Namespaces
namespace	bond_type

namespace	cellular

namespace	chemical

namespace	code

namespace	filter

namespace	genetic

namespace	log

namespace	molecular

namespace	organic

namespace	physical

namespace	property

namespace	random

namespace	state

namespace	string

namespace	symmetry_type

namespace	transcription_factor

namespace	utility

Classes
class	ByteStream

class	Container

class	Iterator

class	SmartIterator

class	Threaded

class	ThreadSafe

class	VirtualBase

Typedefs
typedef std::vector< ByteStream >	ByteStreams

typedef std::vector< const char * >	CharStrings

typedef uint32_t	Index

typedef const char *	Name

typedef std::vector< Name >	Names

typedef std::vector< std::string >	StdStrings

typedef uint32_t	TimeMS

typedef uint32_t	TimeSec

typedef uint32_t	Timestamp

typedef std::vector< Timestamp >	Timestamps

typedef uint32_t	TimeUS

typedef void	TypeNameProber

Enumerations
enum	Position { TOP = 0 , BOTTOM , AFTER , BEFORE , INSERTION_POSITION_TOTAL }

Functions
	BIO_ID (Site, uint8_t) BIO_PERSPECTIVE_SINGLETON(LocalizationSitePerspective

	BIO_ID (StandardDimension, uint32_t) BIO_ID_WITH_PERSPECTIVE(Code

uint8_t	BIO_ID_WITH_PERSPECTIVE (State, uint8_t) BIO_ID_WITH_PERSPECTIVE_WITH_PLURAL(Property

uint8_t uint8_t	BIO_ID_WITH_PERSPECTIVE (SymmetryType, uint8_t) BIO_ID_WITH_PERSPECTIVE(Filter

Site	BIO_PERSPECTIVE_SINGLETON (InsertionSitePerspective, Site) BIO_ID_WITH_PERSPECTIVE(TranscriptionFactor

	BIO_PERSPECTIVE_SINGLETON (OrganismPerspective, StandardDimension) BIO_PERSPECTIVE_SINGLETON(HabitatPerspective

	BIO_SITE_FUNCTION_BODY (InSurface, molecular::Molecule *) BIO_SITE_FUNCTION_BODY(OnMolecule

	BIO_STRONG_TYPEDEF (uint8_t, BondType, 0) BIO_PERSPECTIVE_SINGLETON(BondTypePerspective

template<typename TO , typename FROM >
TO	Cast (FROM toCast)

template<typename TO , typename FROM >
TO	ChemicalCast (FROM toCast)

template<typename T >
T	CloneAndCast (const T toClone)

template<typename TO_FINAL , typename TO_1 , typename FROM >
TO_FINAL	DoubleForceCast (FROM toCast, TO_1 *autoTo)

template<typename TO , typename FROM >
TO	ForceCast (FROM toCast)

const Index	InvalidIndex ()

template<typename T >
const std::string	TypeName ()

template<typename T >
static const std::string	TypeName ()

template<typename T >
const std::string	TypeName (const T t)

template<>
const std::string	TypeName< void > ()

template<typename T >
static const std::string	WrappedTypeName ()

static const std::size_t	WrappedTypeNamePrefixLength ()

static const std::size_t	WrappedTypeNameSuffixLength ()

Variables
uint8_t	Properties

Detailed Description

the random namespace provides functions for generating random numbers. IMPORTANT: random is currently only implemented in c++11. When not using c++ >= 11, 0 is returned.

Common string operations

File of common types used across many classes.

WARNING: THIS FILE USES C++11 for cross platform time management. TODO: add C++98 compatibility for popular operating systems.

Typedef Documentation

◆ ByteStreams

typedef std::vector< ByteStream > bio::ByteStreams

Definition at line 52 of file Types.h.

◆ CharStrings

typedef std::vector< const char* > bio::CharStrings

Definition at line 49 of file Types.h.

◆ Index

typedef uint32_t bio::Index

Indices are used by Arrangements to manage and manipulate what they store.

Definition at line 57 of file Types.h.

◆ Name

typedef const char* bio::Name

Names are used in NameTracker<>s but are defined here for simplicity.

Definition at line 46 of file Types.h.

◆ Names

typedef std::vector< Name > bio::Names

Definition at line 47 of file Types.h.

◆ StdStrings

typedef std::vector< std::string > bio::StdStrings

Definition at line 50 of file Types.h.

◆ TimeMS

typedef uint32_t bio::TimeMS

milliseconds (ms for short)

Definition at line 79 of file Types.h.

