mems::CompactGappedAlignment< BaseType > Class Template Reference

The CompactGappedAlignment stores a gapped alignment as a bit-vector Rather than using one byte per aligned position, this class uses one bit, making particularly space efficient. More...

#include <CompactGappedAlignment.h>

List of all members.

Public Member Functions
CompactGappedAlignment *	Clone () const
template<class MatchType>	CompactGappedAlignment (MatchType &m)
	CompactGappedAlignment (std::vector< bitset_t > &aln_mat, gnSeqI alignment_length)
	CompactGappedAlignment (uint seq_count, gnSeqI align_length)
	CompactGappedAlignment ()
void	CondenseGapColumns ()
	Eliminates any columns that contain only gap characters.
CompactGappedAlignment *	Copy () const
void	copyRange (CompactGappedAlignment &dest, gnSeqI left_column, gnSeqI length)
virtual void	CropEnd (gnSeqI crop_amount)
virtual void	CropLeft (gnSeqI crop_amount, uint seqI)
virtual void	CropRight (gnSeqI crop_amount, uint seqI)
virtual void	CropStart (gnSeqI crop_amount)
virtual void	Free ()
const std::vector< bitset_t > &	GetAlignment () const
	allows a peek at the data inside this alignment.
void	GetAlignment (std::vector< bitset_t > &align_matrix) const
void	GetColumn (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column) const
virtual void	Invert ()
virtual bool	IsGap (uint seq, gnSeqI col) const
	returns true if the given row,column of the alignment has a gap character
gnSeqI	SeqPosToColumn (uint seq, int64 pos)
void	SetAlignment (std::vector< bitset_t > &seq_align)
void	SetAlignment (const std::vector< std::string > &seq_align)
void	swap (CompactGappedAlignment &other)
void	translate (CompactGappedAlignment &cga, uint cga_seq, uint my_seq, bool add_bits=true)
	translate a cga to a new coordinate system
bool	validate () const
bool	validate_bitcount () const
Protected Member Functions
void	create_bitcount ()
gnSeqI	SeqPosToColumn (gnSeqI pos, const bitset_t &bvec, const std::vector< size_t > &index) const
void	swap (CompactGappedAlignment *other)
Protected Attributes
std::vector< bitset_t >	align_matrix
	aligned positions have true values, gaps are false
std::vector< std::vector< size_t > >	bcount

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Detailed Description

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >>
class mems::CompactGappedAlignment< BaseType >

The CompactGappedAlignment stores a gapped alignment as a bit-vector Rather than using one byte per aligned position, this class uses one bit, making particularly space efficient.

Definition at line 38 of file CompactGappedAlignment.h.

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Constructor & Destructor Documentation

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment (   )  [inline]

Definition at line 41 of file CompactGappedAlignment.h. Referenced by mems::CompactGappedAlignment< BaseType >::Clone(), and mems::CompactGappedAlignment< BaseType >::copyRange().

template<class BaseType> mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment (  uint  seq_count, gnSeqI  align_length )

Definition at line 216 of file CompactGappedAlignment.h. References uint.

template<class BaseType> mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment (  std::vector< bitset_t > &  aln_mat, gnSeqI  alignment_length )

Definition at line 206 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::create_bitcount(), and mems::CompactGappedAlignment< BaseType >::validate_bitcount().

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> template<class MatchType> mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment (  MatchType &  m  )  [inline]

Definition at line 46 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::CompactGappedAlignment< BaseType >::create_bitcount(), uint, and mems::CompactGappedAlignment< BaseType >::validate().

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Member Function Documentation

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> CompactGappedAlignment* mems::CompactGappedAlignment< BaseType >::Clone (   )  const [inline]

Definition at line 67 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::CondenseGapColumns (   )

Eliminates any columns that contain only gap characters. Definition at line 772 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, and mems::CompactGappedAlignment< BaseType >::create_bitcount(). Referenced by mems::unalignIslands().

template<class BaseType> CompactGappedAlignment< BaseType > * mems::CompactGappedAlignment< BaseType >::Copy (   )  const

