libbpp-phyl-dev 2.2.0-1+b1 / usr / include / Bpp / Phyl / NodeTemplate.h

//
// File: NodeTemplate.h
// Created by: Vincent Ranwez
//             Julien Dutheil
// Created on: Thu Jun 28 18:11 2005
//

/*
Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or 
data to be ensured and,  more generally, to use and operate it in the 
same conditions as regards security. 

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _NODETEMPLATE_H_
#define _NODETEMPLATE_H_

#include "Node.h"

namespace bpp
{

/**
 * @brief The NodeTemplate class.
 *
 * This class inherits from the Node class.
 * Its is a generic way to store any information to a node.
 * A NodeTemplate only add the setInfos and getInfos methods,
 * which set and retrieve a NodeInfo, whose type is given as a template
 * of the class.
 * This class is mainly for computation conveniency, one may define a NodeInfo
 * class with several results attached.
 * An example is provided in the PGMA class.
 * Another way is to use a map<Node *, NodeInfos>, with the limitation of the
 * map access.
 * One may also wish to use the property system of the Node class, but
 * properties are stored as in a map<string, Clonable *>, with the drawbacks
 * of the slow map access and the systematic use of dynamic_cast<NodeInfo *> to
 * convert from Clonable *.
 *
 * This class redefines all constructors and access methods (get*) with return
 * types as NodeTemplate and not Node (using covariant returns).
 *
 * @see Node, TreeTemplate
 */
template<class NodeInfos>
class NodeTemplate :
  public Node
{
  friend class TreeTemplateTools;

	private:

		NodeInfos infos_;

	public:
		
		/**	
		 * @brief Build a new void NodeTemplate object.
		 */
		NodeTemplate() : Node(), infos_() {}
			
		/**
		 * @brief Build a new NodeTemplate with specified id.
		 */
		NodeTemplate(int id) : Node(id), infos_() {}

		/**
		 * @brief Build a new NodeTemplate with specified name.
		 */
		NodeTemplate(const std::string& name) : Node(name), infos_() {}

		/**
		 * @brief Build a new NodeTemplate with specified id and name.
		 */
		NodeTemplate(int id, const std::string& name) : Node(id, name), infos_() {}

  protected:
		/**
		 * @brief Copy constructor.
		 * 
		 * @param node The node to copy.
		 */
		NodeTemplate(const Node& node) : Node(node), infos_() {}

    /**
		 * @brief Copy constructor.
		 * 
		 * @param node The node to copy.
		 */
		NodeTemplate(const NodeTemplate<NodeInfos>& node):
      Node(node), infos_(node.infos_)
    {}

		/**
		 * @brief Assignation operator.
		 *
		 * @param node the node to copy.
		 * @return A reference toward this node.
		 */
		NodeTemplate<NodeInfos>& operator=(const NodeTemplate<NodeInfos>& node)
		{
      Node::operator=(node);
			infos_ = node.infos_;
			return *this;
		}

    NodeTemplate<NodeInfos>* clone() const { return new NodeTemplate<NodeInfos>(*this); }

  public:
		virtual ~NodeTemplate() {}

  public:

		const NodeTemplate<NodeInfos>* getFather() const { return dynamic_cast<const NodeTemplate<NodeInfos> *>(father_); }
 
		NodeTemplate<NodeInfos>* getFather() { return dynamic_cast<NodeTemplate<NodeInfos> *>(father_); }
				
		NodeTemplate<NodeInfos>* removeFather() { NodeTemplate<NodeInfos>* f = dynamic_cast<NodeTemplate<NodeInfos> *>(father_); father_ = 0; return f; }

		const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
				
		NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
				
    std::vector<const NodeTemplate<NodeInfos>*> getNeighbors() const
		{
      std::vector<const Node*> neighbors = Node::getNeighbors();
      std::vector<const NodeTemplate<NodeInfos>*> neighbors2(neighbors.size());
			for (size_t i = 0; i < neighbors.size(); i++)
				neighbors2[i] = dynamic_cast<const NodeTemplate<NodeInfos>*>(neighbors[i]);
			return neighbors2;
		}
		
    std::vector<NodeTemplate<NodeInfos>*> getNeighbors()
		{
      std::vector<Node*> neighbors = Node::getNeighbors();
      std::vector<NodeTemplate<NodeInfos>*> neighbors2(neighbors.size());
			for (size_t i = 0; i < neighbors.size(); i++)
				neighbors2[i] = dynamic_cast<NodeTemplate<NodeInfos>*>(neighbors[i]);
			return neighbors2;
		}
		
		NodeTemplate<NodeInfos>* operator[](int i) { return dynamic_cast<NodeTemplate<NodeInfos>*>((i < 0) ? father_ : sons_[i]); }
				
		const NodeTemplate<NodeInfos>* operator[](int i) const { return dynamic_cast<const NodeTemplate<NodeInfos> *>((i < 0) ? father_ : sons_[i]); }


		// Specific methods:

    /**
     * @return A reference toward the information object associated to this node.
     */
		virtual const NodeInfos& getInfos() const { return infos_; }
		
    /**
     * @return A reference toward the information object associated to this node.
     */
		virtual NodeInfos& getInfos() { return infos_; }

    /**
     * @brief Set the information to be associated to this node.
     * 
     * @param infos An information object.
     */
		virtual void setInfos(const NodeInfos& infos) { infos_ = infos; }

};

} //end of namespace bpp.

#endif	//_NODETEMPLATE_H_