SubMatrix Class Reference

Implement a standard substitution matrix. More...

Inheritance diagram for SubMatrix:

Collaboration diagram for SubMatrix:

Public Member Functions
	SubMatrix ()
	Default constructor.
	SubMatrix (istream &is)
	istream constructor.
	SubMatrix (const SubMatrix &orig)
	Copy constructor.
virtual	~SubMatrix ()
	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 void	copy (const SubMatrix &orig)
	Copy orig object to this object ("deep copy"). More...
virtual string	getResidues () const
	Implementation of abstract class method.
virtual SubMatrix *	newCopy ()
	Construct a new "deep copy" of this object. More...
SubMatrix &	operator= (const SubMatrix &orig)
	Assignment operator. More...
virtual unsigned int	size () const
	Return the dimension of the matrix.

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 SubMatrix &object)
	Output operator. More...
istream &	operator>> (istream &is, SubMatrix &object)
	Input operator. More...

Detailed Description

Implement a standard substitution matrix.

Member Function Documentation

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

virtualinherited

Build scoring matrix from raw data.

Parameters

residues
residuescores

void copy ( const Substitution &  orig )

virtualinherited

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

Parameters

orig

void copy ( const SubMatrix &  orig )

virtual

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

Parameters

orig

SubMatrix * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements Substitution.

SubMatrix & operator=

(

const SubMatrix &

orig

)

Assignment operator.

Parameters

orig

Returns

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

staticinherited

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

Parameters

is
data

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

staticinherited

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

Parameters

os
data

Friends And Related Function Documentation

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

friend

Output operator.

Parameters

os
object

Returns

istream& operator>> ( istream &  is, SubMatrix &  object  )

friend

Input operator.

Parameters

is
object

Returns

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

• Align2/Sources/SubMatrix.h
• Align2/Sources/SubMatrix.cc