bio::physical::Perspective< DIMENSION > Class Template Reference

#include <Perspective.h>

Inheritance diagram for bio::physical::Perspective< DIMENSION >:

Collaboration diagram for bio::physical::Perspective< DIMENSION >:

Classes
class	Hadit

Public Types
typedef std::vector< Hadit >	Hadits
typedef DIMENSION	Id
typedef std::vector< Id >	Ids

Public Member Functions
	Perspective ()
virtual	~Perspective ()
virtual bool	AssociateType (Id id, Wave *type)
virtual bool	DisassociateType (Id id)
Hadits::iterator	Find (Id id)
Hadits::const_iterator	Find (Id id) const
virtual Id	GetIdFromName (Name name)
virtual Id	GetIdWithoutCreation (Name name) const
virtual Name	GetNameFromId (Id id) const
virtual Wave *	GetNewObjectFromId (Id id) const
template<typename T >
T	GetNewObjectFromIdAs (Id id)
virtual Wave *	GetNewObjectFromName (Name name)
template<typename T >
T	GetNewObjectFromNameAs (Name name)
virtual Id	GetNumUsedIds () const
virtual const Wave *	GetTypeFromId (Id id) const
template<typename T >
const T	GetTypeFromIdAs (Id id) const
virtual const Wave *	GetTypeFromName (Name name) const
template<typename T >
const T	GetTypeFromNameAs (Name name) const
virtual Id	GetUniqueIdFor (Name name)
Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()
	ThreadSafe (const ThreadSafe &toCopy)
virtual	~ThreadSafe ()
void	LockThread () const
void	UnlockThread () const

Static Public Member Functions
static Id	InvalidId ()
static Name	InvalidName ()

Protected Attributes
Hadits	m_hadits
Id	m_nextId

Detailed Description

template<typename DIMENSION>
class bio::physical::Perspective< DIMENSION >

A Perspective keeps track of Names and Ids for a certain set of objects within a DIMENSION and ensures a unique Id <-> Name pairing for all objects it "observes". A DIMENSION is a numeric space in which objects may be defined. The size of the space determines how many objects may be "observed" (i.e. kept track of) by a single Perspective. Together, a Perspective and DIMENSION can be thought to define the "size" of the "lens" used to "observe" "objects", if you'll permit the physical analogy of what is purely imaginative. Only objects that share a DIMENSION may be derived from, combined, etc. You cannot have a child class that derives from 2 different Identifiable templates (without solving diamond inheritance and some other caveats). Thus, functionally, you can think of each DIMENSION as a different library, with its source code hidden, such that only objects within that library, that DIMENSION, may inherit from each other. An example DIMENSION would be uint32_t, with up to 4,294,967,295 unique object names per perspective.

An example use case can be seen with Neurons and Synapses. Both are distinct objects and both can be tracked through different Perspectives. This means a Neuron of Id 1 can have the name "MyNeuron" and a Synapse of Id 1 can have the name "MySynapse". However, Neurons and Synapses share a lot of code and should exist within the same DIMENSION (e.g. in case you wanted to make some strange Neuron/Synapse hybrid). If your DIMENSION is a uint8_t, you could have 255 Neurons and 255 Synapses using a different Perspective for each. Using a single Respective, you could only have 255 uniquely identified Neurons OR Connections, total. Therefore, you'd likely want multiple Perspectives and a much larger DIMENSION (uint32_t, for instance) in order to accommodate a more total objects. See below for a macro for creating singleton of Perspectives.

Definition at line 70 of file Perspective.h.

Member Typedef Documentation

Hadits

template<typename DIMENSION >

typedef std::vector< Hadit > bio::physical::Perspective< DIMENSION >::Hadits

Definition at line 101 of file Perspective.h.

Id

template<typename DIMENSION >

typedef DIMENSION bio::physical::Perspective< DIMENSION >::Id

Definition at line 74 of file Perspective.h.

Ids

template<typename DIMENSION >

typedef std::vector< Id > bio::physical::Perspective< DIMENSION >::Ids

Definition at line 75 of file Perspective.h.

Constructor & Destructor Documentation

Perspective()

template<typename DIMENSION >

bio::physical::Perspective< DIMENSION >::Perspective ( )

inline

Definition at line 106 of file Perspective.h.

        :
        m_nextId(1)
    {
    }

~Perspective()

template<typename DIMENSION >

virtual bio::physical::Perspective< DIMENSION >::~Perspective ( )

inlinevirtual

Definition at line 115 of file Perspective.h.

