Nucleotide Class Reference
[Molecular Datastructures]

#include <nucleotide.h>

Inheritance diagram for Nucleotide:


Public Types
Enums
enum	Property { PROPERTY__5_PRIME = Residue::NUMBER_OF_PROPERTIES + 1, PROPERTY__3_PRIME, PROPERTY__NUCLEOTIDE, NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer.
Public Member Functions
bool	operator== (const Nucleotide &nucleotide) const throw ()
	Equality operator.
bool	operator!= (const Nucleotide &nucleotide) const throw ()
	Inequality operator.
Constructors and Destructors
	Nucleotide () throw ()
	Default constructor.
	Nucleotide (const Nucleotide &nucleotide, bool deep=true) throw ()
	Copy constructor.
	Nucleotide (const String &name, const String &id=BALL_NUCLEOTIDE_DEFAULT_ID, char insertion_code=BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE) throw ()
	Detailled constructor.
virtual	~Nucleotide () throw ()
	Destructor.
virtual void	clear () throw ()
	Clears the nucleotides contents.
virtual void	destroy () throw ()
	Clears the nucleotides contents and removes it from all composite structures.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a Nucleotide object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a Nucleotide object from a persistent stream.
Assignment
void	set (const Nucleotide &nucleotide, bool deep=true) throw ()
	Assignment with cloning facility.
Nucleotide &	operator= (const Nucleotide &nucleotide) throw ()
	Assignment operator.
void	get (Nucleotide &nucleotide, bool deep=true) const throw ()
	Copy this instance to nucleotide .
void	swap (Nucleotide &nucleotide) throw ()
	Swapping of instaces of nucleotide.
Accessors
NucleicAcid *	getNucleicAcid () throw ()
	Get a pointer to the parent NucleicAcid.
const NucleicAcid *	getNucleicAcid () const throw ()
	Get a pointer to the parent NucleicAcid.
void	setID (const String &id) throw ()
	Set the ID of the nucleotide.
const String &	getID () const throw ()
	Retrieve the ID of the nucleotide.
void	setInsertionCode (char insertion_code) throw ()
	Set the insertion code of the nucleotide.
char	getInsertionCode () const throw ()
	Retrieve the insertion code of the nucleotide.
void	prepend (Atom &atom) throw ()
	Prepend an atom at position 0.
void	append (Atom &atom) throw ()
	Append an atom after the last position.
void	insert (Atom &atom) throw ()
	Insert an atom after the last position.
void	insertBefore (Atom &atom, Composite &before) throw ()
	Insert an atom before a given Composite object.
void	insertAfter (Atom &atom, Composite &after) throw ()
	Insert an atom after a given Composite object.
bool	remove (Atom &atom) throw ()
	Remove an atom.
void	spliceBefore (Nucleotide &nucleotide) throw ()
	Cut all children of `nucleotide` and prepend them before the children of this instance.
void	spliceAfter (Nucleotide &nucleotide) throw ()
	Cut all children of `nucleotide` and append them after the children of this instance.
void	splice (Nucleotide &nucleotide) throw ()
	Move the children of `nucleotide` into this instance.
Predicates
bool	isTerminal () const throw ()
	Test if this instance nucleotide is terminal.
bool	is3Prime () const throw ()
	Test if this instance nucleotide is 3-prime.
bool	is5Prime () const throw ()
	Test if this instance nucleotide is 5-prime.
Debugging and Diagnostics
virtual bool	isValid () const throw ()
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	Internal state dump.

Detailed Description

Nucleotide class.

This class is used to represent nucleotides within an NucleicAcid object.

Member Function Documentation

void Nucleotide::append ( Atom & atom ) throw ()

Append an atom after the last position.

Parameters:

atom the atom to append

Reimplemented from AtomContainer.

virtual void Nucleotide::dump ( std::ostream & s = std::cout,

Size depth = 0

) const throw () [virtual]

Internal state dump.
Dump the current internal state of this instance to the output ostream s with dumping depth depth .
Parameters:

s output stream where to output the internal state of this instance nucleotide

depth the dumping depth

Reimplemented from Fragment.

void Nucleotide::get ( Nucleotide & nucleotide,

bool deep = true

) const throw ()

Copy this instance to nucleotide .
The assignment is either deep or shallow (default).
Parameters:

nucleotide the nucleotide to be assigned to

See also:
nucleotide::set

const String& Nucleotide::getID ( ) const throw ()

Retrieve the ID of the nucleotide.

Returns:
String the ID (constant)

char Nucleotide::getInsertionCode ( ) const throw ()

Retrieve the insertion code of the nucleotide.

