Neutral Class Reference

#include <Neutral.h>

Collaboration diagram for Neutral:

Public Member Functions
void	blockNodeBalance (const Eref &e, unsigned int, unsigned int, unsigned int)
unsigned int	buildTree (const Eref &e, vector< Id > &tree) const
void	destroy (const Eref &e, int stage)
void	generalNodeBalance (const Eref &e, unsigned int myNode, vector< unsigned int > nodeAssignment)
vector< Id >	getChildren (const Eref &e) const
string	getClass (const Eref &e) const
vector< string >	getDestFields (const Eref &e) const
	Information function to return names of all DestFinfos. More...
double	getDt (const Eref &e) const
	Returns dt associated with this object based on its clock tick. More...
unsigned int	getFieldIndex (const Eref &e) const
	fieldIndex specifies field entry if FieldElement. Otherwise zero More...
unsigned int	getId (const Eref &e) const
	Id is the Id of the object, converted to unsigned int. More...
vector< ObjId >	getIncomingMsgs (const Eref &e) const
unsigned int	getIndex (const Eref &e) const
	Index is the dataIndex of the object. More...
vector< string >	getMsgDestFunctions (const Eref &e, string src) const
vector< ObjId >	getMsgDests (const Eref &e, string src) const
string	getName (const Eref &e) const
vector< Id >	getNeighbors (const Eref &e, string field) const
unsigned int	getNumData (const Eref &e) const
unsigned int	getNumField (const Eref &e) const
ObjId	getObjId (const Eref &e) const
vector< ObjId >	getOutgoingMsgs (const Eref &e) const
ObjId	getParent (const Eref &e) const
string	getPath (const Eref &e) const
vector< string >	getSourceFields (const Eref &e) const
	Information function to return names of all SrcFinfos. More...
Neutral	getThis () const
int	getTick (const Eref &e) const
	Returns clock tick of this object. More...
vector< string >	getValueFields (const Eref &e) const
	Information function to return names of all value Finfos. More...
bool	isA (const Eref &e, string className) const
	Neutral ()
void	setName (const Eref &e, string name)
void	setNumData (const Eref &e, unsigned int num)
void	setNumField (const Eref &e, unsigned int num)
void	setThis (Neutral v)
void	setTick (const Eref &e, int num)

Static Public Member Functions
static Id	child (const Eref &e, const string &name)
static void	children (const Eref &e, vector< Id > &ret)
static const Cinfo *	initCinfo ()
static bool	isDescendant (Id me, Id ancestor)
static bool	isGlobalField (const string &field)
static ObjId	parent (const Eref &e)
static ObjId	parent (ObjId id)
static string	path (const Eref &e)

Friends
ostream &	operator<< (ostream &s, const Neutral &d)
istream &	operator>> (istream &s, Neutral &d)

Detailed Description

Definition at line 22 of file Neutral.h.

Constructor & Destructor Documentation

Neutral::Neutral

(

)

Definition at line 273 of file Neutral.cpp.

{
    ;
}

Member Function Documentation

void Neutral::blockNodeBalance	(	const Eref &	e,
		unsigned	int,
		unsigned	int,
		unsigned	int
	)

Request conversion of data into a blockDataHandler subclass, and to carry out node balancing of data as per args.

Definition at line 627 of file Neutral.cpp.

Referenced by initCinfo().

{
}

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unsigned int Neutral::buildTree	(	const Eref &	e,
		vector< Id > &	tree
	)		const

Builds a vector of all descendants of e

Definition at line 583 of file Neutral.cpp.

References ALLDATA, Eref::element(), getChildren(), and Element::id().

Referenced by destroy(), and verifyKids().

{
    unsigned int ret = 1;
    Eref er( e.element(), ALLDATA );
    vector< Id > kids = getChildren( er );
    sort( kids.begin(), kids.end() );
    kids.erase( unique( kids.begin(), kids.end() ), kids.end() );
    for ( vector< Id >::iterator i = kids.begin(); i != kids.end(); ++i )
        ret += buildTree( i->eref(), tree );
    tree.push_back( e.element()->id() );
    return ret;
}

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Id Neutral::child ( const Eref &  e, const string &  name  )

static

Finds specific named child

Definition at line 665 of file Neutral.cpp.

References ALLDATA, Eref::dataIndex(), Msg::e2(), Eref::element(), Cinfo::findFinfo(), Msg::findOtherEnd(), SrcFinfo::getBindIndex(), Msg::getE2(), DestFinfo::getFid(), Msg::getMsg(), Element::getMsgAndFunc(), Element::getName(), Element::hasFields(), Element::id(), name, Eref::objId(), and parent().

Referenced by ReadKkit::assignPoolCompartments(), buildFromProto(), ReadKkit::buildSumTotal(), SetGet::checkSet(), doClassSpecificMessaging(), Shell::doCopy(), Shell::doCreate(), Shell::doFind(), Shell::doMove(), setName(), Neuron::setSpineAndPsdMesh(), and testTreeTraversal().

