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SeqDivergenceProfile Class Reference

Calculate a frequency profile or PSSM using SeqDivergence weighting scheme. More...

+ Inheritance diagram for SeqDivergenceProfile:
+ Collaboration diagram for SeqDivergenceProfile:

Public Member Functions

 SeqDivergenceProfile ()
 Default constructor.
 
 SeqDivergenceProfile (const SeqDivergenceProfile &orig)
 Copy constructor.
 
virtual ~SeqDivergenceProfile ()
 Destructor.
 
virtual void copy (const SeqDivergenceProfile &orig)
 Copy orig object to this object ("deep copy"). More...
 
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 SeqDivergenceProfilenewCopy ()
 Construct a new "deep copy" of this object. More...
 
SeqDivergenceProfileoperator= (const SeqDivergenceProfile &orig)
 Assignment operator. More...
 
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 pCalculateWeight (Alignment &ali)
 Calculate alignment weights. 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 using SeqDivergence weighting scheme.

Some explanations can be found in:

            Guoli Wang, Roland L. Dunbrack jr.
            Scoring profile-to-profile sequence alignments.
            Institute for Cancer Research, Fox Chase Cancer Center,
            Philadelphia, Pennsylvania 19111, USA. March 16, 2004.

Member Function Documentation

void copy ( const SeqDivergenceProfile orig)
virtual

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

Parameters
orig
void copy ( const Profile orig)
virtualinherited

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

Parameters
orig
SeqDivergenceProfile * newCopy ( )
virtual

Construct a new "deep copy" of this object.

Returns

Reimplemented from Profile.

SeqDivergenceProfile & operator= ( const SeqDivergenceProfile orig)

Assignment operator.

Parameters
orig
Returns
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 from Profile.

void pCalculateWeight ( Alignment ali)
virtual

Calculate alignment weights.

Parameters
ali
void pConstructData ( Alignment ali)
virtual

Construct data from alignment.

Parameters
ali

Reimplemented from Profile.

void setProfile ( Alignment ali)
virtualinherited

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

Parameters
ali
void setProfile ( Alignment ali,
istream &  is 
)
virtualinherited

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: