PssmInput Class Reference

Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix). More...

Public Member Functions
	PssmInput ()
	Default constructor.
	PssmInput (istream &is)
	istream constructor.
	PssmInput (const PssmInput &orig)
	Copy constructor.
virtual	~PssmInput ()
	Destructor.
virtual void	copy (const PssmInput &orig)
	Copy orig object to this object ("deep copy"). More...
virtual PssmInput *	newCopy ()
	Construct a new "deep copy" of this object. More...
PssmInput &	operator= (const PssmInput &orig)
	Assignment operator. More...
double	score (int i, int j)
	Return the score of the aminoacid j in position i.
virtual unsigned int	size () const
	Return the size of the object referred as the dimension of the PSSM.

Static Public Member Functions
template<class T >
static void	pReadDoubleVector (istream &is, vector< vector< T > > &data, vector< string > &data1, vector< string > &data2)
	Helper function used to read a vector<vector> construct. More...
template<class T >
static void	pWriteDoubleVector (ostream &os, vector< vector< T > > data, vector< string > data1, vector< string > data2)
	Helper function used to write a vector<vector> construct. More...

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

Detailed Description

Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix).

Member Function Documentation

void copy ( const PssmInput &  orig )

virtual

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

Parameters

orig

PssmInput * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

PssmInput & operator=

(

const PssmInput &

orig

)

Assignment operator.

Parameters

orig

Returns

template void pReadDoubleVector ( istream &  is, vector< vector< T > > &  data, vector< string > &  data1, vector< string > &  data2  )

static

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

Parameters

is
data
data1
data2

void pWriteDoubleVector ( ostream &  os, vector< vector< T > >  data, vector< string >  data1, vector< string >  data2  )

static

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

Parameters

os
data
data1
data2

Friends And Related Function Documentation

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

friend

Output operator.

Parameters

os
object

Returns

istream& operator>> ( istream &  is, PssmInput &  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/PssmInput.h
• Align2/Sources/PssmInput.cc