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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 PDTREESET_H
#define PDTREESET_H
#include "tree/mtreeset.h"
#include "pdtree.h"
/**
Vector of PDTree
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class PDTreeSet : public MTreeSet
{
public:
PDTreeSet();
/**
constructor, read trees from user file
@param params program parameters
*/
PDTreeSet(Params ¶ms);
/**
@return a new tree
*/
virtual MTree *newTree() { return (new PDTree()); }
/**
@return true if trees are rooted
*/
bool isRootedTrees();
/**
@return number of taxa
*/
int getNTaxa();
/********************************************************
INITIALZATION
********************************************************/
/**
initialize the tree from program parameters
@param params program parameters
*/
void init(Params ¶ms);
/**
read the parameter from the file
@param params program parameters
*/
void readParams(Params ¶ms);
/**
Identify the root node if specified, include it into the initial set
@param root_name name of the root node
*/
void readRootNode(const char *root_name);
/**
read the initial set of taxa to be included into PD-tree
@param params program parameters
*/
void readInitialSet(Params ¶ms);
protected:
/**
name of initial taxa, to be included into PD set
*/
StrVector init_taxa;
};
#endif
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