1 #ifndef NGALIGN_BANDED_ALIGNER__HPP
2 #define NGALIGN_BANDED_ALIGNER__HPP
74 bool IsAlignmentContained(
const objects::CSeq_align& Align)
const;
75 int GapDistance(
const objects::CSeq_align& Align)
const;
77 double SubjToQueryRatio()
const;
104 string GetName()
const {
return "instanced_mm_aligner"; }
129 const objects::CSeq_id& SubjectId,
135 objects::CScope& Scope);
138 objects::CScope& Scope);
Declares the CBl2Seq (BLAST 2 Sequences) class.
Declares the CBlastNucleotideOptionsHandle class.
Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.
Definitions of special type used in BLAST.
objects::CSeq_interval Subject
CInstance(const objects::CSeq_align_set &AlignSet)
objects::CSeq_align_set Alignments
CInstance(const CRef< objects::CSeq_align > Align)
objects::CSeq_interval Query
TAlignResultsRef GenerateAlignments(objects::CScope &Scope, ISequenceSet *QuerySet, ISequenceSet *SubjectSet, TAlignResultsRef AccumResults)
void SetPathValues(int Match, int Mismatch, int GapOpen, int GapExtend)
void x_FilterInstances(vector< CRef< CInstance > > &Instances, double MaxRatio)
CRef< objects::CSeq_align_set > x_RunCleanup(const objects::CSeq_align_set &AlignSet, objects::CScope &Scope)
void x_RunAligner(objects::CScope &Scope, CQuerySet &QueryAligns, TAlignResultsRef Results)
void x_GetDistanceInstances(CQuerySet &QueryAligns, objects::CScope &Scope, vector< CRef< CInstance > > &Instances)
void x_GetCleanupInstances(CQuerySet &QueryAligns, objects::CScope &Scope, vector< CRef< CInstance > > &Instances)
CRef< objects::CDense_seg > x_RunMMGlobal(const objects::CSeq_id &QueryId, const objects::CSeq_id &SubjectId, objects::ENa_strand Strand, TSeqPos QueryStart, TSeqPos QueryStop, TSeqPos SubjectStart, TSeqPos SubjectStop, objects::CScope &Scope)
CInstancedAligner(int TimeOutSeconds, float MaxRatio, float MinPctCoverage, int Threshold)
bool x_MinCoverageCheck(const CQuerySet &QueryAligns)
Include a standard set of the NCBI C++ Toolkit most basic headers.
unsigned int TSeqPos
Type for sequence locations and lengths.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
ENa_strand
strand of nucleic acid
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.