#include <Arrangement.h>

Inheritance diagram for bio::physical::Arrangement< TYPE >:

Collaboration diagram for bio::physical::Arrangement< TYPE >:

Public Member Functions
	Arrangement (const Index expectedSize=2)

virtual	~Arrangement ()

ByteStream	Access (const Index index)

const ByteStream	Access (const Index index) const

Index	Add (const ByteStream content)

virtual bool	AreEqual (Index internal, const ByteStream external) const

bool	Erase (const Index index)

virtual const std::size_t	GetStepSize () const

virtual TYPE	OptimizedAccess (Index index)

virtual const TYPE	OptimizedAccess (Index index) const

Public Member Functions inherited from bio::Container
	Container (const Container &other)

	Container (const Index expectedSize=2, std::size_t stepSize=sizeof(ByteStream))

virtual	~Container ()

virtual ByteStream	Access (const Index index)

virtual const ByteStream	Access (const Index index) const

ByteStream	Access (const SmartIterator itt)

virtual const ByteStream	Access (const SmartIterator itt) const

virtual Index	Add (const ByteStream content)

template<typename T >
std::vector< T >	AsVector () const

virtual SmartIterator	Begin () const

virtual void	Clear ()

virtual Iterator *	ConstructClassIterator (const Index index=InvalidIndex()) const

virtual SmartIterator	End () const

bool	Erase (const SmartIterator itt)

virtual bool	Erase (Index index)

virtual void	Expand ()

virtual Index	GetAllocatedSize () const

virtual Index	GetBeginIndex () const

virtual Index	GetCapacity () const

virtual Index	GetEndIndex () const

virtual Index	GetNumberOfElements () const

bool	Has (const ByteStream content) const

virtual void	Import (const Container *other)

virtual Index	Insert (const ByteStream content, const Index index)

virtual bool	IsAllocated (const Index index) const

virtual bool	IsFree (const Index index) const

virtual bool	IsInRange (const Index index) const

virtual ByteStream	operator[] (const Index index)

virtual const ByteStream	operator[] (const Index index) const

virtual ByteStream	operator[] (const SmartIterator itt)

virtual const ByteStream	operator[] (const SmartIterator itt) const

Index	SeekTo (const ByteStream content) const

Additional Inherited Members
Protected Member Functions inherited from bio::Container
virtual bool	AreEqual (Index internal, const ByteStream external) const

virtual Index	GetNextAvailableIndex ()

virtual const std::size_t	GetStepSize () const

Protected Attributes inherited from bio::Container
std::deque< Index >	m_deallocated

Index	m_firstFree

Index	m_size

unsigned char *	m_store

Iterator *	m_tempItt

Detailed Description

template<typename TYPE>
class bio::physical::Arrangement< TYPE >

Arrangements provide a more memory-efficient interface of the Container interface for a single type.

Template Parameters

TYPE

Definition at line 35 of file Arrangement.h.

Constructor & Destructor Documentation

◆ Arrangement()

template<typename TYPE >

bio::physical::Arrangement< TYPE >::Arrangement ( const Index expectedSize = 2 )

inline

Parameters

expectedSize

Definition at line 43 of file Arrangement.h.

 :
 Container(
 expectedSize,
 sizeof(TYPE))
 {
 
 }

◆ ~Arrangement()

template<typename TYPE >

virtual bio::physical::Arrangement< TYPE >::~Arrangement ( )

inlinevirtual

Definition at line 55 of file Arrangement.h.

 {
 
 }

Member Function Documentation

◆ Access() [1/2]

template<typename TYPE >

ByteStream bio::physical::Arrangement< TYPE >::Access ( const Index index )

inlinevirtual

Get access to an element. NOTE: THIS DOES NOT CHECK IF THE ELEMENT IsFree!!! Free checks can be done independently. This is done for speed.

Parameters

index

Returns: the value stored in *this at the given index.

Reimplemented from bio::Container.

Definition at line 75 of file Arrangement.h.

 {
 BIO_SANITIZE(this->IsAllocated(index), ,
 return NULL)
 TYPE* ret;
 std::memcpy(
 ret,
 &this->m_store[index * sizeof(TYPE)],
 sizeof(TYPE));
 return *ret;
 }

References BIO_SANITIZE, bio::Container::IsAllocated(), and bio::Container::m_store.

Referenced by bio::physical::Arrangement< TYPE >::AreEqual(), and bio::physical::Arrangement< TYPE >::OptimizedAccess().

◆ Access() [2/2]

template<typename TYPE >

const ByteStream bio::physical::Arrangement< TYPE >::Access ( const Index index ) const

inlinevirtual

Get access to an element. NOTE: THIS DOES NOT CHECK IF THE ELEMENT IsFree!!! Free checks can be done independently. This is done for speed.

Parameters

index

Returns: the value stored in *this at the given index.

Reimplemented from bio::Container.

Definition at line 87 of file Arrangement.h.

