The next step is to create a C++ class encapsulating the notion of a phylogenetic tree.
Create the header file tree.hpp in the src directory and fill it with the following text:
#pragma once
#include <memory>
#include <iostream>
#include "node.hpp"
namespace strom {
//class TreeManip;
//class Likelihood;
//class Updater;
class Tree {
//friend class TreeManip;
//friend class Likelihood;
//friend class Updater;
public:
Tree();
~Tree();
bool isRooted() const;
unsigned numLeaves() const;
unsigned numInternals() const;
unsigned numNodes() const;
private:
void clear();
bool _is_rooted;
Node * _root;
unsigned _nleaves;
unsigned _ninternals;
Node::PtrVector _preorder;
Node::PtrVector _levelorder;
Node::Vector _nodes;
public:
typedef std::shared_ptr< Tree > SharedPtr;
};
inline Tree::Tree() {
std::cout << "Constructing a Tree" << std::endl;
clear();
}
inline Tree::~Tree() {
std::cout << "Destroying a Tree" << std::endl;
}
inline void Tree::clear() {
_is_rooted = false;
_root = 0;
_nodes.clear();
_preorder.clear();
_levelorder.clear();
}
inline bool Tree::isRooted() const {
return _is_rooted;
}
inline unsigned Tree::numLeaves() const {
return _nleaves;
}
inline unsigned Tree::numInternals() const {
return _ninternals;
}
inline unsigned Tree::numNodes() const {
return (unsigned)_nodes.size();
}
}
Just after the pragma directive (explained earlier) are three lines that include header files. The contents of each of these header files (headers, for short) are effectively dumped into this file at the point where they are invoked. The memory header file provides the definition of std::shared_ptr (explained below). The iostream header file provides the definition of std::cout, which is used in the constructor and destructor function bodies. Finally, The node.hpp header file provides our definition of the Node class. The headers that are surrounded by <angled brackets> are system headers, while those surrounded by "quotes" are provided by you. This convention helps the compiler, which will generally look for system header files in a different place than user-provided headers.
You may note that the member functions are all labeled with the inline keyword. The inline keyword is a friendly request made to the compiler that you would like the function body to be simply copied into the place where it is called, which is often more efficient than a function call. The compiler gets to decide, however, whether the body of a particular function will actually be inlined at a particular place in the code.
The class declares a public constructor and a public destructor. As we saw for the Node class, the constructor is responsible for initializing the memory set aside to store a new Tree object, and the destructor is in charge of cleaning up the object before the memory for the object is released. Our Tree constructor calls the member function clear() to initialize the data members of the Tree class. I have (temporarily) placed code in both constructor and destructor to write output. This output will allow us to easily see when a Tree object is being constructed or destructed. We will comment out these output lines after we test the class.
The member function clear() is provided to restore a Tree object to its just-constructed state.
The functions isRooted() and numLeaves() are called accessors or accessor functions because they simply make the value of private data members available. You might ask why make _is_rooted and _nleaves private if you are going to allow public access to their values via these accessor functions. The answer is that this allows us to make the values of these data members available publicly without allowing their values to be changed. The only objects that can change _nleaves and _is_rooted are objects of class Tree or objects of classes that have been declared friends of Tree.
Finally, the member function numNodes() might be called a utility function because it calculates something, namely the length of the _nodes vector. It is a utility function rather than an accessor function because it does more work than simply returning the value of a data member.
A boolean data member _is_rooted indicates whether the Tree object should be considered rooted or unrooted. A Node pointer _root will point to the Node object serving as the root node of the Tree object (note that every tree has a root node, even if _is_rooted is false: the distinction between rooted and unrooted lies in how the likelihood is computed, not in how the tree is stored in memory). An unsigned integer _nleaves stores the number of tip nodes (leaves) in the tree. Finally, two standard vector data members store nodes. The vector _nodes stores the Node objects themselves, while the vector _preorder stores pointers to the Node objects in _nodes.
A SharedPtr type is defined that represents a shared pointer (also known as a smart pointer) to our Tree class. Smart pointers keep track of how many references there are to a particular object. Once no other object is holding on to a reference (i.e. is pointing to) an object, the smart pointer takes care of deleting the object automatically. This makes memory management much easier because you, as the programmer, do not have to remember to delete objects that are no longer being used so long as you always manage them via smart pointers.
Note that the type name we’ve defined is just SharedPtr, which is not specific to Tree. The fact that this type is defined within the Tree class declaration, however, means that we will always know the object referred to by this SharedPtr because to use it we will have to qualify it by the class name: Tree::SharedPtr tree.
As for the Node class, the TreeManip and Likelihood classes will need to have access to the private member functions and data members of the Tree class. Because TreeManip and Likelihood have not yet been created, these friend declarations are currently commented out.