core::sequence::MCAligner Class Reference

#include <MCAligner.hh>

Inheritance diagram for core::sequence::MCAligner:

Collaboration diagram for core::sequence::MCAligner:

Public Member Functions
	MCAligner ()
	constructors More...
	MCAligner (Real kT)
virtual	~MCAligner ()
	destructor More...
void	kT (Real new_kT)
	Sets the kT used in the align method. A optimal value of kT means acceptance of less optimal decisions along the dynamic programming matrix. More...
Real	kT () const
	Returns the kT used in the align method. More...
virtual SequenceAlignment	align (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)
	Align these two Sequences using the given ScoringScheme. Rather than finding an optimal alignment, MCAligner uses a stochastic algorithm to generate an alignment at a given kT. More...
Public Member Functions inherited from core::sequence::Aligner
	Aligner ()
	ctor More...
virtual	~Aligner ()
	dtor More...
void	validate_input (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)
SequenceAlignment	traceback (SequenceOP seq_x, SequenceOP seq_y, DP_Matrix matrix, CellOP start)

Private Attributes
Real	kT_

Detailed Description

Definition at line 28 of file MCAligner.hh.

Constructor & Destructor Documentation

core::sequence::MCAligner::MCAligner ( )

inline

constructors

Definition at line 33 of file MCAligner.hh.

core::sequence::MCAligner::MCAligner ( Real  kT)

inline

Definition at line 34 of file MCAligner.hh.

virtual core::sequence::MCAligner::~MCAligner ( )

inlinevirtual

destructor

Definition at line 37 of file MCAligner.hh.

Member Function Documentation

SequenceAlignment core::sequence::MCAligner::align ( SequenceOP  seq_y, SequenceOP  seq_x, ScoringSchemeOP  ss  )

virtual

Align these two Sequences using the given ScoringScheme. Rather than finding an optimal alignment, MCAligner uses a stochastic algorithm to generate an alignment at a given kT.

Detailed: The Needleman-Wunsch algorithm uses dynamic programming to

generate an optimal alignment between two scoring sequences under a given scoring scheme. Rather than making the best decision at each element of the dynamic programming matrix, MCAligner makes a stochastic decision between introducing a gap in seq_y, introducing a gap in seq_x, or aligning two characters between the two sequences. The decision is made by transforming the scores for each of the three possible decisions into probabilities using Boltzmann weighting of the scores for each possibility at a given kT. The kT is stored as a member variable of the MCAligner class, and accessor methods are provided above.

Implements core::sequence::Aligner.

Definition at line 42 of file MCAligner.cc.

References core::sequence::above, core::sequence::align_RG(), core::sequence::diagonal, core::sequence::NWAligner::init_matrix(), kT(), core::sequence::left, and core::sequence::Aligner::traceback().

void core::sequence::MCAligner::kT ( Real  new_kT)

inline

Sets the kT used in the align method. A optimal value of kT means acceptance of less optimal decisions along the dynamic programming matrix.

Definition at line 41 of file MCAligner.hh.

References kT_.

Real core::sequence::MCAligner::kT ( ) const

inline

Returns the kT used in the align method.

Definition at line 46 of file MCAligner.hh.

References kT_.

Referenced by align().

Member Data Documentation

Real core::sequence::MCAligner::kT_

private

Definition at line 72 of file MCAligner.hh.

Referenced by kT().

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

• src/core/sequence/MCAligner.hh
• src/core/sequence/MCAligner.cc