SequenceData Class Reference

Print alignment of two sequences. More...

Inheritance diagram for SequenceData:

Collaboration diagram for SequenceData:

Public Member Functions
	SequenceData (int n, const string &seq1, const string &seq2, const string &name1="Seq1", const string &name2="Seq2")
	Default constructor. More...
	SequenceData (const SequenceData &orig)
	Copy constructor. More...
virtual	~SequenceData ()
	Destructor.
virtual void	add (string s, int n)
	Insert a sequence at position n of the vector.
virtual void	calculateMatch (int i, int tbi, int j, int tbj)
	Calculate single match positions. More...
virtual void	clear ()
	Insert a void string in all positions of the vector.
virtual void	copy (const SequenceData &orig)
	Copy orig object to this object ("deep copy"). More...
virtual void	copy (const AlignmentData &orig)
	Copy orig object to this object ("deep copy"). More...
virtual Alignment &	generateMatch (double score=0.00)
	Generate and return an ensemble of suboptimal alignments. More...
virtual void	getMatch ()
	Reverse the strings of the vector.
virtual string	getSequence (int n)
	Return the sequence at position n of the vector. More...
virtual SequenceData *	newCopy ()
	Construct a new "deep copy" of this object. More...
SequenceData &	operator= (const SequenceData &orig)
	Assignment operator. More...
virtual void	outputMatch (ostream &os, bool fasta=false)
	Control if the strings of the vector are similar and print them. More...
virtual void	setSequence (string s, int n)
	Set the sequence at position n of the vector. More...
virtual bool	similar (char a, char b)
	Define if two residues are similar. More...

Data Fields
vector< string >	match
	Matching alignment positions.
int	n
	Number of strings in the alignment.
string	name1
	Name of target sequence.
string	name2
	Name of template sequence.

Detailed Description

Print alignment of two sequences.

Constructor & Destructor Documentation

SequenceData	(	int	n,
		const string &	_seq1,
		const string &	_seq2,
		const string &	_n1 = "Seq1",
		const string &	_n2 = "Seq2"
	)

Default constructor.

Parameters

n
_seq1
_seq2
_n1
_n2

SequenceData

(

const SequenceData &

orig

)

Copy constructor.

Parameters

orig

Member Function Documentation

void calculateMatch ( int  i, int  tbi, int  j, int  tbj  )

virtual

Calculate single match positions.

Parameters

i
tbi
j
tbj

Implements AlignmentData.

void copy ( const SequenceData &  orig )

virtual

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

Parameters

orig

void copy ( const AlignmentData &  orig )

virtualinherited

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

Parameters

orig

Alignment & generateMatch ( double  score = 0.00 )

virtual

Generate and return an ensemble of suboptimal alignments.

Parameters

score

Returns

Implements AlignmentData.

string getSequence ( int  n )

virtual

Return the sequence at position n of the vector.

Parameters

n

Returns

Implements AlignmentData.

SequenceData * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements AlignmentData.

SequenceData & operator=

(

const SequenceData &

orig

)

Assignment operator.

Parameters

orig

Returns

void outputMatch ( ostream &  os, bool  fasta = false  )

virtual

Control if the strings of the vector are similar and print them.

Parameters

os
fasta

Implements AlignmentData.

void setSequence ( string  s, int  n  )

virtual

Set the sequence at position n of the vector.

Parameters

s
n

bool similar ( char  a, char  b  )

virtualinherited

Define if two residues are similar.

Parameters

a
b

Returns

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

• Align2/Sources/SequenceData.h
• Align2/Sources/SequenceData.cc