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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 "tree/phylotree.h"
#include "tree/tinatree.h"
#include "parsmultistate.h"
#include "alignment/alignment.h"
#include "tree/parstree.h"
void doParsMultiState(Params ¶ms) {
Alignment alignment(params.aln_file, params.sequence_type, params.intype, "");
alignment.orderPatternByNumChars(PAT_VARIANT);
ParsTree pars_tree;
pars_tree.readTree(params.user_file, params.is_rooted);
if (pars_tree.rooted)
pars_tree.convertToUnrooted();
pars_tree.setAlignment(&alignment);
pars_tree.initCostMatrix(CM_LINEAR);
pars_tree.setParsimonyKernel(params.SSE);
pars_tree.initializeAllPartialPars();
int total_length = pars_tree.computeParsimony();
cout << "total length: " << total_length << endl;
pars_tree.initCostMatrix(CM_UNIFORM);
int pars_score = pars_tree.computeParsimony();
cout.unsetf(ios::fixed);
cout.precision(6);
cout << "mean length: " << double(total_length)/pars_score << endl;
cout << "Parsimony score is: " << pars_score << endl;
//cout << "Parsimony score ver2 is: " << tree.computeParsimony() << endl;
//tree.printParsimonyStates();
}
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