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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. *
***************************************************************************/
#include "superalignmentpairwise.h"
SuperAlignmentPairwise::SuperAlignmentPairwise()
: AlignmentPairwise()
{
}
SuperAlignmentPairwise::SuperAlignmentPairwise(PhyloSuperTree *atree, int seq1, int seq2)
: AlignmentPairwise()
{
tree = atree;
seq_id1 = seq1;
seq_id2 = seq2;
SuperAlignment *aln = (SuperAlignment*) atree->aln;
int part = 0;
for (PhyloSuperTree::iterator it = atree->begin(); it != atree->end(); it++, part++) {
int id1 = aln->taxa_index[seq1][part];
int id2 = aln->taxa_index[seq2][part];
if (id1 >= 0 && id2 >= 0)
partitions.push_back(new AlignmentPairwise((*it), id1, id2));
}
}
double SuperAlignmentPairwise::computeFunction(double value) {
double lh = 0.0;
for (vector<AlignmentPairwise*>::iterator it = partitions.begin(); it != partitions.end(); it++) {
lh += (*it)->computeFunction(value);
}
return lh;
}
void SuperAlignmentPairwise::computeFuncDerv(double value, double &df, double &ddf) {
// double lh = 0.0;
df = 0.0;
ddf = 0.0;
for (vector<AlignmentPairwise*>::iterator it = partitions.begin(); it != partitions.end(); it++) {
double d1, d2;
// lh += (*it)->computeFuncDerv(value, d1, d2);
(*it)->computeFuncDerv(value, d1, d2);
df += d1;
ddf += d2;
}
// return lh;
}
SuperAlignmentPairwise::~SuperAlignmentPairwise()
{
for (vector<AlignmentPairwise*>::reverse_iterator it = partitions.rbegin(); it != partitions.rend(); it++)
delete (*it);
partitions.clear();
}
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