#include <LinearMotif.h>

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

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

Public Types
typedef physical::Line	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 Types inherited from bio::chemical::UnorderedMotif< CONTENT_TYPE >
typedef physical::Arrangement< CONTENT_TYPE >	Contents

Public Member Functions
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< CONTENT_TYPE > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual CONTENT_TYPE	AddImplementation (CONTENT_TYPE content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< CONTENT_TYPE >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual CONTENT_TYPE	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual CONTENT_TYPE	GetByIdImplementation (StandardDimension id)

virtual const CONTENT_TYPE	GetByIdImplementation (StandardDimension id) const

virtual CONTENT_TYPE	GetByNameImplementation (Name name)

virtual const CONTENT_TYPE	GetByNameImplementation (Name name) const

virtual CONTENT_TYPE	GetOrCreateByIdImplementation (StandardDimension id)

virtual CONTENT_TYPE	GetOrCreateByNameImplementation (Name name)

virtual std::string	GetStringFromImplementation (std::string separator=", ")

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const CONTENT_TYPE &content) const

virtual void	ImportImplementation (const LinearMotif< CONTENT_TYPE > *other)

virtual Code	InsertImplementation (CONTENT_TYPE toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< CONTENT_TYPE > >
	Elementary ()

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< CONTENT_TYPE > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< CONTENT_TYPE >) Class(LinearMotif< 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::UnorderedMotif< CONTENT_TYPE >
	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::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)

Static Public Member Functions
static LinearMotif< CONTENT_TYPE > Properties	GetClassProperties ()

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
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< CONTENT_TYPE > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< CONTENT_TYPE > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Additional Inherited Members
Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< CONTENT_TYPE > >
static bool	hasRegistered

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::LinearMotif< CONTENT_TYPE >

LinearMotif objects contain pointers to chemical::Classes.

IMPORTANT: CONTENT_TYPE MUST BE A chemical::Class* (which is in the StandardDimension). YOU CANNOT USE LinearMotif WITH TYPES THAT ARE NOT POINTERS TO CHILDREN OF chemical::Class (i.e. a physical::Identifiable<StandardDimension>) Other Dimensions may be supported in a future release. physical::Line and physical::Linear for why.

NOTE: CONTENT_TYPE cannot be "const". cv qualifiers may be supported in a future release but for now, all CONTENT_TYPEs must have the option of being modified. For more on this, see Linear.h.

Template Parameters

CONTENT_TYPE a pointer type to a child of chemical::Class

Definition at line 54 of file LinearMotif.h.

Member Typedef Documentation

◆ Contents

template<typename CONTENT_TYPE >

typedef physical::Line bio::chemical::LinearMotif< CONTENT_TYPE >::Contents

For cleaner code, we redefine Contents.

Definition at line 64 of file LinearMotif.h.

Constructor & Destructor Documentation

◆ LinearMotif() [1/3]

template<typename CONTENT_TYPE >

bio::chemical::LinearMotif< CONTENT_TYPE >::LinearMotif ( physical::Perspective< StandardDimension > * perspective = NULL )

inlineexplicit

Parameters

perspective

Definition at line 90 of file LinearMotif.h.

        :
        Elementary< LinearMotif< CONTENT_TYPE > >(GetClassProperties()),
        chemical::Class< LinearMotif< CONTENT_TYPE > >(this),
        m_perspective(perspective)
    {
        CtorCommon();
    }

◆ LinearMotif() [2/3]

template<typename CONTENT_TYPE >

bio::chemical::LinearMotif< CONTENT_TYPE >::LinearMotif	(	const Contents *	contents,
		physical::Perspective< StandardDimension > *	perspective = `NULL`
	)

inlineexplicit

Parameters

contents
name
perspective

Definition at line 104 of file LinearMotif.h.

        :
        Elementary< LinearMotif< CONTENT_TYPE > >(GetClassProperties()),
        chemical::Class< LinearMotif< CONTENT_TYPE > >(this),
        m_perspective(perspective)
    {
        CtorCommon();
        this->m_contents->Import(contents);
    }

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

◆ LinearMotif() [3/3]

template<typename CONTENT_TYPE >

bio::chemical::LinearMotif< CONTENT_TYPE >::LinearMotif ( const LinearMotif< CONTENT_TYPE > & toCopy )

inline

Copying a LinearMotif will Clone all contents in toCopy into *this. Keep in mind that dtor will delete the contents of *this.

