Id Class Reference

#include <Id.h>

Collaboration diagram for Id:

Public Member Functions
void	bindIdToElement (Element *e)
void	destroy () const
Element *	element () const
	Synonym for Id::operator()() More...
Eref	eref () const
	Id ()
	Id (unsigned int id)
	Id (const std::string &path, const std::string &separator="/")
	Id (const ObjId &oi)
bool	operator!= (const Id &other) const
bool	operator< (const Id &other) const
bool	operator== (const Id &other) const
std::string	path (const std::string &separator="/") const
unsigned int	value () const
void	zeroOut () const
	~Id ()

Static Public Member Functions
static void	clearAllElements ()
static std::string	id2str (Id id)
static bool	isValid (Id id)
static bool	isValid (unsigned int id)
static Id	nextId ()
static unsigned int	numIds ()
static Id	str2Id (const std::string &s)

Static Private Member Functions
static vector< Element * > &	elements ()

Private Attributes
unsigned int	id_

Friends
ostream &	operator<< (ostream &s, const Id &i)
istream &	operator>> (istream &s, Id &i)

Detailed Description

This class manages id lookups for elements. Ids provide a uniform handle for every object, independent of which node they are located on.

Definition at line 17 of file Id.h.

Constructor & Destructor Documentation

Id::Id

(

)

Returns the root Id

Definition at line 18 of file Id.cpp.

Referenced by Id(), and str2Id().

    : id_( 0 )
{
    ;
}

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Id::Id

(

unsigned int

id

)

Creates an id with the specified Element number

Definition at line 25 of file Id.cpp.

    : id_( id )
{
    ;
}

Id::Id	(	const std::string &	path,
		const std::string &	separator = "/"
	)

Returns an id found by traversing the specified path

Definition at line 31 of file Id.cpp.

References Shell::doFind(), Id(), ObjId::id, and id_.

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    assert( shell );
    id_ = shell->doFind( path ).id.id_;
}

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Id::Id

(

const ObjId &

oi

)

Downconverts an OjbId to an Id

Definition at line 38 of file Id.cpp.

    : id_( oi.id.id_ )
{
    ;
}

Id::~Id ( )

inline

Destroys an Id. Doesn't do anything much.

Definition at line 46 of file Id.h.

{}

Member Function Documentation

void Id::bindIdToElement

(

Element *

e

)

The specified element is placed into current id.

Definition at line 148 of file Id.cpp.

References elements(), and id_.

{
    if ( elements().size() <= id_ )
    {
        if ( elements().size() % 1000 == 0 )
        {
            elements().reserve( elements().size() + 1000 );
        }
        elements().resize( id_ + 1, 0 );
    }
    assert( elements()[ id_ ] == 0 );
    /*
    if ( elements()[ id_ ] != 0 )
        cout << "Warning: assigning Element to existing id " << id_ << "\n";
        */
    elements()[ id_ ] = e;
    // cout << "Id::bindIdToElement '" << e->getName() << "' = " << id_ << endl;
}

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void Id::clearAllElements ( )

static

Used to clean up all Elements when the simulation is terminated

Definition at line 202 of file Id.cpp.

References elements().

Referenced by finalize(), and main().

{
    for ( vector< Element* >::iterator
            i = elements().begin(); i != elements().end(); ++i )
    {
        if ( *i )
        {
            (*i)->clearAllMsgs();
            delete *i;
        }
    }
}

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void Id::destroy

(

)

const

Cleanly deletes the associated Element, and zeroes out contents of elements vector at the location pointed to by this->id_.

Definition at line 176 of file Id.cpp.

References elements(), and id_.

Referenced by Element::destroyElementTree(), Cell::setupf(), testArith(), testFibonacci(), testLookupSetGet(), testMpiFibonacci(), testMsgSrcDestFields(), testSetGetExtField(), testSharedMsg(), and testShellParserStart().

{
    if ( elements()[ id_ ] )
    {
        // cout << "Id::destroy '" << elements()[ id_ ]->getName() << "' = " << id_ << endl;
        delete elements()[ id_ ];
        elements()[ id_ ] = 0;
        // Put id_ on 'available' list
    }
    else
    {
        cout << "Warning: Id::destroy: " << id_ << " already zeroed\n";
    }
}

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Element * Id::element

(

)

const

Synonym for Id::operator()()

Returns the Element pointed to by the id If it is off-node, returns an allocated wrapper element with postmaster and id information. Calling func has to free it. This wrapper element may also point to UNKNOWN NODE, in which case the master node IdManager has to figure out where it belongs. Returns 0 on failure. Deprecated. Element* operator()() const; Returns the Element pointed to by the Id. Perhaps cleaner to use than operator()() as it is an explicit function.

