A template class representing a node from a Newick tree. More...

#include <jade.newick.hpp>

Collaboration diagram for jade::basic_newick_node< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...

typedef const basic_newick_node *	const_pointer_type
	The constant Newick node pointer type. More...

typedef basic_newick_node *	pointer_type
	The Newick node pointer type. More...

typedef std::vector< pointer_type >	children_type
	The children vector type. More...

typedef basic_scanner< char >	scanner_type
	The scanner type. More...

Public Member Functions
	~basic_newick_node ()
	Reclaims resources used by this instance and its children. More...

	basic_newick_node ()
	Initializes a new instance of the class. Initially, the instance has no name, no length, no parent, and no children. More...

	basic_newick_node (std::istream &in)
	Initializes a new instance of the class from the specified input stream. The input stream must end with a semicolon. If an error occurs, the method throws an exception. More...

	basic_newick_node (const std::string &in)
	Initializes a new instance of the class from the specified input string. The input string must end with a semicolon. If an error occurs, the method throws an exception. More...

void	erase_length ()
	Erases the length. More...

template<typename TPredicate >
std::set< const_pointer_type >	find_all (const TPredicate predicate) const

template<typename TPredicate >
std::set< pointer_type >	find_all (const TPredicate predicate)

std::set< const_pointer_type >	find_descendents () const

std::set< pointer_type >	find_descendents ()

template<typename TPredicate >
const_pointer_type	find_first (const TPredicate predicate) const

template<typename TPredicate >
pointer_type	find_first (const TPredicate predicate)

const_pointer_type	find_id (const int id) const

pointer_type	find_id (const int id)

std::set< const_pointer_type >	find_leafs () const

std::set< pointer_type >	find_leafs ()

const_pointer_type	find_name (char const *const name) const

pointer_type	find_name (char const *const name)

const_pointer_type	find_root () const

pointer_type	find_root ()

template<typename TAction >
void	for_each (const TAction action) const
	Executes the specified action for all descendent nodes, including this instance, in depth-first order. More...

template<typename TAction >
void	for_each (const TAction action)
	Executes the specified action for all descendent nodes, including this instance, in depth-first order. More...

const children_type &	get_children () const

int	get_id () const

value_type	get_length () const

const std::string &	get_name () const

const_pointer_type	get_parent () const

pointer_type	get_parent ()

bool	has_length () const

bool	has_name () const

bool	is_leaf () const

bool	is_root () const

pointer_type	reroot () const
	Creates a new tree based on the tree associated with this node; in the tree returned, a copy of this node is the root. More...

void	set_length (const value_type length)
	Assigns the length. More...

void	set_name (char const *const name)
	Assigns the name. More...

std::string	str () const
	Encodes this instance and returns the output as a string. A semicolon is written as the last character of the file. More...

void	write (std::ostream &out) const
	Writes this instance into the specified output stream. The output stream receives a semicolon after the tree data. More...

void	write (char const *const path) const
	Writes this instance into the specified file. A semicolon is written as the last character of the file. More...

void	write (const std::string &path) const
	Writes this instance into the specified file. A semicolon is written as the last character of the file. More...

Static Public Member Functions
static pointer_type	from_file (char const *const path)

static basic_newick_node *	from_file (const std::string &path)

Detailed Description

template<typename TValue>
class jade::basic_newick_node< TValue >

A template class representing a node from a Newick tree.

Definition at line 18 of file jade.newick.hpp.

Member Typedef Documentation

◆ children_type

template<typename TValue >

typedef std::vector<pointer_type> jade::basic_newick_node< TValue >::children_type

The children vector type.

Definition at line 31 of file jade.newick.hpp.

◆ const_pointer_type

template<typename TValue >

typedef const basic_newick_node* jade::basic_newick_node< TValue >::const_pointer_type

The constant Newick node pointer type.

Definition at line 25 of file jade.newick.hpp.

◆ pointer_type

template<typename TValue >

typedef basic_newick_node* jade::basic_newick_node< TValue >::pointer_type

The Newick node pointer type.

Definition at line 28 of file jade.newick.hpp.

◆ scanner_type

template<typename TValue >

typedef basic_scanner<char> jade::basic_newick_node< TValue >::scanner_type

The scanner type.

