bio::chemical::UnorderedStructureInterface Class Reference

#include <UnorderedStructureInterface.h>

Inheritance diagram for bio::chemical::UnorderedStructureInterface:

Collaboration diagram for bio::chemical::UnorderedStructureInterface:

Public Member Functions
	UnorderedStructureInterface ()
virtual	~UnorderedStructureInterface ()
template<typename T >
T	Add (const T t)
template<typename T >
void	Clear ()
template<typename T >
Container *	GetAll ()
template<typename T >
const Container *	GetAll () const
template<typename T >
std::vector< T >	GetAllAsVector ()
template<typename T >
const std::vector< T >	GetAllAsVector () const
template<typename T >
unsigned long	GetCount () const
template<typename T >
unsigned int	GetNumMatching (const Container *other) const
template<typename T >
std::string	GetStringFrom (std::string separator=", ")
template<typename T >
bool	Has (T content) const
template<typename T >
bool	HasAll (const Container *contents) const
template<typename T >
void	Import (const std::vector< T > &other)
template<typename T >
void	Import (const UnorderedMotif< T > *other)
Code	ImportAll (const physical::Wave *other)
template<typename T >
T	Remove (const T t)
Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()
	ThreadSafe (const ThreadSafe &toCopy)
virtual	~ThreadSafe ()
void	LockThread () const
void	UnlockThread () const
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::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

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)
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::chemical::Atom
Bonds	m_bonds
Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object
Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal
Symmetry *	m_symmetry

Detailed Description

Interface methods for all UnorderedMotif classes.

Definition at line 34 of file UnorderedStructureInterface.h.

Constructor & Destructor Documentation

UnorderedStructureInterface()

bio::chemical::UnorderedStructureInterface::UnorderedStructureInterface ( )

inline

Definition at line 43 of file UnorderedStructureInterface.h.

 {
 }

~UnorderedStructureInterface()

virtual bio::chemical::UnorderedStructureInterface::~UnorderedStructureInterface ( )

inlinevirtual

Definition at line 50 of file UnorderedStructureInterface.h.

 {
 }

Member Function Documentation

Add()

template<typename T >

T bio::chemical::UnorderedStructureInterface::Add ( const T  t )

inline

Adds to *this using the appropriate interface for T. Does not allow duplicates.

Template Parameters

T

Parameters

t

Returns

the t inserted or 0; 0 if T is invalid.

Definition at line 63 of file UnorderedStructureInterface.h.

 {
 T ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->AddImplementation(t);
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::AddImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

Referenced by bio::genetic::GenomeDefault::GenomeDefault(), bio::genetic::RNAPolymerase::Activate(), and bio::molecular::Molecule::operator>>().

Clear()

template<typename T >

void bio::chemical::UnorderedStructureInterface::Clear ( )

inline

Removes all T from *this. Does not delete the contents! Does nothing if T is invalid.

Template Parameters

T

Definition at line 302 of file UnorderedStructureInterface.h.

 {
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 implementer->ClearImplementation();
 }
 UnlockThread();
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::ClearImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

GetAll() [1/2]

template<typename T >

Container * bio::chemical::UnorderedStructureInterface::GetAll ( )

inline

USE WITH CAUTION!!!

Template Parameters

T

Returns

A pointer to all contents in *this; 0 if T is invalid.

Definition at line 202 of file UnorderedStructureInterface.h.

 {
 Container* ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->GetAllImplementation();
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::AbstractMotif::GetAllImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

Referenced by bio::genetic::RNAPolymerase::Activate(), and bio::chemical::Axis::Rotate().

GetAll() [2/2]

template<typename T >

const Container * bio::chemical::UnorderedStructureInterface::GetAll ( ) const

inline

Safer, const version of above.

Template Parameters

T

Returns

A pointer to all contents in *this; 0 if T is invalid.

Definition at line 222 of file UnorderedStructureInterface.h.

 {
 Container* ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->GetAllImplementation();
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::AbstractMotif::GetAllImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

GetAllAsVector() [1/2]

template<typename T >

std::vector< T > bio::chemical::UnorderedStructureInterface::GetAllAsVector ( )

inline

Ease of use wrapper around casting the contents of *this as a std::vector.

Template Parameters

T

Returns

the contents of *this casted to an std::vector.

Definition at line 338 of file UnorderedStructureInterface.h.

 {
 return this->template GetAll< T >()->
 template AsVector< T >();
 }

Referenced by bio::chemical::PeriodicTableImplementation::GetPropertiesOf().

GetAllAsVector() [2/2]

template<typename T >

const std::vector< T > bio::chemical::UnorderedStructureInterface::GetAllAsVector ( ) const

inline

Ease of use wrapper around casting the contents of *this as a std::vector.

Template Parameters

T

Returns

the contents of *this casted to an std::vector.

Definition at line 350 of file UnorderedStructureInterface.h.

 {
 return this->template GetAll< T >()->
 template AsVector< T >();
 }

GetCount()

template<typename T >

unsigned long bio::chemical::UnorderedStructureInterface::GetCount ( ) const

inline

Gives the number of T in *this

Template Parameters

T

Returns

the size of contents; 0 if T is invalid.

Definition at line 182 of file UnorderedStructureInterface.h.

 {
 unsigned long ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->GetCountImplementation();
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetCountImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

GetNumMatching()

template<typename T >

unsigned int bio::chemical::UnorderedStructureInterface::GetNumMatching ( const Container *  other ) const

inline

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

Parameters

other

Returns

quantity overlap with other; 0 if T is invalid.

Definition at line 262 of file UnorderedStructureInterface.h.

 {
 unsigned int ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->GetNumMatchingImplementation(other);
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetNumMatchingImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

GetStringFrom()

template<typename T >

std::string bio::chemical::UnorderedStructureInterface::GetStringFrom ( std::string  separator = ", " )

inline

Get the Contents of *this as a string.

