Pairwise sequence and profile alignment. More...

Inheritance diagram for Align:

Collaboration diagram for Align:

Public Types
enum
	Numeric value used to identify invalid alignment positions.

Public Member Functions
	Align (AlignmentData ad, GapFunction gf, ScoringScheme *ss)
	Default constructor.

	Align (const Align &orig)
	Copy constructor.

virtual	~Align ()
	Destructor.

virtual void	copy (const Align &orig)
	Copy orig object to this object ("deep copy"). More...

virtual void	doMatch (ostream &os) const
	Output of alignment result.

virtual void	doMatchPlusHeader (ostream &os, string headerTarget, string headerTemplate) const
	Output of alignment result (including headers of the two sequences).

virtual vector< Alignment >	generateMultiMatch (unsigned int num=1)
	Generate and return an ensemble of suboptimal alignments. More...

virtual vector< double >	generateMultiMatchScore (unsigned int num=10)
	Generate and return scores of an ensemble of suboptimal alignments. More...

AlignmentData *	getAlignmentData ()
	Return AlignmentData pointer.

GapFunction *	getGapFunction ()
	Return GapFunction pointer.

virtual vector< string >	getMatch () const
	Return two-element array containing an alignment with maximal score.

virtual vector< vector< int > >	getMatchSubset ()
	Return subset corresponding to match.

virtual void	getMultiMatch ()=0
	Return two-element array containing an alignment with maximal score.

virtual vector< double >	getMultiMatchScore (unsigned int num=10)
	Return alignment scores of an ensemble of suboptimal alignments.

virtual double	getScore () const
	Return alignment score.

ScoringScheme *	getScoringScheme ()
	Return ScoringScheme pointer.

virtual Align *	newCopy ()=0
	Construct a new "deep copy" of this object.

virtual Traceback	next (const Traceback &tb) const
	Return next Traceback element.

Align &	operator= (const Align &orig)
	Assignment operator.

virtual void	outputMultiMatch (ostream &os, unsigned int num=10, bool fasta=false)
	Generate and output an ensemble of suboptimal alignments.

virtual void	pCalculateMatrix (bool update=true)=0
	Update/create matrix values.

virtual void	pCalculateMatrix (const vector< unsigned int > &v1, const vector< unsigned int > &v2, bool update=true)=0
	Update/create weighted matrix values.

void	pModifyMatrix (int i, int j)
	Modify matrix during suboptimal alignment generation. More...

virtual void	recalculateMatrix ()
	Recalculate the alignment matrix.

void	setPenalties (double mul, double add)
	Set penalties for suboptimal alignments. More...

virtual vector< int >	shiftMatchSubset (vector< int > inputVector, int newStartPos)
	Return vector with positions shifted depending on new position.

Data Fields
AlignmentData *	ad
	Pointer to AlignmentData.

vector< vector< Traceback > >	B
	Traceback matrix.

Traceback	B0
	Starting point of the traceback.

vector< vector< double > >	F
	Score matrix.

GapFunction *	gf
	Pointer to GapFunction.

unsigned int	m
	Length of template sequence.

unsigned int	n
	Length of target sequence.

double	penaltyAdd
	Additive penalty for suboptimal alignment.

double	penaltyMul
	Multiplicative penalty for suboptimal alignment.

vector< int >	res1Pos
	Aligned positions for target sequence.

vector< int >	res2Pos
	Aligned positions for template sequence.

ScoringScheme *	ss
	Pointer to ScoringScheme.

Detailed Description

Pairwise sequence and profile alignment.

originally based on the Java implementation from Peter Sestoft. http://www.dina.dk/~sestoft

Member Function Documentation

void copy ( const Align & orig )

virtual

Copy orig object to this object ("deep copy").

Parameters

orig

vector< Alignment > generateMultiMatch ( unsigned int num = 1 )

virtual

Generate and return an ensemble of suboptimal alignments.

Parameters

num

Returns

vector< double > generateMultiMatchScore ( unsigned int num = 10 )

virtual

Generate and return scores of an ensemble of suboptimal alignments.

Parameters

num

Returns

void pModifyMatrix	(	int	i,
		int	j
	)

Modify matrix during suboptimal alignment generation.

Parameters

i
j

void setPenalties	(	double	mul,
		double	add
	)

Set penalties for suboptimal alignments.

Parameters

mul
add

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

Align2/Sources/Align.h
Align2/Sources/Align.cc

Public Types

Public Member Functions

Data Fields

Detailed Description

Member Function Documentation