PhyloTree< T > Class Template Reference

#include <PhyloTree.h>

List of all members.

Public Member Functions
const T &	back () const
T &	back ()
void	clear ()
double	getHeight (node_id_t nodeI) const
	Determines the height of the tree along the path from nodeI to its left-most descendant leaf node.
double	getHeight () const
	Determines the height of the tree along the path from the root to the left-most leaf node.
PhyloTree< T > &	operator= (const PhyloTree< T > &pt)
const T &	operator[] (const unsigned i) const
T &	operator[] (const unsigned i)
	PhyloTree (const PhyloTree< T > &pt)
	PhyloTree ()
void	push_back (T &t)
void	readTree (std::istream &tree_file)
	Reads a tree in Newick format.
void	resize (const unsigned s)
size_t	size () const
void	swap (PhyloTree< T > &other)
void	writeTree (std::ostream &os) const
	Writes a tree in Newick format.
	~PhyloTree ()
Public Attributes
std::vector< T >	nodes
	nodes of the tree
node_id_t	root
	root of the tree
double	weight
	Overall tree weight.

template<class T>
class PhyloTree< T >

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Constructor & Destructor Documentation

template<class T> PhyloTree< T >::PhyloTree (   )

Definition at line 75 of file PhyloTree.h. References PhyloTree< T >::root.

template<class T> PhyloTree< T >::PhyloTree (  const PhyloTree< T > &  pt  )

Definition at line 82 of file PhyloTree.h.

template<class T> PhyloTree< T >::~PhyloTree (   )

Definition at line 98 of file PhyloTree.h.

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Member Function Documentation

template<class T> const T& PhyloTree< T >::back (   )  const [inline]

Definition at line 60 of file PhyloTree.h.

template<class T> T& PhyloTree< T >::back (   )  [inline]

Definition at line 59 of file PhyloTree.h.

template<class T> void PhyloTree< T >::clear (   )

Definition at line 102 of file PhyloTree.h. References PhyloTree< T >::nodes, and PhyloTree< T >::root. Referenced by PhyloTree< T >::readTree().

template<class T> double PhyloTree< T >::getHeight (  node_id_t  nodeI  )  const

Determines the height of the tree along the path from nodeI to its left-most descendant leaf node. Definition at line 321 of file PhyloTree.h. References PhyloTree< T >::getHeight().

template<class T> double PhyloTree< T >::getHeight (   )  const

Determines the height of the tree along the path from the root to the left-most leaf node. Definition at line 315 of file PhyloTree.h. References PhyloTree< T >::root. Referenced by PhyloTree< T >::getHeight().

template<class T> PhyloTree< T > & PhyloTree< T >::operator= (  const PhyloTree< T > &  pt  )

Definition at line 89 of file PhyloTree.h. References PhyloTree< T >::nodes, PhyloTree< T >::root, and PhyloTree< T >::weight.

template<class T> const T& PhyloTree< T >::operator[] (  const unsigned  i  )  const [inline]

Definition at line 56 of file PhyloTree.h.

template<class T> T& PhyloTree< T >::operator[] (  const unsigned  i  )  [inline]

Definition at line 55 of file PhyloTree.h.

template<class T> void PhyloTree< T >::push_back (  T &  t  )  [inline]

Definition at line 58 of file PhyloTree.h.

template<class T> void PhyloTree< T >::readTree (  std::istream &  tree_file  )

Reads a tree in Newick format. WARNING: only reads rooted trees correctly < read_state of 0 indicates nothing has been parsed yet Definition at line 115 of file PhyloTree.h. References PhyloTree< T >::clear(), node_id_t, PhyloTree< T >::nodes, and uint.

template<class T> void PhyloTree< T >::resize (  const unsigned  s  )  [inline]

Definition at line 61 of file PhyloTree.h.

template<class T> size_t PhyloTree< T >::size (   )  const [inline]

Definition at line 57 of file PhyloTree.h. Referenced by PhyloTree< T >::writeTree().

template<class T> void PhyloTree< T >::swap (  PhyloTree< T > &  other  )  [inline]

Definition at line 64 of file PhyloTree.h. Referenced by std::swap().

template<class T> void PhyloTree< T >::writeTree (  std::ostream &  os  )  const

Writes a tree in Newick format. Definition at line 256 of file PhyloTree.h. References node_id_t, PhyloTree< T >::root, and PhyloTree< T >::size().

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Member Data Documentation

template<class T> std::vector< T > PhyloTree< T >::nodes

nodes of the tree Definition at line 36 of file PhyloTree.h. Referenced by PhyloTree< T >::clear(), PhyloTree< T >::operator=(), PhyloTree< T >::readTree(), and PhyloTree< AlignmentTreeNode >::swap().

template<class T> node_id_t PhyloTree< T >::root

root of the tree Definition at line 35 of file PhyloTree.h. Referenced by PhyloTree< T >::clear(), PhyloTree< T >::getHeight(), PhyloTree< T >::operator=(), PhyloTree< T >::PhyloTree(), PhyloTree< AlignmentTreeNode >::swap(), and PhyloTree< T >::writeTree().

template<class T> double PhyloTree< T >::weight

Overall tree weight. Definition at line 34 of file PhyloTree.h. Referenced by PhyloTree< T >::operator=(), and PhyloTree< AlignmentTreeNode >::swap().

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The documentation for this class was generated from the following file:

• libMems/PhyloTree.h

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