{
    static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();
    static const Finfo* cf = neutralCinfo->findFinfo( "childOut" );
    static const SrcFinfo* cf2 = dynamic_cast< const SrcFinfo* >( cf );
    static const BindIndex bi = cf2->getBindIndex();

    const vector< MsgFuncBinding >* bvec = e.element()->getMsgAndFunc( bi );

    vector< Id > ret;

    for ( vector< MsgFuncBinding >::const_iterator i = bvec->begin();
        i != bvec->end(); ++i ) {
        if ( i->fid == pafid ) {
            const Msg* m = Msg::getMsg( i->mid );
            assert( m );
            Element* e2 = m->e2();
            if ( e2->getName() == name ) {
                if ( e.dataIndex() == ALLDATA ) {// Child of any index is OK
                    return e2->id();
                } else {
                    ObjId parent = m->findOtherEnd( m->getE2() );
                    // If child is a fieldElement, then all parent indices
                    // are permitted. Otherwise insist parent dataIndex OK.
                    if ( e2->hasFields() || parent == e.objId() )
                        return e2->id();
                }
            }
        }
    }
    return Id();
}

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void Neutral::children ( const Eref &  e, vector< Id > &  ret  )

static

return ids of all the children in ret.

Definition at line 342 of file Neutral.cpp.

References ALLDATA, Eref::dataIndex(), Eref::element(), Cinfo::findFinfo(), SrcFinfo::getBindIndex(), DestFinfo::getFid(), Msg::getMsg(), Element::getMsgAndFunc(), and Msg::targets().

Referenced by ReadCell::addChannelMessage(), addSpine(), allChildren(), Neuron::buildSegmentTree(), checkChildren(), Cell::children(), HSolve::children(), Shell::cleanSimulation(), ReadCspace::deployParameters(), ChemCompt::getChildConcs(), getChildren(), hasScaleFormula(), initCinfo(), innerCopyElements(), ReadCspace::makePlots(), ChemCompt::setChildConcs(), singleLevelWildcard(), testCopyFieldElement(), testTable(), and verifyKids().

{
        /*
    vector< Id > temp;
    getNeighbors( ret, neutralCinfo->findFinfo( "childOut" ) );
    for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i ) {
        if ( ret
    }
    */



    static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();
    static const Finfo* cf = neutralCinfo->findFinfo( "childOut" );
    static const SrcFinfo* cf2 = dynamic_cast< const SrcFinfo* >( cf );
    static const BindIndex bi = cf2->getBindIndex();

    const vector< MsgFuncBinding >* bvec = e.element()->getMsgAndFunc( bi );

    for ( vector< MsgFuncBinding >::const_iterator i = bvec->begin();
        i != bvec->end(); ++i ) {
        if ( i->fid == pafid ) {
            const Msg* m = Msg::getMsg( i->mid );
            assert( m );
            vector< vector< Eref > > kids;
            m->targets( kids );
            if ( e.dataIndex() == ALLDATA ) {
                for ( vector< vector< Eref > >::iterator
                    i = kids.begin(); i != kids.end(); ++i ) {
                    for ( vector< Eref >::iterator
                        j = i->begin(); j != i->end(); ++j )
                        ret.push_back( j->id() );
                }
            } else {
                const vector< Eref >& temp = kids[e.dataIndex()];
                for ( vector< Eref >::const_iterator
                            i = temp.begin(); i != temp.end(); ++i )
                    ret.push_back( i->id() );
            }
        }
    }
}

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void Neutral::destroy	(	const Eref &	e,
		int	stage
	)

Destroys Element and all children

Definition at line 605 of file Neutral.cpp.

References ALLDATA, buildTree(), Element::cinfo(), Msg::deleteMsg(), Element::destroyElementTree(), Eref::element(), Cinfo::isA(), and Eref::objId().

Referenced by Shell::destroy(), and initCinfo().

{
    if ( e.element()->cinfo()->isA( "Msg" ) ) {
        Msg::deleteMsg( e.objId() );
        return;
    }
    vector< Id > tree;
    Eref er( e.element(), ALLDATA );
    unsigned int numDescendants = buildTree( er, tree );
    /*
    cout << "Neutral::destroy: id = " << e.id() <<
        ", name = " << e.element()->getName() <<
        ", numDescendants = " << numDescendants << endl;
        */
    assert( numDescendants == tree.size() );
    Element::destroyElementTree( tree );
}

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void Neutral::generalNodeBalance	(	const Eref &	e,
		unsigned int	myNode,
		vector< unsigned int >	nodeAssignment
	)

Request conversion of data into a generalDataHandler subclass, and to carry out node balancing of data as per args.

Definition at line 636 of file Neutral.cpp.

Referenced by initCinfo().

{
}

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vector< Id > Neutral::getChildren

(

const Eref &

e

)

const

Looks up all the Element children of the current Element

Gets Element children, not individual entries in the array.

