Calculate a frequency profile or PSSM. More...

Inheritance diagram for Profile:

Public Member Functions
	Profile ()
	Default constructor.

	Profile (const Profile &orig)
	Copy constructor.

virtual	~Profile ()
	Destructor.

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

virtual double	getAminoFrequency (char amino, unsigned int i)
	Return the frequency of the aminoacid amino for position i.

virtual double	getAminoFrequencyFromCode (AminoAcidCode amino, unsigned int i)
	Return the frequency of the aminoacid amino for position i.

virtual char	getAminoMaxFrequency (unsigned int i)
	Return the most frequent aminoacid for position i.

virtual AminoAcidCode	getAminoMaxFrequencyCode (unsigned int i)
	Return the most frequent aminoacid for position i.

virtual string	getConsensus ()
	Return the consensus of the profile.

virtual double	getFreqMaxAminoFrequency (unsigned int i)
	Return the frequency of the most frequent aminoacid for position i.

virtual unsigned int	getNumGap (unsigned int i)
	Return the number of gaps for position i.

virtual unsigned int	getNumSequences ()
	Return the number of sequences in the profile.

virtual const string	getSeq ()
	Return the master sequence.

virtual unsigned int	getSequenceLength ()
	Return the lenght of sequences in the profile.

virtual Profile *	newCopy ()
	Construct a new "deep copy" of this object.

Profile &	operator= (const Profile &orig)
	Assignment operator.

virtual void	pCalculateRawFrequency (vector< double > &freq, double &gapFreq, Alignment &ali, unsigned int i)
	Calculate the raw (ie. unnormalized) aminoacids frequencies for position i. More...

virtual void	pConstructData (Alignment &ali)
	Construct data from alignment. More...

virtual void	pResetData ()
	Reset all data.

virtual void	reverse ()
	Reverse profile.

virtual void	setAllowGaps (bool g)
	Set wether to include/exclude gaps in the master sequence.

virtual void	setFrequency (double freq, AminoAcidCode amino, int i)
	Set the frequency of the aminoacid amino for position i.

virtual void	setFrequency (double freq, char amino, int i)
	Set the frequency of the aminoacid amino for position i.

virtual void	setNumGap (int numGap, int j)
	Set the number of gaps for position i.

virtual void	setNumSequences (int i)
	Set the number of sequences in the profile.

virtual void	setProfile (Alignment &ali)
	Set the profile with or without gaps in the master sequence. More...

virtual void	setProfile (Alignment &ali, istream &is)
	Set the profile with or without gaps in the master sequence. More...

virtual void	setSeq (string master)
	Set the master sequence.

Data Fields
bool	gap
	If true, consider gaps in the master sequence.

vector< double >	gapFreq
	Gaps frequencies.

unsigned int	numSeq
	Number of sequences.

vector< vector< double > >	profAliFrequency
	Aminoacids frequencies.

string	seq
	Master sequence.

unsigned int	seqLen
	Lenght of sequences.

Detailed Description

Calculate a frequency profile or PSSM.

Member Function Documentation

void copy ( const Profile & orig )

virtual

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

Parameters

orig

void pCalculateRawFrequency	(	vector< double > &	freq,
		double &	freqGap,
		Alignment &	ali,
		unsigned int	i
	)

virtual

Calculate the raw (ie. unnormalized) aminoacids frequencies for position i.

Parameters

freq
freqGap
ali
i

Reimplemented in SeqDivergenceProfile, HenikoffProfile, and PSICProfile.

void pConstructData ( Alignment & ali )

virtual

Construct data from alignment.

Parameters

ali

Reimplemented in SeqDivergenceProfile, HenikoffProfile, and PSICProfile.

void setProfile ( Alignment & ali )

virtual

Set the profile with or without gaps in the master sequence.

Parameters

ali

void setProfile	(	Alignment &	ali,
		istream &	is
	)

virtual

Set the profile with or without gaps in the master sequence.

Parameters

ali
is

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

Align2/Sources/Profile.h
Align2/Sources/Profile.cc

Public Member Functions

Data Fields

Detailed Description

Member Function Documentation