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//
// superalignmentpairwiseplen.h
// iqtree
//
// Created by Olga on 04/05/17.
//
//
#ifndef iqtree_superalignmentpairwiseplen_h
#define iqtree_superalignmentpairwiseplen_h
#include "tree/phylosupertreeplen.h"
#include "superalignmentpairwise.h"
class SuperAlignmentPairwisePlen : public SuperAlignmentPairwise {
public:
/**
constructor
*/
SuperAlignmentPairwisePlen();
/**
construct the pairwise alignment from two sequences of a multiple alignment
@param aln input multiple alignment
@param seq_id1 ID of the first sequence
@param seq_id2 ID of the second sequence
*/
SuperAlignmentPairwisePlen(PhyloSuperTreePlen *atree, int seq1, int seq2);
~SuperAlignmentPairwisePlen();
/**
compute the likelihood for a distance between two sequences. Used for the ML optimization of the distance.
@param value x-value of the function
@return log-likelihood
*/
virtual double computeFunction(double value);
/**
This function calculate f(value), first derivative f'(value) and 2nd derivative f''(value).
used by Newton raphson method to minimize the function.
@param value x-value of the function
@param df (OUT) first derivative
@param ddf (OUT) second derivative
@return f(value) of function f you want to minimize
*/
virtual void computeFuncDerv(double value, double &df, double &ddf);
/**
partition information
*/
vector<PartitionInfo>* part_info;
};
#endif
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