bio::Container Class Reference

#include <Container.h>

Inheritance diagram for bio::Container:

Collaboration diagram for bio::Container:

Public Member Functions
	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

Protected Member Functions
virtual bool	AreEqual (Index internal, const ByteStream external) const
virtual Index	GetNextAvailableIndex ()
virtual const std::size_t	GetStepSize () const

Protected Attributes
std::deque< Index >	m_deallocated
Index	m_firstFree
Index	m_size
unsigned char *	m_store
Iterator *	m_tempItt

Detailed Description

Containers are the singular Biology container construct. Essentially we need a generic, non-template std::vector<> base class, so we'll make our own. Different containers (e.g. the corollaries to std::set vs std::map vs std::vector) are all children of *this and we use typical inheritance to modify the behavior of each specialization. By using inheritance for our Containers, we can pass Container*s around and use a standard interface to manipulate the contents. In other words, we can treat std::sets like std::vectors or even treat std::maps like std::queues, all by overriding virtual methods and handling inputs consistently (obviously containers with key value pairs will need to pull a new piece of information from somewhere if given only a key or only a value).

NOTE: we still use stl containers where the additional features of *this class are not needed. Those usages may be changed to implement *this in a future release.

You can think of Containers as our own internal RAM. We allocated a block of bytes and manipulate them as necessary. By default, we use ByteStreams to store arbitrary data in our allocated memory. ByteStreams can be wasteful though (e.g. a whole extra std::string for every Index); so, overrides of this can use the same internal memory block but store other data structures for more efficient memory usage. We maintain ByteStreams as our data conversion type, as they are flexible but safer than a void.

When using Containers, we make no guarantees regarding the type of data stored. All we provide is a consistent means of accessing those data. To this end, we ensure that a Index's validity follows the lifecycle of the datum at that Index. This is identical to pointers: a Index represents the memory address of what is stored in *this. This means that as data are erased from *this, the memory is not moved, consolidated, or manipulated in any way that destroys the old references. This rule does have some exceptions and you are allowed to break it yourself. However, we try to stick by this as much as possible (e.g. see Insert(), below).

When using an Iterator, you will be given a SmartIterator which dynamically determines its implementation. Thus, we allow for full inheritance of *this base class.

There is another tradeoff here that we are leaning into: our interface does not make for easy use of std:: containers under-the-hood. By enforcing consistency on access, we've made the system less flexible. This may be changed in a major release down the road but its what we're sticking with for now.

When using Containers there are a few guidelines we recommend:

1. If you need direct access to the memory stored, store a pointer. Keep it simple.
2. If you do not need direct access, store the raw type (e.g. for .?int\d+_t types)
3. Containers themselves should be passed by pointer. This consistency helps when the Container needs to be Cast, etc.

Definition at line 61 of file Container.h.

Constructor & Destructor Documentation

Container() [1/2]

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

NOTE: We cannot use GetStepSize() here as virtual functions are not available to ctors.

Definition at line 29 of file Container.cpp.

    :
    m_firstFree(1),
    m_size(expectedSize + 1),
    m_tempItt(NULL)
{
    m_store = (unsigned char*)std::malloc(m_size * stepSize);
    BIO_ASSERT(m_store)
}

References BIO_ASSERT, m_size, and m_store.

Container() [2/2]

bio::Container::Container

(

const Container &

other

)

Copy ctor. Imports all contents from other into *this.

Parameters

other

Definition at line 42 of file Container.cpp.

    :
    m_firstFree(other.m_firstFree),
    m_size(other.m_size),
    m_tempItt(NULL)
{
    m_store = (unsigned char*)std::malloc(m_size * other.GetStepSize());
    BIO_ASSERT(m_store)
    Import(&other); // <- NOT VIRTUAL (in ctor).
}

References BIO_ASSERT, GetStepSize(), Import(), m_size, and m_store.