Parameters

toCopy

Definition at line 122 of file LinearMotif.h.

        :
        Elementary< LinearMotif< CONTENT_TYPE > >(toCopy.GetClassProperties()),
        chemical::Class< LinearMotif< CONTENT_TYPE > >(this),
        m_perspective(toCopy.m_perspective)
    {
        CtorCommon();
        this->m_contents->Import(toCopy.GetAllImplementation());
    }

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

◆ ~LinearMotif()

template<typename CONTENT_TYPE >

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

inlinevirtual

Deletes all the Contents in *this. NOTE: this uses delete, not delete[]. The only way to avoid this is by Clear()ing *this yourself first.

Definition at line 137 of file LinearMotif.h.

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

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

Member Function Documentation

◆ AddImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::AddImplementation ( CONTENT_TYPE content )

inlinevirtual

Adds content to *this.

Parameters

content

Returns: t or NULL.

Reimplemented from bio::chemical::UnorderedMotif< CONTENT_TYPE >.

Definition at line 170 of file LinearMotif.h.

    {
        return ChemicalCast< CONTENT_TYPE >(Cast< physical::Line* >(this->m_contents)->LinearAccess(this->m_contents->Add(content)));
    }

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

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::CreateImplementation().

◆ Attenuate()

template<typename CONTENT_TYPE >

virtual Code bio::chemical::LinearMotif< CONTENT_TYPE >::Attenuate ( const physical::Wave * other )

inlinevirtual

Override of Wave method. See that class for details. If other is an Excitation, call ForEach instead.

Parameters

other

Returns: the result of all Attenuations.

Reimplemented from bio::physical::Wave.

Definition at line 472 of file LinearMotif.h.

    {
        if (physical::Wave::GetResonanceBetween(
            other,
            ExcitationBase::GetClassProperties()).size())
        {
            ForEachImplementation(ChemicalCast< ExcitationBase* >(other));
            return code::Success();
        }
 
        Code ret = code::Success();
        for (
            SmartIterator cnt = this->m_contents;
            !cnt.IsAtBeginning();
            --cnt
            )
        {
            if (cnt.template As< physical::Identifiable< StandardDimension >* >()->Attenuate(other) != code::Success())
            {
                ret = code::UnknownError();
            }
        }
        return ret;
    }

References bio::chemical::Atom::As(), bio::physical::Wave::Attenuate(), bio::chemical::LinearMotif< CONTENT_TYPE >::ForEachImplementation(), bio::chemical::ExcitationBase::GetClassProperties(), bio::physical::Wave::GetResonanceBetween(), bio::chemical::AbstractMotif::m_contents, bio::code::Success(), and bio::code::UnknownError().

◆ BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS()

template<typename CONTENT_TYPE >

bio::chemical::LinearMotif< CONTENT_TYPE >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS	(	chemical	,
		LinearMotif< CONTENT_TYPE >
	)

Ensure virtual methods point to Class implementations. We want to define our own Attenuate & Disattenuate, so we have to ignore the optional class methods for the chemical class.

◆ ClearImplementation()

template<typename CONTENT_TYPE >

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

inlinevirtual

Deletes & clears the contents of *this. NOTE: this uses delete, not delete[].

Reimplemented from bio::chemical::UnorderedMotif< CONTENT_TYPE >.

Definition at line 575 of file LinearMotif.h.

    {
        //No need to delete anything, since our Linear wrapper handles that for us.
        this->m_contents->Clear();
    }

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

◆ CreateImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::CreateImplementation ( StandardDimension id )

inlinevirtual

Create a CONTENT_TYPE from a given Id and adds it to *this. Clones the Wave associated with the given Id. This requires a valid Perspective in *this and for that Perspective to have an Wave registered with the given Id.

Parameters

id

Returns: a newly created CONTENT_TYPE else NULL.

