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//
// superalignmentpairwiseplen.cpp
// iqtree
//
// Created by Olga on 04/05/17.
//
//
#include <stdio.h>
#include "superalignmentpairwiseplen.h"
/**********************************************************
* class SuperAlignmentPairwisePlen
**********************************************************/
SuperAlignmentPairwisePlen::SuperAlignmentPairwisePlen(PhyloSuperTreePlen *atree, int seq1, int seq2)
: SuperAlignmentPairwise((PhyloSuperTree*) atree, seq1, seq2)
{
part_info = &(atree->part_info);
}
double SuperAlignmentPairwisePlen::computeFunction(double value) {
int part = 0;
double lh = 0.0;
for (vector<AlignmentPairwise*>::iterator it = partitions.begin(); it != partitions.end(); it++, part++) {
lh += (*it)->computeFunction(part_info->at(part).part_rate*value);
}
return lh;
}
void SuperAlignmentPairwisePlen::computeFuncDerv(double value, double &df, double &ddf) {
int part = 0;
// double lh = 0.0;
df = 0.0;
ddf = 0.0;
for (vector<AlignmentPairwise*>::iterator it = partitions.begin(); it != partitions.end(); it++, part++) {
double d1, d2;
(*it)->computeFuncDerv(part_info->at(part).part_rate*value, d1, d2);
df += part_info->at(part).part_rate*d1;
ddf += part_info->at(part).part_rate*part_info->at(part).part_rate*d2;
}
// return lh;
}
SuperAlignmentPairwisePlen::~SuperAlignmentPairwisePlen()
{}
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