bio::chemical::UnorderedMotif< CONTENT_TYPE > Class Template Reference

#include <UnorderedMotif.h>

Inheritance diagram for bio::chemical::UnorderedMotif< CONTENT_TYPE >:

Collaboration diagram for bio::chemical::UnorderedMotif< CONTENT_TYPE >:

Public Types
typedef physical::Arrangement< CONTENT_TYPE >	Contents
Public Types inherited from bio::physical::Identifiable< StandardDimension >
typedef StandardDimension	Id
typedef std::vector< Id >	Ids
Public Types inherited from bio::physical::Observer< Perspective< StandardDimension > >
typedef Perspective< StandardDimension >	Perspective

Public Member Functions
	UnorderedMotif (const Contents *contents)
	UnorderedMotif (const UnorderedMotif< CONTENT_TYPE > *toCopy)
virtual	~UnorderedMotif ()
virtual CONTENT_TYPE	AddImplementation (const CONTENT_TYPE content)
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< CONTENT_TYPE >) UnorderedMotif()
virtual void	ClearImplementation ()
virtual unsigned long	GetCountImplementation () const
virtual unsigned int	GetNumMatchingImplementation (const Container *other) const
virtual std::string	GetStringFromImplementation (std::string separator=", ")
virtual bool	HasAllImplementation (const Container *contents) const
virtual bool	HasImplementation (const CONTENT_TYPE content) const
virtual void	ImportImplementation (const UnorderedMotif< CONTENT_TYPE > *other)
virtual CONTENT_TYPE	RemoveImplementation (const CONTENT_TYPE content)
Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< CONTENT_TYPE > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< CONTENT_TYPE >) Class(UnorderedMotif< CONTENT_TYPE > *object
Public Member Functions inherited from bio::physical::Class< T >
	Class (T *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
T *	Convert (Wave *wave)
virtual	operator T* ()
virtual	operator Wave * ()
Public Member Functions inherited from bio::physical::Wave
	Wave (Symmetry *symmetry=NULL)
virtual	~Wave ()
virtual chemical::Atom *	AsAtom ()
virtual const chemical::Atom *	AsAtom () const
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Code	Attenuate (const Wave *other)
virtual Wave *	Clone () const
virtual Wave *	Demodulate ()
virtual const Wave *	Demodulate () const
virtual Code	Disattenuate (const Wave *other)
virtual Properties	GetProperties () const
virtual Wave *	Modulate (Wave *signal)
virtual Wave *	operator* ()
virtual const Wave *	operator* () const
virtual Wave *	operator* (Wave *signal)
virtual void	operator+ (const Wave *other)
virtual void	operator- (const Wave *other)
virtual void	operator| (Symmetry *symmetry)
virtual Code	Reify (Symmetry *symmetry)
virtual Symmetry *	Spin () const
Public Member Functions inherited from bio::physical::Identifiable< StandardDimension >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective
void	CloneIntoName (Name name)
Public Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
	Observer (const Observer &other)
	Observer (Perspective *perspective=NULL)
virtual	~Observer ()
virtual Perspective *	GetPerspective () const
virtual void	SetPerspective (Perspective *perspective)
Public Member Functions inherited from bio::physical::Class< Identifiable< StandardDimension > >
	Class (Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
Identifiable< StandardDimension > *	Convert (Wave *wave)
virtual	operator Identifiable< StandardDimension > * ()
virtual	operator Wave * ()
Public Member Functions inherited from bio::log::Writer
	Writer (Engine *logEngine, Filter logFilter)
virtual	~Writer ()
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Writer) Writer()
void	ExternalLog (Filter logFilter, Level level, const char *format,...) const
Engine *	GetLogEngine ()
const Engine *	GetLogEngine () const
bool	HasLogEngine () const
virtual void	SetLogEngine (Engine *logEngine)
Public Member Functions inherited from bio::physical::Filterable
	Filterable (Filter filter)
virtual	~Filterable ()
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Filterable) Filterable()
Filter	GetFilter () const
virtual void	InitializeImplementation (ByteStreams args)
virtual Code	Reify (Symmetry *symmetry)
virtual void	SetFilter (Filter filter)
virtual Symmetry *	Spin () const
Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Filterable *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
Filterable *	Convert (Wave *wave)
virtual	operator Filterable * ()
virtual	operator Wave * ()
Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Writer *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
Writer *	Convert (Wave *wave)
virtual	operator Wave * ()
virtual	operator Writer * ()
Public Member Functions inherited from bio::chemical::Atom
	Atom (const Atom &other)
virtual	~Atom ()
template<typename T >
T	As ()
template<typename T >
const T	As () const
template<typename T >
T	AsBonded ()
template<typename T >
const T	AsBonded () const
template<typename T >
T	AsBondedQuantum ()
template<typename T >
const T	AsBondedQuantum () const
virtual Code	Attenuate (const Wave *other)
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()
template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())
virtual Code	Disattenuate (const Wave *other)
template<typename T >
bool	FormBond (T toBond, BondType type=bond_type::Unknown())
Bonds *	GetAllBonds ()
const Bonds *	GetAllBonds () const
Wave *	GetBonded (Valence position)
const Wave *	GetBonded (Valence position) const
template<typename T >
Valence	GetBondPosition () const
Valence	GetBondPosition (AtomicNumber bondedId) const
Valence	GetBondPosition (Name typeName) const
template<typename T >
BondType	GetBondType () const
BondType	GetBondType (Valence position) const
template<typename T >
	operator T ()
virtual Code	Reify (physical::Symmetry *symmetry)
virtual physical::Symmetry *	Spin () const
Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Atom *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
Atom *	Convert (Wave *wave)
virtual	operator Atom * ()
virtual	operator Wave * ()
Public Member Functions inherited from bio::chemical::AbstractMotif
	AbstractMotif ()
virtual	~AbstractMotif ()
virtual void	ClearImplementation ()
virtual Container *	GetAllImplementation ()
virtual const Container *	GetAllImplementation () const
virtual unsigned long	GetCountImplementation () const
virtual std::string	GetStringFromImplementation (std::string separator=", ")
virtual void	ImportImplementation (const void *other)