Definition at line 391 of file LinearMotif.h.

    {
        BIO_SANITIZE(this->GetStructuralPerspective(), ,
            return NULL);
        return this->AddImplementation((this->GetStructuralPerspective()->template GetTypeFromIdAs< CONTENT_TYPE >(id)));
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::AddImplementation(), BIO_SANITIZE, and bio::chemical::LinearMotif< CONTENT_TYPE >::GetStructuralPerspective().

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByIdImplementation(), and bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation().

◆ Disattenuate()

template<typename CONTENT_TYPE >

virtual Code bio::chemical::LinearMotif< CONTENT_TYPE >::Disattenuate ( const physical::Wave * other )

inlinevirtual

Override of Wave method. See that class for details.

Parameters

other

Returns: the result of all Disattenuations.

Reimplemented from bio::physical::Wave.

Definition at line 502 of file LinearMotif.h.

    {
        Code ret = code::Success();
        for (
            SmartIterator cnt = this->m_contents;
            !cnt.IsAtBeginning();
            --cnt
            )
        {
            if (cnt.template As< physical::Identifiable< StandardDimension >* >()->Disattenuate(other) != code::Success())
            {
                ret = code::UnknownError();
            }
        }
        return ret;
    }

References bio::chemical::Atom::As(), bio::physical::Wave::Disattenuate(), bio::chemical::AbstractMotif::m_contents, bio::code::Success(), and bio::code::UnknownError().

◆ ForEachImplementation()

template<typename CONTENT_TYPE >

virtual Emission bio::chemical::LinearMotif< CONTENT_TYPE >::ForEachImplementation ( ExcitationBase * excitation )

inlinevirtual

Performs the given Excitation on all contents.

Parameters

excitation

Definition at line 524 of file LinearMotif.h.

    {
        Emission ret;
        for (
            SmartIterator cnt = this->m_contents;
            !cnt.IsAtBeginning();
            --cnt
            )
        {
            ByteStream result;
            excitation->CallDown(
                cnt.template As< physical::Identifiable< StandardDimension >* >()->AsWave(),
                &result
            );
            ret.push_back(result);
        }
        return ret;
    }

References bio::chemical::Atom::As(), bio::physical::Class< T >::AsWave(), bio::chemical::ExcitationBase::CallDown(), and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::Attenuate(), and bio::chemical::LinearStructureInterface::ForEach().

◆ GetByIdImplementation() [1/2]

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation ( StandardDimension id )

inlinevirtual

Implementation for getting by id.

Parameters

id

Returns: a Content of the given id or NULL.

Definition at line 324 of file LinearMotif.h.

    {
        Index ret = Cast< physical::Line* >(this->m_contents)->SeekToId(id);
        BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
            return NULL) //level 2 for GetOrCreate.
 
        return ChemicalCast< CONTENT_TYPE >(Cast< physical::Line* >(this->m_contents)->LinearAccess(ret));
    }

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::LinearStructureInterface::GetById(), bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByIdImplementation(), and bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation().

◆ GetByIdImplementation() [2/2]

template<typename CONTENT_TYPE >

virtual const CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation ( StandardDimension id ) const

inlinevirtual

const interface for getting by id.

Parameters

id

Returns: a Content of the given id or NULL.

Definition at line 340 of file LinearMotif.h.

    {
        Index ret = Cast< physical::Line* >(this->m_contents)->SeekToId(id);
        BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
            return NULL) //level 2 for GetOrCreate.
 
        return ChemicalCast< CONTENT_TYPE >(Cast< physical::Line* >(this->m_contents)->LinearAccess(ret));
    }

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, and bio::chemical::AbstractMotif::m_contents.

◆ GetByNameImplementation() [1/2]

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetByNameImplementation ( Name name )

inlinevirtual

Implementation for getting by name.

Parameters

name

Returns: a CONTENT_TYPE of the given name or NULL.

Definition at line 357 of file LinearMotif.h.

