static Protected Member Functions

static void x_SimplifyTSeqLocVector (const TSeqLocVector &slv, vector< CConstRef< objects::CSeq_id > > &query_ids)

Convert the TSeqLocVector to a vector of Seq-ids.

Private Member Functions

void x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)

Common initialization code for all c-tors.

CBl2Seq (const CBl2Seq &rhs)

Prohibit copy constructor.

CBl2Seq & operator= (const CBl2Seq &rhs)

Prohibit assignment operator.

void x_ResetQueryDs ()

Resets query data structures.

void x_ResetSubjectDs ()

Resets subject data structures.

Private Attributes

TSeqLocVector m_tQueries

query sequence(s)

TSeqLocVector m_tSubjects

sequence(s) to BLAST against

CRef< CBlastOptionsHandle > m_OptsHandle

Blast options.

bool mi_bQuerySetUpDone

internal: query processing already done?

CBLAST_SequenceBlk mi_clsQueries

internal: one for all queries

CBlastQueryInfo mi_clsQueryInfo

internal: one for all queries

BlastSeqSrc * mi_pSeqSrc

internal: Subject sequences source

BlastScoreBlk * mi_pScoreBlock

internal: score block

CLookupTableWrap mi_pLookupTable

internal: one for all queries

BlastSeqLoc * mi_pLookupSegments

internal: regions of queries to scan during lookup table creation

TSearchMessages m_Messages

Stores any warnings emitted during query setup.

BlastHSPResults * mi_pResults

Results for all queries and subjects together.

BlastDiagnostics * mi_pDiagnostics

Return search statistics data.

BlastMaskLoc * m_ipFilteredRegions

Regions filtered out from the query sequences.

TInterruptFnPtr m_fnpInterrupt

User-provided interrupt callback.

CSBlastProgress m_ProgressMonitor

Structure to aid in progress monitoring/interruption.

CSearchResultSet::TAncillaryVector m_AncillaryData

Ancillary BLAST data.

vector< TSeqLocInfoVector > m_SubjectMasks

Subject masks for those which intersect hits.

Friends

class ::CBlastFilterTest

Constructor & Destructor Documentation

CBl2Seq::CBl2Seq ( const CBl2Seq & rhs ) [private]

Prohibit copy constructor.

Member Function Documentation

CBl2Seq& CBl2Seq::operator= ( const CBl2Seq & rhs ) [private]

Prohibit assignment operator.

Friends And Related Function Documentation

friend class ::CBlastFilterTest [friend]

Definition at line 245 of file bl2seq.hpp.

Member Data Documentation

CSearchResultSet::TAncillaryVector CBl2Seq::m_AncillaryData [private]

Ancillary BLAST data.

Definition at line 236 of file bl2seq.hpp.
Referenced by GetAncillaryResults(), RunEx(), x_BuildAncillaryData(), and x_ResetSubjectDs().

TInterruptFnPtr CBl2Seq::m_fnpInterrupt [private]

User-provided interrupt callback.

Definition at line 232 of file bl2seq.hpp.
Referenced by RunFullSearch(), SetInterruptCallback(), and x_Init().

BlastMaskLoc* CBl2Seq::m_ipFilteredRegions [private]

Regions filtered out from the query sequences.

Definition at line 229 of file bl2seq.hpp.
Referenced by GetFilteredQueryRegions(), SetupSearch(), x_Init(), and x_ResetQueryDs().

TSearchMessages CBl2Seq::m_Messages [private]

Stores any warnings emitted during query setup.

Definition at line 221 of file bl2seq.hpp.
Referenced by GetMessages(), RunEx(), SetupSearch(), and x_ResetQueryDs().

CRef<CBlastOptionsHandle> CBl2Seq::m_OptsHandle [private]

Blast options.

Definition at line 200 of file bl2seq.hpp.
Referenced by CBl2Seq(), GetOptionsHandle(), Run(), RunEx(), RunWithoutSeqalignGeneration(), SetOptionsHandle(), SetupSearch(), x_BuildAncillaryData(), and x_Results2SeqAlign().

CSBlastProgress CBl2Seq::m_ProgressMonitor [private]

Structure to aid in progress monitoring/interruption.

Definition at line 234 of file bl2seq.hpp.
Referenced by RunFullSearch(), SetInterruptCallback(), and x_Init().

vector<TSeqLocInfoVector> CBl2Seq::m_SubjectMasks [private]

Subject masks for those which intersect hits.