Definition at line 34 of file jade.newick.hpp.

◆ value_type

template<typename TValue >

typedef TValue jade::basic_newick_node< TValue >::value_type

The value type.

Definition at line 22 of file jade.newick.hpp.

Constructor & Destructor Documentation

◆ ~basic_newick_node()

template<typename TValue >

jade::basic_newick_node< TValue >::~basic_newick_node ( )

inline

Reclaims resources used by this instance and its children.

Definition at line 39 of file jade.newick.hpp.

         {
             _destruct();
         }

◆ basic_newick_node() [1/3]

template<typename TValue >

jade::basic_newick_node< TValue >::basic_newick_node ( )

inline

Initializes a new instance of the class. Initially, the instance has no name, no length, no parent, and no children.

Definition at line 48 of file jade.newick.hpp.

             : _children   ()
             , _has_length (false)
             , _id         (0)
             , _length     (0)
             , _name       ()
             , _parent     ()
         {
         }

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◆ basic_newick_node() [2/3]

template<typename TValue >

jade::basic_newick_node< TValue >::basic_newick_node ( std::istream & in )

inlineexplicit

Initializes a new instance of the class from the specified input stream. The input stream must end with a semicolon. If an error occurs, the method throws an exception.

Exceptions

jade::error Thrown if there is an error parsing the tree.

Parameters

in	The input stream to read.

Definition at line 65 of file jade.newick.hpp.

             : basic_newick_node ()
         {
             scanner_type s (in);
             _read(s);
         }

◆ basic_newick_node() [3/3]

template<typename TValue >

jade::basic_newick_node< TValue >::basic_newick_node ( const std::string & in )

inlineexplicit

Initializes a new instance of the class from the specified input string. The input string must end with a semicolon. If an error occurs, the method throws an exception.

Exceptions

jade::error Thrown if there is an error parsing the tree.

Parameters

in	The input string to read.

Definition at line 80 of file jade.newick.hpp.

             : basic_newick_node ()
         {
             scanner_type s (in);
             _read(s);
         }

Member Function Documentation

◆ erase_length()

template<typename TValue >

void jade::basic_newick_node< TValue >::erase_length ( )

inline

Erases the length.

Definition at line 91 of file jade.newick.hpp.

         {
             _length = 0;
             _has_length = false;
         }

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◆ find_all() [1/2]

template<typename TValue >

template<typename TPredicate >

std::set<pointer_type> jade::basic_newick_node< TValue >::find_all ( const TPredicate predicate )

inline

Returns: A colleciton of all descendents that match the specified predicate. The method searches in depth-first order and examines this node as well.

Parameters

predicate The predicate to match.

Definition at line 126 of file jade.newick.hpp.

         {
             std::set<pointer_type> container;
  
             this->for_each([predicate, &container](
                      pointer_type node)
                      -> void
             {
                 if (predicate(node))
                     container.insert(node);
             });
  
             return container;
         }

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◆ find_all() [2/2]

template<typename TValue >

template<typename TPredicate >

std::set<const_pointer_type> jade::basic_newick_node< TValue >::find_all ( const TPredicate predicate ) const

inline

Returns: A colleciton of all descendents that match the specified predicate. The method searches in depth-first order and examines this node as well.

Parameters

predicate The predicate to match.

Definition at line 103 of file jade.newick.hpp.

         {
             std::set<const_pointer_type> container;
  
             this->for_each([predicate, &container](
                      const_pointer_type node)
                      -> void
             {
                 if (predicate(node))
                     container.insert(node);
             });
  
             return container;
         }

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◆ find_descendents() [1/2]

template<typename TValue >

std::set<pointer_type> jade::basic_newick_node< TValue >::find_descendents ( )

inline

Returns: The collection of descendents of this node.

Definition at line 156 of file jade.newick.hpp.

         {
             return find_all([this](pointer_type node) -> bool
             {
                 return node != this;
             });
         }

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◆ find_descendents() [2/2]

template<typename TValue >

std::set<const_pointer_type> jade::basic_newick_node< TValue >::find_descendents ( ) const

inline

Returns: The collection of descendents of this node.

Definition at line 145 of file jade.newick.hpp.