Returns:
String the insertion code (constant)

const NucleicAcid* Nucleotide::getNucleicAcid ( ) const throw ()

Get a pointer to the parent NucleicAcid.
The pointer is 0 if this instance nucleotide does not have a parent NucleicAcid.
Returns:
NucleicAcid* - constant pointer to the parent NucleicAcid

NucleicAcid* Nucleotide::getNucleicAcid ( ) throw ()

Get a pointer to the parent NucleicAcid.
The pointer is 0 if this instance nucleotide does not have a parent NucleicAcid.
Returns:
NucleicAcid* - mutable pointer to the parent NucleicAcid

void Nucleotide::insert ( Atom & atom ) throw ()

Insert an atom after the last position.

Parameters:

atom the atom to insert

Reimplemented from AtomContainer.

void Nucleotide::insertAfter ( Atom & atom,

Composite & after

) throw ()

Insert an atom after a given Composite object.

Parameters:

atom the atom to insert

after the Composite object to insert after

Reimplemented from AtomContainer.

void Nucleotide::insertBefore ( Atom & atom,

Composite & before

) throw ()

Insert an atom before a given Composite object.

Parameters:

atom the atom to insert

before the Composite object to insert before

Reimplemented from AtomContainer.

bool Nucleotide::is3Prime ( ) const throw ()

Test if this instance nucleotide is 3-prime.
Returns true, if this instance is the first nucleotide in its parent NucleicAcid.
Returns:
bool

bool Nucleotide::is5Prime ( ) const throw ()

Test if this instance nucleotide is 5-prime.
Returns true, if this instance is the last nucleotide in its parent NucleicAcid.
Returns:
bool

bool Nucleotide::isTerminal ( ) const throw ()

Test if this instance nucleotide is terminal.
Returns true, if this instance is the first or last nucleotide in its parent NucleicAcid.
Returns:
bool

virtual bool Nucleotide::isValid ( ) const throw () [virtual]

Internal state and consistency self-validation.

Returns:
bool - true if the internal state of this instance nucleotide is correct (self-validated) and consistent, false otherwise

Reimplemented from AtomContainer.

bool Nucleotide::operator!= ( const Nucleotide & nucleotide ) const throw ()

Inequality operator.

See also:
operator ==

Nucleotide& Nucleotide::operator= ( const Nucleotide & nucleotide ) throw ()

Assignment operator.
The assignment is either deep or shallow (default).
Parameters:

nucleotide the nucleotide to be copied (cloned)

Returns:
nucleotide& - this instance nucleotide

See also:
nucleotide::set

bool Nucleotide::operator== ( const Nucleotide & nucleotide ) const throw ()

Equality operator.
Two nucleotides are equal if they have the same handle.
See also:
Object::operator ==.

void Nucleotide::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Reads a Nucleotide object from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from Fragment.

void Nucleotide::persistentWrite ( PersistenceManager & pm,

const char * name = 0

) const throw (Exception::GeneralException) [virtual]

Writes a Nucleotide object to a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from Fragment.

void Nucleotide::prepend ( Atom & atom ) throw ()

Prepend an atom at position 0.

Parameters:

atom the atom to prepend

Reimplemented from AtomContainer.

bool Nucleotide::remove ( Atom & atom ) throw ()

Remove an atom.

Parameters:

atom the atom to remove

Reimplemented from AtomContainer.

void Nucleotide::set ( const Nucleotide & nucleotide,

bool deep = true

) throw ()

Assignment with cloning facility.
The assignment is either deep or shallow (default).
Parameters:

nucleotide the nucleotide to be copied (cloned)

deep make a deep (=true) or shallow (=false) copy

void Nucleotide::setID ( const String & id ) throw ()

Set the ID of the nucleotide.

Parameters:

id the new ID

void Nucleotide::setInsertionCode ( char insertion_code ) throw ()

Set the insertion code of the nucleotide.

Parameters:

insertion_code the new insertion code

void Nucleotide::splice ( Nucleotide & nucleotide ) throw ()

Move the children of nucleotide into this instance.
The children are inserted using spliceBefore .

void Nucleotide::spliceAfter ( Nucleotide & nucleotide ) throw ()

Cut all children of nucleotide and append them after the children of this instance.

Parameters:

nucleotide the nucleotide to access

void Nucleotide::spliceBefore ( Nucleotide & nucleotide ) throw ()

Cut all children of nucleotide and prepend them before the children of this instance.

Parameters:

nucleotide the nucleotide to access

void Nucleotide::swap ( Nucleotide & nucleotide ) throw ()

Swapping of instaces of nucleotide.

Parameters:

nucleotide the instance of nucleotide to swap with

Nucleotide Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Detailed Description

Member Function Documentation

Nucleotide Class Reference
[Molecular Datastructures]