bio::physical::Line Class Reference

#include <Line.h>

Inheritance diagram for bio::physical::Line:

Collaboration diagram for bio::physical::Line:

Public Member Functions
	Line (Index expectedSize=2)
virtual	~Line ()
ByteStream	Access (const Index index)
const ByteStream	Access (const Index index) const
virtual bool	AreEqual (Index internal, const ByteStream external) const
virtual Identifiable< StandardDimension > *	LinearAccess (Index index)
virtual const Identifiable< StandardDimension > *	LinearAccess (Index index) const
virtual Index	SeekToId (StandardDimension id)
virtual Index	SeekToName (Name name)
Public Member Functions inherited from bio::physical::Arrangement< Linear >
	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 Linear	OptimizedAccess (Index index)
virtual const Linear	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

Lines are Linear Arrangements.

NOTE: We reserve Position 0 as invalid.

Template Parameters

STORE

Definition at line 37 of file Line.h.

Constructor & Destructor Documentation

Line()

bio::physical::Line::Line

(

Index

expectedSize = 2

)

Parameters

expectedSize

Definition at line 28 of file Line.cpp.

 :
 Arrangement< Linear >(expectedSize)
{
 
}

~Line()

bio::physical::Line::~Line ( )

virtual

Definition at line 35 of file Line.cpp.

{
 
}

Member Function Documentation

Access() [1/2]

ByteStream bio::physical::Line::Access ( const Index  index )

virtual

We want to return an Identifiable< StandardDimension >*, not a Linear.

Parameters

index

Returns

an Identifiable< StandardDimension >* from the Linear at the given Index.

Reimplemented from bio::Container.

Definition at line 40 of file Line.cpp.

{
 return Cast< Identifiable< StandardDimension >* >(OptimizedAccess(index));
}

References bio::physical::Arrangement< Linear >::OptimizedAccess().

Access() [2/2]

const ByteStream bio::physical::Line::Access ( const Index  index ) const

virtual

We want to return an Identifiable< StandardDimension >*, not a Linear.

Parameters

index

Returns

an Identifiable< StandardDimension >* from the Linear at the given Index.

Reimplemented from bio::Container.

Definition at line 45 of file Line.cpp.

{
 return Cast< Identifiable< StandardDimension >* >(OptimizedAccess(index));
}

References bio::physical::Arrangement< Linear >::OptimizedAccess().

AreEqual()

bool bio::physical::Line::AreEqual ( Index  internal, const ByteStream  external  ) const

virtual

Since we operate on Identifiable< StandardDimension >*, not Linears, we want to treat the external datum as Identifiable< StandardDimension >*.

Parameters

internal
external

Returns

whether or not the Linear at the given Index is equal to the provided Identifiable< StandardDimension >*.

Reimplemented from bio::physical::Arrangement< Linear >.

Definition at line 50 of file Line.cpp.

{
 BIO_SANITIZE(external.Is< Identifiable< StandardDimension >* >(),,return false)
 return OptimizedAccess(internal) == external.template As< const Identifiable< StandardDimension >* >();
}

References BIO_SANITIZE, bio::ByteStream::Is(), and bio::physical::Arrangement< Linear >::OptimizedAccess().

LinearAccess() [1/2]

Identifiable< StandardDimension > * bio::physical::Line::LinearAccess ( Index  index )

virtual

Convenience wrapper around OptimizedAccess.

Parameters

index

Returns

the given position casted to an Identifiable< StandardDimension >*

Definition at line 56 of file Line.cpp.

{
 return OptimizedAccess(index);
}

References bio::physical::Arrangement< Linear >::OptimizedAccess().

Referenced by SeekToId(), and SeekToName().

LinearAccess() [2/2]

const Identifiable< StandardDimension > * bio::physical::Line::LinearAccess ( Index  index ) const

virtual

Convenience wrapper around OptimizedAccess.

Parameters

index

Returns

the given position casted to an Identifiable< StandardDimension >*

Definition at line 61 of file Line.cpp.

{
 return OptimizedAccess(index);
}

References bio::physical::Arrangement< Linear >::OptimizedAccess().

SeekToId()

Index bio::physical::Line::SeekToId ( StandardDimension  id )

virtual

Get the position of an Identifiable< StandardDimension >* with the given id in *this.

Parameters

id

Returns

an Index matching the given id or InvalidIndex().

Definition at line 83 of file Line.cpp.

{
 if (!m_tempItt)
 {
 m_tempItt = ConstructClassIterator();
 }
 m_tempItt->MoveTo(GetEndIndex());
 for (; !m_tempItt->IsAtBeginning(); --m_tempItt)
 {
 if (LinearAccess(m_tempItt->GetIndex())->IsId(id))
 {
 return m_tempItt->GetIndex();
 }
 }
 return InvalidIndex();
}

References bio::Container::ConstructClassIterator(), bio::Container::GetEndIndex(), bio::Iterator::GetIndex(), bio::InvalidIndex(), bio::Iterator::IsAtBeginning(), LinearAccess(), bio::Container::m_tempItt, and bio::Iterator::MoveTo().

SeekToName()

Index bio::physical::Line::SeekToName ( Name  name )

virtual

Get the position of an Identifiable< StandardDimension >* with the given name in *this.

Parameters

name

Returns

an Index matching the given name or InvalidIndex().

Definition at line 66 of file Line.cpp.

{
 if (!m_tempItt)
 {
 m_tempItt = ConstructClassIterator();
 }
 m_tempItt->MoveTo(GetEndIndex());
 for (; !m_tempItt->IsAtBeginning(); --m_tempItt)
 {
 if (LinearAccess(m_tempItt->GetIndex())->IsName(name))
 {
 return m_tempItt->GetIndex();
 }
 }
 return InvalidIndex();
}

References bio::Container::ConstructClassIterator(), bio::Container::GetEndIndex(), bio::Iterator::GetIndex(), bio::InvalidIndex(), bio::Iterator::IsAtBeginning(), LinearAccess(), bio::Container::m_tempItt, and bio::Iterator::MoveTo().

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

• /home/eons/git/biology/lib_bio/inc/bio/physical/arrangement/Line.h
• /home/eons/git/biology/lib_bio/src/physical/arrangement/Line.cpp