◆ TimeSec

typedef uint32_t bio::TimeSec

seconds (s or sec for short)

Definition at line 84 of file Types.h.

◆ Timestamp

typedef uint32_t bio::Timestamp

milliseconds (ms for short)

Definition at line 68 of file Types.h.

◆ Timestamps

typedef std::vector< Timestamp > bio::Timestamps

Definition at line 69 of file Types.h.

◆ TimeUS

typedef uint32_t bio::TimeUS

microseconds (us for short)

Definition at line 74 of file Types.h.

◆ TypeNameProber

typedef void bio::TypeNameProber

Used to determine magic numbers in extracting symbols as type.

Definition at line 49 of file TypeName.h.

Enumeration Type Documentation

◆ Position

enum bio::Position

Mainly used for inserting children into Nested classes.

Enumerator
TOP
BOTTOM
AFTER
BEFORE
INSERTION_POSITION_TOTAL

Definition at line 45 of file Types.h.

{
 TOP = 0,
 BOTTOM,
 AFTER,
 BEFORE,
 INSERTION_POSITION_TOTAL
} Position;

Function Documentation

◆ BIO_ID() [1/2]

bio::BIO_ID	(	Site	,
		uint8_t
	)

Sites are types of places. The place itself should be specified by Name or Id. Because places can be anything, we rely on Perspective::AssociateType and chemical::Excitation in order to turn a Site into an actionable function. Sites are identical to Sites except they have an insertion method, rather than an extraction method. See Localization.h for more info.

◆ BIO_ID() [2/2]

bio::BIO_ID	(	StandardDimension	,
		uint32_t
	)

Id type used for all Ids until Named classes can be properly derived from. See physical::Identifiable.h for more info. StandardDimension is NOT used when the type itself is the id, e.g. for Code, etc. Value returned by many bio methods. You may make your own Codes by using the macro defined in common/Codes.h

◆ BIO_ID_WITH_PERSPECTIVE() [1/2]

uint8_t bio::BIO_ID_WITH_PERSPECTIVE	(	State	,
		uint8_t
	)

States determine the condition of an object (e.g. a chemical::Substance) at runtime. The most common State is Enabled() (see "bio/chemical/States.h") Properties are feature flags that give some hint of what a Wave can do (i.e. be cast as). For example, having the Periodic() Property means the class derives from Periodic and thus implements the Peak() method. You might not know that the derived Wave included inheritance of Periodic without being able to ProbeFor() the Periodic Property. See Wave.h for more info.

While the State of an object might change often, the Properties should remain constant. However, that is not enforced. The properties of water change when its chemical state changes from liquid to solid, so the Properties of your objects could change in whatever way you'd like, though doing so is generally not recommended.

◆ BIO_ID_WITH_PERSPECTIVE() [2/2]

uint8_t uint8_t bio::BIO_ID_WITH_PERSPECTIVE	(	SymmetryType	,
		uint8_t
	)

SymmetryTypes determine what to do with a particular Symmetry. They should contain the generic building blocks of all Axes (e.g. programming languages) such that Waves can be Spun around any Axis.

References BIO_PERSPECTIVE_SINGLETON().

◆ BIO_PERSPECTIVE_SINGLETON() [1/2]

Site bio::BIO_PERSPECTIVE_SINGLETON	(	InsertionSitePerspective	,
		Site
	)

TranscriptionFactors determine which Proteins are expressed in which Cells. They exist as unique numbers only, which are added to Expressors in order to direct Plasmid expression on startup. For example, if you want to add functionality to a Cell, you would start by defining YourFavoritePlasmid (genetic::Plasmid), which contains YourFavoriteProtein (cellular::Protein). You would then specify which TranscriptionFactors are required for YourFavoriteProtein in YourFavoriteGene. Once that is done, you can add the previous TranscriptionFactor to any number of Cells, all of which will begin expressing YourFavoriteProtein on startup. TranscriptionFactors thus allow you to pick and choose which features of your loaded modules you would like in your Cells. In practice, you'll likely be using other people's Plasmids, so TranscriptionFactors give you a level of control over how you want to consume external libraries in your networks.

Referenced by BIO_ID_WITH_PERSPECTIVE().