Additional Inherited Members
Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (const Wave *wave, const Properties &properties)
static Properties	GetResonanceBetween (const Wave *wave1, const Wave *wave2)
static Properties	GetResonanceBetween (ConstWaves waves)
Static Public Member Functions inherited from bio::chemical::AbstractMotif
static Properties	GetClassProperties ()
Public Attributes inherited from bio::chemical::Class< UnorderedMotif< CONTENT_TYPE > >
physical::Perspective< StandardDimension > Filter	filter
physical::Perspective< StandardDimension > *	perspective
Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id
Protected Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
virtual void	InitializeImplementation (ByteStreams args)
Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()
virtual	~VirtualBase ()
void	Initialize (ByteStream arg1)
void	Initialize (ByteStream arg1, ByteStream arg2)
void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)
void	Initialize (ByteStreams args)
virtual void	InitializeImplementation (ByteStreams args)=0
Protected Member Functions inherited from bio::log::Writer
virtual void	InitializeImplementation (ByteStreams args)
void	Log (Level level, const char *format,...) const
Protected Member Functions inherited from bio::chemical::Atom
virtual bool	BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)
virtual bool	FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)
Protected Attributes inherited from bio::physical::Class< T >
T *	m_object
Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal
Symmetry *	m_symmetry
Protected Attributes inherited from bio::VirtualBase
bool	m_hasBeenInitialized
Protected Attributes inherited from bio::physical::Class< Identifiable< StandardDimension > >
Identifiable< StandardDimension > *	m_object
Protected Attributes inherited from bio::physical::Filterable
Filter	m_filter
Protected Attributes inherited from bio::physical::Class< Filterable >
Filterable *	m_object
Protected Attributes inherited from bio::physical::Class< Writer >
Writer *	m_object
Protected Attributes inherited from bio::chemical::Atom
Bonds	m_bonds
Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object
Protected Attributes inherited from bio::chemical::AbstractMotif
Container *	m_contents

Detailed Description

template<typename CONTENT_TYPE>
class bio::chemical::UnorderedMotif< CONTENT_TYPE >

UnorderedMotif classes have Content classes stored within them. They are simple containers.

Definition at line 40 of file UnorderedMotif.h.

Member Typedef Documentation

Contents

template<typename CONTENT_TYPE >

typedef physical::Arrangement< CONTENT_TYPE > bio::chemical::UnorderedMotif< CONTENT_TYPE >::Contents

Definition at line 46 of file UnorderedMotif.h.

Constructor & Destructor Documentation

UnorderedMotif() [1/2]

template<typename CONTENT_TYPE >

bio::chemical::UnorderedMotif< CONTENT_TYPE >::UnorderedMotif ( const Contents *  contents )

inline

Parameters

contents

Definition at line 67 of file UnorderedMotif.h.

 :
 chemical::Class< UnorderedMotif< CONTENT_TYPE > >(this) //TODO: Define Symmetry.
 {
 this->m_contents = new Contents(*contents);
 }

References bio::chemical::AbstractMotif::m_contents.