    {
        LockThread();
        for (
            typename Hadits::iterator itt = m_hadits.begin();
            itt != m_hadits.end();
            ++itt
            )
        {
            if (itt->m_name)
            {
                delete[] itt->m_name;
                itt->m_name = NULL;
            }
            if (itt->m_type)
            {
                PerspectiveUtilities::Delete(itt->m_type);
                itt->m_type = NULL;
            }
        }
        m_hadits.clear();
        UnlockThread();
    }

References bio::physical::PerspectiveUtilities::Delete(), bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, and bio::ThreadSafe::UnlockThread().

Member Function Documentation

AssociateType()

template<typename DIMENSION >

virtual bool bio::physical::Perspective< DIMENSION >::AssociateType ( Id  id, Wave *  type  )

inlinevirtual

Associates the given Wave type with the given id. This is only necessary if you want to use GetTypeFromId later on. NOTE: There is no GetIdFromType(). For that behavior, see chemical::PeriodicTable and chemical::Atom.

Parameters

id
type

Returns

true if the association completed successfully else false

Definition at line 354 of file Perspective.h.

    {
        typename Hadits::iterator hdt = Find(id);
        if (hdt == m_hadits.end() || hdt->m_type)
        {
            return false;
        }
 
        LockThread();
        BIO_SANITIZE(type,
            hdt->m_type = PerspectiveUtilities::Clone(type),
            hdt->m_type = type);
        UnlockThread();
 
        return true;
    }

References BIO_SANITIZE, bio::physical::PerspectiveUtilities::Clone(), bio::physical::Perspective< DIMENSION >::Find(), bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, and bio::ThreadSafe::UnlockThread().

DisassociateType()

template<typename DIMENSION >

virtual bool bio::physical::Perspective< DIMENSION >::DisassociateType ( Id  id )

inlinevirtual

Removes the type association created by AssociateType().

Parameters

id

Returns

true if the association was removed else false.

Definition at line 379 of file Perspective.h.

    {
        typename Hadits::iterator hdt = Find(id);
        if (hdt == m_hadits.end())
        {
            return false;
        }
 
        LockThread();
        BIO_SANITIZE_AT_SAFETY_LEVEL_2(hdt->m_type,
            PerspectiveUtilities::Delete(hdt->m_type),);
        hdt->m_type = NULL;
        UnlockThread();
 
        return true;
    }

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, bio::physical::PerspectiveUtilities::Delete(), bio::physical::Perspective< DIMENSION >::Find(), bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, and bio::ThreadSafe::UnlockThread().

Find() [1/2]

template<typename DIMENSION >

Hadits::iterator bio::physical::Perspective< DIMENSION >::Find ( Id  id )

inline

Gives an iterator fos the given id.

Parameters

id

Returns

a Hadits::iterator or m_hadits.end();

Definition at line 162 of file Perspective.h.

    {
 
        LockThread();
        typename Hadits::iterator hdt = m_hadits.begin();
        for (
            ; hdt != m_hadits.end();
            ++hdt
            )
        {
            if (hdt->m_id == id)
            {
                UnlockThread();
                return hdt;
            }
        }
        UnlockThread();
        return hdt;
    }

References bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, and bio::ThreadSafe::UnlockThread().

Referenced by bio::physical::Perspective< DIMENSION >::AssociateType(), bio::physical::Perspective< DIMENSION >::DisassociateType(), bio::physical::Perspective< DIMENSION >::GetNameFromId(), and bio::physical::Perspective< DIMENSION >::GetTypeFromId().

Find() [2/2]

template<typename DIMENSION >

Hadits::const_iterator bio::physical::Perspective< DIMENSION >::Find ( Id  id ) const

inline

Gives an iterator fos the given id.

Parameters

id

Returns

a Hadits::const_iterator or m_hadits.end();

Definition at line 187 of file Perspective.h.

    {
        LockThread();
        typename Hadits::const_iterator hdt = m_hadits.begin();
        for (
            ; hdt != m_hadits.end();
            ++hdt
            )
        {
            if (hdt->m_id == id)
            {
                UnlockThread();
                return hdt;
            }
        }
        UnlockThread();
        return hdt;
    }

References bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, and bio::ThreadSafe::UnlockThread().

GetIdFromName()

template<typename DIMENSION >

virtual Id bio::physical::Perspective< DIMENSION >::GetIdFromName ( Name  name )

inlinevirtual

This will create a new Id for the given name if one does not exist.

Parameters

name

Returns

the Id associated with the given name

Definition at line 212 of file Perspective.h.