~Container()

bio::Container::~Container ( )

virtual

Definition at line 53 of file Container.cpp.

{
    Clear(); // <- NOT VIRTUAL (in dtor).
    if (m_tempItt)
    {
        delete m_tempItt;
        m_tempItt = NULL;
    }
    std::free(m_store);
}

References Clear(), m_store, and m_tempItt.

Member Function Documentation

Access() [1/4]

ByteStream bio::Container::Access ( const Index  index )

virtual

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 in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, bio::physical::Arrangement< Bond * >, and bio::physical::Line.

Definition at line 185 of file Container.cpp.

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

References BIO_SANITIZE, IsAllocated(), and m_store.

Referenced by Access(), bio::chemical::UnorderedMotif< CONTENT_TYPE >::AddImplementation(), AreEqual(), bio::Iterator::operator*(), operator[](), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::RemoveImplementation().

Access() [2/4]

const ByteStream bio::Container::Access ( const Index  index ) const

virtual

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 in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, bio::physical::Arrangement< Bond * >, and bio::physical::Line.

Definition at line 197 of file Container.cpp.

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

References BIO_SANITIZE, IsAllocated(), and m_store.

Access() [3/4]

ByteStream bio::Container::Access ( const SmartIterator  itt )

inline

Access wrapper for SmartIterators.

Parameters

itt

Returns

the value stored in *this at the given index.

Definition at line 183 of file Container.h.

    {
        return Access(itt.GetIndex());
    }

References Access(), and bio::SmartIterator::GetIndex().

Access() [4/4]

virtual const ByteStream bio::Container::Access ( const SmartIterator  itt ) const

inlinevirtual

Access wrapper for SmartIterators.

Parameters

itt

Returns

the value stored in *this at the given index.

Definition at line 193 of file Container.h.

    {
        return Access(itt.GetIndex());
    }

References Access(), and bio::SmartIterator::GetIndex().

Add()

Index bio::Container::Add ( const ByteStream  content )

virtual

Adds content to *this.

Parameters

content

Returns

the Index of the added content.

Reimplemented in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, and bio::physical::Arrangement< Bond * >.

Definition at line 129 of file Container.cpp.

{
    Index ret = GetNextAvailableIndex();
    BIO_SANITIZE(ret, ,
        return ret)
    std::memcpy(
        &m_store[ret * sizeof(ByteStream)],
        content,
        sizeof(ByteStream));
    return ret;
}

References BIO_SANITIZE, GetNextAvailableIndex(), and m_store.

Referenced by bio::chemical::UnorderedMotif< CONTENT_TYPE >::AddImplementation(), bio::chemical::LinearMotif< CONTENT_TYPE >::AddImplementation(), Import(), Insert(), and bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

AreEqual()

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

protectedvirtual

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 in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, bio::physical::Arrangement< Bond * >, and bio::physical::Line.

Definition at line 345 of file Container.cpp.

{
    return Access(internal) == external;
}

References Access().

Referenced by SeekTo().

AsVector()

template<typename T >

std::vector< T > bio::Container::AsVector ( ) const

inline

Ease of use wrapper around casting *this to a std::vector. Since template methods are not virtual, you must make sure to properly implement Access() and make sure that *this contains the given type.

Template Parameters

T

Returns

a std::vector containing the contents from *this.

Definition at line 297 of file Container.h.

    {
        std::vector< T > ret;
        for (
            SmartIterator rct = End();
            !rct.IsAtBeginning();
            --rct
            )
        {
            ret.push_back(rct.As< T >());
        }
        return ret;
    }

References End(), and bio::SmartIterator::IsAtBeginning().

Begin()

SmartIterator bio::Container::Begin ( ) const

virtual

NOTE: This does not need to be overridden if you've already defined ConstructClassIterator().

Returns

A new Iterator pointing to the beginning of *this.

Definition at line 295 of file Container.cpp.

{
    return SmartIterator(
        this,
        GetBeginIndex());
}

References GetBeginIndex().

