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mems::UngappedLocalAlignment< AbstractMatchImpl > Class Template Reference

The UngappedLocalAlignment class stores the location of an equal size (inexact or exactly) matching region between several sequences. More...

#include <UngappedLocalAlignment.h>

Inheritance diagram for mems::UngappedLocalAlignment< AbstractMatchImpl >:

Inheritance graph
[legend]
List of all members.

Public Member Functions

gnSeqI AlignmentLength () const
UngappedLocalAlignment * Clone () const
UngappedLocalAlignment * Copy () const
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 ExtendEnd (gnSeqI extend_amount)
virtual void ExtendStart (gnSeqI extend_amount)
virtual void Free ()
void GetAlignment (std::vector< bitset_t > &align_matrix) const
void GetColumn (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column) const
bool IsGap (uint seqI, gnSeqI col) const
gnSeqI Length (uint seqI=(std::numeric_limits< uint >::max)()) const
virtual void Move (int64 distance)
boolean operator== (const UngappedLocalAlignment &mhe) const
 comparison operator, compares two UngappedLocalAlignmentes to see if they are the same

void SetLength (gnSeqI len, uint seqI=0)
 UngappedLocalAlignment (const uint seq_count)
 Creates a new UngappedLocalAlignment.

 UngappedLocalAlignment ()

Protected Attributes

gnSeqI m_length

Friends

template<typename AMImpl> std::ostream & operator<< (std::ostream &os, const UngappedLocalAlignment< AMImpl > &ula)
 Writes the location of this UngappedLocalAlignment to the specified output stream (e.g.

Detailed Description

template<class AbstractMatchImpl>
class mems::UngappedLocalAlignment< AbstractMatchImpl >

The UngappedLocalAlignment class stores the location of an equal size (inexact or exactly) matching region between several sequences.

This class can use one of several storage schemes such as DenseAbstractMatch or SparseAbstractMatch

Definition at line 28 of file UngappedLocalAlignment.h.

Constructor & Destructor Documentation

template<class AbstractMatchImpl>
mems::UngappedLocalAlignment< AbstractMatchImpl >::UngappedLocalAlignment (   ) 
 

Definition at line 89 of file UngappedLocalAlignment.h.

Referenced by mems::UngappedLocalAlignment< AbstractMatchImpl >::Clone().

template<class AbstractMatchImpl>
mems::UngappedLocalAlignment< AbstractMatchImpl >::UngappedLocalAlignment (  const uint  seq_count  ) 
 

Creates a new UngappedLocalAlignment.

Parameters:
seq_count The total number of sequences in the alignment

Definition at line 95 of file UngappedLocalAlignment.h.

References uint.

Member Function Documentation

template<class AbstractMatchImpl>
gnSeqI mems::UngappedLocalAlignment< AbstractMatchImpl >::AlignmentLength (   )  const [inline]
 

Definition at line 57 of file UngappedLocalAlignment.h.

template<class AbstractMatchImpl>
UngappedLocalAlignment< AbstractMatchImpl > * mems::UngappedLocalAlignment< AbstractMatchImpl >::Clone (   )  const
 

Reimplemented in mems::MatchHashEntry.

Definition at line 103 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::UngappedLocalAlignment().

template<class AbstractMatchImpl>
UngappedLocalAlignment< AbstractMatchImpl > * mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy (   )  const
 

Reimplemented in mems::MatchHashEntry.

Definition at line 109 of file UngappedLocalAlignment.h.

References mems::m_allocateAndCopy().

Referenced by mems::AddGapMatches(), mems::addUnalignedIntervals(), mems::addUnalignedIntervals_v2(), mems::createBackboneList(), mems::EliminateOverlaps(), mems::ProgressiveAligner::extractAlignment(), mems::ProgressiveAligner::getAncestralMatches(), mems::ProgressiveAligner::getPairwiseMatches(), mems::ProgressiveAligner::getRepresentativeAncestralMatches(), mems::makeAlignmentTree(), mems::mergePairwiseHomologyPredictions(), mems::ReadList(), mems::GenericIntervalList< MatchType >::ReadList(), and mems::ProgressiveAligner::recurseOnPairs().

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::CropEnd (  gnSeqI  crop_amount  )  [virtual]
 

Definition at line 147 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length.

Referenced by mems::UngappedLocalAlignment< AbstractMatchImpl >::CropLeft(), mems::UngappedLocalAlignment< AbstractMatchImpl >::CropRight(), mems::EliminateOverlaps(), and mems::transposeMatches().

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

Definition at line 169 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::CropEnd(), mems::UngappedLocalAlignment< AbstractMatchImpl >::CropStart(), and uint.

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

Definition at line 178 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::CropEnd(), mems::UngappedLocalAlignment< AbstractMatchImpl >::CropStart(), and uint.