    {
        if (strcmp(
            InvalidName(),
            name
        ))
        {
            return InvalidId();
        }
 
        Id ret = GetIdWithoutCreation(name);
        if (ret)
        {
            return ret;
        }
 
        Name usedName;
        string::CloneInto(
            name,
            usedName
        );
 
        LockThread();
        ret = m_nextId++;
        m_hadits.push_back(
            Hadit(
                ret,
                usedName,
                NULL
            ));
        UnlockThread();
 
        return ret;
    }

References bio::string::CloneInto(), bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), bio::physical::Perspective< DIMENSION >::InvalidId(), bio::physical::Perspective< DIMENSION >::InvalidName(), bio::ThreadSafe::LockThread(), bio::physical::Perspective< DIMENSION >::m_hadits, bio::physical::Perspective< DIMENSION >::m_nextId, and bio::ThreadSafe::UnlockThread().

Referenced by bio::physical::Perspective< DIMENSION >::GetNewObjectFromName(), bio::chemical::LinearMotif< CONTENT_TYPE >::GetOrCreateByNameImplementation(), bio::physical::Perspective< DIMENSION >::GetUniqueIdFor(), and bio::genetic::Plasmid::TranscribeFor().

GetIdWithoutCreation()

template<typename DIMENSION >

virtual Id bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation ( Name  name ) const

inlinevirtual

the same as GetIdFromName but will RETURN 0 instead of making a new association, if name is not found.

Parameters

name

Returns

the Id associated with name else InvalidId().

Definition at line 310 of file Perspective.h.

    {
        if (strcmp(
            InvalidName(),
            name
        ))
        {
            return InvalidId();
        }
 
        typename Hadits::const_iterator itt = m_hadits.begin();
        for (
            ; itt != m_hadits.end();
            ++itt
            )
        {
            if (!strcmp(
                itt->m_name,
                name
            ))
            {
                return itt->m_id;
            }
        }
        return InvalidId();
    }

References bio::physical::Perspective< DIMENSION >::InvalidId(), bio::physical::Perspective< DIMENSION >::InvalidName(), and bio::physical::Perspective< DIMENSION >::m_hadits.

Referenced by bio::physical::Perspective< DIMENSION >::GetIdFromName(), bio::physical::Perspective< DIMENSION >::GetTypeFromName(), and bio::physical::Perspective< DIMENSION >::GetUniqueIdFor().

GetNameFromId()

template<typename DIMENSION >

virtual Name bio::physical::Perspective< DIMENSION >::GetNameFromId ( Id  id ) const

inlinevirtual

This requires that the Id has been previously associated with the name, perhaps from a call to GetIdFromName.

Parameters

id

Returns

the Name associated with the given Id

Definition at line 253 of file Perspective.h.

    {
        if (id == InvalidId())
        {
            return InvalidName();
        }
 
        typename Hadits::const_iterator result = Find(id);
        if (result == m_hadits.end())
        {
            return InvalidName();
        }
        return result->m_name;
    }

References bio::physical::Perspective< DIMENSION >::Find(), bio::physical::Perspective< DIMENSION >::InvalidId(), bio::physical::Perspective< DIMENSION >::InvalidName(), and bio::physical::Perspective< DIMENSION >::m_hadits.

GetNewObjectFromId()

template<typename DIMENSION >

virtual Wave * bio::physical::Perspective< DIMENSION >::GetNewObjectFromId ( Id  id ) const

inlinevirtual

Creates a new object by Clone()ing the associated type.

Parameters

id

Returns

a Clone() of the Wave* associated with the given id else NULL.

Definition at line 430 of file Perspective.h.

    {
        const Wave* ret = GetTypeFromId(id);
        if (ret)
        {
            return PerspectiveUtilities::Clone(ret);
        }
        return NULL;
    }

References bio::physical::PerspectiveUtilities::Clone(), and bio::physical::Perspective< DIMENSION >::GetTypeFromId().

Referenced by bio::physical::Perspective< DIMENSION >::GetNewObjectFromIdAs(), and bio::physical::Perspective< DIMENSION >::GetNewObjectFromName().

GetNewObjectFromIdAs()

template<typename DIMENSION >

template<typename T >

T bio::physical::Perspective< DIMENSION >::GetNewObjectFromIdAs ( Id  id )

inline

Ease of use method for casting the result of GetNewObjectFromId()

Template Parameters

T

Parameters

id

Returns

a new T* from Clone()ing the type associated with the given id else NULL.

Definition at line 485 of file Perspective.h.

    {
        BIO_SANITIZE_WITH_CACHE(GetNewObjectFromId(id),
            BIO_SINGLE_ARG(return ForceCast< T, Wave* >(RESULT)),
            return NULL);
    }

References BIO_SANITIZE_WITH_CACHE, BIO_SINGLE_ARG, and bio::physical::Perspective< DIMENSION >::GetNewObjectFromId().

