CModelCompare Class Reference

Search Toolkit Book for CModelCompare

#include <algo/gnomon/annot.hpp>

Static Public Member Functions
static bool	CanBeConnectedIntoOne (const CGeneModel &a, const CGeneModel &b)
static size_t	CountCommonSplices (const CGeneModel &a, const CGeneModel &b)
static bool	AreSimilar (const CGeneModel &a, const CGeneModel &b, int tolerance)
static bool	BadOverlapTest (const CGeneModel &a, const CGeneModel &b)
static bool	RangeNestedInIntron (TSignedSeqRange r, const CGeneModel &algn, bool check_in_holes=true)
static bool	HaveCommonExonOrIntron (const CGeneModel &a, const CGeneModel &b)

Detailed Description

Definition at line 137 of file annot.hpp.

Member Function Documentation

AreSimilar()

bool CModelCompare::AreSimilar ( const CGeneModel &  a, const CGeneModel &  b, int  tolerance  )

static

Definition at line 76 of file select_alignments_alt.cpp.

References a, abs, b, bmax, CRange_Base::GetFrom(), CRange_Base::GetTo(), int, max(), and min().

Referenced by CChainer::CChainerImpl::FilterOutSimilarsWithLowerScore().

BadOverlapTest()

bool CModelCompare::BadOverlapTest ( const CGeneModel &  a, const CGeneModel &  b  )

static

Definition at line 131 of file select_alignments_alt.cpp.

References a, b, and CountCommonSplices().

CanBeConnectedIntoOne()

bool CModelCompare::CanBeConnectedIntoOne ( const CGeneModel &  a, const CGeneModel &  b  )

static

Definition at line 45 of file select_alignments_alt.cpp.

References a, b, and Precede().

CountCommonSplices()

size_t CModelCompare::CountCommonSplices ( const CGeneModel &  a, const CGeneModel &  b  )

static

Definition at line 60 of file select_alignments_alt.cpp.

References a, b, i, and ncbi::grid::netcache::search::fields::size.

Referenced by BadOverlapTest(), and CGene::IsAlternative().

HaveCommonExonOrIntron()

bool CModelCompare::HaveCommonExonOrIntron ( const CGeneModel &  a, const CGeneModel &  b  )

static

Definition at line 153 of file select_alignments_alt.cpp.

References a, b, i, and ncbi::grid::netcache::search::fields::size.

Referenced by CChainer::CChainerImpl::FilterOutTandemOverlap().

RangeNestedInIntron()

bool CModelCompare::RangeNestedInIntron ( TSignedSeqRange  r, const CGeneModel &  algn, bool  check_in_holes = true  )

static

Definition at line 141 of file select_alignments_alt.cpp.

References CGeneModel::Exons(), i, Include(), int, and r().

Referenced by CChain::HarborsNested(), CGene::HarborsRange(), CGnomonAnnotator::Predict(), and CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes().

---

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

• include/algo/gnomon/annot.hpp
• src/algo/gnomon/select_alignments_alt.cpp