    {
        Index ret = Cast< physical::Line* >(this->m_contents)->SeekToName(name);
        BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
            return NULL) //level 2 for GetOrCreate.
 
        return ChemicalCast< CONTENT_TYPE >(Cast< physical::Line* >(this->m_contents)->LinearAccess(ret));
    }

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, and bio::chemical::AbstractMotif::m_contents.

Referenced by bio::chemical::LinearStructureInterface::GetByName().

◆ GetByNameImplementation() [2/2]

template<typename CONTENT_TYPE >

virtual const CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetByNameImplementation ( Name name ) const

inlinevirtual

Implementation for getting by name.

Parameters

name

Returns: a CONTENT_TYPE of the given name or NULL.

Definition at line 373 of file LinearMotif.h.

    {
        Index ret = Cast< physical::Line* >(this->m_contents)->SeekToName(name);
        BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
            return NULL) //level 2 for GetOrCreate.
 
        return ChemicalCast< CONTENT_TYPE >(Cast< physical::Line* >(this->m_contents)->LinearAccess(ret));
    }

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, and bio::chemical::AbstractMotif::m_contents.

◆ GetClassProperties()

template<typename CONTENT_TYPE >

static LinearMotif< CONTENT_TYPE > Properties bio::chemical::LinearMotif< CONTENT_TYPE >::GetClassProperties ( )

inlinestatic

Add property::Linear() to what is given by AbstractMotif.

Returns: {Structural(), Linear()}

Definition at line 80 of file LinearMotif.h.

    {
        Properties ret = AbstractMotif::GetClassProperties();
        ret.push_back(property::Linear());
        return ret;
    }

References bio::chemical::AbstractMotif::GetClassProperties(), bio::property::Linear(), and bio::Properties.

◆ GetOrCreateByIdImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByIdImplementation ( StandardDimension id )

inlinevirtual

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.

Parameters

id

Returns: A CONTENT_TYPE of the given id.

Definition at line 406 of file LinearMotif.h.

    {
        CONTENT_TYPE ret = this->GetByIdImplementation(
            id
        );
        if (ret)
        {
            return ret;
        }
        return this->CreateImplementation(id);
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::CreateImplementation(), and bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation().

Referenced by bio::chemical::LinearStructureInterface::GetOrCreateById().

◆ GetOrCreateByNameImplementation()

template<typename CONTENT_TYPE >

virtual CONTENT_TYPE bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation ( Name name )

inlinevirtual

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.

Parameters

name

Returns: A CONTENT_TYPE of the given id.

Definition at line 426 of file LinearMotif.h.

    {
        BIO_SANITIZE(this->GetStructuralPerspective(), ,
            return NULL);
        //We convert to Id in case the Name is not already registered in the desired Perspective.
        StandardDimension id = this->GetStructuralPerspective()->GetIdFromName(name);
        CONTENT_TYPE ret = this->GetByIdImplementation(id);
        if (ret)
        {
            return ret;
        }
        return this->CreateImplementation(id);
    }

References BIO_SANITIZE, bio::chemical::LinearMotif< CONTENT_TYPE >::CreateImplementation(), bio::chemical::LinearMotif< CONTENT_TYPE >::GetByIdImplementation(), bio::physical::Perspective< DIMENSION >::GetIdFromName(), and bio::chemical::LinearMotif< CONTENT_TYPE >::GetStructuralPerspective().

Referenced by bio::chemical::LinearStructureInterface::GetOrCreateByName().

◆ GetStringFromImplementation()

template<typename CONTENT_TYPE >

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

inlinevirtual

Gets the Names of all Contents and puts them into a string.

Parameters

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

Returns: the Contents of *this as a string.

Reimplemented from bio::chemical::UnorderedMotif< CONTENT_TYPE >.

Definition at line 550 of file LinearMotif.h.

    {
        std::string ret = "";
 
        for (
            SmartIterator cnt(
                this->m_contents,
                this->m_contents->GetBeginIndex());
            !cnt.IsAtEnd();
            ++cnt
            )
        {
            ret += cnt.template As< physical::Identifiable< StandardDimension >* >()->GetName();
            if (cnt.GetIndex() != this->m_contents->GetEndIndex() - 1)
            {
                ret += separator;
            }
        }
        return ret;
    }

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

◆ GetStructuralPerspective() [1/2]

template<typename CONTENT_TYPE >

physical::Perspective< StandardDimension > * bio::chemical::LinearMotif< CONTENT_TYPE >::GetStructuralPerspective ( )

inline

Returns: the m_perspective used by *this.