Referenced by bio::organic::Habitat::AdaptInhabitants(), bio::cellular::Tissue::DifferentiateCells(), bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetStringFromImplementation(), bio::organic::Organism::Morphogenesis(), bio::cellular::OrganSystem::Organogenesis(), bio::chemical::Axis::Rotate(), and bio::cellular::Organ::SpecializeTissues().

Clear()

void bio::Container::Clear ( )

virtual

Remove all elements from *this.

Definition at line 265 of file Container.cpp.

{
    //Call destructors before clearing the array.
    if (!m_tempItt)
    {
        m_tempItt = ConstructClassIterator();
    }
    m_tempItt->MoveTo(GetEndIndex());
    for (
        ; !m_tempItt->IsAtBeginning();
        --m_tempItt
        )
    {
        Erase(m_tempItt->GetIndex());
    }
 
    m_firstFree = 1;
    m_deallocated.clear();
}

References ConstructClassIterator(), Erase(), GetEndIndex(), bio::Iterator::GetIndex(), bio::Iterator::IsAtBeginning(), m_deallocated, m_firstFree, m_tempItt, and bio::Iterator::MoveTo().

Referenced by ~Container(), bio::chemical::LinearMotif< CONTENT_TYPE >::~LinearMotif(), bio::chemical::LinearMotif< CONTENT_TYPE >::ClearImplementation(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::ClearImplementation().

ConstructClassIterator()

Iterator * bio::Container::ConstructClassIterator ( const Index  index = InvalidIndex() ) const

virtual

Override this to construct Iterators for your Containers.

Parameters

index

Returns

a new Iterator pointing to the given Index in *this or NULL.

Definition at line 285 of file Container.cpp.

{
    BIO_SANITIZE(IsAllocated(index), ,
        return NULL)
    return new Iterator(
        this,
        index
    );
}

References BIO_SANITIZE, and IsAllocated().

Referenced by Clear(), SeekTo(), bio::physical::Line::SeekToId(), and bio::physical::Line::SeekToName().

End()

SmartIterator bio::Container::End ( ) const

virtual

NOTE: This does not need to be overridden if you've already defined ConstructClassIterator().

Returns

An Iterator pointing to the end of *this.

Definition at line 302 of file Container.cpp.

{
    return SmartIterator(
        this,
        GetEndIndex());
}

References GetEndIndex().

Referenced by bio::molecular::Surface::~Surface(), AsVector(), bio::chemical::Atom::Attenuate(), bio::chemical::Atom::Disattenuate(), bio::chemical::Atom::GetBondPosition(), bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetNumMatchingImplementation(), Import(), bio::chemical::UnorderedStructureInterface::ImportAll(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), bio::molecular::Surface::Release(), and bio::molecular::Surface::ReleaseAll().

Erase() [1/2]

bool bio::Container::Erase ( const SmartIterator  itt )

inline

Erase wrapper for SmartIterators.

Parameters

itt

Returns

whether or not the erasure was successful.

Definition at line 223 of file Container.h.

    {
        return Erase(itt.GetIndex());
    }

References Erase(), and bio::SmartIterator::GetIndex().

Erase() [2/2]

bool bio::Container::Erase ( Index  index )

virtual

Removes content from *this.

Parameters

index

Returns

whether or not the erasure was successful.

Reimplemented in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, and bio::physical::Arrangement< Bond * >.

Definition at line 237 of file Container.cpp.

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

References BIO_SANITIZE, IsAllocated(), m_deallocated, and m_store.

Referenced by Clear(), Erase(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::RemoveImplementation().

Expand()

void bio::Container::Expand ( )

virtual

Grow store to accommodate dynamic allocation.

Parameters

datumSize

the memory size a Index should jump over.

Definition at line 112 of file Container.cpp.

