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/***************************************************************************
* Copyright (C) 2006 by BUI Quang Minh, Steffen Klaere, Arndt von Haeseler *
* 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 MPDABLOCK_H
#define MPDABLOCK_H
#include "ncl/ncl.h"
#include "tools.h"
class SplitGraph;
/**
PdaBlock to read from nexus file
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class MPdaBlock : public NxsBlock
{
public:
friend class SplitGraph;
friend class PDNetwork;
friend class CircularNetwork;
/**
constructor, assigning an associated splits graph
@param asgraph a splits graph
*/
MPdaBlock(SplitGraph *asgraph);
/**
destructor
*/
virtual ~MPdaBlock();
/**
print info to an output stream
@param out output stream, cout for output to screen
*/
virtual void Report(ostream &out);
/**
reset the block
*/
virtual void Reset();
/**
called when some commands are skipped
@param commandName command name
*/
virtual void SkippingCommand(NxsString commandName);
/**
read the file containing total budget and taxa costs informations
@param params program parameters
*/
void readBudgetFile(Params ¶ms);
/**
read the file containing total budget and area costs informations
@param params program parameters
*/
void readBudgetAreaFile(Params ¶ms);
/**
@return total budget
*/
double getBudget() {
return budget;
}
/**
@return min budget
*/
double getMinBudget() {
return min_budget;
}
/**
@return size of PD set
*/
int getSubSize() {
return sub_size;
}
/**
@return cost of a taxon
*/
double getCost(int tax_id) {
assert(tax_id < (int) costs.size());
return costs[tax_id];
}
protected:
/**
the associated splits graph
*/
SplitGraph *sgraph;
/**
total budget
*/
double budget;
/**
min budget, to compute PD sets with preservation
costs from min_budget to budget
*/
double min_budget;
/**
size of PD set
*/
int sub_size;
/**
true if cost constrained PD problem
*/
bool cost_constrained;
/**
cost of each taxon
*/
vector<double> costs;
/**
main method to read block from file
@param token a token reader
*/
virtual void Read(NxsToken &token);
};
#endif
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