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NCBI C++ ToolKit: src/algo/align/splign/splign_simple.cpp Source File

blast::

(genomic, scope),

m_TranscriptId(&sequence::

(transcript, &scope)),

m_GenomicId (&sequence::

(genomic, &scope))

((*ii)->IsSet()) {

(hitref->GetQueryStrand() ==

) {

hitref->FlipStrands();

hitrefs.push_back(hitref);

(hitrefs.size()) {

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

@ eMegablast

Nucl-Nucl (traditional megablast)

Runs the BLAST algorithm between 2 sequences.

CRef< objects::CSeq_align_set > AsSeqAlignSet(const CSplign::TResults *results=0, int flags=eAF_SplicedSegWithParts) const

Format alignment as a seq-align-set.

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

CRef< objects::CSeq_align_set > GetResultsAsAln(CSplignFormatter::EAsnFlags flags=CSplignFormatter::eAF_Disc) const

Format the resulting alignment as a seq-align-set.

CConstRef< CSplign > GetSplign(void) const

CConstRef< objects::CSeq_id > m_GenomicId

CRef< blast::CBl2Seq > & SetBlast(void)

CConstRef< blast::CBl2Seq > GetBlast(void) const

CConstRef< objects::CSeq_id > m_TranscriptId

CRef< blast::CBl2Seq > m_Blast

const CSplign::TResults & Run(void)

CSplignSimple(const objects::CSeq_loc &transcript, ETranscriptQuality tq, const objects::CSeq_loc &genomic, objects::CScope &scope)

CRef< CSplign > & SetSplign(void)

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

void Run(THitRefs *hitrefs)

CRef< objects::CScope > & SetScope(void)

void PreserveScope(bool preserve=true)

Controls whether to clean the scope object's cache on a new sequence.

const TResults & GetResult(void) const

vector< SAlignedCompartment > TResults

vector< THitRef > THitRefs

CRef< TAligner > & SetAligner(void)

Access the spliced aligner core object.

static CRef< CSplicedAligner > s_CreateDefaultAligner(void)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

list< CRef< CSeq_align > > Tdata

Structure to represent a single sequence to be fed to BLAST.

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