#include <Wave.h>

Inheritance diagram for bio::physical::Wave:

Collaboration diagram for bio::physical::Wave:

Public Member Functions
	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

Static Public Member Functions
static Properties	GetResonanceBetween (const Wave *wave, const Properties &properties)

static Properties	GetResonanceBetween (const Wave wave1, const Wave wave2)

static Properties	GetResonanceBetween (ConstWaves waves)

Protected Attributes
Wave *	m_signal

Symmetry *	m_symmetry

Detailed Description

A Wave is a base class for all Biology objects. Waves can be Periodic but do not have to be. By default, we assume Waves have no discernible frequency, amplitude, or any other Property. This is similar to a chaotic pattern or a wave modulated with enough signals that it becomes indiscernible from white noise / randomness. We do not / cannot make any assumptions about the ordering / pattern of a Wave at this level. Such Properties will only manifest in derived classes.

You should be able to upcast to Wave from any other class. Cloning a Wave should produce a functional fully derived class. This means that all diamond inheritance should be resolved by all children when calling Clone For downcasting to a derived class, you will need to use the chemical::Atom::Bond(...) methodology. See chemical/Atom.h for more info.

Waves may be Modulated to store additional signals and subsequently Demodulated in order to retrieve that original signal. In this way, any Wave can carry any other.

Definition at line 64 of file Wave.h.

Constructor & Destructor Documentation

◆ Wave()

bio::physical::Wave::Wave ( Symmetry * symmetry = NULL )

Definition at line 32 of file Wave.cpp.

    :
    m_symmetry(
        symmetry
    ),
    m_signal(
        NULL
    )
{
}

Referenced by Clone().

◆ ~Wave()

bio::physical::Wave::~Wave ( )

virtual

Definition at line 45 of file Wave.cpp.

{
    BIO_SANITIZE_AT_SAFETY_LEVEL_2(m_symmetry,
        delete m_symmetry;
        m_symmetry = NULL,);
}

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, and m_symmetry.

Member Function Documentation

◆ AsAtom() [1/2]

virtual chemical::Atom * bio::physical::Wave::AsAtom ( )

inlinevirtual

For Downcasting. Because Wave cannot be virtually inherited and will likely become an ambiguous base, we commit a sin and provide a cheat. This method can be used to resolve any downcasting. For example: this->AsAtom()->As<Whatever>().

Returns: this as an Atom, if possible.

Definition at line 209 of file Wave.h.

    {
        return NULL;
    }

Referenced by bio::chemical::UnorderedStructureInterface::ImportAll(), and bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

◆ AsAtom() [2/2]

virtual const chemical::Atom * bio::physical::Wave::AsAtom ( ) const

inlinevirtual

For Downcasting. Because Wave cannot be virtually inherited and will likely become an ambiguous base, we commit a sin and provide a cheat. This method can be used to resolve any downcasting. For example: this->AsAtom()->As<Whatever>().

Returns: this as an Atom, if possible.

Definition at line 221 of file Wave.h.

    {
        return NULL;
    }

◆ AsWave() [1/2]

virtual Wave * bio::physical::Wave::AsWave ( )

inlinevirtual

For Upcasting. Used for resolving ambiguous inheritance without the need to explicitly derive from Wave. NOTE: operator Wave*() and various perturbations fail to resolve ambiguous implicit upcasting.

Returns: this

Definition at line 186 of file Wave.h.

    {
        return this;
    }

◆ AsWave() [2/2]

virtual const Wave * bio::physical::Wave::AsWave ( ) const

inlinevirtual

For Upcasting. Used for resolving ambiguous inheritance without the need to explicitly derive from Wave. NOTE: operator Wave*() and various perturbations fail to resolve ambiguous implicit upcasting.

Returns: this

Definition at line 197 of file Wave.h.

    {
        return this;
    }

◆ Attenuate()

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

virtual

Moves other through *this, taking something from it. Used for += operator This is a nop unless implemented by children.

Parameters

other

Definition at line 81 of file Wave.cpp.

{
    return code::NotImplemented();
}

References bio::code::NotImplemented().

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::Attenuate(), bio::chemical::Atom::Attenuate(), and operator+().

◆ Clone()

Wave * bio::physical::Wave::Clone ( ) const

virtual

Returns: a copy of the most derived object of *this.

