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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 GREEDY_H
#define GREEDY_H
#include "pdtree.h"
/**
Implementation of greedy algorithm with complexity O(n*logk)
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class Greedy : public PDTree
{
public:
/**
construct from program parameters
@param params program parameters
*/
Greedy(Params ¶ms) :
PDTree(params) {}
/**
construct from a tree
@param tree a tree class
*/
Greedy(PDTree &tree) :
PDTree(tree) {}
/**
constructor
*/
Greedy() : PDTree() {};
/**
run the algorithm
@param params program parameters
@param taxa_set (OUT) vector of PD sets
*/
void run(Params ¶ms, vector<PDTaxaSet> &taxa_set);
/**
update the ordered list based on the recent longest path
@param node the starting node
@param subtree (OUT) resulted subtree
@param cur_set the current set
*/
void updateOnLongestPath(Node *node, NodeVector &subtree, PDTaxaSet &cur_set);
/**
build the initial subtree based on the initial set of taxa
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
@param subtree (OUT) resulted subtree
@param nodestack (TEMP) stack of node, used only by function
*/
void buildOnInitialSet(NodeVector &subtree, NodeVector &nodestack, Node *node = NULL, Node *dad = NULL);
/**
initialize the ordered list based on the initial subtree structure
@param subtree vector containing nodes in the subtree
@return the subtree length
*/
double updateOnInitialSet(NodeVector &subtree);
/**
@return innodes.begin().
*/
NeighborSet::iterator highestNeighbor();
/**
add an edge into the NeighborSet
*/
void addNeighbor(Neighbor* neigh);
//NodeSet innodes;
/**
neighbor set
*/
NeighborSet neighset;
/**
list of nodes in the subtree
*/
NodeVector subtree;
private:
/**
size of list of nodes, used internally during greedy search
*/
int list_size;
};
#endif
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