Here we work with a single big array of all ids. Off-node elements are represented by their postmasters. When we hit a postmaster we put the id into a special field on it. Note that this is horrendously thread-unsafe.

Definition at line 113 of file Id.cpp.

Referenced by ReadCell::addCaConc(), ReadCell::addCanonicalChannel(), ReadCell::addChannel(), addClockMsg(), ReadCell::addSpikeGen(), Streamer::addTable(), Shell::adopt(), assignParam(), ReadCell::buildChannels(), ReadCell::buildCompartment(), buildFromProto(), Dsolve::buildMeshJunctions(), Dsolve::buildNeuroMeshJunctions(), ReadKkit::buildSumTotal(), Dsolve::calcJunction(), checkChildren(), checkForSpine(), SetGet::checkSet(), OneToAllMsg::copy(), OneToOneDataIndexMsg::copy(), OneToOneMsg::copy(), SingleMsg::copy(), DiagonalMsg::copy(), SparseMsg::copy(), FieldElement::data(), HSolve::deepSearchForCompartment(), HSolve::deleteIncomingMessages(), Shell::doAddMsg(), doClassSpecificMessaging(), Shell::doLoadModel(), Shell::doMove(), Element::dropAllMsgsFromSrc(), fillSegIndex(), fillSegments(), VoxelPoolsBase::filterCrossRateTerms(), NeuroNode::filterSpines(), NeuroMesh::filterSpines(), findAllConnectedCompartments(), findFuncMsgSrc(), findMeshOfEnz(), findModelParent(), DiagonalMsg::findOtherEnd(), findParentComptOfReac(), FieldElement::getNode(), FieldElement::getNumOnNode(), Stoich::getProxyPools(), LookupField< L, A >::getVec(), Shell::innerAddMsg(), innerCopyElements(), Shell::innerMove(), Stoich::installAndUnschedFunc(), Stoich::installAndUnschedFuncRate(), Stoich::installAndUnschedFuncReac(), isDoingReinit(), FieldElement::isGlobal(), isOffSolverReac(), Shell::isRunning(), ReadKkit::loadTab(), FieldElement::localDataStart(), main(), Dsolve::mapXfersBetweenDsolves(), FieldElement::numData(), FieldElement::numField(), FieldElement::numLocalData(), FieldElementFinfoBase::postCreationFunc(), FieldElement::rawIndex(), ReadCell::read(), Streamer::reinit(), FieldElement::resizeField(), SrcFinfo1< T >::sendTo(), SrcFinfo2< T1, T2 >::sendTo(), Gsolve::setCompartment(), ZombiePoolInterface::setCompartment(), Stoich::setCompartment(), Ksolve::setDsolve(), Gsolve::setDsolve(), Stoich::setDsolve(), Stoich::setKsolve(), HSolve::setSeed(), ZombieFunction::setSolver(), ZombieReac::setSolver(), ZombieMMenz::setSolver(), ZombieEnz::setSolver(), Neuron::setSpineAndPsdMesh(), Gsolve::setStoich(), SteadyState::setStoich(), Ksolve::setStoich(), Dsolve::setStoich(), ReadKkit::setupSlaveMsg(), showFields(), FieldElement::startDataIndex(), test2ArgSetVec(), testAssortedMsg(), testCellDiffn(), testCopy(), testCopyFieldElement(), testCreateMsg(), testCylDiffnWithStoich(), testFilterOffNodeTargets(), testGet(), testMsgField(), testMsgSrcDestFields(), testSendMsg(), testSendSpike(), testSetGet(), testSetGetDouble(), testSetGetVec(), testSharedMsg(), testSmallCellDiffn(), testStrGet(), testStrSet(), testTaperingCylDiffn(), testTreeTraversal(), testTwoReacGetNeighbors(), ZombiePool::vSetSolver(), ZombieCaConc::vSetSolver(), ZombieHHChannel::vSetSolver(), ZombieCompartment::vSetSolver(), Stoich::zombifyModel(), and Stoich::zombifyPoolFuncWithScaling().