Definition at line 334 of file Neutral.cpp.

References children().

Referenced by buildTree(), initCinfo(), testCopy(), and testMove().

{
    vector< Id > ret;
    children( e, ret );
    return ret;
}

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string Neutral::getClass

(

const Eref &

e

)

const

Looks up the Class name of the current Element

Definition at line 393 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), and Cinfo::name().

Referenced by initCinfo().

{
    return e.element()->cinfo()->name();
}

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vector< string > Neutral::getDestFields

(

const Eref &

e

)

const

Information function to return names of all DestFinfos.

Definition at line 481 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), Cinfo::getDestFinfo(), Cinfo::getNumDestFinfo(), and Finfo::name().

Referenced by initCinfo().

{
    unsigned int num = e.element()->cinfo()->getNumDestFinfo();
    vector< string > ret( num );
    for ( unsigned int i = 0; i < num; ++i ) {
        const Finfo *f = e.element()->cinfo()->getDestFinfo( i );
        assert( f );
        ret[i] = f->name();
    }
    return ret;
}

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double Neutral::getDt

(

const Eref &

e

)

const

Returns dt associated with this object based on its clock tick.

Definition at line 447 of file Neutral.cpp.

References Eref::element(), LookupField< L, A >::get(), and Element::getTick().

Referenced by initCinfo().

{
    int tick = e.element()->getTick();
    if ( tick < 0 )
        return 0.0;
    Id clockId( 1 );
    return LookupField< unsigned int, double >::get(
        clockId, "tickDt", tick );
}

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unsigned int Neutral::getFieldIndex

(

const Eref &

e

)

const

fieldIndex specifies field entry if FieldElement. Otherwise zero

Definition at line 432 of file Neutral.cpp.

References Eref::fieldIndex().

Referenced by initCinfo().

{
    return e.fieldIndex();
}

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unsigned int Neutral::getId

(

const Eref &

e

)

const

Id is the Id of the object, converted to unsigned int.

Definition at line 422 of file Neutral.cpp.

References Eref::id(), and Id::value().

Referenced by initCinfo().

{
    return e.id().value();
}

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vector< ObjId > Neutral::getIncomingMsgs

(

const Eref &

e

)

const

Readonly field access function for getting all incoming Msgs.

Definition at line 511 of file Neutral.cpp.

References Msg::e2(), Eref::element(), Msg::getMsg(), Msg::mid(), and Element::msgIn().

Referenced by initCinfo().

{
    vector< ObjId > ret;
    const vector< ObjId >& msgIn = e.element()->msgIn();

    for (unsigned int i = 0; i < msgIn.size(); ++i ) {
        const Msg* m = Msg::getMsg( msgIn[i] );
            assert( m );
            if ( m->e2() == e.element() )
                ret.push_back( m->mid() );
    }
    return ret;
}

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unsigned int Neutral::getIndex

(

const Eref &

e

)

const

Index is the dataIndex of the object.

Definition at line 427 of file Neutral.cpp.

References Eref::dataIndex().

Referenced by initCinfo().

{
    return e.dataIndex();
}

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vector< string > Neutral::getMsgDestFunctions	(	const Eref &	e,
		string	src
	)		const

Return vector of function names called on each target ObjId of the specified SrcFinfo, by the current object. Twin function to getMsgDests.

Definition at line 557 of file Neutral.cpp.

References Element::cinfo(), Eref::dataIndex(), Eref::element(), Cinfo::findFinfo(), Element::getMsgTargetAndFunctions(), Eref::id(), and Id::path().

Referenced by initCinfo().

{
    vector< string > ret( 0 );
    const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
    const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( finfo );
    if ( sf ) {
        vector< ObjId > tgt;
        vector< string > func;
        e.element()->getMsgTargetAndFunctions( e.dataIndex(), sf,
            tgt, func );
        return func;
    } else {
        cout << "Warning: Neutral::getMsgDestFunctions: Id.Field '" <<
                e.id().path() << "." << field <<
                "' not found or not a SrcFinfo\n";
    }
    return ret;
}

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vector< ObjId > Neutral::getMsgDests	(	const Eref &	e,
		string	src
	)		const

Return vector of target ObjIds called by the specified SrcFinfo, by the current object. Twin function to getMsgDestFunctions.

Definition at line 538 of file Neutral.cpp.

References Element::cinfo(), Eref::dataIndex(), Eref::element(), Cinfo::findFinfo(), Element::getMsgTargetAndFunctions(), Eref::id(), and Id::path().

Referenced by initCinfo().

{
    const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
    const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( finfo );
    if ( sf ) {
        vector< ObjId > tgt;
        vector< string > func;
        e.element()->getMsgTargetAndFunctions( e.dataIndex(), sf,
            tgt, func );
        return tgt;
    } else {
        cout << "Warning: Neutral::getMsgDests: Id.Field '" <<
                e.id().path() << "." << field <<
                "' not found or not a SrcFinfo\n";
    }
    static vector< ObjId > ret( 0 );
    return ret;
}

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string Neutral::getName

(

const Eref &

e

)

const

Definition at line 316 of file Neutral.cpp.