Parameters

separator

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

Returns

the Contents of *this as a string; "" if T is invalid.

Definition at line 319 of file UnorderedStructureInterface.h.

 {
 std::string ret = "";
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->GetStringFromImplementation(separator);
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetStringFromImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

Has()

template<typename T >

bool bio::chemical::UnorderedStructureInterface::Has ( T  content ) const

inline

Check for content.

Template Parameters

T

Parameters

content

Returns

whether or not content exists in *this; false if T is invalid.

Definition at line 243 of file UnorderedStructureInterface.h.

 {
 bool ret = false;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->HasImplementation(content);
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

HasAll()

template<typename T >

bool bio::chemical::UnorderedStructureInterface::HasAll ( const Container *  contents ) const

inline

Check if *this contains all of the given contents Should NOT check if the given contents contain all those of *this.

Parameters

content

Returns

whether or not the given contents exists in *this

Definition at line 282 of file UnorderedStructureInterface.h.

 {
 bool ret = false;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->HasAllImplementation(contents);
 }
 UnlockThread();
 return ret;
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasAllImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

Referenced by bio::genetic::RNAPolymerase::Activate(), and bio::chemical::Reaction::ReactantsMeetRequirements().

Import() [1/2]

template<typename T >

void bio::chemical::UnorderedStructureInterface::Import ( const std::vector< T > &  other )

inline

Copy the contents of a vector into *this. Will only work if *this contains an UnorderedMotif of the given type. Does nothing if T is invalid.

Template Parameters

T

Parameters

other

Definition at line 124 of file UnorderedStructureInterface.h.

 {
 for (
 typename std::vector< T >::const_iterator otr = other.begin();
 otr != other.end();
 ++otr
 )
 {
 this->Add< T >(*otr);
 }
 }

Import() [2/2]

template<typename T >

void bio::chemical::UnorderedStructureInterface::Import ( const UnorderedMotif< T > *  other )

inline

Copy the contents of another container into *this. Does nothing if T is invalid.

Template Parameters

T

Parameters

other

Definition at line 105 of file UnorderedStructureInterface.h.

 {
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 implementer->ImportImplementation(other);
 }
 UnlockThread();
 }

References bio::chemical::UnorderedMotif< CONTENT_TYPE >::ImportImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

Referenced by bio::cellular::Tissue::DifferentiateCells(), bio::molecular::Molecule::operator>>(), bio::molecular::Vesicle::operator>>=(), and bio::chemical::PeriodicTableImplementation::RecordPropertiesOf().

ImportAll()

Code bio::chemical::UnorderedStructureInterface::ImportAll ( const physical::Wave *  other )

inline

This method does way more than it should reasonably be able to. Here, we take advantage of some of the Biology features that are starting to form. Primarily, we leverage physical::Properties and Bonds (per Atom) to search through the pseudo-vtable of Atom, find all StructuralComponents in *this and attempt to Import the corresponding StructuralComponents of other. This method side-steps the typical inheritance encapsulation in order to prevent child classes from having to override this method and account for each new UnorderedMotif they add. In other words, complexity here removes repeated code downstream.

Parameters

other

Definition at line 142 of file UnorderedStructureInterface.h.

 {
 BIO_SANITIZE(other && other->AsAtom(), ,
 return code::BadArgument1())
 
 Code ret = code::Success();
 
 LockThread(); // in case m_bonds changes.
 Bond* bondBuffer;
 for (
 SmartIterator bnd = other->AsAtom()->GetAllBonds()->End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->IsEmpty())
 {
 continue;
 }
 if (physical::Wave::GetResonanceBetween(
 bondBuffer->GetBonded(),
 AbstractMotif::GetClassProperties()).size() == 0)
 {
 continue;
 }
 const physical::Wave* otherBond = other->AsAtom()->GetBonded(other->AsAtom()->GetBondPosition(bondBuffer->GetId()));
 (Cast< AbstractMotif* >(bondBuffer->GetBonded()))->ImportImplementation(otherBond); //actual work
 }
 UnlockThread();
 
 return ret;
 }

References bio::physical::Wave::AsAtom(), bio::code::BadArgument1(), BIO_SANITIZE, bio::Container::End(), bio::chemical::Atom::GetAllBonds(), bio::chemical::Bond::GetBonded(), bio::chemical::Atom::GetBonded(), bio::chemical::Atom::GetBondPosition(), bio::chemical::AbstractMotif::GetClassProperties(), bio::chemical::Bond::GetId(), bio::physical::Wave::GetResonanceBetween(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Bond::IsEmpty(), bio::ThreadSafe::LockThread(), bio::code::Success(), and bio::ThreadSafe::UnlockThread().

Remove()

template<typename T >

T bio::chemical::UnorderedStructureInterface::Remove ( const T  t )

inline

Removes t from *this using the appropriate handler for T.

Template Parameters

T

Parameters

t

Returns

the removed content or 0; 0 if T is invalid.

Definition at line 84 of file UnorderedStructureInterface.h.

 {
 T ret = 0;
 LockThread();
 UnorderedMotif< T >* implementer = this->AsBonded< UnorderedMotif< T >* >();
 if (implementer)
 {
 ret = implementer->RemoveImplementation(t);
 }
 UnlockThread();
 return ret;
 }

References bio::ThreadSafe::LockThread(), bio::chemical::UnorderedMotif< CONTENT_TYPE >::RemoveImplementation(), and bio::ThreadSafe::UnlockThread().

Referenced by bio::molecular::Molecule::TransferFrom().

---

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

• /home/eons/git/biology/lib_bio/inc/bio/chemical/structure/interface/UnorderedStructureInterface.h