Definition at line 127 of file CompactGappedAlignment.h. References mems::m_allocateAndCopy(). Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), mems::ProgressiveAligner::ConstructSuperIntervalFromMSA(), mems::detectAndApplyBackbone(), mems::ProgressiveAligner::extractAlignment(), mems::HssArrayToCga(), mems::makeAllPairwiseGenomeHSS(), mems::ProgressiveAligner::translateGappedCoordinates(), and mems::unalignIslands().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::copyRange (  CompactGappedAlignment< BaseType > &  dest, gnSeqI  left_column, gnSeqI  length )

Definition at line 675 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::bitset_t, mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::GetColumn(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), and mems::HssArrayToCga().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::create_bitcount (   )  [protected]

Definition at line 273 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::bitset_t, mems::INDEX_INTERVAL, and uint. Referenced by mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::CondenseGapColumns(), mems::CompactGappedAlignment< BaseType >::copyRange(), mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropStart(), mems::CompactGappedAlignment< BaseType >::Invert(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), and mems::CompactGappedAlignment< BaseType >::translate().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::CropEnd (  gnSeqI  crop_amount  )  [virtual]

Definition at line 537 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::GetColumn(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by mems::CompactGappedAlignment< BaseType >::CropLeft(), and mems::CompactGappedAlignment< BaseType >::CropRight().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::CropLeft (  gnSeqI  crop_amount, uint  seqI )  [virtual]

Definition at line 582 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropStart(), mems::CompactGappedAlignment< BaseType >::SeqPosToColumn(), uint, and mems::CompactGappedAlignment< BaseType >::validate().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::CropRight (  gnSeqI  crop_amount, uint  seqI )  [virtual]

Definition at line 614 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropStart(), mems::CompactGappedAlignment< BaseType >::SeqPosToColumn(), uint, and mems::CompactGappedAlignment< BaseType >::validate().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::CropStart (  gnSeqI  crop_amount  )  [virtual]

Definition at line 485 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::GetColumn(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by mems::CompactGappedAlignment< BaseType >::CropLeft(), and mems::CompactGappedAlignment< BaseType >::CropRight().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::Free (   )  [virtual]

Definition at line 133 of file CompactGappedAlignment.h. References mems::m_free(). Referenced by mems::ProgressiveAligner::extractAlignment(), mems::HssArrayToCga(), and mems::ProgressiveAligner::translateGappedCoordinates().

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> const std::vector< bitset_t >& mems::CompactGappedAlignment< BaseType >::GetAlignment (   )  const [inline]

allows a peek at the data inside this alignment. don't change it or the CompactGappedAlignment will become corrupt Definition at line 86 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix.

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

Definition at line 259 of file CompactGappedAlignment.h. Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), and mems::ProgressiveAligner::extractAlignment().

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

Definition at line 649 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::INDEX_INTERVAL, and uint. Referenced by mems::CompactGappedAlignment< BaseType >::copyRange(), mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropStart(), and mems::writeBackboneSeqCoordinates().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::Invert (   )  [virtual]

Definition at line 464 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::bitset_t, mems::CompactGappedAlignment< BaseType >::create_bitcount(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), and mems::ProgressiveAligner::ConstructSuperIntervalFromMSA().

template<class BaseType> bool mems::CompactGappedAlignment< BaseType >::IsGap (  uint  seq, gnSeqI  col )  const [virtual]

returns true if the given row,column of the alignment has a gap character Definition at line 265 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, and uint.

template<class BaseType> gnSeqI mems::CompactGappedAlignment< BaseType >::SeqPosToColumn (  gnSeqI  pos, const bitset_t &  bvec, const std::vector< size_t > &  index )  const [protected]

Definition at line 331 of file CompactGappedAlignment.h. References mems::bitset_t, and mems::INDEX_INTERVAL.

template<class BaseType> gnSeqI mems::CompactGappedAlignment< BaseType >::SeqPosToColumn (  uint  seq, int64  pos )

Definition at line 321 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, and uint. Referenced by mems::CompactGappedAlignment< BaseType >::CropLeft(), mems::CompactGappedAlignment< BaseType >::CropRight(), and mems::CompactGappedAlignment< BaseType >::translate().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::SetAlignment (  std::vector< bitset_t > &  seq_align  )

Definition at line 245 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::CompactGappedAlignment< BaseType >::create_bitcount(), std::swap(), and mems::CompactGappedAlignment< BaseType >::validate_bitcount().