Definition at line 52 of file Wave.cpp.

{
    return new Wave(
        *this
    );
}

References Wave().

Referenced by bio::physical::PerspectiveUtilities::Clone().

◆ Demodulate() [1/2]

Wave * bio::physical::Wave::Demodulate ( )

virtual

Treats *this as a carrier wave.

Returns: the signal carried by *this.

Definition at line 99 of file Wave.cpp.

{
    return m_signal;
}

References m_signal.

Referenced by bio::chemical::Atom::Attenuate(), bio::chemical::Atom::Disattenuate(), and operator*().

◆ Demodulate() [2/2]

const Wave * bio::physical::Wave::Demodulate ( ) const

virtual

Treats *this as a carrier wave.

Returns: the signal carried by *this.

Definition at line 104 of file Wave.cpp.

{
    return m_signal;
}

References m_signal.

◆ Disattenuate()

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

virtual

Pulls other out of *this, maybe giving something back? The opposite of Attenuation. Used for -= operator. This is a nop unless implemented by children.

Parameters

other

Definition at line 86 of file Wave.cpp.

{
    return code::NotImplemented();
}

References bio::code::NotImplemented().

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::Disattenuate(), bio::chemical::Atom::Disattenuate(), and operator-().

◆ GetProperties()

Properties bio::physical::Wave::GetProperties ( ) const

virtual

Waves, depending on their behavior, can have different Properties. GetProperties can be used for determining how to downcast *this. The Properties returned dictate what a Wave can do and / or what can be done with one. If we treat Properties as fourier components of a waveform, we could restate GetProperties as GetPeriodicComponents. In this context, "what a wave can do" and "what can be done with a wave" can be expressed as "which systems resonate with the wave in question" or "which systems have comparable periodic components", which is true here as well: when 2 Waves have the same Properties (i.e. Resonate with each other) they can be treated the same in some regard (perhaps they are "numeric" and can be "added") and when 2 waves have comparable properties, they can interact with each other. It is up to you and other users of this framework to determine which Properties to use where. This is your space, so make use of it when you feel it's appropriate. NOTE: Waves do not actually have m_properties. This method MUST be implemented by children in order to work. If using any chemical::Class or beyond, this method will be implemented for you. See chemical/Class.h for more info.

Returns: the Properties of *this (empty vector unless overridden).

Reimplemented in bio::cellular::PeakCarrierWave, bio::chemical::ExcitationBase, bio::chemical::ExcitationWithoutArgument< WAVE, RETURN >, bio::chemical::ExcitationWithArgument< WAVE, RETURN, ARGUMENT >, bio::chemical::ExcitationWithTwoArguments< WAVE, RETURN, ARGUMENT1, ARGUMENT2 >, and bio::physical::Periodic.

Definition at line 142 of file Wave.cpp.

{
    Properties ret;
    return ret;
}

References bio::Properties.

Referenced by GetResonanceBetween().

◆ GetResonanceBetween() [1/3]

Properties bio::physical::Wave::GetResonanceBetween	(	const Wave *	wave,
		const Properties &	properties
	)

static

Ease of use method for getting the Resonance between a Wave and a set of Properties

Parameters

wave
properties

Returns: the number of overlapping Properties between the Wave and Properties given.

Definition at line 148 of file Wave.cpp.

{
    class TempWave :
        public Wave
    {
    public:
        TempWave(Properties p)
            :
            m_properties(p)
        {
        }
 
        ~TempWave()
        {
        }
 
        virtual Properties GetProperties() const
        {
            return m_properties;
        }
 
        Properties m_properties;
    };
 
    ConstWaves waves;
    waves.push_back(
        wave
    );
    TempWave* twave = new TempWave(properties);
    waves.push_back(
        twave
    );
 
    Properties ret = GetResonanceBetween(
        waves
    );
 
    delete twave;
    return ret;
}

References GetProperties(), GetResonanceBetween(), and bio::Properties.

◆ GetResonanceBetween() [2/3]

Properties bio::physical::Wave::GetResonanceBetween	(	const Wave *	wave1,
		const Wave *	wave2
	)

static

Ease of use method for getting the Resonance between just 2 waves, rather than n.