References Eref::element(), and Element::getName().

Referenced by initCinfo().

{
    return e.element()->getName();
}

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vector< Id > Neutral::getNeighbors	(	const Eref &	e,
		string	field
	)		const

Readonly field access function for getting Ids connected to current Id via specified Field. Field is specified by its name. Returns an empty vector if it fails.

Definition at line 525 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), Cinfo::findFinfo(), Element::getNeighbors(), Eref::id(), and Id::path().

Referenced by initCinfo().

{
    vector< Id > ret;
    const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
    if ( finfo )
        e.element()->getNeighbors( ret, finfo );
    else
        cout << "Warning: Neutral::getNeighbors: Id.Field '" <<
                e.id().path() << "." << field <<
                "' not found\n";
    return ret;
}

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unsigned int Neutral::getNumData

(

const Eref &

e

)

const

Definition at line 398 of file Neutral.cpp.

References Eref::element(), and Element::numData().

Referenced by initCinfo().

{
    return e.element()->numData();
}

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unsigned int Neutral::getNumField

(

const Eref &

e

)

const

Definition at line 408 of file Neutral.cpp.

References Eref::dataIndex(), Eref::element(), Eref::isDataHere(), Element::numField(), and Element::rawIndex().

Referenced by initCinfo().

{
    assert( e.isDataHere() );
    unsigned int rawIndex = e.element()->rawIndex( e.dataIndex() );
    return e.element()->numField( rawIndex );
}

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ObjId Neutral::getObjId

(

const Eref &

e

)

const

Simply returns own ObjId

Definition at line 321 of file Neutral.cpp.

References Eref::objId().

Referenced by initCinfo().

{
    return e.objId();
}

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vector< ObjId > Neutral::getOutgoingMsgs

(

const Eref &

e

)

const

Readonly field access function for getting all outgoing Msgs.

Definition at line 493 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), Element::getMsgAndFunc(), and Cinfo::numBindIndex().

Referenced by initCinfo().

{
    vector< ObjId > ret;
    unsigned int numBindIndex = e.element()->cinfo()->numBindIndex();

    for ( unsigned int i = 0; i < numBindIndex; ++i ) {
        const vector< MsgFuncBinding >* v =
            e.element()->getMsgAndFunc( i );
        if ( v ) {
            for ( vector< MsgFuncBinding >::const_iterator mb = v->begin();
                mb != v->end(); ++mb ) {
                ret.push_back( mb->mid );
            }
        }
    }
    return ret;
}

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ObjId Neutral::getParent

(

const Eref &

e

)

const

Looks up the full Id info for the parent of the current Element

Definition at line 326 of file Neutral.cpp.

References parent().

Referenced by initCinfo(), and testCopy().

{
    return parent( e );
}

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string Neutral::getPath

(

const Eref &

e

)

const

Traverses to root, building path.

Definition at line 388 of file Neutral.cpp.

References path().

Referenced by initCinfo().

{
    return path( e );
}

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vector< string > Neutral::getSourceFields

(

const Eref &

e

)

const

Information function to return names of all SrcFinfos.

Definition at line 469 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), Cinfo::getNumSrcFinfo(), Cinfo::getSrcFinfo(), and Finfo::name().

Referenced by initCinfo().

{
    unsigned int num = e.element()->cinfo()->getNumSrcFinfo();
    vector< string > ret( num );
    for ( unsigned int i = 0; i < num; ++i ) {
        const Finfo *f = e.element()->cinfo()->getSrcFinfo( i );
        assert( f );
        ret[i] = f->name();
    }
    return ret;
}

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Neutral Neutral::getThis

(

)

const

Field access functions for the entire object. For Neutrals the getThis function does return the Neutral object, but it has no data to set. However, the function name acts as a placeholder and derived objects can override the function so that the entire object can be accessed as a field and also used for inter-node data transfer.

Definition at line 289 of file Neutral.cpp.

Referenced by initCinfo().

{
    return *this;
}

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int Neutral::getTick

(

const Eref &

e

)

const

Returns clock tick of this object.

Definition at line 437 of file Neutral.cpp.

References Eref::element(), and Element::getTick().

Referenced by initCinfo().

{
    return e.element()->getTick();
}

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vector< string > Neutral::getValueFields

(

const Eref &

e

)

const

Information function to return names of all value Finfos.

Definition at line 457 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), Cinfo::getNumValueFinfo(), Cinfo::getValueFinfo(), and Finfo::name().

Referenced by initCinfo().

