Tree.h

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//
// File: Tree.h
// Created by: Julien Dutheil
// Created on: Thu Mar 13 12:03:18 2003
//

/*
  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 _TREE_H_
#define _TREE_H_

#include "TreeExceptions.h"

// From Utils:
#include <Bpp/Clonable.h>

// From the STL:
#include <string>
#include <vector>
#include <map>

namespace bpp
{

  class Tree:
    public virtual Clonable
  {

  public: // Constructors and destructor:
    
    Tree() {}
    virtual ~Tree() {}

    Tree* clone() const = 0;

    virtual Tree* cloneSubtree(int newRootId) const = 0;
  public:
    
    virtual std::string getName() const = 0;
    
    virtual void setName(const std::string& name) = 0;
    virtual size_t getNumberOfLeaves() const = 0;
    
    virtual size_t getNumberOfNodes() const = 0;

    virtual std::vector<double> getBranchLengths() const = 0;

    virtual std::vector<std::string> getLeavesNames() const = 0;

    virtual int getRootId() const = 0;

    virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
  
    virtual std::vector<int> getLeavesId() const = 0;

    virtual std::vector<int> getNodesId() const = 0;
    
    virtual std::vector<int> getInnerNodesId() const = 0;
    
    virtual std::vector<int> getBranchesId() const = 0;

    virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;

    virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;

    virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;

    virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;

    virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
    
    virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
    
    virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
    
    virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
    virtual bool hasNode(int nodeId) const = 0;

    virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;

    virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
    void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
  
    virtual double getDistanceToFather(int nodeId) const = 0;
    
    virtual void setDistanceToFather(int nodeId, double length) = 0;
    
    virtual void deleteDistanceToFather(int nodeId) = 0;
    
    virtual bool hasDistanceToFather(int nodeId) const = 0;
    virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
    
    virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
        
    virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
        
    virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
        
    virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;

    virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
    virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
    
    virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
        
    virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
        
    virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
        
    virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;

    virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
    virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;

    virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
    
    virtual bool isRooted() const = 0;
    
    virtual bool unroot() throw (UnrootedTreeException) = 0;

    virtual void resetNodesId() = 0;
    
    // Works on (multi)furcations:
    
    virtual bool isMultifurcating() const = 0;
    
    virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;

    virtual double getTotalLength() throw (NodeException) = 0;

    virtual void setBranchLengths(double brLen) = 0;
    
    virtual void setVoidBranchLengths(double brLen) = 0;
  
    virtual void scaleTree(double factor) throw (NodeException) = 0;

    virtual int getNextId() = 0;

  };

} //end of namespace bpp.

#endif  //_TREE_H_