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/***************************************************************************
* Copyright (C) 2018 by Lukasz Reszczynski *
* lukasz.reszczynski@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 "terrace.h"
Terrace::Terrace(PhyloTree &tree, SuperAlignment* saln) :
coverage(tree.aln->getSeqNames().size(), saln->taxa_index[0].size())
{
stringstream nwk;
tree.printTree(nwk, 0);
terraces::index cols{};
terraces::index rows{};
terraces::bitmatrix coverage_matrix{rows, cols};
vector<string> labels = tree.aln->getSeqNames();
names.resize(labels.size());
for (int i=0; i<labels.size(); i++) {
string label = labels[i];
names[i] = label;
indices[label] = i;
}
auto terraphast_nwk = terraces::parse_nwk(nwk.str(), indices);
int n_partitions = saln->taxa_index[0].size();
for (int i=0; i<labels.size(); i++) {
for (int j=0; j<n_partitions; j++) {
bool value = (saln->taxa_index[i][j] != -1);
coverage.set(i, j, value);
}
}
supertree = terraces::create_supertree_data(terraphast_nwk, coverage);
init();
}
void Terrace::init()
{
}
uint64_t Terrace::getSize()
{
return terraces::count_terrace(supertree);
}
void Terrace::printTrees(ostream &out)
{
terraces::print_terrace(supertree, names, out);
}
void Terrace::printTreesCompressed(ostream &out)
{
terraces::print_terrace_compressed(supertree, names, out);
}
Terrace::~Terrace()
{
}
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