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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef SUPERALIGNMENTPAIRWISE_H
#define SUPERALIGNMENTPAIRWISE_H
#include "alignmentpairwise.h"
#include "superalignment.h"
#include "tree/phylosupertree.h"
/**
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class SuperAlignmentPairwise : public AlignmentPairwise
{
public:
SuperAlignmentPairwise();
/**
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
*/
SuperAlignmentPairwise(PhyloSuperTree *atree, int seq1, int seq2);
~SuperAlignmentPairwise();
/**
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);
vector<AlignmentPairwise*> partitions;
};
#endif
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