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

Search Toolkit Book for CSearchResults

#include <blast_results.hpp>

Inheritance diagram for CSearchResults:

[legend]Collaboration diagram for CSearchResults:

[legend]List of all members.

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Detailed Description

Search Results for One Query.

This class encapsulates all the search results and related data corresponding to one of the input queries.

Definition at line 150 of file blast_results.hpp.

Public Member Functions
	CSearchResults (CConstRef< objects::CSeq_id > query, CRef< objects::CSeq_align_set > align, const TQueryMessages &errs, CRef< CBlastAncillaryData > ancillary_data, const TMaskedQueryRegions *query_masks=NULL, const string &rid=kEmptyStr, const SPHIQueryInfo *phi_query_info=NULL)
	Constructor.
	~CSearchResults ()
	Our destructor.
void	SetRID (const string &rid)
	Sets the RID for these results.
string	GetRID () const
	Returns the RID for these results (if applicable), otherwise returns an empty string.
CConstRef< objects::CSeq_align_set >	GetSeqAlign () const
	Accessor for the Seq-align results.
bool	HasAlignments () const
	Return true if there are any alignments for this query.
CConstRef< objects::CSeq_id >	GetSeqId () const
	Accessor for the query's sequence identifier.
CRef< CBlastAncillaryData >	GetAncillaryData () const
	Accessor for the query's search ancillary.
TQueryMessages	GetErrors (int min_severity=eBlastSevError) const
	Accessor for the error/warning messsages for this query.
bool	HasErrors () const
	Returns true if there are errors among the results for this object.
bool	HasWarnings () const
	Returns true if there are warnings among the results for this object.
string	GetErrorStrings () const
	Retrieve a string with the query identifier followed by the errors produced, returns a empty string if HasErrors() returns false.
string	GetWarningStrings () const
	Retrieve a string with the query identifier followed by the warnings produced, returns a empty string if HasWarnings() returns false.
void	GetMaskedQueryRegions (TMaskedQueryRegions &flt_query_regions) const
	Retrieve the query regions which were masked by BLAST.
void	SetMaskedQueryRegions (const TMaskedQueryRegions &flt_query_regions)
	Mutator for the masked query regions, intended to be used by internal BLAST APIs to populate this object.
void	GetSubjectMasks (TSeqLocInfoVector &subj_masks) const
	Retrieve the masked locations for the subject sequences in the contained alignment.
void	SetSubjectMasks (const TSeqLocInfoVector &subj_masks)
	Set the masked locations for the subject sequences in the contained alignment.
const SPHIQueryInfo *	GetPhiQueryInfo () const
	Retrieves PHI-BLAST information about pattern on query.
Private Member Functions
	CSearchResults (const CSearchResults &rhs)
	Prohibit copy constructor.
CSearchResults &	operator= (const CSearchResults &rhs)
	Prohibit assignment operator.
Private Attributes
CConstRef< objects::CSeq_id >	m_QueryId
	this query's id
CRef< objects::CSeq_align_set >	m_Alignment
	alignments for this query
TQueryMessages	m_Errors
	error/warning messages for this query
TMaskedQueryRegions	m_Masks
	this query's masked regions
TSeqLocInfoVector	m_SubjectMasks
	the matching subjects masks
CRef< CBlastAncillaryData >	m_AncillaryData
	non-alignment ancillary data for this query
string	m_RID
	The RID, if applicable (otherwise it's empty).
SPHIQueryInfo *	m_PhiQueryInfo
	PHI-BLAST information.

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Constructor & Destructor Documentation

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

Prohibit copy constructor.

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Member Function Documentation

CRef<CBlastAncillaryData> CSearchResults::GetAncillaryData (   )  const [inline]

Accessor for the query's search ancillary. Definition at line 192 of file blast_results.hpp. References m_AncillaryData.

const SPHIQueryInfo* CSearchResults::GetPhiQueryInfo (   )  const [inline]

Retrieves PHI-BLAST information about pattern on query. Definition at line 233 of file blast_results.hpp. References m_PhiQueryInfo.

string CSearchResults::GetRID (   )  const [inline]

Returns the RID for these results (if applicable), otherwise returns an empty string. Definition at line 177 of file blast_results.hpp. References m_RID.

CConstRef<objects::CSeq_align_set> CSearchResults::GetSeqAlign (   )  const [inline]

Accessor for the Seq-align results. Definition at line 180 of file blast_results.hpp. References m_Alignment.

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

Prohibit assignment operator.

void CSearchResults::SetRID (  const string &  rid  )  [inline]

Sets the RID for these results. Parameters: rid  RID to set [in] Definition at line 173 of file blast_results.hpp. References m_RID.

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Member Data Documentation

CRef<objects::CSeq_align_set> CSearchResults::m_Alignment [private]

alignments for this query Definition at line 242 of file blast_results.hpp. Referenced by GetSeqAlign(), and HasAlignments().

CRef<CBlastAncillaryData> CSearchResults::m_AncillaryData [private]

non-alignment ancillary data for this query Definition at line 254 of file blast_results.hpp. Referenced by GetAncillaryData().

TQueryMessages CSearchResults::m_Errors [private]

error/warning messages for this query Definition at line 245 of file blast_results.hpp. Referenced by GetErrors(), GetErrorStrings(), GetWarningStrings(), HasErrors(), and HasWarnings().

TMaskedQueryRegions CSearchResults::m_Masks [private]

this query's masked regions Definition at line 248 of file blast_results.hpp.

SPHIQueryInfo* CSearchResults::m_PhiQueryInfo [private]

PHI-BLAST information. Definition at line 260 of file blast_results.hpp. Referenced by CSearchResults(), GetPhiQueryInfo(), and ~CSearchResults().

CConstRef<objects::CSeq_id> CSearchResults::m_QueryId [private]

this query's id Definition at line 239 of file blast_results.hpp. Referenced by GetSeqId().

string CSearchResults::m_RID [private]

The RID, if applicable (otherwise it's empty). Definition at line 257 of file blast_results.hpp. Referenced by GetRID(), and SetRID().

TSeqLocInfoVector CSearchResults::m_SubjectMasks [private]

the matching subjects masks Definition at line 251 of file blast_results.hpp. Referenced by GetSubjectMasks(), and SetSubjectMasks().

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

• include/algo/blast/api/blast_results.hpp
• src/algo/blast/api/blast_results.cpp

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