DIAlign::AlignObj Struct Reference

An alignment object (for non-affine alignment) More...

#include <alignment.h>

Collaboration diagram for DIAlign::AlignObj:

Public Member Functions
	AlignObj (int ROW_SIZE, int COL_SIZE)
	Constructor for AlignObj. More...

Public Attributes
std::vector< double >	s_data
	similarity score matrix.
std::vector< Traceback::TracebackType >	Traceback
	Traceback matrices store source matrix name and direction as matrices are filled with dynamic programming.
std::vector< 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.
std::vector< double >	M_forw
	Not needed, will be removed.
std::vector< bool >	Path
	Path matrix would represent alignment path through similarity matrix as binary-hot encoding.
std::vector< bool >	simPath
	Not needed, will be removed.
std::vector< int >	OptionalPaths
	Highlight the number of all optimal paths.
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 = n*GapOpen.
double	GapExten
	Not needed, will be removed.
bool	FreeEndGaps
	True for Overlap alignment.
std::vector< int >	indexA_aligned
	Aligned signalA indices after alignment.
std::vector< int >	indexB_aligned
	Aligned signalB indices after alignment.
std::vector< double >	score
	Cumulative score along the aligned path.
double	score_forw
	Not needed, will be removed.
double	simScore_forw
	Summation of similarity score along the alignment path-band.
double	alterAlignScore
	Alignment score of 2nd best peak alignment.
int	nGaps
	Total number of gaps in the alignment path.

Detailed Description

An alignment object (for non-affine alignment)

It contains similarity matrix, matrix M to store cumulative-scores for dynamic programming. Traceback matrices store source matrix 'M' 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::AlignObj::AlignObj ( int  ROW_SIZE, int  COL_SIZE  )

inline

Constructor for AlignObj.

Allocates memory for s_data, M, Traceback, Path matrices.

Parameters

ROW_SIZE	Number of rows in matrix M.
COL_SIZE	Number of columns in matrix M.

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

• alignment.h