#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().

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Line()

◆ ~Line()

Member Function Documentation

◆ Access() [1/2]

◆ Access() [2/2]

◆ AreEqual()

◆ LinearAccess() [1/2]

◆ LinearAccess() [2/2]

◆ SeekToId()

◆ SeekToName()