{
    unsigned int num = e.element()->cinfo()->getNumValueFinfo();
    vector< string > ret( num );
    for ( unsigned int i = 0; i < num; ++i ) {
        const Finfo *f = e.element()->cinfo()->getValueFinfo( i );
        assert( f );
        ret[i] = f->name();
    }
    return ret;
}

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const Cinfo * Neutral::initCinfo ( )

static

Standard initialization function, used whenever we want to look up the class Cinfo

Definition at line 16 of file Neutral.cpp.

References blockNodeBalance(), children(), destroy(), generalNodeBalance(), getChildren(), getClass(), getDestFields(), getDt(), getFieldIndex(), getId(), getIncomingMsgs(), getIndex(), getMsgDestFunctions(), getMsgDests(), getName(), getNeighbors(), getNumData(), getNumField(), getObjId(), getOutgoingMsgs(), getParent(), getPath(), getSourceFields(), getThis(), getTick(), getValueFields(), id, isA(), name, neutralCinfo, parent(), path(), setName(), setNumData(), setNumField(), setThis(), and setTick().

Referenced by Shell::adopt(), init(), Group::initCinfo(), Boundary::initCinfo(), Mstring::initCinfo(), MMPump::initCinfo(), Species::initCinfo(), Synapse::initCinfo(), RandSpike::initCinfo(), Annotator::initCinfo(), ConcChan::initCinfo(), VectorTable::initCinfo(), SpikeGen::initCinfo(), IntFire::initCinfo(), Nernst::initCinfo(), DiffAmp::initCinfo(), Stats::initCinfo(), MarkovGslSolver::initCinfo(), Arith::initCinfo(), RC::initCinfo(), TableBase::initCinfo(), Cell::initCinfo(), PIDController::initCinfo(), GapJunction::initCinfo(), EnzBase::initCinfo(), ChanBase::initCinfo(), Spine::initCinfo(), moose::VClamp::initCinfo(), Variable::initCinfo(), ReacBase::initCinfo(), SynHandlerBase::initCinfo(), IzhikevichNrn::initCinfo(), SteadyState::initCinfo(), HHGate2D::initCinfo(), Clock::initCinfo(), Interpol2D::initCinfo(), Func::initCinfo(), Neuron::initCinfo(), PyRun::initCinfo(), MarkovSolverBase::initCinfo(), PulseGen::initCinfo(), CaConcBase::initCinfo(), DifBufferBase::initCinfo(), MeshEntry::initCinfo(), DifShellBase::initCinfo(), Ksolve::initCinfo(), Gsolve::initCinfo(), Function::initCinfo(), Finfo::initCinfo(), MarkovRateTable::initCinfo(), HSolve::initCinfo(), PoolBase::initCinfo(), PostMaster::initCinfo(), Msg::initCinfo(), Adaptor::initCinfo(), HHGate::initCinfo(), Dsolve::initCinfo(), moose::CompartmentBase::initCinfo(), Cinfo::initCinfo(), ChemCompt::initCinfo(), Stoich::initCinfo(), Shell::initCinfo(), TestId::initCinfo(), Msg::initMsgManagers(), innerCopyMsgs(), Shell::innerMove(), Cinfo::isA(), FieldElementFinfoBase::postCreationFunc(), showFields(), testCinfoFields(), testFinfoFields(), testIsA(), and testSetGetExtField().

{
    // Element Value Finfos

    static ElementValueFinfo< Neutral, string > name(
        "name",
        "Name of object",
        &Neutral::setName,
        &Neutral::getName );

    // Should be renamed to myId
    static ReadOnlyElementValueFinfo< Neutral, ObjId > me(
        "me",
        "ObjId for current object",
            &Neutral::getObjId );

    static ReadOnlyElementValueFinfo< Neutral, ObjId > parent(
        "parent",
        "Parent ObjId for current object",
            &Neutral::getParent );

    static ReadOnlyElementValueFinfo< Neutral, vector< Id > > children(
        "children",
        "vector of ObjIds listing all children of current object",
            &Neutral::getChildren );

    static ReadOnlyElementValueFinfo< Neutral, string > path(
        "path",
        "text path for object",
            &Neutral::getPath );

    /*
            */
    static ReadOnlyElementValueFinfo< Neutral, string > className(
        "className",
        "Class Name of object",
            &Neutral::getClass );

    static ElementValueFinfo< Neutral, unsigned int > numData(
        "numData",
        "# of Data entries on Element."
        "Note that on a FieldElement this does NOT refer to field entries,"
        "but to the number of DataEntries on the parent of the "
        "FieldElement.",
            &Neutral::setNumData,
            &Neutral::getNumData );

    static ElementValueFinfo< Neutral, unsigned int > numField(
        "numField",
        "For a FieldElement: number of entries of self."
        "For a regular Element: One.",
            &Neutral::setNumField,
            &Neutral::getNumField );

    static ReadOnlyElementValueFinfo< Neutral, unsigned int > id(
        "idValue",
        "Object id of self, converted to an unsigned int.",
            &Neutral::getId );