GetNewObjectFromName()

template<typename DIMENSION >

virtual Wave * bio::physical::Perspective< DIMENSION >::GetNewObjectFromName ( Name  name )

inlinevirtual

Creates a new object by Clone()ing the associated type.

Parameters

name

Returns

a Clone() of the Wave* associated with the given name else NULL.

Definition at line 445 of file Perspective.h.

    {
        return this->GetNewObjectFromId(this->GetIdFromName(name));
    }

References bio::physical::Perspective< DIMENSION >::GetIdFromName(), and bio::physical::Perspective< DIMENSION >::GetNewObjectFromId().

Referenced by bio::physical::Perspective< DIMENSION >::GetNewObjectFromNameAs().

GetNewObjectFromNameAs()

template<typename DIMENSION >

template<typename T >

T bio::physical::Perspective< DIMENSION >::GetNewObjectFromNameAs ( Name  name )

inline

Ease of access method for casting the result of GetNewObjectFromName()

Template Parameters

T

Parameters

name

Returns

a new T* from Clone()ing the type associated with the given name else NULL.

Definition at line 499 of file Perspective.h.

    {
        BIO_SANITIZE_WITH_CACHE(GetNewObjectFromName(name),
            BIO_SINGLE_ARG(return ForceCast< T, Wave* >(RESULT)),
            return NULL);
    }

References BIO_SANITIZE_WITH_CACHE, BIO_SINGLE_ARG, and bio::physical::Perspective< DIMENSION >::GetNewObjectFromName().

GetNumUsedIds()

template<typename DIMENSION >

virtual Id bio::physical::Perspective< DIMENSION >::GetNumUsedIds ( ) const

inlinevirtual

Returns

the number of ids stored in *this.

Definition at line 340 of file Perspective.h.

    {
        return this->m_nextId - 1;
    }

References bio::physical::Perspective< DIMENSION >::m_nextId.

GetTypeFromId()

template<typename DIMENSION >

virtual const Wave * bio::physical::Perspective< DIMENSION >::GetTypeFromId ( Id  id ) const

inlinevirtual

Only works if AssociateType has been called with the given id.

Parameters

id

Returns

the pointer to the Wave type associated with the given id else NULL.

Definition at line 402 of file Perspective.h.

    {
        BIO_SANITIZE(id == InvalidId(), ,
            return NULL)
 
        typename Hadits::const_iterator result = Find(id);
        if (result == m_hadits.end())
        {
            return NULL;
        }
        return result->m_type;
    }

References BIO_SANITIZE, bio::physical::Perspective< DIMENSION >::Find(), bio::physical::Perspective< DIMENSION >::InvalidId(), and bio::physical::Perspective< DIMENSION >::m_hadits.

Referenced by bio::physical::Perspective< DIMENSION >::GetNewObjectFromId(), bio::physical::Perspective< DIMENSION >::GetTypeFromIdAs(), and bio::physical::Perspective< DIMENSION >::GetTypeFromName().

GetTypeFromIdAs()

template<typename DIMENSION >

template<typename T >

const T bio::physical::Perspective< DIMENSION >::GetTypeFromIdAs ( Id  id ) const

inline

Ease of access method for casting the result of GetTypeFromId().

Template Parameters

T

Parameters

id

Returns

a T* associated with the given name id NULL.

Definition at line 457 of file Perspective.h.

    {
        BIO_SANITIZE_WITH_CACHE(GetTypeFromId(id),
            BIO_SINGLE_ARG(return ForceCast< T, const Wave* >(RESULT)),
            return NULL);
    }

References BIO_SANITIZE_WITH_CACHE, BIO_SINGLE_ARG, and bio::physical::Perspective< DIMENSION >::GetTypeFromId().

GetTypeFromName()

template<typename DIMENSION >

virtual const Wave * bio::physical::Perspective< DIMENSION >::GetTypeFromName ( Name  name ) const

inlinevirtual

Only works if AssociateType has been called with the given id.

Parameters

name

Returns

the pointer to the Wave type associated with the given id else NULL.

Definition at line 420 of file Perspective.h.

    {
        return GetTypeFromId(GetIdWithoutCreation(name));
    }

References bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), and bio::physical::Perspective< DIMENSION >::GetTypeFromId().

Referenced by bio::physical::Perspective< DIMENSION >::GetTypeFromNameAs().

