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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 PRUNING_H
#define PRUNING_H
#include "pdtree.h"
/**
Implementation of Pruning algorithm with complexity O(n*log(n-k))
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class Pruning : public PDTree
{
public:
/**
construct from program parameters
@param params program parameters
*/
Pruning(Params ¶ms) :
PDTree(params) {}
/**
constructor, get from another tree
@param tree another MTree
*/
Pruning(PDTree &tree) :
PDTree(tree) {}
/**
constructor
*/
Pruning() : PDTree() {};
/**
run the algorithm
@param params program parameters
@param taxa_set (OUT) vector of PD sets
*/
void run(Params ¶ms, vector<PDTaxaSet> &taxa_set);
/**
delete an external node
@param pos the position of the node in the LeafSet
*/
void deleteExNode(LeafSet::iterator pos);
/**
build the list of all leaves into field leaves.
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
void buildLeaves(Node *node = NULL, Node *dad = NULL);
/**
print all leaves into screen
*/
void printLeaves();
/**
find the iterator to the leaf node in leaves field
@param node a leaf node.
@return iterator to the leaf node in leaves field
*/
LeafSet::iterator findNode(Node *node);
/**
@return leaves.begin().
*/
LeafSet::iterator nearestLeaf();
/**
mark the node in the initial set to be not PRUNABLE
*/
void doInitialSet();
/**
insert a leaf into the LeafSet
@param leaf leaf node to be inserted
*/
void addLeaf(Node* leaf);
/**
leaf set of the tree, used for pruning algorithm
*/
LeafSet leaves;
/**
maximum size of the ordered list of leaves
*/
int list_size;
};
#endif
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