UnorderedMotif() [2/2]

template<typename CONTENT_TYPE >

bio::chemical::UnorderedMotif< CONTENT_TYPE >::UnorderedMotif ( const UnorderedMotif< CONTENT_TYPE > *  toCopy )

inline

Parameters

toCopy

Definition at line 77 of file UnorderedMotif.h.

 :
 chemical::Class< UnorderedMotif< CONTENT_TYPE > >(this) //TODO: Define Symmetry.
 {
 this->m_contents = new Contents(*toCopy->m_contents);
 }

References bio::chemical::AbstractMotif::m_contents.

~UnorderedMotif()

template<typename CONTENT_TYPE >

virtual bio::chemical::UnorderedMotif< CONTENT_TYPE >::~UnorderedMotif ( )

inlinevirtual

Definition at line 87 of file UnorderedMotif.h.

 {
 //NOTE: Children are responsible for clearing m_contents (e.g. through ClearImplementation()).
 }

Member Function Documentation

AddImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::UnorderedMotif< CONTENT_TYPE >::AddImplementation ( const CONTENT_TYPE  content )

inlinevirtual

Adds content to *this.

Parameters

content

Returns

the added content or 0.

Reimplemented in bio::chemical::LinearMotif< CONTENT_TYPE >.

Definition at line 114 of file UnorderedMotif.h.

 {
 CONTENT_TYPE ret = this->m_contents->Access(this->m_contents->Add(content));
 return ret;
 }

References bio::Container::Access(), bio::Container::Add(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedStructureInterface::Add().

BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

template<typename CONTENT_TYPE >

bio::chemical::UnorderedMotif< CONTENT_TYPE >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( chemical  , UnorderedMotif< CONTENT_TYPE >    )

inline

Ensure virtual methods point to Class implementations.

Definition at line 51 of file UnorderedMotif.h.

 :
 chemical::Class< UnorderedMotif< CONTENT_TYPE > >(this) //TODO: Define Symmetry.
 {
 this->m_contents = new Contents(4);
 }

References bio::chemical::AbstractMotif::m_contents.

ClearImplementation()

template<typename CONTENT_TYPE >

virtual void bio::chemical::UnorderedMotif< CONTENT_TYPE >::ClearImplementation ( )

inlinevirtual

Clears the contents of *this.

Reimplemented from bio::chemical::AbstractMotif.

Reimplemented in bio::chemical::LinearMotif< CONTENT_TYPE >, bio::chemical::LinearMotif< Organelle * >, bio::chemical::LinearMotif< genetic::Plasmid * >, bio::chemical::LinearMotif< Tissue * >, bio::chemical::LinearMotif< Organ * >, bio::chemical::LinearMotif< Cell * >, bio::chemical::LinearMotif< Substance * >, bio::chemical::LinearMotif< Symmetry * >, bio::chemical::LinearMotif< Plasmid * >, bio::chemical::LinearMotif< molecular::Protein * >, bio::chemical::LinearMotif< Gene * >, bio::chemical::LinearMotif< Surface * >, bio::chemical::LinearMotif< chemical::Reaction * >, bio::chemical::LinearMotif< Protein * >, bio::chemical::LinearMotif< Molecule * >, bio::chemical::LinearMotif< Organism * >, and bio::chemical::LinearMotif< cellular::OrganSystem * >.

Definition at line 95 of file UnorderedMotif.h.

 {
 this->m_contents->Clear();
 }

References bio::Container::Clear(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedStructureInterface::Clear().

GetCountImplementation()

template<typename CONTENT_TYPE >

virtual unsigned long bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetCountImplementation ( ) const

inlinevirtual

Implementation for counting Contents.

Returns

the number of Contents in *this.

Reimplemented from bio::chemical::AbstractMotif.

Definition at line 104 of file UnorderedMotif.h.

 {
 return this->m_contents->GetNumberOfElements();
 }

References bio::Container::GetNumberOfElements(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedStructureInterface::GetCount().

GetNumMatchingImplementation()

template<typename CONTENT_TYPE >

virtual unsigned int bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetNumMatchingImplementation ( const Container *  other ) const

inlinevirtual

Gives the number of matching contents between *this & other.

Parameters

other

Returns

quantity overlap with other.

Definition at line 159 of file UnorderedMotif.h.

 {
 BIO_SANITIZE(other, ,
 return 0);
 
 unsigned int ret = 0;
 for (
 SmartIterator otr = other->End();
 !otr.IsAtBeginning();
 --otr
 )
 {
 if (this->HasImplementation(*otr))
 {
 ++ret;
 }
 }
 return ret;
 }

References BIO_SANITIZE, bio::Container::End(), bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasImplementation(), and bio::SmartIterator::IsAtBeginning().