Definition at line 238 of file bl2seq.hpp.
Referenced by GetFilteredSubjectRegions(), RunEx(), x_ResetSubjectDs(), and x_Results2SeqAlign().

TSeqLocVector CBl2Seq::m_tQueries [private]

query sequence(s)

Definition at line 198 of file bl2seq.hpp.
Referenced by GetFilteredQueryRegions(), GetQueries(), GetQuery(), RunEx(), SetQueries(), SetQuery(), SetupSearch(), x_BuildAncillaryData(), x_Init(), and x_Results2SeqAlign().

TSeqLocVector CBl2Seq::m_tSubjects [private]

sequence(s) to BLAST against

Definition at line 199 of file bl2seq.hpp.
Referenced by GetSubject(), GetSubjects(), SetSubject(), SetSubjects(), SetupSearch(), x_Init(), and x_Results2SeqAlign().

bool CBl2Seq::mi_bQuerySetUpDone [private]

internal: query processing already done?

Definition at line 211 of file bl2seq.hpp.
Referenced by SetOptionsHandle(), SetupSearch(), and x_ResetQueryDs().

CBLAST_SequenceBlk CBl2Seq::mi_clsQueries [private]

internal: one for all queries

Definition at line 212 of file bl2seq.hpp.
Referenced by RunFullSearch(), SetupSearch(), and x_ResetQueryDs().

CBlastQueryInfo CBl2Seq::mi_clsQueryInfo [private]

internal: one for all queries

Definition at line 213 of file bl2seq.hpp.
Referenced by RunEx(), RunFullSearch(), SetupSearch(), x_BuildAncillaryData(), and x_ResetQueryDs().

BlastDiagnostics* CBl2Seq::mi_pDiagnostics [private]

Return search statistics data.

Definition at line 226 of file bl2seq.hpp.
Referenced by GetDiagnostics(), RunFullSearch(), x_Init(), and x_ResetSubjectDs().

BlastSeqLoc* CBl2Seq::mi_pLookupSegments [private]

internal: regions of queries to scan during lookup table creation

Definition at line 218 of file bl2seq.hpp.
Referenced by SetupSearch(), x_Init(), and x_ResetQueryDs().

CLookupTableWrap CBl2Seq::mi_pLookupTable [private]

internal: one for all queries

Definition at line 217 of file bl2seq.hpp.
Referenced by RunFullSearch(), SetupSearch(), x_Init(), and x_ResetQueryDs().

BlastHSPResults* CBl2Seq::mi_pResults [private]

Results for all queries and subjects together.

Definition at line 224 of file bl2seq.hpp.
Referenced by GetResults(), RunFullSearch(), x_Init(), x_ResetSubjectDs(), and x_Results2SeqAlign().

BlastScoreBlk* CBl2Seq::mi_pScoreBlock [private]

internal: score block

Definition at line 216 of file bl2seq.hpp.
Referenced by RunEx(), RunFullSearch(), SetupSearch(), x_BuildAncillaryData(), x_Init(), and x_ResetQueryDs().

BlastSeqSrc* CBl2Seq::mi_pSeqSrc [private]

internal: Subject sequences source

Definition at line 215 of file bl2seq.hpp.
Referenced by RunFullSearch(), SetupSearch(), x_Init(), and x_ResetSubjectDs().