◆ BIO_PERSPECTIVE_SINGLETON() [2/2]

bio::BIO_PERSPECTIVE_SINGLETON	(	OrganismPerspective	,
		StandardDimension
	)

◆ BIO_SITE_FUNCTION_BODY()

bio::BIO_SITE_FUNCTION_BODY	(	InSurface	,
		molecular::Molecule *
	)

◆ BIO_STRONG_TYPEDEF()

bio::BIO_STRONG_TYPEDEF	(	uint8_t	,
		BondType	,
		0
	)

The BondType of an Atom::Bond provides a simple description of the nature of the Bond. This can be used to inform other systems (e.g. molecular) of how to treat the Bonded Wave. NOTE: Atoms can Bond things that are not Atoms. The only requirement is that they are Wave.

◆ Cast()

template<typename TO , typename FROM >

TO bio::Cast ( FROM toCast )

Simple casting wrapper. It continues to function when RTTI is disabled.

Template Parameters

TO
FROM	Dynamically determined template type.

Parameters

toCast a FROM.

Returns: toCast as a TO

Definition at line 35 of file Cast.h.

{
 #ifdef RTTI_ENABLED
 return dynamic_cast<TO>(toCast);
 #else
 return (TO)(toCast);
 //Is reinterpret_cast the appropriate substitute here? Need to check usages.
 #endif
}

◆ ChemicalCast()

template<typename TO , typename FROM >

TO bio::ChemicalCast ( FROM toCast )

Definition at line 31 of file Cast.h.

{
 return toCast->AsAtom()->template As< TO >();
}

◆ CloneAndCast()

template<typename T >

T bio::CloneAndCast ( const T toClone )

Ease of use method for Cloning.

Template Parameters

T

Returns: a Clone of T casted to back to T.

Definition at line 42 of file Cast.h.

{
 //Dereference here might be dangerous & need sanitization.
 return ChemicalCast< T, ::bio::physical::Wave* >(toClone->Clone()->AsWave());
}

◆ DoubleForceCast()

template<typename TO_FINAL , typename TO_1 , typename FROM >

TO_FINAL bio::DoubleForceCast	(	FROM	toCast,
		TO_1 *	autoTo
	)

DANGEROUS!!! Same as ForceCast, except uses a dummy parameter to automatically determine an intermediate type.

Template Parameters

TO	Dynamically determined by autoTo dummy parameter.
FROM	Dynamically determined template type.

Parameters

toCast	a FROM.
autoTo	dummy.

Returns: toCast as a TO, regardless of what it was before.

Definition at line 76 of file Cast.h.

{
 return (TO_FINAL)(TO_1)(void*)(toCast);
}

◆ ForceCast()

template<typename TO , typename FROM >

TO bio::ForceCast ( FROM toCast )

DANGEROUS!!!

DO NOT USE THIS UNLESS YOU KNOW WHAT YOU ARE DOING!

THIS DOES NO ERROR CHECKING AND WILL BREAK YOUR CODE IF MISUSED!

Example use case: void* toCast = new MyClass(); //void* might be an ambiguous base class but MyClass is the same for toCast and casted. MyClass* casted = ForceCast<MyClass*>(toCast);

Template Parameters

TO
FROM	Dynamically determined template type.

Parameters

toCast a FROM.

Returns: toCast as a TO, regardless of what it was before.

Definition at line 61 of file Cast.h.

{
 return (TO)(void*)(toCast);
}

◆ InvalidIndex()

const Index bio::InvalidIndex ( )

We sacrifice our first index for the ability to do error checking.

Returns: a Index that holds no content.

Definition at line 26 of file Types.cpp.

{
 return 0;
}

Referenced by bio::physical::Arrangement< TYPE >::Add(), bio::Container::GetNextAvailableIndex(), bio::Container::Insert(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), bio::Container::SeekTo(), bio::physical::Line::SeekToId(), and bio::physical::Line::SeekToName().

◆ TypeName() [1/3]

template<typename T >

const std::string bio::TypeName ( )

FORWARD DECLARATION

Template Parameters

T

Returns: Just T as a string.

◆ TypeName() [2/3]

template<typename T >

static const std::string bio::TypeName ( )

static

Converts the T symbol to a string.

Template Parameters

T

Returns: Just T as a string.

Definition at line 95 of file TypeName.h.

{
 static const std::string wrappedName = WrappedTypeName< T >();
 static const std::size_t prefixLength = WrappedTypeNamePrefixLength();
 static const std::size_t suffixLength = WrappedTypeNameSuffixLength();
 static const std::size_t typeNameLength = wrappedName.length() - prefixLength - suffixLength;
 return wrappedName.substr(
 prefixLength,
 typeNameLength
 );
}

References WrappedTypeNamePrefixLength(), and WrappedTypeNameSuffixLength().