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

Definition at line 222 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::bitset_t, and mems::CompactGappedAlignment< BaseType >::create_bitcount(). Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), mems::ProgressiveAligner::ConstructSuperIntervalFromMSA(), mems::CompactGappedAlignment< BaseType >::copyRange(), mems::ProgressiveAligner::extractAlignment(), and mems::GenericIntervalList< MatchType >::ReadStandardAlignmentCompact().

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> void mems::CompactGappedAlignment< BaseType >::swap (  CompactGappedAlignment< BaseType > *  other  )  [inline, protected]

Definition at line 110 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, and std::swap().

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> void mems::CompactGappedAlignment< BaseType >::swap (  CompactGappedAlignment< BaseType > &  other  )  [inline]

Definition at line 106 of file CompactGappedAlignment.h. Referenced by std::swap().

template<class BaseType> void mems::CompactGappedAlignment< BaseType >::translate (  CompactGappedAlignment< BaseType > &  cga, uint  cga_seq, uint  my_seq, bool  add_bits = true )

translate a cga to a new coordinate system Definition at line 348 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::bitset_t, mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::SeqPosToColumn(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by mems::ProgressiveAligner::constructLcbTrackingMatches(), and mems::ProgressiveAligner::translateGappedCoordinates().

template<class BaseType> bool mems::CompactGappedAlignment< BaseType >::validate (   )  const

Definition at line 139 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::debug_cga, uint, and mems::CompactGappedAlignment< BaseType >::validate_bitcount(). Referenced by mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::copyRange(), mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropLeft(), mems::CompactGappedAlignment< BaseType >::CropRight(), mems::CompactGappedAlignment< BaseType >::CropStart(), mems::ProgressiveAligner::FixLeftEnds(), mems::CompactGappedAlignment< BaseType >::Invert(), and mems::CompactGappedAlignment< BaseType >::translate().

template<class BaseType> bool mems::CompactGappedAlignment< BaseType >::validate_bitcount (   )  const

Definition at line 294 of file CompactGappedAlignment.h. References mems::CompactGappedAlignment< BaseType >::align_matrix, mems::CompactGappedAlignment< BaseType >::bcount, mems::debug_cga, mems::INDEX_INTERVAL, and uint. Referenced by mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), and mems::CompactGappedAlignment< BaseType >::validate().

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Member Data Documentation

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> std::vector< bitset_t > mems::CompactGappedAlignment< BaseType >::align_matrix [protected]

aligned positions have true values, gaps are false Definition at line 116 of file CompactGappedAlignment.h. Referenced by mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::CondenseGapColumns(), mems::CompactGappedAlignment< BaseType >::copyRange(), mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::CropEnd(), mems::CompactGappedAlignment< BaseType >::CropLeft(), mems::CompactGappedAlignment< BaseType >::CropRight(), mems::CompactGappedAlignment< BaseType >::CropStart(), mems::CompactGappedAlignment< BaseType >::GetAlignment(), mems::CompactGappedAlignment< BaseType >::GetColumn(), mems::CompactGappedAlignment< BaseType >::Invert(), mems::CompactGappedAlignment< BaseType >::IsGap(), mems::CompactGappedAlignment< BaseType >::SeqPosToColumn(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), mems::CompactGappedAlignment< BaseType >::swap(), mems::CompactGappedAlignment< BaseType >::translate(), mems::CompactGappedAlignment< BaseType >::validate(), and mems::CompactGappedAlignment< BaseType >::validate_bitcount().

template<class BaseType = AbstractGappedAlignment< HybridAbstractMatch<> >> std::vector< std::vector< size_t > > mems::CompactGappedAlignment< BaseType >::bcount [protected]

Definition at line 117 of file CompactGappedAlignment.h. Referenced by mems::CompactGappedAlignment< BaseType >::CompactGappedAlignment(), mems::CompactGappedAlignment< BaseType >::create_bitcount(), mems::CompactGappedAlignment< BaseType >::CropLeft(), mems::CompactGappedAlignment< BaseType >::CropRight(), mems::CompactGappedAlignment< BaseType >::GetColumn(), mems::CompactGappedAlignment< BaseType >::SeqPosToColumn(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), mems::CompactGappedAlignment< BaseType >::swap(), mems::CompactGappedAlignment< BaseType >::translate(), and mems::CompactGappedAlignment< BaseType >::validate_bitcount().

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

• libMems/CompactGappedAlignment.h

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