#include <Element.h>

Inheritance diagram for Element:

Collaboration diagram for Element:

Public Member Functions
void	addMsg (ObjId mid)

void	addMsgAndFunc (ObjId mid, FuncId fid, BindIndex bindIndex)

const Cinfo *	cinfo () const

void	clearAllMsgs ()
	Used upon ending of MOOSE session, to rapidly clear out messages. More...

void	clearBinding (BindIndex b)

virtual Element *	copyElement (Id newParent, Id newId, unsigned int n, bool toGlobal) const =0

virtual char *	data (unsigned int rawIndex, unsigned int fieldIndex=0) const =0

void	digestMessages ()

void	dropAllMsgsFromSrc (Id src)

void	dropMsg (ObjId mid)

	Element (Id id, const Cinfo *c, const string &name)

unsigned int	findBinding (MsgFuncBinding b) const

ObjId	findCaller (FuncId fid) const

unsigned int	getFieldsOfOutgoingMsg (ObjId mid, vector< pair< BindIndex, FuncId > > &ret) const

unsigned int	getInputMsgs (vector< ObjId > &caller, FuncId fid) const

unsigned int	getInputsWithTgtIndex (vector< pair< Id, unsigned int > > &ret, const DestFinfo *finfo) const

const vector< MsgFuncBinding > *	getMsgAndFunc (BindIndex b) const

unsigned int	getMsgSourceAndSender (FuncId fid, vector< ObjId > &src, vector< string > &sender) const

unsigned int	getMsgTargetAndFunctions (DataId srcDataId, const SrcFinfo *finfo, vector< ObjId > &tgt, vector< string > &func) const

vector< ObjId >	getMsgTargets (DataId srcDataId, const SrcFinfo *finfo) const

const string &	getName () const

unsigned int	getNeighbors (vector< Id > &ret, const Finfo *finfo) const

virtual unsigned int	getNode (unsigned int dataIndex) const =0
	Returns node number of specified dataIndex. More...

virtual unsigned int	getNumOnNode (unsigned int node) const =0

int	getTick () const

virtual bool	hasFields () const =0

bool	hasMsgs (BindIndex b) const

Id	id () const

void	innerSetTick (unsigned int tick)

bool	isDoomed () const

virtual bool	isGlobal () const =0
	True if there is a copy of every dataEntry on all nodes. More...

virtual unsigned int	localDataStart () const =0
	Returns index of first data entry on this node. More...

void	markAsDoomed ()

void	markRewired ()

const vector< MsgDigest > &	msgDigest (unsigned int index)

const vector< ObjId > &	msgIn () const

virtual unsigned int	numData () const =0
	Returns number of data entries across all nodes. More...

virtual unsigned int	numField (unsigned int rawIndex) const =0
	Returns number of field entries for specified data. More...

virtual unsigned int	numLocalData () const =0
	Returns number of local data entries on this node. More...

void	printMsgDigest (unsigned int srcIndex, unsigned int dataIndex) const

void	putOffNodeTargetsInDigest (unsigned int srcNum, vector< vector< bool > > &targetNodes)

void	putTargetsInDigest (unsigned int srcNum, const MsgFuncBinding &mfb, const FuncOrder &fo, vector< vector< bool > > &targetNodes)

virtual unsigned int	rawIndex (unsigned int dataIndex) const =0

void	replaceCinfo (const Cinfo *newCinfo)
	Support function for zombieSwap, replaces Cinfo. More...

virtual void	resize (unsigned int newNumData)=0

virtual void	resizeField (unsigned int rawIndex, unsigned int newNumField)=0

void	setName (const string &val)

void	setTick (int t)

void	showFields () const

void	showMsg () const

virtual unsigned int	startDataIndex (unsigned int nodeNum) const =0
	Returns start dataIndex on specified node. More...

virtual unsigned int	totNumLocalField () const =0

virtual void	zombieSwap (const Cinfo *zCinfo)
	virtual func, this base version must be called by all derived classes More...

virtual	~Element ()

Static Public Member Functions
static void	destroyElementTree (const vector< Id > &tree)

Private Member Functions
unsigned int	getInputs (vector< Id > &ret, const DestFinfo *finfo) const

unsigned int	getOutputs (vector< Id > &ret, const SrcFinfo *finfo) const

Private Attributes
const Cinfo *	cinfo_
	Stores the unique identifier for Element. More...

Id	id_
	Name of the Element. More...

bool	isDoomed_
	True if the element is marked for destruction. More...

bool	isRewired_
	True if messages have been changed and need to digestMessages. More...

vector< ObjId >	m_

vector< vector< MsgFuncBinding > >	msgBinding_

vector< vector< MsgDigest > >	msgDigest_

string	name_

int	tick_
	Returns tick on which element is scheduled. -1 for disabled. More...

Detailed Description

Base class for all object lookups. Provides the MOOSE interface so that it handles messaging, class info, and basic fields. Does not do data.

Definition at line 20 of file Element.h.

Constructor & Destructor Documentation

Element::Element	(	Id	id,
		const Cinfo *	c,
		const string &	name
	)

This is the main constructor, used by Shell::innerCreate which makes most Elements. Also used to create base Elements to init the simulator in main.cpp. Id is the Id of the new Element Cinfo is the class name is its name numData is the number of data entries, defaults to a singleton. The isGlobal flag specifies whether the created objects should be replicated on all nodes, or partitioned without replication.

Definition at line 17 of file Element.cpp.