{
    return elements()[ id_ ];
}

vector< Element * > & Id::elements ( )

staticprivate

Definition at line 59 of file Id.cpp.

Referenced by bindIdToElement(), clearAllElements(), destroy(), eref(), isValid(), nextId(), numIds(), and zeroOut().

{
    static vector< Element* > e;
    return e;
}

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Eref Id::eref

(

)

const

Returns the Eref to the element plus index

Definition at line 125 of file Id.cpp.

References elements(), and id_.

Referenced by ReadCell::addChannelMessage(), addClockMsg(), addSpine(), Streamer::addTable(), ReadKkit::assignPoolCompartments(), benchmarkMsg(), ReadSwc::build(), Dsolve::build(), Neuron::buildElist(), ReadKkit::buildEnz(), buildFromProto(), Dsolve::calcJunction(), checkChildren(), Cell::children(), HSolve::children(), SteadyState::classifyState(), Shell::cleanSimulation(), OneToOneDataIndexMsg::copy(), OneToOneMsg::copy(), doClassSpecificMessaging(), ReadCspace::expandEnzyme(), ReadCspace::expandReaction(), Neuron::getExprElist(), Neuron::getExprVal(), getShell(), handle_keyboard_interrupts(), init(), MarkovSolverBase::init(), innerCopyElements(), Neutral::isDescendant(), isDoingReinit(), Shell::isRunning(), Shell::launchParser(), makeCompt(), ReadCspace::makeMolecule(), ReadCspace::makePlots(), makeReacTest(), makeStandardElements(), Dsolve::mapChansBetweenDsolves(), Dsolve::mapDiffPoolsBetweenDsolves(), mapVoxelsBetweenMeshes(), Dsolve::mapXfersBetweenDsolves(), path(), FieldElementFinfoBase::postCreationFunc(), HSolveUtils::rates(), Table::reinit(), Streamer::reinit(), Clock::reportClock(), Ksolve::setDsolve(), Gsolve::setDsolve(), Stoich::setDsolve(), Stoich::setElist(), MarkovRateTable::setInt2dChildTable(), Stoich::setKsolve(), ZombieReac::setSolver(), ZombieMMenz::setSolver(), ZombieEnz::setSolver(), Neuron::setSpineAndPsdMesh(), Gsolve::setStoich(), SteadyState::setStoich(), Ksolve::setStoich(), Dsolve::setStoich(), Cell::setupSolver(), MarkovRateTable::setVtChildTable(), Element::showFields(), storeFunctionMsgs(), testAssortedMsg(), testBuildStoich(), testCalcJunction(), testCellDiffn(), testChildren(), testClock(), testClockMessaging(), testCopy(), testCopyFieldElement(), testCopyMsgOps(), testCreateMsg(), testCylDiffn(), testCylDiffnWithStoich(), testDescendant(), testFibonacci(), testFilterOffNodeTargets(), testFindModelParent(), testGetMsg(), testGetMsgs(), testInterNodeOps(), testMMenz(), testMMenzProcess(), testMove(), testMpiFibonacci(), testMsgElementListing(), testMsgField(), testMsgSrcDestFields(), testObjIdToAndFromPath(), testPoolVolumeScaling(), testReacVolumeScaling(), testReadKkit(), ReadCspace::testReadModel(), testReMesh(), testRunGsolve(), testRunKsolve(), testSendMsg(), testSendSpike(), testSetupReac(), testSharedMsg(), testShellAddMsg(), testShellParserCreateDelete(), testShellParserQuit(), testShellParserStart(), testShellSetGet(), testSmallCellDiffn(), testStats(), testSyncSynapseSize(), testTable(), testTaperingCylDiffn(), testTreeTraversal(), testTwoReacGetNeighbors(), testVolScaling(), testWildcard(), verifyKids(), ZombieCaConc::vSetSolver(), ZombieHHChannel::vSetSolver(), and ZombieCompartment::vSetSolver().

{
    return Eref( elements()[ id_ ], 0 );
    // return Eref( elements()[ id_ ], index_ );
}

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string Id::id2str ( Id  id )

static

Returns a string holding the ascii value of the id_ .

Definition at line 70 of file Id.cpp.