 {
 BIO_SANITIZE(this->IsAllocated(index), ,
 return NULL)
 TYPE* ret;
 std::memcpy(
 ret,
 &this->m_store[index * sizeof(TYPE)],
 sizeof(TYPE));
 return *ret;
 }

References BIO_SANITIZE, bio::Container::IsAllocated(), and bio::Container::m_store.

◆ Add()

template<typename TYPE >

Index bio::physical::Arrangement< TYPE >::Add ( const ByteStream content )

inlinevirtual

Adds content to *this.

Parameters

content

Returns: the Index of the added content.

Reimplemented from bio::Container.

Definition at line 60 of file Arrangement.h.

 {
 BIO_SANITIZE(content.Is< TYPE >(), ,
 return InvalidIndex())
 Index ret = this->GetNextAvailableIndex();
 BIO_SANITIZE(ret, ,
 return InvalidIndex())
 TYPE toAdd = content;
 std::memcpy(
 &this->m_store[ret * sizeof(TYPE)],
 &toAdd,
 sizeof(TYPE));
 return ret;
 }

References BIO_SANITIZE, bio::Container::GetNextAvailableIndex(), bio::InvalidIndex(), bio::ByteStream::Is(), and bio::Container::m_store.

Referenced by bio::chemical::Atom::FormBondImplementation().

◆ AreEqual()

template<typename TYPE >

virtual bool bio::physical::Arrangement< TYPE >::AreEqual	(	Index	internal,
		const ByteStream	external
	)		const

inlinevirtual

To make comparisons easier and reduce the work needed to optimize *this, children can define a comparison method which will be used for all searches.

Parameters

internal
external

Returns: whether or not the contents of *this at the given Index match the given datum.

Reimplemented from bio::Container.

Reimplemented in bio::physical::Line.

Definition at line 113 of file Arrangement.h.

 {
 BIO_SANITIZE(external.Is< TYPE >(), ,
 return false)
 return this->Access(internal).template As< TYPE >() == external.template As< TYPE >();
 }

References bio::physical::Arrangement< TYPE >::Access(), BIO_SANITIZE, and bio::ByteStream::Is().

◆ Erase()

template<typename TYPE >

bool bio::physical::Arrangement< TYPE >::Erase ( const Index index )

inlinevirtual

Removes content from *this.

Parameters

index

Returns: whether or not the erasure was successful.

Reimplemented from bio::Container.

Definition at line 99 of file Arrangement.h.

 {
 BIO_SANITIZE(this->IsAllocated(index), ,
 return false)
 TYPE* toDelete;
 std::memcpy(
 toDelete,
 &this->m_store[index * sizeof(TYPE)],
 sizeof(TYPE));
 delete toDelete;
 this->m_deallocated.push_back(index);
 return true;
 }

References BIO_SANITIZE, bio::Container::IsAllocated(), bio::Container::m_deallocated, and bio::Container::m_store.

◆ GetStepSize()

template<typename TYPE >

virtual const std::size_t bio::physical::Arrangement< TYPE >::GetStepSize ( ) const

inlinevirtual

Please override this to return the size of the type your Container interface is working with.

Returns: the size of the data type stored in *this.

Reimplemented from bio::Container.

Definition at line 147 of file Arrangement.h.

 {
 return sizeof(TYPE);
 }

◆ OptimizedAccess() [1/2]

template<typename TYPE >

virtual TYPE bio::physical::Arrangement< TYPE >::OptimizedAccess ( Index index )

inlinevirtual

Convenience wrapper for accessing without casting.

Parameters

index

Returns: the given position in *this as a TYPE.

Definition at line 128 of file Arrangement.h.

 {
 return this->Access(index);
 }

References bio::physical::Arrangement< TYPE >::Access().

Referenced by bio::chemical::Atom::AsBonded(), bio::chemical::Atom::BreakBondImplementation(), bio::chemical::Atom::FormBondImplementation(), bio::chemical::Atom::GetBonded(), and bio::chemical::Atom::GetBondType().

◆ OptimizedAccess() [2/2]

template<typename TYPE >

virtual const TYPE bio::physical::Arrangement< TYPE >::OptimizedAccess ( Index index ) const

inlinevirtual

Convenience wrapper for accessing without casting.

Parameters

index

Returns: the given position in *this as a TYPE.

Definition at line 138 of file Arrangement.h.

 {
 return this->Access(index).template As< TYPE >();
 }

References bio::physical::Arrangement< TYPE >::Access().

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

/home/eons/git/biology/lib_bio/inc/bio/physical/arrangement/Arrangement.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Arrangement()

◆ ~Arrangement()

Member Function Documentation

◆ Access() [1/2]

◆ Access() [2/2]

◆ Add()

◆ AreEqual()

◆ Erase()

◆ GetStepSize()

◆ OptimizedAccess() [1/2]

◆ OptimizedAccess() [2/2]