    static ReadOnlyElementValueFinfo< Neutral, unsigned int > index(
        "index",
        "For a FieldElement: Object index of parent."
        "For a regular Element: Object index (dataId) of self.",
            &Neutral::getIndex );

    static ReadOnlyElementValueFinfo< Neutral, unsigned int > fieldIndex(
        "fieldIndex",
        "For a FieldElement: field Index of self."
        "For a regular Element: zero.",
            &Neutral::getFieldIndex );

    static ElementValueFinfo< Neutral, int >
        tick(
        "tick",
        "Clock tick for this Element for periodic execution in the "
        "main simulation event loop. A default is normally assigned, "
        "based on object class, but one can override to any value "
        "between 0 and 19. Assigning to -1 means that the object is "
        "disabled and will not be called during simulation execution "
        "The actual timestep (dt) belonging to a clock tick is defined "
        "by the Clock object.",
            &Neutral::setTick,
            &Neutral::getTick );

    static ReadOnlyElementValueFinfo< Neutral, double >
            dt(
            "dt",
            "Timestep used for this Element. Zero if not scheduled.",
            &Neutral::getDt );


    static ReadOnlyElementValueFinfo< Neutral, vector< string > >
            valueFields(
            "valueFields",
            "List of all value fields on Element."
            "These fields are accessed through the assignment operations "
            "in the Python interface."
            "These fields may also be accessed as functions through the "
            "set<FieldName> and get<FieldName> commands.",
            &Neutral::getValueFields
    );

    static ReadOnlyElementValueFinfo< Neutral, vector< string > >
            sourceFields(
            "sourceFields",
            "List of all source fields on Element, that is fields that "
            "can act as message sources. ",
            &Neutral::getSourceFields
    );

    static ReadOnlyElementValueFinfo< Neutral, vector< string > >
            destFields(
            "destFields",
            "List of all destination fields on Element, that is, fields"
            "that are accessed as Element functions.",
            &Neutral::getDestFields
    );

    static ReadOnlyElementValueFinfo< Neutral, vector< ObjId > > msgOut(
        "msgOut",
        "Messages going out from this Element",
            &Neutral::getOutgoingMsgs );

    static ReadOnlyElementValueFinfo< Neutral, vector< ObjId > > msgIn(
        "msgIn",
        "Messages coming in to this Element",
            &Neutral::getIncomingMsgs );

    static ReadOnlyLookupElementValueFinfo< Neutral, string, vector< Id > > neighbors(
        "neighbors",
        "Ids of Elements connected this Element on specified field.",
            &Neutral::getNeighbors );

    static ReadOnlyLookupElementValueFinfo< Neutral, string, vector< ObjId > > msgDests(
        "msgDests",
        "ObjIds receiving messages from the specified SrcFinfo",
            &Neutral::getMsgDests );

    static ReadOnlyLookupElementValueFinfo< Neutral, string, vector< string > > msgDestFunctions(
        "msgDestFunctions",
        "Matching function names for each ObjId receiving a msg from "
        "the specified SrcFinfo",
            &Neutral::getMsgDestFunctions );

    static ReadOnlyLookupElementValueFinfo< Neutral, string, bool >isA(
        "isA",
        "Returns true if the current object is derived from the specified "
        "the specified class",
            &Neutral::isA );

    // Value Finfos
    static ValueFinfo< Neutral, Neutral > thisFinfo (
        "this",
        "Access function for entire object",
        &Neutral::setThis,
        &Neutral::getThis
    );
    // SrcFinfos
    static SrcFinfo1< int > childOut( "childOut",
        "Message to child Elements");

    // DestFinfos
    static DestFinfo parentMsg( "parentMsg",
        "Message from Parent Element(s)",
        new EpFunc1< Neutral, int >( &Neutral::destroy ) );

    static DestFinfo blockNodeBalance( "blockNodeBalance",
        "Request conversion of data into a blockDataHandler subclass,"
        "and to carry out node balancing of data."
        "The amount of data is not altered, and if the data is already a"
        "blockDataHandler subclass it retains its original dimensions"
        "If converting from a generalDataHandler to blockHandler it treats"
        "it as a linear array"
        "The function preserves the old data and shuffles info around"
        "between nodes to complete the balancing."
        "Arguments are: myNode, startNode, endNode",
        new EpFunc3< Neutral, unsigned int, unsigned int, unsigned int >(
            &Neutral::blockNodeBalance ) );

    static DestFinfo generalNodeBalance( "generalNodeBalance",
        "Request conversion of data into a generalDataHandler subclass,"
        "and to carry out node balancing of data as per specified args."
        "The amount of data is not altered. The generalDataHandler loses"
        "any dimensional information that may have been present in an "
        "earlier blockDataHandler incarnation."
        "Arguments are: myNode, nodeAssignment",
        new EpFunc2< Neutral, unsigned int, vector< unsigned int > >(
            &Neutral::generalNodeBalance ) );