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::CropStart (  gnSeqI  crop_amount  )  [virtual]
 

Definition at line 138 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length.

Referenced by mems::UngappedLocalAlignment< AbstractMatchImpl >::CropLeft(), mems::UngappedLocalAlignment< AbstractMatchImpl >::CropRight(), mems::EliminateOverlaps(), mems::MatchHashEntry::end_to_start_compare(), and mems::transposeMatches().

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::ExtendEnd (  gnSeqI  extend_amount  )  [virtual]
 

Definition at line 162 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length.

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::ExtendStart (  gnSeqI  extend_amount  )  [virtual]
 

Definition at line 155 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length.

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::Free (   )  [virtual]
 

Reimplemented in mems::MatchHashEntry.

Definition at line 114 of file UngappedLocalAlignment.h.

References mems::m_free().

Referenced by mems::addUnalignedIntervals(), mems::EliminateOverlaps(), and mems::makeAlignmentTree().

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

Definition at line 187 of file UngappedLocalAlignment.h.

References mems::bitset_t, and uint.

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

Definition at line 210 of file UngappedLocalAlignment.h.

References uint.

template<class AbstractMatchImpl>
bool mems::UngappedLocalAlignment< AbstractMatchImpl >::IsGap (  uint  seqI,
gnSeqI  col
)  const [inline]
 

Definition at line 78 of file UngappedLocalAlignment.h.

template<class AbstractMatchImpl>
gnSeqI mems::UngappedLocalAlignment< AbstractMatchImpl >::Length (  uint  seqI = (std::numeric_limits<uint>::max)()  )  const [inline]
 

Definition at line 48 of file UngappedLocalAlignment.h.

Referenced by mems::MatchHashEntry::CalculateOffset(), mems::MatchHashEntry::Contains(), mems::EliminateOverlaps(), mems::MatchHashEntry::end_to_start_compare(), mems::getInterveningCoordinates(), mems::operator<<(), mems::Aligner::Recursion(), mems::MatchHashEntry::start_compare(), mems::MatchHashEntry::start_lessthan_ptr(), mems::MatchHashEntry::strict_start_lessthan_ptr(), and mems::transposeMatches().

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::Move (  int64  distance  )  [virtual]
 

Definition at line 128 of file UngappedLocalAlignment.h.

References mems::uint32.

template<class AbstractMatchImpl>
boolean mems::UngappedLocalAlignment< AbstractMatchImpl >::operator== (  const UngappedLocalAlignment< AbstractMatchImpl > &  mhe  )  const
 

comparison operator, compares two UngappedLocalAlignmentes to see if they are the same

Definition at line 120 of file UngappedLocalAlignment.h.

References mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length.

template<class AbstractMatchImpl>
void mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength (  gnSeqI  len,
uint  seqI = 0
)  [inline]
 

Definition at line 56 of file UngappedLocalAlignment.h.

Referenced by mems::AddGapMatches(), mems::addUnalignedIntervals(), mems::addUnalignedIntervals_v2(), mems::createBackboneList(), mems::ProgressiveAligner::extractAlignment(), mems::ProgressiveAligner::getAncestralMatches(), mems::ProgressiveAligner::getPairwiseMatches(), mems::ProgressiveAligner::getRepresentativeAncestralMatches(), mems::RepeatHash::HashMatch(), mems::MemHash::HashMatch(), mems::MaskedMemHash::HashMatch(), mems::MemHash::LoadFile(), mems::makeAlignmentTree(), mems::readBackboneColsFile(), mems::RepeatMatchList::ReadList(), mems::ReadList(), mems::GenericIntervalList< MatchType >::ReadList(), and mems::ProgressiveAligner::recurseOnPairs().

Friends And Related Function Documentation

template<class AbstractMatchImpl>
template<typename AMImpl>
std::ostream& operator<< (  std::ostream &  os,
const UngappedLocalAlignment< AMImpl > &  ula
)  [friend]
 

Writes the location of this UngappedLocalAlignment to the specified output stream (e.g.

cout).

Member Data Documentation

template<class AbstractMatchImpl>
gnSeqI mems::UngappedLocalAlignment< AbstractMatchImpl >::m_length [protected]
 

Definition at line 84 of file UngappedLocalAlignment.h.

Referenced by mems::UngappedLocalAlignment< AbstractMatchImpl >::CropEnd(), mems::UngappedLocalAlignment< AbstractMatchImpl >::CropStart(), mems::UngappedLocalAlignment< AbstractMatchImpl >::ExtendEnd(), mems::UngappedLocalAlignment< AbstractMatchImpl >::ExtendStart(), and mems::UngappedLocalAlignment< AbstractMatchImpl >::operator==().

The documentation for this class was generated from the following file:
Generated on Fri Mar 14 06:01:44 2008 for libMems by doxygen 1.3.6