Definition at line 152 of file LinearMotif.h.

    {
        return m_perspective;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::m_perspective.

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::CreateImplementation(), and bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation().

◆ GetStructuralPerspective() [2/2]

template<typename CONTENT_TYPE >

const physical::Perspective< StandardDimension > * bio::chemical::LinearMotif< CONTENT_TYPE >::GetStructuralPerspective ( ) const

inline

Returns: the m_perspective used by *this.

Definition at line 160 of file LinearMotif.h.

    {
        return m_perspective;
    }

References bio::chemical::LinearMotif< CONTENT_TYPE >::m_perspective.

◆ HasImplementation()

template<typename CONTENT_TYPE >

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

inlinevirtual

Check for content. Dereferences content (i.e. prevents pointer comparison (unless**)).

Parameters

content

Returns: whether or not the given content exists in *this

Definition at line 448 of file LinearMotif.h.

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

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

◆ ImportImplementation()

template<typename CONTENT_TYPE >

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

inlinevirtual

Copy the contents of another container into *this. Clone()s each element.

Parameters

other

Definition at line 458 of file LinearMotif.h.

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

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

◆ InsertImplementation()

template<typename CONTENT_TYPE >

virtual Code bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation	(	CONTENT_TYPE	toAdd,
		const Position	position = `BOTTOM`,
		const StandardDimension	optionalPositionArg = `0`,
		const bool	transferSubContents = `false`
	)

inlinevirtual

Adds a Content in *this at the indicated position. Multiple contents of the same id will cause the previously existing Content to be removed.

NOTE: THIS DESTROYS INDEX INTEGRITY. Indices will be rearranged to accommodate the insertion, making any cached Index invalid.

Parameters

toAdd	what to add. IMPORTANT: This must not already be in a LinearMotif (i.e. create a clone() before adding it to another destination).
position	determines where in *this the Content is added.
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 conflicting Content to be copied into the new Content, before the conflicting Content is deleted (similar to renaming an upper directory while preserving it's contents).

Returns: Status of addition (e.g. success or failure).

Definition at line 188 of file LinearMotif.h.

    {
        BIO_SANITIZE(toAdd, ,
            return code::MissingArgument1())
 
        Code ret = code::Success();
 
        SmartIterator toReplace(
            this->m_contents,
            InvalidIndex());
 
        //Remove conflicts
        for (
            SmartIterator cnt = this->m_contents->End();
            !cnt.IsAtBeginning();
            --cnt
            )
        {
            if (cnt.template As< CONTENT_TYPE >()->IsId(toAdd->GetId()))
            {
                //Not an error, but potentially worth noting.
                ret = code::SuccessfullyReplaced();
 
                toReplace = cnt;
                break; //Only find 1 conflict, as no others should exist.
            }
        }
 
        CONTENT_TYPE addition = CloneAndCast< CONTENT_TYPE >(toAdd);
        BIO_SANITIZE(addition, ,
            return code::GeneralFailure())
 
        if (this->m_contents->IsAllocated(toReplace.GetIndex())) //i.e. GetIndex() != 0.
        {
            if (transferSubContents)
            {
                //NOTE: THIS REMOVES ALL STRUCTURAL COMPONENTS IN toReplace
                // WHICH ARE NOT EXPLICITLY IN addition
                //This makes sense but is bound to be a bug at some point...
 
                CONTENT_TYPE toReplaceCasted = toReplace.template As< CONTENT_TYPE >();
                //addition->ImportAll(toReplaceCasted); //<- inaccessible, so we replicate the function here.
 