{
    BIO_SANITIZE(m_size < std::numeric_limits< Index >::max(), ,
        return)
    Index targetSize = m_size * m_size; //squared.
    if (targetSize < m_size)
    {
        targetSize = std::numeric_limits< Index >::max();
    }
    m_store = (unsigned char*)std::realloc(
        m_store,
        targetSize * GetStepSize());
    BIO_SANITIZE(m_store, ,
        return)
    m_size = targetSize;
}

References BIO_SANITIZE, GetStepSize(), m_size, and m_store.

Referenced by GetNextAvailableIndex(), and Insert().

GetAllocatedSize()

Index bio::Container::GetAllocatedSize ( ) const

virtual

GetCapacity - the number of free Indices at the end (ignores any deallocated Indices in the middle).

Returns

the number of Indices that have been allocated in *this.

Definition at line 79 of file Container.cpp.

{
    return m_firstFree;
}

References m_firstFree.

Referenced by GetEndIndex(), GetNumberOfElements(), bio::Iterator::Increment(), Insert(), and bio::Iterator::IsAtEnd().

GetBeginIndex()

Index bio::Container::GetBeginIndex ( ) const

virtual

Returns

where to start.

Definition at line 64 of file Container.cpp.

{
    return 1;
}

Referenced by Begin(), bio::chemical::LinearMotif< CONTENT_TYPE >::GetStringFromImplementation(), and bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

GetCapacity()

Index bio::Container::GetCapacity ( ) const

virtual

Returns

the number of allocatable Indices in *this.

Definition at line 74 of file Container.cpp.

{
    return m_size;
}

References m_size.

Referenced by Insert().

GetEndIndex()

Index bio::Container::GetEndIndex ( ) const

virtual

Returns

where to end.

Definition at line 69 of file Container.cpp.

{
    return GetAllocatedSize();
}

References GetAllocatedSize().

Referenced by Clear(), End(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), SeekTo(), bio::physical::Line::SeekToId(), and bio::physical::Line::SeekToName().

GetNextAvailableIndex()

Index bio::Container::GetNextAvailableIndex ( )

protectedvirtual

For ease of use when Add()ing. NOTE: This will mark the returned Index as filled, so please make sure it actually receives content.

Returns

a Index to fill with new content.

Definition at line 329 of file Container.cpp.

{
    Index ret = InvalidIndex();
    if (!m_deallocated.empty())
    {
        ret = m_deallocated.front();
        m_deallocated.pop_front();
    }
    else if (m_firstFree == m_size)
    {
        Expand();
        ret = m_firstFree++;
    }
    return ret;
}

References Expand(), bio::InvalidIndex(), m_deallocated, m_firstFree, and m_size.

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

GetNumberOfElements()

Index bio::Container::GetNumberOfElements ( ) const

virtual

GetAllocatedSize - the number of deallocated Indices.

Returns

the number of elements in *this.

Definition at line 84 of file Container.cpp.

{
    return GetAllocatedSize() - m_deallocated.size();
}

References GetAllocatedSize(), and m_deallocated.

Referenced by bio::chemical::UnorderedMotif< CONTENT_TYPE >::GetCountImplementation(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasAllImplementation().

GetStepSize()

const std::size_t bio::Container::GetStepSize ( ) const

protectedvirtual

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 in bio::physical::Arrangement< TYPE >, bio::physical::Arrangement< Linear >, and bio::physical::Arrangement< Bond * >.

Definition at line 353 of file Container.cpp.

{
    return sizeof(ByteStream);
}

Referenced by Container(), Expand(), and Insert().

Has()

bool bio::Container::Has

(

const ByteStream

content

)

const

Parameters

content

Returns

whether or not *this contains the given content.

Definition at line 232 of file Container.cpp.

{
    return SeekTo(content); //implicit cast to bool should work.
}

References SeekTo().

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::HasImplementation(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::HasImplementation().

Import()

void bio::Container::Import ( const Container *  other )

virtual

Copy the contents of other into *this.

