DIAlign::AffineAlignObj Struct Reference

An affine alignment object. More...

#include <affinealignobj.h>

Collaboration diagram for DIAlign::AffineAlignObj:

Public Member Functions
	AffineAlignObj (int ROW_SIZE, int COL_SIZE, bool clearMemory=true)
	Constructor for AffineAlignObj. More...
void	reset (int ROW_SIZE, int COL_SIZE)
	Reset object to initial state (without allocating new memory)
AffineAlignObj &	operator= (const AffineAlignObj &rhs)
	Overloading copy assignment operator.
	AffineAlignObj (const AffineAlignObj &rhs)
	Copy constructor.
	~AffineAlignObj ()
	Destructor: frees memory.

Public Attributes
double *	s_data
	similarity score matrix.
double *	M
	Match or Mismatch matrix, residues of A and B are aligned without a gap. M(i,j) = Best score upto (i,j) given Ai is aligned to Bj.
double *	A
	Insert in sequence A, residue in A is aligned to gap in B. A(i,j) is the best score given that Ai is aligned to a gap in B.
double *	B
	Insert in sequence B, residue in B is aligned to gap in A. B(i,j) is the best score given that Bj is aligned to a gap in A.
Traceback::TracebackType *	Traceback
	Traceback matrices store source matrix name and direction as matrices are filled with dynamic programming.
bool *	Path
	Path matrix would represent alignment path through similarity matrix as binary-hot encoding.
bool *	simPath
	Not needed, will be removed.
int	signalA_len
	Number of data-points in signal A.
int	signalB_len
	Number of data-points in signal B.
double	GapOpen
	Penalty for Gap opening. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
double	GapExten
	Penalty for Gap extension. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
bool	FreeEndGaps
	True for Overlap alignment.
std::vector< int >	indexA_aligned
	Aligned signalA indices after affine alignment.
std::vector< int >	indexB_aligned
	Aligned signalB indices after affine alignment.
std::vector< double >	score
	Cumulative score along the aligned path.
int	nGaps
	Total number of gaps in the alignment path.

Detailed Description

An affine alignment object.

This object contains similarity matrix, three matrices M, A and B storing cumulative-scores for dynamic programming. Traceback matrices store source matrix name and direction as matrices are filled with dynamic programming. Path matrix encode alignment path that results in the highest cumulative score. The aligned indices are also stored for signal A and signal B.

Constructor & Destructor Documentation

DIAlign::AffineAlignObj::AffineAlignObj ( int  ROW_SIZE, int  COL_SIZE, bool  clearMemory = true  )

inline

Constructor for AffineAlignObj.

Allocates memory for s_data, M, A, B, Traceback, Path matrices. Initialize them with zero if clearMemory is set true.

Parameters

ROW_SIZE	Number of rows in matrix M.
COL_SIZE	Number of columns in matrix M.
clearMemory	If true, matrices are initialized with zero.

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

• affinealignobj.h