    // Setting up the Finfo list.
    static Finfo* neutralFinfos[] = {
        &childOut,              // SrcFinfo
        &parentMsg,             // DestFinfo
        &thisFinfo,             // Value
        &name,                  // Value
        &me,                    // ReadOnlyValue
        &parent,                // ReadOnlyValue
        &children,              // ReadOnlyValue
        &path,                  // ReadOnlyValue
        &className,             // ReadOnlyValue
        &numData,               // Value
        &numField,              // Value
        &id,                    // ReadOnlyValue
        &index,                 // ReadOnlyValue
        &fieldIndex,            // ReadOnlyValue
        &tick,                  // Value
        &dt,                    // ReadOnlyValue
        &valueFields,           // ReadOnlyValue
        &sourceFields,          // ReadOnlyValue
        &destFields,            // ReadOnlyValue
        &msgOut,                // ReadOnlyValue
        &msgIn,                 // ReadOnlyValue
        &neighbors,         // ReadOnlyLookupValue
        &msgDests,              // ReadOnlyLookupValue
        &msgDestFunctions,      // ReadOnlyLookupValue
        &isA,                   // ReadOnlyLookupValue
    };

    // Setting up the Cinfo.

    static string doc[] =
    {
        "Name", "Neutral",
        "Author", "Upinder S. Bhalla, 2007, NCBS",
        "Description", "Neutral: Base class for all MOOSE classes. Provides"
        "access functions for housekeeping fields and operations, message"
        "traversal, and so on."
    };
    static Dinfo< Neutral > dinfo;
    static Cinfo neutralCinfo (
        "Neutral",
        0, // No base class.
        neutralFinfos,
        sizeof( neutralFinfos ) / sizeof( Finfo* ),
        &dinfo,
                doc,
                sizeof(doc)/sizeof(string)
    );

    return &neutralCinfo;
}

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bool Neutral::isA	(	const Eref &	e,
		string	className
	)		const

Returns True if the object is derived from the specified class

Definition at line 576 of file Neutral.cpp.

References Element::cinfo(), Eref::element(), and Cinfo::isA().

Referenced by initCinfo().

{
    return e.element()->cinfo()->isA( className );
}

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bool Neutral::isDescendant ( Id  me, Id  ancestor  )

static

Checks if 'me' is a descendant of 'ancestor'

Definition at line 647 of file Neutral.cpp.

References Eref::element(), ObjId::eref(), Id::eref(), Element::findCaller(), Cinfo::findFinfo(), Msg::findOtherEnd(), DestFinfo::getFid(), Msg::getMsg(), Element::id(), and Eref::objId().

Referenced by Shell::doCopy(), Shell::doMove(), and testDescendant().

{
    static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();

    Eref e = me.eref();

    while ( e.element()->id() != Id() && e.element()->id() != ancestor ) {
        ObjId mid = e.element()->findCaller( pafid );
        assert( mid != ObjId() );
        ObjId fid = Msg::getMsg( mid )->findOtherEnd( e.objId() );
        e = fid.eref();
    }
    return ( e.element()->id() == ancestor );
}

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bool Neutral::isGlobalField ( const string &  field )

static

Checks if specified field is a global, typically because it is present on the Element and therefore should be assigned uniformly on all nodes

Definition at line 781 of file Neutral.cpp.

{
    if ( field.length() < 8 )
        return 0;
    if ( field.substr( 0, 4 ) == "set_" ) {
        if ( field == "set_name" )
            return 1;
        if ( field == "set_group" )
            return 1;
        if ( field == "set_lastDimension" ) // This is the critical one!
            return 1;
    }
    return 0;
}

ObjId Neutral::parent ( const Eref &  e )

static

Returns parent object

Definition at line 701 of file Neutral.cpp.

References Eref::objId().

Referenced by Synapse::addMsgCallback(), addSpine(), child(), doClassSpecificMessaging(), Shell::doFind(), Synapse::dropMsgCallback(), findModelParent(), getCompt(), getParent(), initCinfo(), innerCopyElements(), ReadCspace::printMol(), MeshEntry::reinit(), setName(), storeFunctionMsgs(), and testObjIdToAndFromPath().

{
    return Neutral::parent( e.objId() );
}

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ObjId Neutral::parent ( ObjId  id )

static

Definition at line 706 of file Neutral.cpp.

References ObjId::element(), Element::findCaller(), Cinfo::findFinfo(), Msg::findOtherEnd(), DestFinfo::getFid(), Msg::getMsg(), and ObjId::id.

{
    static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();

    if ( oid.id == Id() ) {
        cout << "Warning: Neutral::parent: tried to take parent of root\n";
        return Id();
    }

    ObjId mid = oid.element()->findCaller( pafid );
    assert( mid != ObjId() );

    ObjId pa = Msg::getMsg( mid )->findOtherEnd( oid );
    return pa;
}

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string Neutral::path ( const Eref &  e )

static

Finds the path of element e

Definition at line 725 of file Neutral.cpp.

