#include <LinearStructureInterface.h>

Inheritance diagram for bio::chemical::LinearStructureInterface:

Collaboration diagram for bio::chemical::LinearStructureInterface:

Public Member Functions
	LinearStructureInterface ()

virtual	~LinearStructureInterface ()

template<typename T >
Emission	ForEach (ExcitationBase *excitation)

template<typename T >
T	GetById (StandardDimension id)

template<typename T >
const T	GetById (StandardDimension id) const

template<typename T >
T	GetByName (Name name)

template<typename T >
const T	GetByName (Name name) const

template<typename T >
T	GetOrCreateById (StandardDimension id)

template<typename T >
T	GetOrCreateByName (Name name)

template<typename T >
Code	Insert (T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

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 LinearMotif classes.

Definition at line 34 of file LinearStructureInterface.h.

Constructor & Destructor Documentation

◆ LinearStructureInterface()

bio::chemical::LinearStructureInterface::LinearStructureInterface ( )

inline

Definition at line 42 of file LinearStructureInterface.h.

43 {

44 }

◆ ~LinearStructureInterface()

virtual bio::chemical::LinearStructureInterface::~LinearStructureInterface ( )

inlinevirtual

Definition at line 49 of file LinearStructureInterface.h.

50 {

51 }

Member Function Documentation

◆ ForEach()

template<typename T >

Emission bio::chemical::LinearStructureInterface::ForEach ( ExcitationBase * excitation )

inline

Performs the given Reaction on all contents.

Parameters

excitation

Definition at line 236 of file LinearStructureInterface.h.

    {
        Emission ret;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->ForEachImplementation(excitation);
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::ForEachImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetById() [1/2]

template<typename T >

T bio::chemical::LinearStructureInterface::GetById ( StandardDimension id )

inline

Gets a T* by its id.

Template Parameters

T

Parameters

id

Returns: a T of the given id or NULL; NULL if T is invalid.

Definition at line 93 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetByIdImplementation(
                id
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetById() [2/2]

template<typename T >

const T bio::chemical::LinearStructureInterface::GetById ( StandardDimension id ) const

inline

Gets a const T* by its id.

Template Parameters

T

Parameters

id

Returns: a T of the given id or NULL; NULL if T is invalid.

Definition at line 115 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetByIdImplementation(
                id
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetByName() [1/2]

template<typename T >

T bio::chemical::LinearStructureInterface::GetByName ( Name name )

inline

Gets a T* by its name.

Template Parameters

T

Parameters

name

Returns: a T of the given id or NULL; NULL if T is invalid.

Definition at line 139 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetByNameImplementation(
                name
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetByNameImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetByName() [2/2]

template<typename T >

const T bio::chemical::LinearStructureInterface::GetByName ( Name name ) const

inline

Gets a const T* by its name.

Template Parameters

T

Parameters

name

Returns: a T of the given id or NULL; NULL if T is invalid.

Definition at line 163 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetByNameImplementation(
                name
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetByNameImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetOrCreateById()

template<typename T >

T bio::chemical::LinearStructureInterface::GetOrCreateById ( StandardDimension id )

inline

Tries to find a Content of the given id in *this and, optionally, the Contents beneath. If such an object doesn't exist, one is created from its Wave.

Template Parameters

T

Parameters

id

Returns: A T* of the given id; NULL if T is invalid.

Definition at line 188 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetOrCreateByIdImplementation(
                id
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByIdImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ GetOrCreateByName()

template<typename T >

T bio::chemical::LinearStructureInterface::GetOrCreateByName ( Name name )

inline

Tries to find a Content of the given name in *this and, optionally, the Contents beneath. If such an object doesn't exist, one is created from its Wave.

Template Parameters

T

Parameters

name

Returns: A T* of the given id; NULL if T is invalid.

Definition at line 213 of file LinearStructureInterface.h.

    {
        T ret = NULL;
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->GetOrCreateByNameImplementation(
                name
            );
        }
        UnlockThread();
        return ret;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

◆ Insert()

template<typename T >

Code bio::chemical::LinearStructureInterface::Insert	(	T	toAdd,
		const Position	position = `BOTTOM`,
		const StandardDimension	optionalPositionArg = `0`,
		const bool	transferSubContents = `false`
	)

inline

Inserts toAdd into *this at then indicated position. Removes any conflicting Contents of the same Id as toAdd.

Template Parameters

T	the type of Content

Parameters

toAdd	what to add.
position	where toAdd is inserted (e.g. the TOP or BOTTOM).
optionalPositionArg	If a position is specified, the optionalPositionArg is the id of the Content referenced (e.g. BEFORE, MyContentId()).
transferSubContents	allows all of the Contents within a Content that conflicts with toAdd to be copied into toAdd, before the conflicting Content is deleted (similar to renaming an upper directory while preserving it's contents).

Definition at line 63 of file LinearStructureInterface.h.

    {
        Code ret = code::GeneralFailure();
        LockThread();
        LinearMotif< T >* implementer = this->AsBonded< LinearMotif< T >* >();
        if (implementer)
        {
            ret = implementer->InsertImplementation(
                toAdd,
                position,
                optionalPositionArg,
                transferSubContents
            );
        }
        UnlockThread();
        return ret;
    }

References bio::code::GeneralFailure(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), bio::ThreadSafe::LockThread(), and bio::ThreadSafe::UnlockThread().

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LinearStructureInterface()

◆ ~LinearStructureInterface()

Member Function Documentation

◆ ForEach()

◆ GetById() [1/2]

◆ GetById() [2/2]

◆ GetByName() [1/2]

◆ GetByName() [2/2]

◆ GetOrCreateById()

◆ GetOrCreateByName()

◆ Insert()