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// File: TreeParsimonyData.h
// Created by: Julien Dutheil
// Created on: Tue Jan 09 17:15 2007
// From file AbstractTreeParsimonyScore.h
//
/*
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 _TREEPARSIMONYDATA_H_
#define _TREEPARSIMONYDATA_H_
#include "../Node.h"
#include "../TreeTemplate.h"
#include <Bpp/Clonable.h>
namespace bpp
{
/**
* @brief TreeParsimonyScore node data structure.
*
* Stores inner computation for a given node.
*
* @see TreeParsimonyData
*/
class TreeParsimonyNodeData :
public virtual Clonable
{
public:
TreeParsimonyNodeData() {}
virtual ~TreeParsimonyNodeData() {}
#ifndef NO_VIRTUAL_COV
TreeParsimonyNodeData* clone() const = 0;
#endif
public:
/**
* @brief Get the node associated to this data structure.
*
* @return The node associated to this structure.
*/
virtual const Node* getNode() const = 0;
/**
* @brief Set the node associated to this data
*
* @param node A pointer toward the node to be associated to this data.
*/
virtual void setNode(const Node* node) = 0;
};
/**
* @brief TreeParsimonyScore data structure.
*
* Stores all the inner computations:
* - subtree scores and ancestral states for each node,
* - correspondance between sites in the dataset and array indices.
*
* @see TreeParsimonyNodeData
*/
class TreeParsimonyData :
public virtual Clonable
{
public:
TreeParsimonyData() {}
virtual ~TreeParsimonyData() {}
#ifndef NO_VIRTUAL_COV
TreeParsimonyData* clone() const = 0;
#endif
public:
virtual const TreeTemplate<Node>* getTree() const = 0;
virtual size_t getArrayPosition(int parentId, int sonId, size_t currentPosition) const = 0;
virtual size_t getRootArrayPosition(size_t site) const = 0;
virtual TreeParsimonyNodeData& getNodeData(int nodeId) = 0;
virtual const TreeParsimonyNodeData& getNodeData(int nodeId) const = 0;
};
} // end of namespace bpp.
#endif // _TREEPARSIMONYDATA_H_
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