CModelCompare Class Reference

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#include <annot.hpp>

List of all members.

Detailed Description

Definition at line 137 of file 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)
static bool HaveCommonExonOrIntron (const CGeneModel &a, const CGeneModel &b)
static bool CodingCompatible (const CGeneModel &a, const CGeneModel &b, const CResidueVec &seq, bool check_outside=true)

Static Private Member Functions

static bool CodingCompatibleTwoCDS (const CGeneModel &a, const CGeneModel &b)
static bool CodingCompatibleOneCDS (const CGeneModel &a, const CGeneModel &b, const CResidueVec &seq, bool check_outside)
static bool IsConfirmedStartOrStopInsideOtherModelHole (const CGeneModel &theModel, const CGeneModel &otherModel)
static TSignedSeqRange ExtendedMaxCdsLimits (const CGeneModel &a)
static TSignedSeqPos CommonReadingFramePoint (const CGeneModel &a, const CGeneModel &b)

Member Function Documentation

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

Definition at line 248 of file select_alignments_alt.cpp.

References abs, CGeneModel::Exons(), COpenRange< Position >::GetFrom(), COpenRange< Position >::GetTo(), COpenRange< Position >::IntersectingWith(), CGeneModel::Limits(), CGeneModel::ReadingFrame(), and CGeneModel::Strand().

Referenced by CModelFilters::FilterOutSimilarsWithLowerScore().

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

Definition at line 396 of file select_alignments_alt.cpp.

References CountCommonSplices(), CGeneModel::Exons(), COpenRange< Position >::IntersectingWith(), CGeneModel::Limits(), CGeneModel::TrustedmRNA(), and CGeneModel::TrustedProt().

Referenced by CAltSplice::BadOverlapTest().

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

Definition at line 85 of file select_alignments_alt.cpp.

References CGeneModel::Limits(), CGeneModel::OpenLeftEnd(), CGeneModel::OpenRightEnd(), Precede(), and CGeneModel::Strand().

bool CModelCompare::CodingCompatible (  const CGeneModel &  a,
const CGeneModel &  b,
const CResidueVec &  seq,
bool  check_outside = true
)  [static]
 

Definition at line 514 of file chainer.cpp.

References _ASSERT, CodingCompatibleTwoCDS(), COpenRange< Position >::Empty(), CGeneModel::isCompatible(), COpenRange< Position >::NotEmpty(), and CGeneModel::ReadingFrame().

Referenced by CChainMembers::FillGapsInAlignments(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::LeftRight(), and CChainer::CChainerImpl::RightLeft().

bool CModelCompare::CodingCompatibleOneCDS (  const CGeneModel &  a,
const CGeneModel &  b,
const CResidueVec &  seq,
bool  check_outside
)  [static, private]
 

Definition at line 443 of file chainer.cpp.

References _ASSERT, COpenRange< Position >::NotEmpty(), CGeneModel::ReadingFrame(), and swap().

bool CModelCompare::CodingCompatibleTwoCDS (  const CGeneModel &  a,
const CGeneModel &  b
)  [static, private]
 

Definition at line 401 of file chainer.cpp.

References _ASSERT, CommonReadingFramePoint(), CGeneModel::Exons(), ExtendedMaxCdsLimits(), CGeneModel::FrameShifts(), CGeneModel::GetCdsInfo(), COpenRange< Position >::GetFrom(), COpenRange< Position >::GetTo(), Include(), IsConfirmedStartOrStopInsideOtherModelHole(), CCDSInfo::MaxCdsLimits(), COpenRange< Position >::NotEmpty(), CGeneModel::ReadingFrame(), CGeneModel::Strand(), and swap().

Referenced by CodingCompatible().

TSignedSeqPos CModelCompare::CommonReadingFramePoint (  const CGeneModel &  a,
const CGeneModel &  b
)  [static, private]
 

Definition at line 347 of file chainer.cpp.

References CGeneModel::Exons(), CGeneModel::FrameShifts(), ITERATE, and CGeneModel::ReadingFrame().

Referenced by CodingCompatibleTwoCDS().

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

Definition at line 108 of file select_alignments_alt.cpp.

References CGeneModel::Exons(), CGeneModel::IntersectingWith(), and CGeneModel::Strand().

Referenced by BadOverlapTest().

TSignedSeqRange CModelCompare::ExtendedMaxCdsLimits (  const CGeneModel &  a  )  [static, private]
 

Definition at line 377 of file chainer.cpp.

References limits.

Referenced by CodingCompatibleTwoCDS().

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

Definition at line 636 of file select_alignments_alt.cpp.

References CGeneModel::Exons(), CGeneModel::IntersectingWith(), and CGeneModel::Strand().

Referenced by CModelFilters::FilterOutTandemOverlap().

bool CModelCompare::IsConfirmedStartOrStopInsideOtherModelHole (  const CGeneModel &  theModel,
const CGeneModel &  otherModel
)  [static, private]
 

Definition at line 384 of file chainer.cpp.

References CGeneModel::ConfirmedStart(), CGeneModel::Exons(), CGeneModel::GetCdsInfo(), CGeneModel::HasStop(), COpenRange< Position >::IntersectingWith(), CCDSInfo::Start(), and CCDSInfo::Stop().

Referenced by CodingCompatibleTwoCDS().

bool CModelCompare::RangeNestedInIntron (  TSignedSeqRange  r,
const CGeneModel &  algn
)  [static]
 

Definition at line 412 of file select_alignments_alt.cpp.

References CGeneModel::Exons(), and Include().

Referenced by CGeneSelector::CheckCompatibility().

The documentation for this class was generated from the following files:
Generated on Wed Dec 9 08:02:39 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:19:28 2009 by modify_doxy.py rev. 173732