Parameters

wave1
wave2

Returns: the number of overlapping Properties between both waves given.

Definition at line 192 of file Wave.cpp.

{
    ConstWaves waves;
    waves.push_back(
        wave1
    );
    waves.push_back(
        wave2
    );
    return GetResonanceBetween(
        waves
    );
}

References GetResonanceBetween().

◆ GetResonanceBetween() [3/3]

Properties bio::physical::Wave::GetResonanceBetween ( ConstWaves waves )

static

Check how (and if) 2 Waves Resonate with each other. Resonance is defined as a commonality between 2 or more Waves. This is a little bit more generic than real life resonance, which is strictly a measure of increased amplitude when 2 or more waves interact. Here, Waves interacting could mean an increase in aperiodic behavior, where no frequency has any single discernible change to it, or any number of other complex transformations.

Parameters

waves

Returns: the number of overlapping Properties between both waves given.

Definition at line 209 of file Wave.cpp.

{
    Properties overlap;
    BIO_SANITIZE(waves.size() && waves[0], ,
        return overlap);
    overlap = waves[0]->GetProperties();
    BIO_SANITIZE_AT_SAFETY_LEVEL_2(waves.size() > 1, ,
        return overlap);
    std::vector< Properties::iterator > remBuffer;
 
    for (
        ConstWaves::const_iterator wav = waves.begin()++;
        wav != waves.end();
        ++wav
        )
    {
        BIO_SANITIZE(*wav, ,
            continue);
 
        Properties wavProperties = (*wav)->GetProperties();
        remBuffer.clear();
        for (
            Properties::iterator prp = overlap.begin();
            prp != overlap.end();
            ++prp
            )
        {
            if (std::find(
                wavProperties.begin(),
                wavProperties.end(),
                *prp
            ) != wavProperties.end())
            {
                remBuffer.push_back(
                    prp
                );
            }
        }
        for (
            std::vector< Properties::iterator >::iterator rem = remBuffer.begin();
            rem != remBuffer.end();
            ++rem
            )
        {
            overlap.erase(
                *rem
            );
        }
    }
    return overlap;
}

References BIO_SANITIZE, BIO_SANITIZE_AT_SAFETY_LEVEL_2, and bio::Properties.

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::Attenuate(), bio::chemical::Atom::Attenuate(), bio::chemical::Atom::Disattenuate(), GetResonanceBetween(), bio::chemical::UnorderedStructureInterface::ImportAll(), and bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

◆ Modulate()

Wave * bio::physical::Wave::Modulate ( Wave * signal )

virtual

This will overwrite any signal currently carried by *this.

Returns: the signal Modulated.

Definition at line 91 of file Wave.cpp.

{
    m_signal = signal;
    return this;
}

References m_signal.

Referenced by bio::cellular::PeakCarrierWave::PeakCarrierWave(), and operator*().

◆ operator*() [1/3]

Wave * bio::physical::Wave::operator* ( )

virtual

Demodulate operator (i.e. not "dereference")

Returns: Demodulate()

Definition at line 118 of file Wave.cpp.

{
    return Demodulate();
}

References Demodulate().

◆ operator*() [2/3]

const Wave * bio::physical::Wave::operator* ( ) const

virtual

Demodulate operator (i.e. not "dereference")

Returns: Demodulate()

Definition at line 123 of file Wave.cpp.

{
    return Demodulate();
}

References Demodulate().

◆ operator*() [3/3]

Wave * bio::physical::Wave::operator* ( Wave * signal )

virtual

Modulate operator (i.e. not "multiply")

Parameters

signal

Returns: Modulate(signal)

Definition at line 109 of file Wave.cpp.

{
    return Modulate(
        signal
    );
}

References Modulate().

◆ operator+()

void bio::physical::Wave::operator+ ( const Wave * other )

virtual

Makes other interfere with *this. Attenuates other.

Parameters

other

Definition at line 128 of file Wave.cpp.

{
    Attenuate(other);
}

References Attenuate().

◆ operator-()

void bio::physical::Wave::operator- ( const Wave * other )

virtual

Removes the interference of other from *this. Disattenuates other.

Parameters

other

Definition at line 135 of file Wave.cpp.

{
    Disattenuate(other);
}

References Disattenuate().

