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NCBI C++ ToolKit: include/algo/align/mergetree/equiv_range.hpp Source File

(objects::CBioseq_Handle QueryHandle,

objects::CBioseq_Handle SubjtHandle,

void CalcMatches(objects::CBioseq_Handle QueryHandle, objects::CBioseq_Handle SubjtHandle, TEquivList &Equivs)

CEquivRange SliceOnSubjt(const CEquivRange &Original, const CRange< TSeqPos > &pSubjt)

bool MergeAbuttings(const TEquivList &Originals, TEquivList &Merges)

void ExtractRangesFromSeqAlign(const objects::CSeq_align &Alignment, TEquivList &Equivs)

CEquivRange Merge(const CEquivRange &First, const CEquivRange &Second)

CEquivRange SliceOnQuery(const CEquivRange &Original, const CRange< TSeqPos > &pQuery)

bool SplitIntersections(const TEquivList &Originals, TEquivList &Splits)

ERelative CalcRelative(const CEquivRange &Check) const

bool AbuttingWith(const CEquivRange &Other) const

ERelative CalcRelativeDuo(const CEquivRange &Check) const

static TSeqPos Distance(const CEquivRange &A, const CEquivRange &B)

objects::ENa_strand Strand

vector< TSeqPos > MisMatchSubjtPoints

bool IntersectingWith(const CEquivRange &Other) const

bool s_SortEquivBySubjt(const CEquivRange &A, const CEquivRange &B)

bool operator<(const CEquivRange &A, const CEquivRange &B)

string s_RelToStr(CEquivRange::ERelative rel)

vector< CEquivRange > TEquivList

bool operator==(const CEquivRange &A, const CEquivRange &B)

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

std::ofstream out("events_result.xml")

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

bool NotEmpty(void) const

bool AbuttingWith(const TThisType &r) const

bool IntersectingWith(const TThisType &r) const

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

ENa_strand

strand of nucleic acid

Magic spell ;-) needed for some weird compilers... very empiric.

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