{
    return id.path();
}

static bool Id::isValid ( Id  id )

inlinestatic

Definition at line 145 of file Id.h.

References elements(), and id_.

Referenced by moose_connect(), moose_copy(), moose_ElementField_getPath(), moose_ElementField_setattro(), moose_Field_hash(), moose_Field_init(), moose_Field_repr(), moose_getField(), moose_Id_delete(), moose_Id_getattro(), moose_Id_getItem(), moose_Id_getLength(), moose_Id_getPath(), moose_Id_getShape(), moose_Id_getSlice(), moose_Id_repr(), moose_Id_setattro(), moose_Id_setField(), moose_Id_str(), moose_move(), moose_ObjId_connect(), moose_ObjId_get_destField_attr(), moose_ObjId_get_elementField_attr(), moose_ObjId_get_lookupField_attr(), moose_ObjId_getDataIndex(), moose_ObjId_getField(), moose_ObjId_getFieldIndex(), moose_ObjId_getFieldNames(), moose_ObjId_getFieldType(), moose_ObjId_getId(), moose_ObjId_getLookupField(), moose_ObjId_getNeighbors(), moose_ObjId_hash(), moose_ObjId_init_from_id(), moose_ObjId_repr(), moose_ObjId_richcompare(), moose_ObjId_setattro(), moose_ObjId_setDestField(), moose_ObjId_setLookupField(), and moose_ObjId_str().

    {
        return (id.id_ < elements().size()) && (elements()[id.id_] != 0);
    }

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static bool Id::isValid ( unsigned int  id )

inlinestatic

Definition at line 150 of file Id.h.

References elements(), and id.

    {
        return (id < elements().size()) && (elements()[id] != 0);
    }

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Id Id::nextId ( )

static

Reserves an id for assigning to an Element. Each time it is called a new id is reserved, even if previous ones have not been used yet.

Definition at line 132 of file Id.cpp.

References elements().

Referenced by buildFinfoElement(), Shell::doCopy(), Shell::doCreate(), init(), Msg::initMsgManagers(), innerCopyElements(), Cinfo::makeCinfoElements(), FieldElementFinfoBase::postCreationFunc(), Cell::setupSolver(), showFields(), test2ArgSetVec(), testArith(), testClock(), testCreateMsg(), testFibonacci(), testGet(), testLookupSetGet(), testMsgField(), testMsgSrcDestFields(), testSendMsg(), testSendSpike(), testSetGet(), testSetGetDouble(), testSetGetExtField(), testSetGetSynapse(), testSetGetVec(), testSetRepeat(), testSharedMsg(), testSparseMsg(), testStrGet(), and testStrSet().

{
    // Should really look up 'available' list.
    // Should really put the returned value onto the 'reserved' list
    // so they don't go dangling.
    Id ret( elements().size() );
    elements().push_back( 0 );
    return ret;
}

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unsigned int Id::numIds ( )

static

Returns the number of Ids in use.

Definition at line 143 of file Id.cpp.

References elements().

{
    return elements().size();
}

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bool Id::operator!= ( const Id &  other ) const

inline

Definition at line 130 of file Id.h.

References id_.

    {
        // return id_ != other.id_ || index_ != other.index_;
        return id_ != other.id_;
    }

bool Id::operator< ( const Id &  other ) const

inline

Definition at line 136 of file Id.h.

References id_.

    {
        //  return ( id_ < other.id_ ) ||
        //      ( id_ == other.id_ && index_ < other.index_ );
        return ( id_ < other.id_ );
    }

bool Id::operator== ( const Id &  other ) const

inline

Definition at line 124 of file Id.h.

References id_.

    {
        // return id_ == other.id_ && index_ == other.index_;
        return id_ == other.id_;
    }

string Id::path

(

const std::string &

separator = "/"

)

const

Returns the full pathname of the object on the id.

Definition at line 76 of file Id.cpp.

References eref(), and Neutral::path().