◆ TypeName() [3/3]

template<typename T >

const std::string bio::TypeName ( const T t )

Converts the T symbol to a string.

Template Parameters

T

Parameters

t	used for auto type determination.

Returns: Just T as a string.

Definition at line 114 of file TypeName.h.

{
 return TypeName< T >();
}

◆ TypeName< void >()

template<>

const std::string bio::TypeName< void > ( )

inline

Returns: "void"

Definition at line 41 of file TypeName.h.

{
 return "void";
}

◆ WrappedTypeName()

template<typename T >

static const std::string bio::WrappedTypeName ( )

static

Converts the T symbol to a string. Only supported on a limited number of compilers.

Template Parameters

T

Returns: T as a string with wrapping symbols.

Definition at line 58 of file TypeName.h.

{
 #ifdef __clang__
 return __PRETTY_FUNCTION__;
 #elif defined(__GNUC__)
 return __PRETTY_FUNCTION__;
 #elif defined(_MSC_VER)
 return __FUNCSIG__;
 #else
 #error "Unsupported compiler"
 #endif
}

◆ WrappedTypeNamePrefixLength()

static const std::size_t bio::WrappedTypeNamePrefixLength ( )

static

Used to trim leading characters from symbol string.

Returns: magic number for prefix length.

Definition at line 75 of file TypeName.h.

{
 return WrappedTypeName< TypeNameProber >().find(TypeName< TypeNameProber >());
}

Referenced by TypeName(), and WrappedTypeNameSuffixLength().

◆ WrappedTypeNameSuffixLength()

static const std::size_t bio::WrappedTypeNameSuffixLength ( )

static

Used to trim trailing characters from symbol string.

Returns: magic number for suffix length.

Definition at line 84 of file TypeName.h.

{
 return WrappedTypeName< TypeNameProber >().length() - WrappedTypeNamePrefixLength() - TypeName< TypeNameProber >().length();
}

References WrappedTypeNamePrefixLength().

Referenced by TypeName().

Variable Documentation

◆ Properties

uint8_t bio::Properties

Definition at line 58 of file Types.h.

Referenced by bio::chemical::ExcitationBase::GetClassProperties(), bio::chemical::AbstractMotif::GetClassProperties(), bio::chemical::LinearMotif< CONTENT_TYPE >::GetClassProperties(), bio::physical::Periodic::GetClassProperties(), bio::cellular::PeakCarrierWave::GetProperties(), bio::chemical::ExcitationWithoutArgument< WAVE, RETURN >::GetProperties(), bio::chemical::ExcitationWithArgument< WAVE, RETURN, ARGUMENT >::GetProperties(), bio::chemical::ExcitationWithTwoArguments< WAVE, RETURN, ARGUMENT1, ARGUMENT2 >::GetProperties(), bio::physical::Wave::GetProperties(), bio::chemical::PeriodicTableImplementation::GetPropertiesOf(), bio::physical::Wave::GetResonanceBetween(), bio::chemical::PeriodicTableImplementation::RecordPropertyOf(), and bio::chemical::Reaction::Require().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ ByteStreams

◆ CharStrings

◆ Index

◆ Name

◆ Names

◆ StdStrings

◆ TimeMS

◆ TimeSec

◆ Timestamp

◆ Timestamps

◆ TimeUS

◆ TypeNameProber

Enumeration Type Documentation

◆ Position

Function Documentation

◆ BIO_ID() [1/2]

◆ BIO_ID() [2/2]

◆ BIO_ID_WITH_PERSPECTIVE() [1/2]

◆ BIO_ID_WITH_PERSPECTIVE() [2/2]

◆ BIO_PERSPECTIVE_SINGLETON() [1/2]

◆ BIO_PERSPECTIVE_SINGLETON() [2/2]

◆ BIO_SITE_FUNCTION_BODY()

◆ BIO_STRONG_TYPEDEF()

◆ Cast()

◆ ChemicalCast()

◆ CloneAndCast()

◆ DoubleForceCast()

◆ ForceCast()

◆ InvalidIndex()

◆ TypeName() [1/3]

◆ TypeName() [2/3]

◆ TypeName() [3/3]

◆ TypeName< void >()

◆ WrappedTypeName()

◆ WrappedTypeNamePrefixLength()

◆ WrappedTypeNameSuffixLength()

Variable Documentation

◆ Properties