mems::GenericInterval< GappedBaseImpl > Class Template Reference

#include <Interval.h>

List of all members.

Public Member Functions
void	add (AbstractMatch *am)
virtual void	CalculateOffset ()
GenericInterval *	Clone () const
GenericInterval *	Copy () const
void	CropEnd (gnSeqI crop_amount)
void	CropLeft (gnSeqI amount, uint seqI)
void	CropRight (gnSeqI amount, uint seqI)
void	CropStart (gnSeqI crop_amount)
virtual void	Free ()
	GenericInterval (const GenericInterval &iv)
template<typename BidIt>	GenericInterval (BidIt it_begin, const BidIt &it_end)
	construct from a MatchList or a vector of pointers to AbstractMatches
	GenericInterval ()
virtual void	GetAlignedSequences (gnAlignedSequences &gnas, const std::vector< genome::gnSequence * > &seq_table) const
	Get a gnAlignedSequences object TODO: get rid of this.
void	GetAlignment (std::vector< bitset_t > &align_matrix) const
void	GetColumn (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column) const
const std::vector< AbstractMatch * > &	GetMatches () const
void	Invert ()
bool	IsGap (uint seq, gnSeqI col) const
void	Marble (gnSeqI size)
	marbles the gaps so that no sequence has more than "size" contiguous gaps
void	MoveEnd (int64 move_amount)
void	MoveStart (int64 move_amount)
GenericInterval &	operator= (const GenericInterval &iv)
void	SetAlignment (const std::vector< std::string > &seq_align)
template<class MatchVector> void	SetMatches (MatchVector &matches)
	Set the matches in this interval *without* making a copy.
template<class MatchVector> void	SetMatchesTemp (MatchVector &matches)
	Set the matches in this interval *without* cloberring the interval.
void	StealMatches (std::vector< AbstractMatch * > &matches)
void	swap (GenericInterval &other)
void	ValidateMatches () const
	self test code
	~GenericInterval ()
Protected Member Functions
void	swap (GenericInterval *other)
Protected Attributes
std::vector< AbstractMatch * >	matches
Private Member Functions
void	addUnalignedRegions ()
void	CalculateAlignmentLength ()
void	FindMatchPos (uint seqI, gnSeqI pos, size_t &matchI, gnSeqI &match_pos)
void	GetColumnAndMatch (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column, size_t &matchI, gnSeqI &match_col) const
Friends
template<typename BaseImpl> std::ostream &	operator<< (std::ostream &os, const GenericInterval< BaseImpl > &iv)
	Writes this GenericInterval to the specified output stream (e.g.
template<typename BaseImpl> std::istream &	operator>> (std::istream &is, const GenericInterval< BaseImpl > &iv)
	Reads a GenericInterval from the specified input stream (e.g.

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >>
class mems::GenericInterval< GappedBaseImpl >

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Constructor & Destructor Documentation

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> mems::GenericInterval< GappedBaseImpl >::GenericInterval (   )  [inline]

Definition at line 49 of file Interval.h. Referenced by mems::GenericInterval< GappedBaseImpl >::Clone(), and mems::GenericInterval< GappedBaseImpl >::SetMatches().

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> template<typename BidIt> mems::GenericInterval< GappedBaseImpl >::GenericInterval (  BidIt  it_begin, const BidIt &  it_end )  [inline]

construct from a MatchList or a vector of pointers to AbstractMatches Definition at line 55 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::addUnalignedRegions(), mems::GenericInterval< GappedBaseImpl >::CalculateAlignmentLength(), mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), and mems::GenericInterval< GappedBaseImpl >::ValidateMatches().

template<class GappedBaseImpl> mems::GenericInterval< GappedBaseImpl >::GenericInterval (  const GenericInterval< GappedBaseImpl > &  iv  )

Definition at line 219 of file Interval.h.

template<class GappedBaseImpl> mems::GenericInterval< GappedBaseImpl >::~GenericInterval (   )

Definition at line 200 of file Interval.h.

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Member Function Documentation

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> void mems::GenericInterval< GappedBaseImpl >::add (  AbstractMatch *  am  )  [inline]

Definition at line 140 of file Interval.h. References mems::AbstractMatch::Copy().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::addUnalignedRegions (   )  [private]

Definition at line 783 of file Interval.h. References mems::AddGapMatches(), and uint. Referenced by mems::GenericInterval< GappedBaseImpl >::GenericInterval(), mems::GenericInterval< GappedBaseImpl >::SetMatches(), and mems::GenericInterval< GappedBaseImpl >::SetMatchesTemp().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CalculateAlignmentLength (   )  [private]