References ObjId::dataIndex, Eref::element(), ObjId::element(), ObjId::eref(), Eref::fieldIndex(), Element::findCaller(), Cinfo::findFinfo(), Msg::findOtherEnd(), DestFinfo::getFid(), Msg::getMsg(), Element::getName(), Element::hasFields(), ObjId::id, and Eref::objId().

Referenced by getPath(), initCinfo(), ObjId::path(), and Id::path().

{
    static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();

    vector< ObjId > pathVec;
    ObjId curr = e.objId();
    stringstream ss;

    pathVec.push_back( curr );
    while ( curr.id != Id() ) {
        ObjId mid = curr.eref().element()->findCaller( pafid );
        if ( mid == ObjId() ) {
            cout << "Error: Neutral::path:Cannot follow msg of ObjId: " <<
                    e.objId() << " for func: " << pafid << endl;
            break;
        }
        curr = Msg::getMsg( mid )->findOtherEnd( curr );
        pathVec.push_back( curr );
    }
    if ( pathVec.size() <= 1 )
        return "/";
    for ( unsigned int i = 1; i < pathVec.size(); ++i ) {
        ss << "/";
        ObjId& oid = pathVec[ pathVec.size() - i - 1 ];
        ss << oid.element()->getName();
        if ( !oid.element()->hasFields() )
            ss << "[" << oid.dataIndex << "]";
        /*
        if ( !oid.element()->hasFields() )
            ss << "[" << oid.dataIndex << "]";
        if ( oid.element()->numData() > 1 )
            ss << "[" << oid.dataIndex << "]";
            */
    }
    // Append braces if Eref was for a fieldElement. This should
    // work even if it is off-node.
    if ( e.element()->hasFields() ) {
        ss << "[" << e.fieldIndex() << "]";
    }

    return ss.str();
}

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void Neutral::setName	(	const Eref &	e,
		string	name
	)

Field access functions for the name of the Element/Neutral

Definition at line 294 of file Neutral.cpp.

References child(), Eref::element(), ObjId::eref(), Eref::id(), Shell::isNameValid(), name, parent(), Id::path(), Element::setName(), and Id::value().

Referenced by initCinfo().

{
    if ( e.id().value() <= 3 ) {
        cout << "Warning: Neutral::setName on '" << e.id().path() <<
               "'. Cannot rename core objects\n";
        return;
    }
    if ( !Shell::isNameValid( name ) ) {
        cout << "Warning: Neutral::setName on '" << e.id().path() <<
               "'. Illegal character in name.\n";
        return;
    }
    ObjId pa = parent( e );
    Id sibling = Neutral::child( pa.eref(), name );
    if ( sibling == Id() ) { // OK, no existing object with same name.
        e.element()->setName( name );
    } else {
        cout << "Warning: Neutral::setName: an object with the name '" <<
            name << "'\n already exists on the same parent. Not changed\n";
    }
}

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void Neutral::setNumData	(	const Eref &	e,
		unsigned int	num
	)

numData is the number of data entries on this Element.

Definition at line 403 of file Neutral.cpp.

References Eref::element(), and Element::resize().

Referenced by initCinfo().

{
    e.element()->resize( num );
}

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void Neutral::setNumField	(	const Eref &	e,
		unsigned int	num
	)

numField is the size of the field array on the FieldElement specified by the Eref including its data index.

Definition at line 415 of file Neutral.cpp.

References Eref::dataIndex(), Eref::element(), Eref::isDataHere(), Element::rawIndex(), and Element::resizeField().

Referenced by initCinfo().

{
    assert( e.isDataHere() );
    unsigned int rawIndex = e.element()->rawIndex( e.dataIndex() );
    e.element()->resizeField( rawIndex, num );
}

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void Neutral::setThis

(

Neutral

v

)

Field access functions for the entire object. For Neutrals the setThis function is a dummy: it doesn't do anything because the Neutral has no data to set. However, the function name acts as a placeholder and derived objects can override the function so that the entire object can be accessed as a field and also for inter-node data transfer.

Definition at line 284 of file Neutral.cpp.

Referenced by initCinfo().

{
    ;
}

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void Neutral::setTick	(	const Eref &	e,
		int	num
	)

The clock Tick specifies the timing and order of execution of the 'process' action of this object in the simulation. The timing is set by assigning the appropriate dt to this tick in the Clock object. A value of -1 means that the object is disabled.

Definition at line 442 of file Neutral.cpp.

References Eref::element(), and Element::setTick().

Referenced by initCinfo().

{
    e.element()->setTick( num );
}

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Friends And Related Function Documentation

ostream& operator<< ( ostream &  s, const Neutral &  d  )

friend

istream& operator>> ( istream &  s, Neutral &  d  )

friend

---

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

• moose-core/shell/Neutral.h
• moose-core/shell/Neutral.cpp