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

include/algo/blast/api/bl2seq.hpp
src/algo/blast/api/bl2seq.cpp

Generated on Mon Dec 7 10:17:20 2009 for NCBI C++ ToolKit by

1.4.6

Modified on Mon Dec 07 16:22:39 2009 by modify_doxy.py rev. 173732


Public Member Functions
	CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
	Constructor to compare 2 sequences with default options.
	CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p)
	Constructor to compare query against all subject sequences with default options.
	CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p)
	Constructor to allow query concatenation with default options.
	CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)
	Constructor to compare 2 sequences with specified options.
	CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)
	Constructor to compare query against all subject sequences with specified options.
	CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)
	Constructor to allow query concatenation with specified options.
virtual	~CBl2Seq ()
	Destructor.
void	SetQuery (const SSeqLoc &query)
	Set the query.
const SSeqLoc &	GetQuery () const
	Retrieve the query sequence.
void	SetQueries (const TSeqLocVector &queries)
	Set a vector of query sequences for a concatenated search.
const TSeqLocVector &	GetQueries () const
	Retrieve a vector of query sequences.
void	SetSubject (const SSeqLoc &subject)
	Set the subject sequence.
const SSeqLoc &	GetSubject () const
	Retrieve the subject sequence.
void	SetSubjects (const TSeqLocVector &subjects)
	Set a vector of subject sequences.
const TSeqLocVector &	GetSubjects () const
	Retrieve a vector of subject sequences.
CBlastOptionsHandle &	SetOptionsHandle ()
	Set the options handle.
const CBlastOptionsHandle &	GetOptionsHandle () const
	Retrieve the options handle.
virtual TSeqAlignVector	Run ()
	Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, .
CRef< CSearchResultSet >	RunEx ()
	Performs the same functionality as Run(), but it returns a different data type.
virtual NCBI_DEPRECATED void	RunWithoutSeqalignGeneration ()
	Runs the search but does not produce seqalign output (useful if the raw search results are needed, rather than a set of complete Seq-aligns).
NCBI_DEPRECATED BlastHSPResults *	GetResults () const
	Retrieves the list of HSP results from the engine (to be used after RunWithoutSeqalignGeneration() method).
TSeqLocInfoVector	GetFilteredQueryRegions () const
	Retrieves regions filtered on the query/queries.
void	GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const
	Retrieves regions filtered on the subject sequence(s).
BlastDiagnostics *	GetDiagnostics () const
	Retrieves the diagnostics information returned from the engine.
void	GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
	Get the ancillary results for a BLAST search (to be used with the Run() method).
void	GetMessages (TSearchMessages &messages) const
	Returns error messages/warnings.
TInterruptFnPtr	SetInterruptCallback (TInterruptFnPtr fnptr, void *user_data=NULL)
	Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.
Protected Member Functions
virtual void	SetupSearch ()
	Process the queries, do setup, and build the lookup table.
virtual void	RunFullSearch ()
	Creates a BlastHSPStream and calls the engine.
virtual TSeqAlignVector	x_Results2SeqAlign ()
	Return a seqalign list for each query/subject pair, even if it is empty.
void	x_BuildAncillaryData (const TSeqAlignVector &alignments)
	Populate the internal m_AncillaryData member.
Static Protected Member Functions
static void	x_SimplifyTSeqLocVector (const TSeqLocVector &slv, vector< CConstRef< objects::CSeq_id > > &query_ids)
	Convert the TSeqLocVector to a vector of Seq-ids.
Private Member Functions
void	x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
	Common initialization code for all c-tors.
	CBl2Seq (const CBl2Seq &rhs)
	Prohibit copy constructor.
CBl2Seq &	operator= (const CBl2Seq &rhs)
	Prohibit assignment operator.
void	x_ResetQueryDs ()
	Resets query data structures.
void	x_ResetSubjectDs ()
	Resets subject data structures.
Private Attributes
TSeqLocVector	m_tQueries
	query sequence(s)
TSeqLocVector	m_tSubjects
	sequence(s) to BLAST against
CRef< CBlastOptionsHandle >	m_OptsHandle
	Blast options.
bool	mi_bQuerySetUpDone
	internal: query processing already done?
CBLAST_SequenceBlk	mi_clsQueries
	internal: one for all queries
CBlastQueryInfo	mi_clsQueryInfo
	internal: one for all queries
BlastSeqSrc *	mi_pSeqSrc
	internal: Subject sequences source
BlastScoreBlk *	mi_pScoreBlock
	internal: score block
CLookupTableWrap	mi_pLookupTable
	internal: one for all queries
BlastSeqLoc *	mi_pLookupSegments
	internal: regions of queries to scan during lookup table creation
TSearchMessages	m_Messages
	Stores any warnings emitted during query setup.
BlastHSPResults *	mi_pResults
	Results for all queries and subjects together.
BlastDiagnostics *	mi_pDiagnostics
	Return search statistics data.
BlastMaskLoc *	m_ipFilteredRegions
	Regions filtered out from the query sequences.
TInterruptFnPtr	m_fnpInterrupt
	User-provided interrupt callback.
CSBlastProgress	m_ProgressMonitor
	Structure to aid in progress monitoring/interruption.
CSearchResultSet::TAncillaryVector	m_AncillaryData
	Ancillary BLAST data.
vector< TSeqLocInfoVector >	m_SubjectMasks
	Subject masks for those which intersect hits.
Friends
class	::CBlastFilterTest

CBl2Seq Class Reference [BLAST (Basic Local Alignment Search Tool)]

Detailed Description

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

CBl2Seq Class Reference
[BLAST (Basic Local Alignment Search Tool)]