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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. *
***************************************************************************/
#ifndef SUPERNODE_H
#define SUPERNODE_H
#include "phylonode.h"
typedef vector<PhyloNeighbor*> PhyloNeighborVec;
/**
A neighbor in a phylogenetic SUPER tree
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class SuperNeighbor : public PhyloNeighbor {
friend class SuperNode;
friend class PhyloSuperTree;
public:
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
*/
SuperNeighbor(Node *anode, double alength) : PhyloNeighbor(anode, alength) {
}
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
@param aid branch ID
*/
SuperNeighbor(Node *anode, double alength, int aid) : PhyloNeighbor(anode, alength, aid) {
}
/**
construct class with another Neighbor
@param nei another Neighbor
*/
SuperNeighbor(SuperNeighbor *nei) : PhyloNeighbor(nei) {
}
/**
allocate a new Neighbor by just copying from this one
@return pointer to newly created Neighbor
*/
virtual Neighbor* newNeighbor() {
return (new SuperNeighbor(this));
}
/**
vector of size m (m = #partitions)
*/
PhyloNeighborVec link_neighbors;
};
/**
Node of a super tree
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class SuperNode : public PhyloNode
{
friend class PhyloSuperTree;
public:
/**
constructor
*/
SuperNode();
/**
constructor
@param aid id of this node
*/
SuperNode(int aid);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
SuperNode(int aid, int aname);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
SuperNode(int aid, const char *aname);
/**
initialization
*/
void init();
/**
add a neighbor
@param node the neighbor node
@param length branch length
@param id branch ID
*/
virtual void addNeighbor(Node *node, double length, int id = -1);
~SuperNode();
};
#endif
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