                Bond* bondBuffer;
                for (
                    SmartIterator bnd = addition->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 = toReplaceCasted->AsAtom()->GetBonded(toReplaceCasted->AsAtom()->GetBondPosition(bondBuffer->GetId()));
                    Cast< AbstractMotif* >(bondBuffer->GetBonded())->ImportImplementation(otherBond); //actual work
                }
            }
            this->m_contents->Erase(toReplace);
        }
 
        switch (position)
        {
            case TOP:
            {
                this->m_contents->Insert(
                    addition,
                    this->m_contents->GetBeginIndex());
                break;
            }
            case BEFORE:
            {
                Index placement = Cast< physical::Line* >(this->m_contents)->SeekToId(optionalPositionArg);
                if (!placement)
                {
                    return code::GeneralFailure();
                }
                BIO_SANITIZE(Cast< physical::Line* >(this->m_contents)->LinearAccess(placement)->GetPerspective() == addition->GetPerspective(), ,
                    return code::GeneralFailure());
 
                this->m_contents->Insert(
                    addition,
                    placement
                );
                break;
            }
            case AFTER:
            {
                Index placement = Cast< physical::Line* >(this->m_contents)->SeekToId(optionalPositionArg);
                if (!placement)
                {
                    return code::GeneralFailure();
                }
                BIO_SANITIZE(Cast< physical::Line* >(this->m_contents)->LinearAccess(placement)->GetPerspective() == addition->GetPerspective(), ,
                    return code::GeneralFailure());
 
                this->m_contents->Insert(
                    addition,
                    ++placement
                );
                break;
            }
            case BOTTOM:
            {
                this->m_contents->Insert(
                    addition,
                    this->m_contents->GetEndIndex());
                break;
            }
            default:
            {
                this->m_contents->Add(addition);
                break;
            }
        } //switch
 
        return ret;
    }

References bio::Container::Add(), bio::AFTER, bio::physical::Wave::AsAtom(), bio::BEFORE, BIO_SANITIZE, bio::BOTTOM, bio::Container::End(), bio::Container::Erase(), bio::code::GeneralFailure(), bio::Container::GetBeginIndex(), bio::chemical::Bond::GetBonded(), bio::chemical::Atom::GetBonded(), bio::chemical::AbstractMotif::GetClassProperties(), bio::Container::GetEndIndex(), bio::chemical::Bond::GetId(), bio::SmartIterator::GetIndex(), bio::physical::Observer< Perspective< StandardDimension > >::GetPerspective(), bio::physical::Wave::GetResonanceBetween(), bio::Container::Insert(), bio::InvalidIndex(), bio::Container::IsAllocated(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Bond::IsEmpty(), bio::chemical::AbstractMotif::m_contents, bio::code::MissingArgument1(), bio::code::Success(), bio::code::SuccessfullyReplaced(), and bio::TOP.

Referenced by bio::chemical::LinearStructureInterface::Insert().

Member Data Documentation

◆ m_perspective

template<typename CONTENT_TYPE >

physical::Perspective< StandardDimension >* bio::chemical::LinearMotif< CONTENT_TYPE >::m_perspective

Each LinearMotif may use a different Perspective for identifying its contents. This Perspective will be used for Name <-> Id matching, Wave->Clone()ing, etc. See bio/physical/Perspective.h for more details.

Definition at line 147 of file LinearMotif.h.

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::GetStructuralPerspective().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Contents

Constructor & Destructor Documentation

◆ LinearMotif() [1/3]

◆ LinearMotif() [2/3]

◆ LinearMotif() [3/3]

◆ ~LinearMotif()

Member Function Documentation

◆ AddImplementation()

◆ Attenuate()

◆ BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS()

◆ ClearImplementation()

◆ CreateImplementation()

◆ Disattenuate()

◆ ForEachImplementation()

◆ GetByIdImplementation() [1/2]

◆ GetByIdImplementation() [2/2]

◆ GetByNameImplementation() [1/2]

◆ GetByNameImplementation() [2/2]

◆ GetClassProperties()

◆ GetOrCreateByIdImplementation()

◆ GetOrCreateByNameImplementation()

◆ GetStringFromImplementation()

◆ GetStructuralPerspective() [1/2]

◆ GetStructuralPerspective() [2/2]

◆ HasImplementation()

◆ ImportImplementation()

◆ InsertImplementation()

Member Data Documentation

◆ m_perspective