Referenced by Streamer::addTable(), ReadCell::buildCompartment(), Dsolve::buildMeshJunctions(), Dsolve::buildNeuroMeshJunctions(), Neuron::buildSegmentTree(), SetGet::checkSet(), HHChannel2D::createGate(), HHChannel2D::destroyGate(), HHChannel::destroyGate(), diagnoseTree(), Shell::doCopy(), findModelParent(), HSolveUtils::gates(), Neutral::getMsgDestFunctions(), Neutral::getMsgDests(), Neutral::getNeighbors(), LookupField< L, A >::getVec(), HHChannel2D::innerCreateGate(), HHChannel::innerCreateGate(), HHChannel2D::innerDestroyGate(), HHChannel::innerDestroyGate(), installDummy(), isOffSolverReac(), ReadCspace::makePlots(), makeStandardElements(), Ksolve::print(), printJunction(), ReadKkit::read(), ReadCell::ReadCell(), ReadCspace::readModelString(), ReadCell::readScript(), Table::reinit(), Streamer::reinit(), Streamer::removeTable(), HHGate::setAlpha(), HHGate::setBeta(), Ksolve::setDsolve(), Gsolve::setDsolve(), Stoich::setFunctionExpr(), setMethod(), HHGate::setMinfinity(), Neutral::setName(), HSolve::setSeed(), ZombieFunction::setSolver(), ZombieEnz::setSolver(), Neuron::setSpineAndPsdMesh(), HHGate::setTableA(), HHGate::setTau(), Cell::setupf(), ReadCell::startGraftCell(), storePlotMsgs(), ReadCspace::testReadModel(), testTreeTraversal(), Conv< Id >::val2str(), HHChannel::vCreateGate(), ZombieCaConc::vSetSolver(), ZombieHHChannel::vSetSolver(), ZombieCompartment::vSetSolver(), writeGroup(), and writeKkit().

{
    string ret = Neutral::path( eref() );
    // Trim off trailing []
    assert( ret.length() > 0 );
    // the 'back' operation is not supported by pre 2011 compilers

    while ( ret[ ret.length() - 1 ] == ']' )
    {
        size_t pos = ret.find_last_of( '[' );
        if ( pos != string::npos && pos > 0 )
        {
            ret = ret.substr( 0, pos );
        }
    }

    return ret;
}

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Id Id::str2Id ( const std::string &  s )

static

Returns an id whose value is string-converted from the specified string.

Static func to extract an id from a string. We need to accept ids out of the existing range, but it would be nice to have a heuristic on how outrageous the incoming value is.

Definition at line 49 of file Id.cpp.

References Id().

{
    // unsigned int val = atoi( s.c_str() );
    return Id( s );
}

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unsigned int Id::value

(

)

const

Definition at line 197 of file Id.cpp.

References id_.

Referenced by ReadKkit::buildSumTotal(), HHChannel2D::createGate(), Dsolve::fillConcChans(), Neutral::getId(), Neuron::getSpineIdsFromCompartmentIds(), PsdMesh::handlePsdList(), SpineMesh::handleSpineList(), init(), Dsolve::innerBuildMeshJunctions(), Stoich::installAndUnschedFunc(), Stoich::installAndUnschedFuncRate(), Stoich::installAndUnschedFuncReac(), makeReacTest(), std::hash< Id >::operator()(), Neutral::setName(), Dsolve::setStoich(), storeFunctionMsgs(), testCopyFieldElement(), testObjIdToAndFromPath(), testPoolVolumeScaling(), testReacVolumeScaling(), testSendSpike(), testSetGetExtField(), testSetGetSynapse(), testSetGetVec(), testSetRepeat(), testSparseMsg(), testSyncSynapseSize(), testTreeTraversal(), testTwoReacGetNeighbors(), and HHChannel::vCreateGate().

{
    return id_;
}

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void Id::zeroOut

(

)

const

Used to clean out any specific Id.

Definition at line 191 of file Id.cpp.

References elements(), and id_.

Referenced by Element::~Element().

{
    assert ( id_ < elements().size() );
    elements()[ id_ ] = 0;
}

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Friends And Related Function Documentation

ostream& operator<< ( ostream &  s, const Id &  i  )

friend

istream& operator>> ( istream &  s, Id &  i  )

friend

Member Data Documentation

unsigned int Id::id_

private

Definition at line 172 of file Id.h.

Referenced by bindIdToElement(), destroy(), eref(), Id(), isValid(), moose_copy(), moose_Id_richCompare(), moose_move(), moose_ObjId_setattro(), operator!=(), operator<(), operator<<(), operator==(), operator>>(), setDestFinfo(), setDestFinfo1(), setDestFinfo2(), value(), and zeroOut().

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

• moose-core/basecode/Id.h
• moose-core/basecode/Id.cpp