◆ operator|()

void bio::physical::Wave::operator| ( Symmetry * symmetry )

virtual

Reifies *this. (*myParticle) | jsonAxis("...");

Parameters

symmetry

Definition at line 72 of file Wave.cpp.

{
    Reify(
        symmetry
    );
}

References Reify().

◆ Reify()

Code bio::physical::Wave::Reify ( Symmetry * symmetry )

virtual

Reifying a Wave takes a Symmetry and realizes it by copying the values supplied into *this. Will update m_symmetry to the Symmetry provided but do nothing else. You should override Reify to update the contents of *this from the given Symmetry. Calling the parent method after is optional. See Quantum.h for an example interface.

Parameters

symmetry

Reimplemented in bio::chemical::Atom, bio::molecular::Molecule, bio::molecular::Surface, bio::physical::Filterable, bio::physical::Periodic, and bio::physical::Quantum< T >.

Definition at line 64 of file Wave.cpp.

{
    (*m_symmetry) = *symmetry;
    return code::Success();
}

References bio::code::Success().

Referenced by operator|().

◆ Spin()

Symmetry * bio::physical::Wave::Spin ( ) const

virtual

Spinning a Wave produces a Symmetry. Waves can be Rotated about any number of Axes. Spinning a Wave along one dimension (one Axis) would be the equivalent of reflecting that Wave or, possibly, refracting, dispersing, or otherwise altering the wave (e.g. if the Axis acted like a prism, rather than a mirror). When a Wave is Spun around multiple dimensions, the resulting Symmetry and effected transformations may not fall under any single property characteristic of real waves. Thus we treat Waves more like particles with a discrete spin.

You can visualize this by imagining a triangle that is then folded over to produce a polygon. Reflecting a triangle about 1 axis generates a rectangle, 2 a square, 3 a hexagon, 4 an octagon, and so on (sides = 3 + fibonacci sequence, starting at 0). Though, in this system, Axes do not overlap, so 1/2 of the polygon is discarded, once n >= 2. In this way, Spin() generates a triangle and you decide the shape by specifying how many Axes to Rotate the Symmetry about.

You should override Spin to update m_symmetry, then return the parent method. See Quantum.h for an example interface.

Returns: m_symmetry.

Reimplemented in bio::chemical::Atom, bio::molecular::Molecule, bio::molecular::Surface, bio::physical::Filterable, bio::physical::Periodic, and bio::physical::Quantum< T >.

Definition at line 59 of file Wave.cpp.

{
    return m_symmetry;
}

References m_symmetry.

Referenced by bio::physical::Axis::operator|(), bio::physical::Filterable::Spin(), bio::physical::Periodic::Spin(), and bio::physical::Quantum< T >::Spin().

Member Data Documentation

◆ m_signal

Wave* bio::physical::Wave::m_signal

protected

for Modulation.

Definition at line 277 of file Wave.h.

Referenced by Demodulate(), and Modulate().

◆ m_symmetry

Symmetry* bio::physical::Wave::m_symmetry

protected

We cache our Symmetry here to avoid excessive new & deletes when Spinning & Reifying *this.

Definition at line 272 of file Wave.h.

Referenced by ~Wave(), bio::physical::Filterable::Spin(), bio::physical::Periodic::Spin(), bio::physical::Quantum< T >::Spin(), and Spin().

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

/home/eons/git/biology/lib_bio/inc/bio/physical/Wave.h
/home/eons/git/biology/lib_bio/src/physical/Wave.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Wave()

◆ ~Wave()

Member Function Documentation

◆ AsAtom() [1/2]

◆ AsAtom() [2/2]

◆ AsWave() [1/2]

◆ AsWave() [2/2]

◆ Attenuate()

◆ Clone()

◆ Demodulate() [1/2]

◆ Demodulate() [2/2]

◆ Disattenuate()

◆ GetProperties()

◆ GetResonanceBetween() [1/3]

◆ GetResonanceBetween() [2/3]

◆ GetResonanceBetween() [3/3]

◆ Modulate()

◆ operator*() [1/3]

◆ operator*() [2/3]

◆ operator*() [3/3]

◆ operator+()

◆ operator-()

◆ operator|()

◆ Reify()

◆ Spin()

Member Data Documentation

◆ m_signal

◆ m_symmetry