Parameters

other

Definition at line 251 of file Container.cpp.

{
    BIO_SANITIZE(other, ,
        return)
    Iterator* otr = other->End();
    for (
        ; !otr->IsAtBeginning();
        --otr
        )
    {
        Add(**otr);
    }
}

References Add(), BIO_SANITIZE, End(), and bio::Iterator::IsAtBeginning().

Referenced by Container(), bio::chemical::LinearMotif< CONTENT_TYPE >::LinearMotif(), bio::chemical::LinearMotif< CONTENT_TYPE >::ImportImplementation(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::ImportImplementation().

Insert()

Index bio::Container::Insert ( const ByteStream  content, const Index  index  )

virtual

Adds content to *this at the specified position. All content past the given position is shifted down. NOTE: This explicitly breaks our rule about Indices being preserved. However, this logic is necessary if the items being inserted need to be accessed in the specified order; for example: the items in *this are molecular::Proteins that have a set execution order.

To make implementing your own Containers easier, this method simply hacks the GetNextAvailableIndex method to return the desired index and then calls Add. Thus, by implementing Add, you also implement Insert.

Parameters

content

Returns

the Index of the added content.

Definition at line 141 of file Container.cpp.

{
    BIO_SANITIZE(index, ,
        return InvalidIndex())
 
    if (index == m_firstFree)
    {
        //no adjustment necessary.
        Add(content);
    }
 
    if (GetAllocatedSize() == GetCapacity())
    {
        Expand();
    }
 
    //move all memory down 1.
    std::memcpy(
        &m_store[index * GetStepSize()],
        &m_store[(index + 1) * GetStepSize()],
        (m_firstFree - index) * GetStepSize());
 
    //adjust all deallocated positions.
    std::deque< Index > adjustedDeallocations;
    for (
        std::deque< Index >::iterator dlc = m_deallocated.begin();
        dlc != m_deallocated.end();
        ++dlc
        )
    {
        adjustedDeallocations.push_front(*dlc + 1);
    }
    m_deallocated = adjustedDeallocations;
 
    //make sure we add to the desired index.
    m_deallocated.push_front(index);
 
    //add the content.
    return Add(content);
}

References Add(), BIO_SANITIZE, Expand(), GetAllocatedSize(), GetCapacity(), GetStepSize(), bio::InvalidIndex(), m_deallocated, m_firstFree, and m_store.

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

IsAllocated()

bool bio::Container::IsAllocated ( const Index  index ) const

virtual

Parameters

index

Returns

IsInRange && !IsFree.

Definition at line 107 of file Container.cpp.

{
    return IsInRange(index) && !IsFree(index);
}

References IsFree(), and IsInRange().

Referenced by Access(), bio::physical::Arrangement< TYPE >::Access(), bio::chemical::Atom::BreakBondImplementation(), ConstructClassIterator(), bio::physical::Arrangement< TYPE >::Erase(), Erase(), bio::chemical::Atom::FormBondImplementation(), bio::chemical::Atom::GetBonded(), bio::chemical::Atom::GetBondType(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), and bio::Iterator::MoveTo().

IsFree()

bool bio::Container::IsFree ( const Index  index ) const

virtual

Checks if the given Index is available to be allocated, i.e. the Index should not be used. NOTE: Just because a Index is not free does not necessarily mean the Index has been allocated.

Parameters

index

Returns

whether or not the given Index is free to use.

Definition at line 94 of file Container.cpp.

{
    if (index >= m_firstFree)
    {
        return true;
    }
    return std::find(
        m_deallocated.begin(),
        m_deallocated.end(),
        index
    ) != m_deallocated.end();
}

References m_deallocated, and m_firstFree.

Referenced by bio::Iterator::Decrement(), bio::Iterator::Increment(), and IsAllocated().

IsInRange()

bool bio::Container::IsInRange ( const Index  index ) const

virtual

NOTE: Just because a Index IsInRange does not mean it is free or allocated.