         {
             return find_all([this](const_pointer_type node) -> bool
             {
                 return node != this;
             });
         }

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◆ find_first() [1/2]

template<typename TValue >

template<typename TPredicate >

pointer_type jade::basic_newick_node< TValue >::find_first ( const TPredicate predicate )

inline

Returns: The first descendent that matches the specified predicate. The method searches in depth-first order and examines this node as well.

Parameters

predicate The predicate to match.

Definition at line 190 of file jade.newick.hpp.

         {
             for (auto child : _children)
             {
                 const pointer_type first = child->find_first(predicate);
                 if (nullptr != first)
                     return first;
             }
  
             return predicate(this) ? this : nullptr;
         }

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◆ find_first() [2/2]

template<typename TValue >

template<typename TPredicate >

const_pointer_type jade::basic_newick_node< TValue >::find_first ( const TPredicate predicate ) const

inline

Returns: The first descendent that matches the specified predicate. The method searches in depth-first order and examines this node as well.

Parameters

predicate The predicate to match.

Definition at line 170 of file jade.newick.hpp.

         {
             for (auto child : _children)
             {
                 const auto first = child->find_first(predicate);
                 if (nullptr != first)
                     return first;
             }
  
             return predicate(this) ? this : nullptr;
         }

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◆ find_id() [1/2]

template<typename TValue >

pointer_type jade::basic_newick_node< TValue >::find_id ( const int id )

inline

Returns: The node with the specified id.

Parameters

id	The id of the node to find.

Definition at line 219 of file jade.newick.hpp.

         {
             return find_first([id](pointer_type node) -> bool
             {
                 return node->_id == id;
             });
         }

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◆ find_id() [2/2]

template<typename TValue >

const_pointer_type jade::basic_newick_node< TValue >::find_id ( const int id ) const

inline

Returns: The node with the specified id.

Parameters

id	The id of the node to find.

Definition at line 206 of file jade.newick.hpp.

         {
             return find_first([id](const_pointer_type node) -> bool
             {
                 return node->_id == id;
             });
         }

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◆ find_leafs() [1/2]

template<typename TValue >

std::set<pointer_type> jade::basic_newick_node< TValue >::find_leafs ( )

inline

Returns: The set of leaf nodes. If this node is a leaf node, it is returned in the collection.

Definition at line 244 of file jade.newick.hpp.

         {
             return find_all([](pointer_type node) -> bool
             {
                 return node->is_leaf();
             });
         }

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◆ find_leafs() [2/2]

template<typename TValue >

std::set<const_pointer_type> jade::basic_newick_node< TValue >::find_leafs ( ) const

inline

Returns: The set of leaf nodes. If this node is a leaf node, it is returned in the collection.

Definition at line 232 of file jade.newick.hpp.

         {
             return find_all([](const_pointer_type node) -> bool
             {
                 return node->is_leaf();
             });
         }

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◆ find_name() [1/2]

template<typename TValue >

pointer_type jade::basic_newick_node< TValue >::find_name ( char const *const name )

inline

Returns: The node with the specified name.

Parameters

name	The name of the node to find.

Definition at line 268 of file jade.newick.hpp.

         {
             return find_first([name](pointer_type node) -> bool
             {
                 return node->_name == name;
             });
         }

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◆ find_name() [2/2]

template<typename TValue >

const_pointer_type jade::basic_newick_node< TValue >::find_name ( char const *const name ) const

inline

Returns: The node with the specified name.

Parameters

name	The name of the node to find.

Definition at line 255 of file jade.newick.hpp.

         {
             return find_first([name](const_pointer_type node) -> bool
             {
                 return node->_name == name;
             });
         }

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◆ find_root() [1/2]

template<typename TValue >

pointer_type jade::basic_newick_node< TValue >::find_root ( )

inline

Returns: The root of the tree associated with this node.

Definition at line 288 of file jade.newick.hpp.

         {
             return is_root() ? this : _parent->find_root();
         }

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◆ find_root() [2/2]

template<typename TValue >

const_pointer_type jade::basic_newick_node< TValue >::find_root ( ) const

inline

Returns: The root of the tree associated with this node.

Definition at line 280 of file jade.newick.hpp.

         {
             return is_root() ? this : _parent->find_root();
         }

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◆ for_each() [1/2]

template<typename TValue >

template<typename TAction >

void jade::basic_newick_node< TValue >::for_each ( const TAction action )

inline

Executes the specified action for all descendent nodes, including this instance, in depth-first order.

