bio::genetic::Insertion Class Reference

#include <Insertion.h>

Inheritance diagram for bio::genetic::Insertion:

Collaboration diagram for bio::genetic::Insertion:

Public Member Functions
virtual BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Insertion) explicit Insertion(chemical	~Insertion ()
virtual chemical::Substance *	GetWhatWillBeInserted ()
virtual void	InsertThis (chemical::Substance *toInsert)
virtual chemical::Substance *	Seek (chemical::Substance *insertIn) const
virtual void	SetSite (Site site)
Public Member Functions inherited from bio::physical::Class< Insertion >
	Class (Insertion *object, Symmetry *symmetry=NULL)
virtual	~Class ()
virtual Wave *	AsWave ()
virtual const Wave *	AsWave () const
virtual Wave *	Clone () const
Insertion *	Convert (Wave *wave)
virtual	operator Insertion * ()
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::genetic::Localization
virtual	~Localization ()
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Localization) explicit Localization(Site site
virtual Name	GetNameOfSite () const
virtual Site	GetSite () const
virtual chemical::Substance *	Seek (chemical::Substance *seekIn) const
virtual void	SetNameOfSite (Name name)
virtual void	SetSite (Site site)

Protected Attributes
chemical::Substance *	m_toInsert
Protected Attributes inherited from bio::physical::Class< Insertion >
Insertion *	m_object
Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal
Symmetry *	m_symmetry
Protected Attributes inherited from bio::genetic::Localization
Name	m_name
Localization *	m_previous
Site	m_site
chemical::ExcitationBase *	mc_method

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)
Public Attributes inherited from bio::genetic::Localization
Name	name
Protected Member Functions inherited from bio::genetic::Localization
chemical::Substance *	ResolvePrevious (chemical::Substance *seekIn) const

Detailed Description

Insertions are a type of Insertion which, instead of just finding a place, add something to a place. This is used to move Proteins to their correct position after Transcription.

NOTE: All Sites currently have a 1 to 1 mapping with Sites and should always be the same value. i.e. Cast< Site >(mySiteId) == InsertionSitePerspective::Instance().GetIdWithoutCreation(mySiteName)

Definition at line 36 of file Insertion.h.

Constructor & Destructor Documentation

~Insertion()

bio::genetic::Insertion::~Insertion ( )

virtual

Ensure virtual methods point to Class implementations.

Parameters

whatToInsert
site
name

Definition at line 46 of file Insertion.cpp.

{
 
}

Member Function Documentation

GetWhatWillBeInserted()

chemical::Substance * bio::genetic::Insertion::GetWhatWillBeInserted ( )

virtual

Returns

what *this will try to insert in its Localization

Definition at line 93 of file Insertion.cpp.

{
    return m_toInsert;
}

InsertThis()

void bio::genetic::Insertion::InsertThis ( chemical::Substance *  toInsert )

virtual

Tells *this to insert toInsert in its Localization.

Parameters

toInsert

Definition at line 88 of file Insertion.cpp.

{
    m_toInsert = toInsert;
}

Seek()

chemical::Substance * bio::genetic::Insertion::Seek ( chemical::Substance *  insertIn ) const

virtual

Override of Localization system. This is what does the inserting. Will recurse upward, following m_previous for as long as possible.

Parameters

insertIn

Returns

a Substance somewhere within the Substance provided or NULL.

Reimplemented from bio::genetic::Localization.

Definition at line 51 of file Insertion.cpp.

{
    insertIn = ResolvePrevious(insertIn);
 
    BIO_SANITIZE(insertIn && m_toInsert, ,
        return insertIn);
 
    if (m_site == InsertionSitePerspective::InvalidId())
    {
        return insertIn;
    }
 
    BIO_SANITIZE(mc_method, ,
        return NULL)
    ByteStream insertion(m_toInsert);
    (const_cast< chemical::ExcitationBase* >(mc_method))->EditArg(
        0,
        insertion
    );
    ByteStream result;
    mc_method->CallDown(
        insertIn->AsWave(),
        result
    );
    chemical::Substance* insert = ChemicalCast< chemical::Substance* >(Cast< physical::Wave* >(result.IKnowWhatImDoing())); //This is about as safe as we can get right now.
    BIO_SANITIZE(insert, ,
        return NULL)
    return insert;
}

References bio::physical::Class< T >::AsWave(), BIO_SANITIZE, and bio::ByteStream::IKnowWhatImDoing().

Referenced by bio::genetic::Expressor::Translate().

SetSite()

void bio::genetic::Insertion::SetSite ( Site  site )

virtual

Set m_site.

Parameters

site

Reimplemented from bio::genetic::Localization.

Definition at line 81 of file Insertion.cpp.

{
    //Assume Sites & Sites always match exactly.
    m_site = site;
    mc_method = InsertionSitePerspective::Instance().GetNewObjectFromIdAs< chemical::ExcitationBase* >(m_site);
}

Member Data Documentation

m_toInsert

chemical::Substance* bio::genetic::Insertion::m_toInsert

protected

Definition at line 92 of file Insertion.h.

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

• /home/eons/git/biology/lib_bio/inc/bio/genetic/localization/Insertion.h
• /home/eons/git/biology/lib_bio/src/genetic/localization/Insertion.cpp