Definition at line 913 of file Interval.h. Referenced by mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::GenericInterval(), mems::GenericInterval< GappedBaseImpl >::SetMatches(), and mems::GenericInterval< GappedBaseImpl >::SetMatchesTemp().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CalculateOffset (   )  [virtual]

Definition at line 848 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::CalculateAlignmentLength(), mems::FindBoundaries(), and uint. Referenced by mems::GenericInterval< GappedBaseImpl >::CropEnd(), mems::GenericInterval< GappedBaseImpl >::CropLeft(), mems::GenericInterval< GappedBaseImpl >::CropRight(), mems::GenericInterval< GappedBaseImpl >::CropStart(), mems::GenericInterval< GappedBaseImpl >::GenericInterval(), mems::GenericInterval< GappedBaseImpl >::SetMatches(), and mems::GenericInterval< GappedBaseImpl >::SetMatchesTemp().

template<class GappedBaseImpl> GenericInterval< GappedBaseImpl > * mems::GenericInterval< GappedBaseImpl >::Clone (   )  const

Definition at line 237 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::GenericInterval().

template<class GappedBaseImpl> GenericInterval< GappedBaseImpl > * mems::GenericInterval< GappedBaseImpl >::Copy (   )  const

Definition at line 189 of file Interval.h. References mems::m_allocateAndCopy(). Referenced by mems::addGuy(), mems::addUnalignedIntervals_v2(), and mems::ProgressiveAligner::alignProfileToProfile().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CropEnd (  gnSeqI  crop_amount  )

Definition at line 512 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::GetColumnAndMatch(), and mems::GenericInterval< GappedBaseImpl >::ValidateMatches(). Referenced by mems::SuperInterval::CropRight(), and mems::mergeUnalignedIntervals().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CropLeft (  gnSeqI  amount, uint  seqI )

Definition at line 564 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::FindMatchPos(), uint, and mems::GenericInterval< GappedBaseImpl >::ValidateMatches().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CropRight (  gnSeqI  amount, uint  seqI )

Definition at line 615 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::FindMatchPos(), uint, and mems::GenericInterval< GappedBaseImpl >::ValidateMatches().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::CropStart (  gnSeqI  crop_amount  )

Definition at line 486 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::GetColumnAndMatch(), and mems::GenericInterval< GappedBaseImpl >::ValidateMatches(). Referenced by mems::SuperInterval::CropLeft(), and mems::mergeUnalignedIntervals().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::FindMatchPos (  uint  seqI, gnSeqI  pos, size_t &  matchI, gnSeqI &  match_pos )  [private]

Definition at line 818 of file Interval.h. References uint. Referenced by mems::GenericInterval< GappedBaseImpl >::CropLeft(), and mems::GenericInterval< GappedBaseImpl >::CropRight().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::Free (   )  [virtual]

Definition at line 194 of file Interval.h. References mems::m_free(). Referenced by mems::addUnalignedRegions().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::GetAlignedSequences (  gnAlignedSequences &  gnas, const std::vector< genome::gnSequence * > &  seq_table )  const [virtual]

Get a gnAlignedSequences object TODO: get rid of this. Definition at line 923 of file Interval.h. References mems::GetAlignment(), mems::gnAlignedSequences::names, mems::gnAlignedSequences::positions, mems::gnAlignedSequences::sequences, and uint. Referenced by mems::simpleFindBackbone(), and mems::simpleFindIslands().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::GetAlignment (  std::vector< bitset_t > &  align_matrix  )  const

Definition at line 539 of file Interval.h. References mems::bitset_t, and uint. Referenced by mems::SuperInterval::ValidateSelf().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::GetColumn (  gnSeqI  col, std::vector< gnSeqI > &  pos, std::vector< bool > &  column )  const

Definition at line 810 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::GetColumnAndMatch(). Referenced by mems::GenericInterval< GappedBaseImpl >::IsGap().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::GetColumnAndMatch (  gnSeqI  col, std::vector< gnSeqI > &  pos, std::vector< bool > &  column, size_t &  matchI, gnSeqI &  match_col )  const [private]

Definition at line 300 of file Interval.h. References uint. Referenced by mems::GenericInterval< GappedBaseImpl >::CropEnd(), mems::GenericInterval< GappedBaseImpl >::CropStart(), and mems::GenericInterval< GappedBaseImpl >::GetColumn().

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> const std::vector<AbstractMatch*>& mems::GenericInterval< GappedBaseImpl >::GetMatches (   )  const [inline]

Definition at line 156 of file Interval.h. Referenced by mems::ProgressiveAligner::alignProfileToProfile(), and mems::SuperInterval::ValidateSelf().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::Invert (   )

Definition at line 801 of file Interval.h. References uint.

template<class GappedBaseImpl> bool mems::GenericInterval< GappedBaseImpl >::IsGap (  uint  seq, gnSeqI  col )  const

Definition at line 937 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::GetColumn(), and uint.