Parameters

index

Returns

whether or not the Index is expected to yield a valid result when used with *this.

Definition at line 89 of file Container.cpp.

{
    return index && index < m_size;
}

References m_size.

Referenced by IsAllocated().

operator[]() [1/4]

ByteStream bio::Container::operator[] ( const Index  index )

virtual

Ease of use wrapper around Access. See Access for details.

Parameters

index

Returns

Access(Index).

Definition at line 309 of file Container.cpp.

{
    return Access(index);
}

References Access().

operator[]() [2/4]

const ByteStream bio::Container::operator[] ( const Index  index ) const

virtual

Ease of use wrapper around Access. See Access for details.

Parameters

index

Returns

Access(Index).

Definition at line 314 of file Container.cpp.

{
    return Access(index);
}

References Access().

operator[]() [3/4]

ByteStream bio::Container::operator[] ( const SmartIterator  itt )

virtual

Ease of use wrapper around Access. See Access for details.

Parameters

itt

Returns

Access(itt).

Definition at line 319 of file Container.cpp.

{
    return Access(itt);
}

References Access().

operator[]() [4/4]

const ByteStream bio::Container::operator[] ( const SmartIterator  itt ) const

virtual

Ease of use wrapper around Access. See Access for details.

Parameters

itt

Returns

Access(itt).

Definition at line 324 of file Container.cpp.

{
    return Access(itt);
}

References Access().

SeekTo()

Index bio::Container::SeekTo

(

const ByteStream

content

)

const

Find the Index of content within *this.

Parameters

content

Returns

the Index of content within *this or InvalidIndex.

Definition at line 209 of file Container.cpp.

{
    if (!m_tempItt)
    {
        m_tempItt = ConstructClassIterator();
    }
    m_tempItt->MoveTo(GetEndIndex());
    for (
        ; !m_tempItt->IsAtBeginning();
        --m_tempItt
        )
    {
        if (AreEqual(
            m_tempItt->GetIndex(),
            content
        ))
        {
            return m_tempItt->GetIndex();
        }
    }
    return InvalidIndex();
}

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

Referenced by Has(), and bio::chemical::UnorderedMotif< CONTENT_TYPE >::RemoveImplementation().

Member Data Documentation

m_deallocated

std::deque< Index > bio::Container::m_deallocated

protected

Definition at line 344 of file Container.h.

Referenced by Clear(), bio::physical::Arrangement< TYPE >::Erase(), Erase(), GetNextAvailableIndex(), GetNumberOfElements(), Insert(), and IsFree().

m_firstFree

Index bio::Container::m_firstFree

protected

Definition at line 343 of file Container.h.

Referenced by Clear(), GetAllocatedSize(), GetNextAvailableIndex(), Insert(), and IsFree().

m_size

Index bio::Container::m_size

protected

Definition at line 342 of file Container.h.

Referenced by Container(), Expand(), GetCapacity(), GetNextAvailableIndex(), and IsInRange().

m_store

unsigned char* bio::Container::m_store

protected

cannot be void* as we need an object type for pointer arithmetic.

Definition at line 340 of file Container.h.

Referenced by Container(), ~Container(), Access(), bio::physical::Arrangement< TYPE >::Access(), Add(), bio::physical::Arrangement< TYPE >::Add(), bio::physical::Arrangement< TYPE >::Erase(), Erase(), Expand(), and Insert().

m_tempItt

Iterator* bio::Container::m_tempItt

mutableprotected

An iterator for use in loops. Matches lifecycle of object for better performance.

Definition at line 350 of file Container.h.

Referenced by ~Container(), Clear(), SeekTo(), bio::physical::Line::SeekToId(), and bio::physical::Line::SeekToName().

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

• /home/eons/git/biology/lib_bio/inc/bio/common/container/Container.h
• /home/eons/git/biology/lib_bio/src/common/container/Container.cpp