GetTypeFromNameAs()

template<typename DIMENSION >

template<typename T >

const T bio::physical::Perspective< DIMENSION >::GetTypeFromNameAs ( Name  name ) const

inline

Ease of access method for casting the result of GetTypeFromId().

Template Parameters

T

Parameters

name

Returns

a T* associated with the given name id NULL.

Definition at line 471 of file Perspective.h.

    {
        BIO_SANITIZE_WITH_CACHE(GetTypeFromName(name),
            BIO_SINGLE_ARG(return ForceCast< T, const Wave* >(RESULT)),
            return NULL);
    }

References BIO_SANITIZE_WITH_CACHE, BIO_SINGLE_ARG, and bio::physical::Perspective< DIMENSION >::GetTypeFromName().

GetUniqueIdFor()

template<typename DIMENSION >

virtual Id bio::physical::Perspective< DIMENSION >::GetUniqueIdFor ( Name  name )

inlinevirtual

There can be up to 256 additional names.

Parameters

name

Returns

a new Id for the given Name. However, the Name associated with the returned Id may not be the one provided. For example, consider: GetNameFromId(GetUniqueIdFor("MyName")); //Returns "MyName" GetNameFromId(GetUniqueIdFor("MyName")); //Returns "MyName_1"

Definition at line 274 of file Perspective.h.

    {
        if (strcmp(
            InvalidName(),
            name
        ))
        {
            return InvalidId();
        }
 
        std::ostringstream usedName;
        usedName.str(""); //TODO: can we do this all in the ctor?
        usedName << name;
 
        Id ret = GetIdWithoutCreation(usedName.str().c_str());
 
        uint8_t nameCount = 0;
        while (!ret)
        {
            usedName.clear();
            usedName.str(""); //TODO: is this right?
            usedName << name;
            usedName << "_" << nameCount++;
            ret = GetIdWithoutCreation(usedName.str().c_str());
        }
 
        //this creates the unique id.
        return GetIdFromName(usedName.str().c_str());
    }

References bio::physical::Perspective< DIMENSION >::GetIdFromName(), bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), bio::physical::Perspective< DIMENSION >::InvalidId(), and bio::physical::Perspective< DIMENSION >::InvalidName().

InvalidId()

template<typename DIMENSION >

static Id bio::physical::Perspective< DIMENSION >::InvalidId ( )

inlinestatic

When overloading other methods of *this, make sure to check your inputs for invalid Ids. See the functions below for examples.

Returns

0.

Definition at line 143 of file Perspective.h.

    {
        return 0;
    }

Referenced by bio::physical::Perspective< DIMENSION >::GetIdFromName(), bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), bio::physical::Perspective< DIMENSION >::GetNameFromId(), bio::physical::Perspective< DIMENSION >::GetTypeFromId(), and bio::physical::Perspective< DIMENSION >::GetUniqueIdFor().

InvalidName()

template<typename DIMENSION >

static Name bio::physical::Perspective< DIMENSION >::InvalidName ( )

inlinestatic

When overloading other methods of *this, make sure to check your inputs for invalid Names. See the functions below for examples.

Returns

"INVALID_NAME".

Definition at line 152 of file Perspective.h.

    {
        return "INVALID_NAME";
    }

Referenced by bio::physical::Perspective< DIMENSION >::GetIdFromName(), bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), bio::physical::Perspective< DIMENSION >::GetNameFromId(), and bio::physical::Perspective< DIMENSION >::GetUniqueIdFor().

Member Data Documentation

m_hadits

template<typename DIMENSION >

Hadits bio::physical::Perspective< DIMENSION >::m_hadits

protected

Definition at line 508 of file Perspective.h.

Referenced by bio::physical::Perspective< DIMENSION >::~Perspective(), bio::physical::Perspective< DIMENSION >::AssociateType(), bio::physical::Perspective< DIMENSION >::DisassociateType(), bio::physical::Perspective< DIMENSION >::Find(), bio::physical::Perspective< DIMENSION >::GetIdFromName(), bio::physical::Perspective< DIMENSION >::GetIdWithoutCreation(), bio::physical::Perspective< DIMENSION >::GetNameFromId(), and bio::physical::Perspective< DIMENSION >::GetTypeFromId().

m_nextId

template<typename DIMENSION >

Id bio::physical::Perspective< DIMENSION >::m_nextId

protected

Definition at line 509 of file Perspective.h.

Referenced by bio::physical::Perspective< DIMENSION >::GetIdFromName(), and bio::physical::Perspective< DIMENSION >::GetNumUsedIds().

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

• /home/eons/git/biology/lib_bio/inc/bio/physical/Perspective.h