Substitution Class Reference

Base class for deriving substitution matrices. More...

Inheritance diagram for Substitution:

Public Member Functions
	Substitution ()
	Default constructor.
	Substitution (const Substitution &orig)
	Copy constructor.
virtual	~Substitution ()
	Destructor.
virtual void	buildscore (const string &residues, const vector< vector< int > > &residuescores)
	Build scoring matrix from raw data. More...
virtual void	copy (const Substitution &orig)
	Copy orig object to this object ("deep copy"). More...
virtual string	getResidues () const =0
	Dummy implementation.
virtual Substitution *	newCopy ()=0
	Construct a new "deep copy" of this object.
Substitution &	operator= (const Substitution &orig)
	Assignment operator. More...

Static Public Member Functions
template<class T >
static void	pReadDoubleVector (istream &is, vector< vector< T > > &data)
	Helper function used to read a vector<vector> construct. More...
static void	pWriteDoubleVector (ostream &os, vector< vector< int > > data)
	Helper function used to write a vector<vector> construct. More...

Data Fields
vector< vector< int > >	score
	Substitution score.

Friends
ostream &	operator<< (ostream &os, const Substitution &object)
	Output operator. More...
istream &	operator>> (istream &is, Substitution &object)
	Input operator.

Detailed Description

Base class for deriving substitution matrices.

Member Function Documentation

void buildscore ( const string &  residues, const vector< vector< int > > &  residuescores  )

virtual

Build scoring matrix from raw data.

Parameters

residues
residuescores

void copy ( const Substitution &  orig )

virtual

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

Parameters

orig

Substitution & operator=

(

const Substitution &

orig

)

Assignment operator.

Parameters

orig

Returns

template void pReadDoubleVector ( istream &  is, vector< vector< T > > &  data  )

static

Helper function used to read a vector<vector> construct.

Parameters

is
data

void pWriteDoubleVector ( ostream &  os, vector< vector< int > >  data  )

static

Helper function used to write a vector<vector> construct.

Parameters

os
data

Friends And Related Function Documentation

ostream& operator<< ( ostream &  os, const Substitution &  object  )

friend

Output operator.

Parameters

os
object

Returns

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

• Align2/Sources/Substitution.h
• Align2/Sources/Substitution.cc