Parameters

action The action to perform.

Definition at line 313 of file jade.newick.hpp.

         {
             for (auto child : _children)
                 child->for_each(action);
  
             action(this);
         }

◆ for_each() [2/2]

template<typename TValue >

template<typename TAction >

void jade::basic_newick_node< TValue >::for_each ( const TAction action ) const

inline

Executes the specified action for all descendent nodes, including this instance, in depth-first order.

Parameters

action The action to perform.

Definition at line 298 of file jade.newick.hpp.

         {
             for (auto child : _children)
                 child->for_each(action);
  
             action(this);
         }

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◆ from_file() [1/2]

template<typename TValue >

static pointer_type jade::basic_newick_node< TValue >::from_file ( char const *const path )

inlinestatic

Returns: A new instance based on the specified file.

Exceptions

jade::error Thrown if there is an error parsing the tree.

Parameters

path	The path to the file.

Definition at line 327 of file jade.newick.hpp.

         {
             std::ifstream in (path);
             return new basic_newick_node(in);
         }

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◆ from_file() [2/2]

template<typename TValue >

static basic_newick_node* jade::basic_newick_node< TValue >::from_file ( const std::string & path )

inlinestatic

Returns: A new instance based on the specified file.

Exceptions

jade::error Thrown if there is an error parsing the tree.

Parameters

path	The path to the file to decode.

Definition at line 339 of file jade.newick.hpp.

         {
             return from_file(path.c_str());
         }

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◆ get_children()

template<typename TValue >

const children_type& jade::basic_newick_node< TValue >::get_children ( ) const

inline

Returns: The collection of immediate children of this node.

Definition at line 348 of file jade.newick.hpp.

         {
             return _children;
         }

◆ get_id()

template<typename TValue >

int jade::basic_newick_node< TValue >::get_id ( ) const

inline

Returns: The unique ID for this node within the tree. If the tree is rerooted, this id persists into the new tree.

Definition at line 357 of file jade.newick.hpp.

         {
             return _id;
         }

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◆ get_length()

template<typename TValue >

value_type jade::basic_newick_node< TValue >::get_length ( ) const

inline

Returns: The length of this node; the length is valid only if the has_length method returns true.

Definition at line 366 of file jade.newick.hpp.

         {
             return _length;
         }

◆ get_name()

template<typename TValue >

const std::string& jade::basic_newick_node< TValue >::get_name ( ) const

inline

Returns: The name of this node.

Definition at line 374 of file jade.newick.hpp.

         {
             return _name;
         }

◆ get_parent() [1/2]

template<typename TValue >

pointer_type jade::basic_newick_node< TValue >::get_parent ( )

inline

Returns: The parent of this node.

Definition at line 390 of file jade.newick.hpp.

         {
             return _parent;
         }

◆ get_parent() [2/2]

template<typename TValue >

const_pointer_type jade::basic_newick_node< TValue >::get_parent ( ) const

inline

Returns: The parent of this node.

Definition at line 382 of file jade.newick.hpp.

         {
             return _parent;
         }

◆ has_length()

template<typename TValue >

bool jade::basic_newick_node< TValue >::has_length ( ) const

inline

Returns: True if the node has a defined length.

Definition at line 398 of file jade.newick.hpp.

         {
             return _has_length;
         }

◆ has_name()

template<typename TValue >

bool jade::basic_newick_node< TValue >::has_name ( ) const

inline

Returns: True if the node has a name.

Definition at line 406 of file jade.newick.hpp.

         {
             return !_name.empty();
         }

◆ is_leaf()

template<typename TValue >

bool jade::basic_newick_node< TValue >::is_leaf ( ) const

inline

Returns: True if the node has no children; i.e. it is a leaf node.

Definition at line 414 of file jade.newick.hpp.

         {
             return _children.empty();
         }

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◆ is_root()

template<typename TValue >

bool jade::basic_newick_node< TValue >::is_root ( ) const

inline

Returns: True if the node has no parent; i.e. it is a root node.

Definition at line 422 of file jade.newick.hpp.