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::Marble (  gnSeqI  size  )

marbles the gaps so that no sequence has more than "size" contiguous gaps Definition at line 393 of file Interval.h. References mems::AbstractMatch::AlignmentLength(), mems::AbstractMatch::CropEnd(), RandTwisterDouble(), uint, and mems::GenericInterval< GappedBaseImpl >::ValidateMatches().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::MoveEnd (  int64  move_amount  )

Definition at line 676 of file Interval.h.

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::MoveStart (  int64  move_amount  )

Definition at line 668 of file Interval.h.

template<class GappedBaseImpl> GenericInterval< GappedBaseImpl > & mems::GenericInterval< GappedBaseImpl >::operator= (  const GenericInterval< GappedBaseImpl > &  iv  )

Definition at line 225 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::matches.

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::SetAlignment (  const std::vector< std::string > &  seq_align  )

Definition at line 876 of file Interval.h. References mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), and uint.

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> template<class MatchVector> void mems::GenericInterval< GappedBaseImpl >::SetMatches (  MatchVector &  matches  )  [inline]

Set the matches in this interval *without* making a copy. The GenericInterval takes ownership of matches Definition at line 76 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::addUnalignedRegions(), mems::GenericInterval< GappedBaseImpl >::CalculateAlignmentLength(), mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), mems::GenericInterval< GappedBaseImpl >::GenericInterval(), mems::Match, and mems::GenericInterval< GappedBaseImpl >::ValidateMatches(). Referenced by mems::addGuy(), mems::addUnalignedIntervals_v2(), mems::Aligner::align(), mems::Aligner::AlignLCB(), mems::AlignLCBInParallel(), and mems::propagateInvert().

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> template<class MatchVector> void mems::GenericInterval< GappedBaseImpl >::SetMatchesTemp (  MatchVector &  matches  )  [inline]

Set the matches in this interval *without* cloberring the interval. Definition at line 102 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::addUnalignedRegions(), mems::GenericInterval< GappedBaseImpl >::CalculateAlignmentLength(), mems::GenericInterval< GappedBaseImpl >::CalculateOffset(), and mems::GenericInterval< GappedBaseImpl >::ValidateMatches().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::StealMatches (  std::vector< AbstractMatch * > &  matches  )

Definition at line 207 of file Interval.h. References uint. Referenced by mems::mergeUnalignedIntervals(), and mems::propagateInvert().

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> void mems::GenericInterval< GappedBaseImpl >::swap (  GenericInterval< GappedBaseImpl > *  other  )  [inline, protected]

Definition at line 173 of file Interval.h. References mems::GenericInterval< GappedBaseImpl >::matches, and std::swap().

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> void mems::GenericInterval< GappedBaseImpl >::swap (  GenericInterval< GappedBaseImpl > &  other  )  [inline]

Definition at line 169 of file Interval.h. Referenced by mems::SuperInterval::swap(), and std::swap().

template<class GappedBaseImpl> void mems::GenericInterval< GappedBaseImpl >::ValidateMatches (   )  const

self test code Definition at line 246 of file Interval.h. References mems::debug_interval, and uint. Referenced by mems::GenericInterval< GappedBaseImpl >::CropEnd(), mems::GenericInterval< GappedBaseImpl >::CropLeft(), mems::GenericInterval< GappedBaseImpl >::CropRight(), mems::GenericInterval< GappedBaseImpl >::CropStart(), mems::GenericInterval< GappedBaseImpl >::GenericInterval(), mems::GenericInterval< GappedBaseImpl >::Marble(), mems::GenericInterval< GappedBaseImpl >::SetMatches(), and mems::GenericInterval< GappedBaseImpl >::SetMatchesTemp().

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Friends And Related Function Documentation

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> template<typename BaseImpl> std::ostream& operator<< (  std::ostream &  os, const GenericInterval< BaseImpl > &  iv )  [friend]

Writes this GenericInterval to the specified output stream (e.g. cout).

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> template<typename BaseImpl> std::istream& operator>> (  std::istream &  is, const GenericInterval< BaseImpl > &  iv )  [friend]

Reads a GenericInterval from the specified input stream (e.g. cin).

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Member Data Documentation

template<class GappedBaseImpl = AbstractGappedAlignment< SparseAbstractMatch<> >> std::vector< AbstractMatch* > mems::GenericInterval< GappedBaseImpl >::matches [protected]

Definition at line 177 of file Interval.h. Referenced by mems::GenericInterval< GappedBaseImpl >::operator=(), and mems::GenericInterval< GappedBaseImpl >::swap().

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

• libMems/Interval.h

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