Referenced by bio::chemical::UnorderedStructureInterface::GetNumMatching(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasAllImplementation().

GetStringFromImplementation()

template<typename CONTENT_TYPE >

virtual std::string bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetStringFromImplementation ( std::string  separator = ", " )

inlinevirtual

Get the Contents of *this as a string.

Parameters

separator

e.g. ", ", the default, or just " ".

Returns

the Contents of *this as a string.

Reimplemented from bio::chemical::AbstractMotif.

Reimplemented in bio::chemical::LinearMotif< CONTENT_TYPE >, bio::chemical::LinearMotif< Organelle * >, bio::chemical::LinearMotif< genetic::Plasmid * >, bio::chemical::LinearMotif< Tissue * >, bio::chemical::LinearMotif< Organ * >, bio::chemical::LinearMotif< Cell * >, bio::chemical::LinearMotif< Substance * >, bio::chemical::LinearMotif< Symmetry * >, bio::chemical::LinearMotif< Plasmid * >, bio::chemical::LinearMotif< molecular::Protein * >, bio::chemical::LinearMotif< Gene * >, bio::chemical::LinearMotif< Surface * >, bio::chemical::LinearMotif< chemical::Reaction * >, bio::chemical::LinearMotif< Protein * >, bio::chemical::LinearMotif< Molecule * >, bio::chemical::LinearMotif< Organism * >, and bio::chemical::LinearMotif< cellular::OrganSystem * >.

Definition at line 196 of file UnorderedMotif.h.

 {
 std::string ret = "";
 SmartIterator cnt = this->m_contents->Begin();
 while (true)
 {
 ret += string::From< CONTENT_TYPE >(*cnt);
 ++cnt;
 if (cnt.IsAtEnd())
 {
 break;
 }
 ret += separator;
 }
 return ret;
 }

References bio::Container::Begin(), bio::SmartIterator::IsAtEnd(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedStructureInterface::GetStringFrom().

HasAllImplementation()

template<typename CONTENT_TYPE >

virtual bool bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasAllImplementation ( const Container *  contents ) const

inlinevirtual

Check for all contents

Parameters

contents

Returns

whether or not the given contents exists in *this

Definition at line 184 of file UnorderedMotif.h.

 {
 BIO_SANITIZE(contents, ,
 return false);
 return this->GetNumMatchingImplementation(contents) == contents->GetNumberOfElements();
 }

References BIO_SANITIZE, bio::Container::GetNumberOfElements(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetNumMatchingImplementation().

Referenced by bio::chemical::UnorderedStructureInterface::HasAll().

HasImplementation()

template<typename CONTENT_TYPE >

virtual bool bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasImplementation ( const CONTENT_TYPE  content ) const

inlinevirtual

Check for content.

Parameters

content

Returns

whether or not the given content exists in *this

Definition at line 137 of file UnorderedMotif.h.

 {
 return this->m_contents->Has(content);
 }

References bio::Container::Has(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetNumMatchingImplementation(), and bio::chemical::UnorderedStructureInterface::Has().

ImportImplementation()

template<typename CONTENT_TYPE >

virtual void bio::chemical::UnorderedMotif< CONTENT_TYPE >::ImportImplementation ( const UnorderedMotif< CONTENT_TYPE > *  other )

inlinevirtual

Copy the contents of another container into *this.

Parameters

other

Definition at line 146 of file UnorderedMotif.h.

 {
 BIO_SANITIZE(other, ,
 return);
 
 this->m_contents->Import(other->GetAllImplementation());
 }

References BIO_SANITIZE, bio::chemical::AbstractMotif::GetAllImplementation(), bio::Container::Import(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::UnorderedStructureInterface::Import().

RemoveImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::UnorderedMotif< CONTENT_TYPE >::RemoveImplementation ( const CONTENT_TYPE  content )

inlinevirtual

Removes content from *this and deletes it.

Parameters

content

Definition at line 124 of file UnorderedMotif.h.

 {
 Index toErase = this->m_contents->SeekTo(content);
 CONTENT_TYPE ret = this->m_contents->Access(toErase);
 this->m_contents->Erase(toErase);
 return ret;
 }

References bio::Container::Access(), bio::Container::Erase(), bio::chemical::AbstractMotif::m_contents, and bio::Container::SeekTo().

Referenced by bio::chemical::UnorderedStructureInterface::Remove().

---

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

• /home/eons/git/biology/lib_bio/inc/bio/chemical/structure/motif/UnorderedMotif.h