         {
             return _parent == nullptr;
         }

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◆ reroot()

template<typename TValue >

pointer_type jade::basic_newick_node< TValue >::reroot ( ) const

inline

Creates a new tree based on the tree associated with this node; in the tree returned, a copy of this node is the root.

Returns: A new Newick node, the root of an equivalent tree.

Definition at line 433 of file jade.newick.hpp.

         {
             //
             // Reroot the structure of the tree.
             //
             auto root = _clone();
             _copy_children(this, root, nullptr);
             _copy_parents(this, root);
  
             //
             // To preserve information, assign the length
             // to the old root to this new root.
             //
             auto old_root = find_root();
             root->_length = old_root->_length;
             root->_has_length = old_root->_has_length;
  
             return root;
         }

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◆ set_length()

template<typename TValue >

void jade::basic_newick_node< TValue >::set_length ( const value_type length )

inline

Assigns the length.

Parameters

length The length to assign.

Definition at line 456 of file jade.newick.hpp.

         {
             assert(!std::isnan(length));
             assert(!std::isinf(length));
             _length = length;
             _has_length = true;
         }

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◆ set_name()

template<typename TValue >

void jade::basic_newick_node< TValue >::set_name ( char const *const name )

inline

Assigns the name.

Parameters

name	The name to assign.

Definition at line 468 of file jade.newick.hpp.

         {
             assert(name != nullptr);
             _name = name;
         }

◆ str()

template<typename TValue >

std::string jade::basic_newick_node< TValue >::str ( ) const

inline

Encodes this instance and returns the output as a string. A semicolon is written as the last character of the file.

Returns: The encoded string.

Definition at line 481 of file jade.newick.hpp.

         {
             std::ostringstream out;
             write(out);
             return out.str();
         }

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◆ write() [1/3]

template<typename TValue >

void jade::basic_newick_node< TValue >::write ( char const *const path ) const

inline

Writes this instance into the specified file. A semicolon is written as the last character of the file.

Parameters

path	The path to the output file.

Definition at line 504 of file jade.newick.hpp.

         {
             std::ofstream out (path);
             write(out);
             out << std::endl;
         }

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◆ write() [2/3]

template<typename TValue >

void jade::basic_newick_node< TValue >::write ( const std::string & path ) const

inline

Writes this instance into the specified file. A semicolon is written as the last character of the file.

Parameters

path	The path to the output file.

Definition at line 517 of file jade.newick.hpp.

         {
             write(path.c_str());
         }

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◆ write() [3/3]

template<typename TValue >

void jade::basic_newick_node< TValue >::write ( std::ostream & out ) const

inline

Writes this instance into the specified output stream. The output stream receives a semicolon after the tree data.

Parameters

out	The output stream.

Definition at line 492 of file jade.newick.hpp.

         {
             _write(out);
             out << ';';
         }

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

jade.newick.hpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

template<typename TValue> class jade::basic_newick_node< TValue >

Member Typedef Documentation

◆ children_type

◆ const_pointer_type

◆ pointer_type

◆ scanner_type

◆ value_type

Constructor & Destructor Documentation

◆ ~basic_newick_node()

◆ basic_newick_node() [1/3]

◆ basic_newick_node() [2/3]

◆ basic_newick_node() [3/3]

Member Function Documentation

◆ erase_length()

◆ find_all() [1/2]

◆ find_all() [2/2]

◆ find_descendents() [1/2]

◆ find_descendents() [2/2]

◆ find_first() [1/2]

◆ find_first() [2/2]

◆ find_id() [1/2]

◆ find_id() [2/2]

◆ find_leafs() [1/2]

◆ find_leafs() [2/2]

◆ find_name() [1/2]

◆ find_name() [2/2]

◆ find_root() [1/2]

◆ find_root() [2/2]

◆ for_each() [1/2]

◆ for_each() [2/2]

◆ from_file() [1/2]

◆ from_file() [2/2]

◆ get_children()

◆ get_id()

◆ get_length()

◆ get_name()

◆ get_parent() [1/2]

◆ get_parent() [2/2]

◆ has_length()

◆ has_name()

◆ is_leaf()

◆ is_root()

◆ reroot()

◆ set_length()

◆ set_name()

◆ str()

◆ write() [1/3]

◆ write() [2/3]

◆ write() [3/3]

template<typename TValue>
class jade::basic_newick_node< TValue >