Base class for printing alignments. More...

Inheritance diagram for AlignmentData:

Public Member Functions
	AlignmentData (int n, const string &name1="Seq1", const string &name2="Seq2")
	Default constructor. More...

	AlignmentData (const AlignmentData &orig)
	Copy constructor. More...

virtual	~AlignmentData ()
	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)=0
	Calculate single match positions.

virtual void	clear ()
	Insert a void string in all positions of the vector.

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

virtual Alignment &	generateMatch (double score=0.00)=0
	Generate and return an ensemble of suboptimal alignments.

virtual void	getMatch ()=0
	Reverse the strings of the vector.

virtual string	getSequence (int n)=0
	Return the sequence at position n of the vector.

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

AlignmentData &	operator= (const AlignmentData &orig)
	Assignment operator. More...

virtual void	outputMatch (ostream &os, bool fasta=false)=0
	Control if the strings of the vector are similar and print them.

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

Base class for printing alignments.

Constructor & Destructor Documentation

Default constructor.

Parameters

AlignmentData ( const AlignmentData & orig )

Copy constructor.

Parameters

orig

void copy ( const AlignmentData & orig )

virtual

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

Parameters

orig

AlignmentData & operator= ( const AlignmentData & orig )

Assignment operator.

Parameters

orig

virtual

Define if two residues are similar.

Parameters

a
b

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