17 #ifndef __SeqDivergenceProfile_H__
18 #define __SeqDivergenceProfile_H__
20 #include <AGPFunction.h>
23 #include <ScoringS2S.h>
24 #include <SequenceData.h>
25 #include <SubMatrix.h>
92 vector<double> aliWeight;
Calculate a frequency profile or PSSM.
Definition: Profile.h:35
SeqDivergenceProfile()
Default constructor.
Definition: SeqDivergenceProfile.cc:36
virtual ~SeqDivergenceProfile()
Destructor.
Definition: SeqDivergenceProfile.cc:44
vector< double > gapFreq
Gaps frequencies.
Definition: Profile.h:142
virtual void pCalculateWeight(Alignment &ali)
Calculate alignment weights.
Definition: SeqDivergenceProfile.cc:93
Implement a simple alignment type.
Definition: Alignment.h:32
SeqDivergenceProfile & operator=(const SeqDivergenceProfile &orig)
Assignment operator.
Definition: SeqDivergenceProfile.cc:55
virtual SeqDivergenceProfile * newCopy()
Construct a new "deep copy" of this object.
Definition: SeqDivergenceProfile.cc:81
virtual void copy(const SeqDivergenceProfile &orig)
Copy orig object to this object ("deep copy").
Definition: SeqDivergenceProfile.cc:69
virtual void pCalculateRawFrequency(vector< double > &freq, double &gapFreq, Alignment &ali, unsigned int i)
Calculate the raw (ie. unnormalized) aminoacids frequencies for position i.
Definition: SeqDivergenceProfile.cc:193
virtual void pConstructData(Alignment &ali)
Construct data from alignment.
Definition: SeqDivergenceProfile.cc:211
Calculate a frequency profile or PSSM using SeqDivergence weighting scheme.
Definition: SeqDivergenceProfile.h:44