     :   name_( name ),
       id_( id ),
       cinfo_( c ),
       msgBinding_( c->numBindIndex() ),
       msgDigest_( c->numBindIndex() ),
       tick_( -1 ),
       isRewired_( false ),
       isDoomed_( false )
 {
     id.bindIdToElement( this );
 }

Element::~Element ( )

virtual

Destructor

Definition at line 31 of file Element.cpp.

References Msg::deleteMsg(), id_, m_, markAsDoomed(), msgBinding_, and Id::zeroOut().

 {
     // A flag that the Element is doomed, used to avoid lookups
     // when deleting Msgs.
     id_.zeroOut();
     markAsDoomed();
     for ( vector< vector< MsgFuncBinding > >::iterator
             i = msgBinding_.begin(); i != msgBinding_.end(); ++i )
     {
         for ( vector< MsgFuncBinding >::iterator
                 j = i->begin(); j != i->end(); ++j )
         {
             // This call internally protects against double deletion.
             Msg::deleteMsg( j->mid );
         }
     }
 
     for ( vector< ObjId >::iterator i = m_.begin(); i != m_.end(); ++i )
         Msg::deleteMsg( *i );
 }

Here is the call graph for this function:

Member Function Documentation

void Element::addMsg ( ObjId mid )

Pushes the Msg mid onto the list. The position on the list does not matter.

Definition at line 79 of file Element.cpp.

References m_, and markRewired().

Referenced by Msg::Msg().

 {
     while ( m_.size() > 0 )
     {
         if ( m_.back().bad() )
             m_.pop_back();
         else
             break;
     }
     m_.push_back( m );
     markRewired();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::addMsgAndFunc	(	ObjId	mid,
		FuncId	fid,
		BindIndex	bindIndex
	)

Pushes back the specified Msg and Func pair into the properly indexed place on the msgBinding_ vector.

Definition at line 128 of file Element.cpp.

References markRewired(), and msgBinding_.

Referenced by SrcFinfo::addMsg(), OneToAllMsg::copy(), OneToOneDataIndexMsg::copy(), OneToOneMsg::copy(), SingleMsg::copy(), DiagonalMsg::copy(), SparseMsg::copy(), testMsgField(), and testSendMsg().

 {
     if ( msgBinding_.size() < bindIndex + 1U )
         msgBinding_.resize( bindIndex + 1 );
     msgBinding_[ bindIndex ].push_back( MsgFuncBinding( mid, fid ) );
     markRewired();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

const Cinfo * Element::cinfo ( ) const

Gets the class information for this Element

Definition at line 66 of file Element.cpp.

References cinfo_.

Referenced by ReadCell::addCaConc(), ReadCell::addCanonicalChannel(), addClockMsg(), ReadCell::addSpikeGen(), Stoich::allocateModelObject(), assignParam(), Dsolve::buildMeshJunctions(), Dsolve::buildNeuroMeshJunctions(), Dsolve::calcJunction(), SetGet::checkSet(), PostMaster::clearPendingRecv(), convertConcToNumRateUsingMesh(), FieldElement::copyElement(), DataElement::DataElement(), HSolve::deepSearchForCompartment(), HSolve::deleteIncomingMessages(), Neutral::destroy(), Shell::doAddMsg(), doClassSpecificMessaging(), Shell::doLoadModel(), fillSegIndex(), fillSegments(), VoxelPoolsBase::filterCrossRateTerms(), findAllConnectedCompartments(), findFuncMsgSrc(), Neutral::getClass(), getCompt(), Neutral::getDestFields(), Msg::getDestFieldsOnE1(), Msg::getDestFieldsOnE2(), Neutral::getMsgDestFunctions(), Neutral::getMsgDests(), getMsgSourceAndSender(), getMsgTargetAndFunctions(), Neutral::getNeighbors(), Neutral::getOutgoingMsgs(), Stoich::getProxyPools(), getReactantVols(), Neutral::getSourceFields(), Msg::getSrcFieldsOnE1(), Msg::getSrcFieldsOnE2(), Neutral::getValueFields(), Shell::innerAddMsg(), innerCopyElements(), Neutral::isA(), isOffSolverReac(), isPartOfDend(), ReadKkit::loadTab(), localGet(), Stoich::locateOffSolverReacs(), Eref::msgDigest(), GetOpFunc1< T, L, A >::op(), GetEpFunc1< T, L, A >::op(), ReadCspace::printMol(), putFuncsInOrder(), putOffNodeTargetsInDigest(), ReadCell::read(), DataElement::resize(), Gsolve::setCompartment(), ZombiePoolInterface::setCompartment(), Stoich::setCompartment(), Ksolve::setDsolve(), Gsolve::setDsolve(), Stoich::setDsolve(), Stoich::setKsolve(), Gsolve::setN(), Gsolve::setNinit(), HSolve::setSeed(), ZombieFunction::setSolver(), ZombieReac::setSolver(), ZombieMMenz::setSolver(), ZombieEnz::setSolver(), Neuron::setSpineAndPsdMesh(), Gsolve::setStoich(), SteadyState::setStoich(), Ksolve::setStoich(), Dsolve::setStoich(), EndoMesh::setSurround(), setTick(), ReadKkit::setupSlaveMsg(), SetGet::strGet(), SetGet::strSet(), HSolveUtils::targets(), Stoich::unZombifyModel(), Stoich::unZombifyPools(), Pool::vGetIsBuffered(), ZombiePool::vSetSolver(), ZombieCaConc::vSetSolver(), ZombieHHChannel::vSetSolver(), ZombieCompartment::vSetSolver(), DataElement::zombieSwap(), ZombieFunction::zombify(), CplxEnzBase::zombify(), ReacBase::zombify(), EnzBase::zombify(), CaConcBase::zombify(), PoolBase::zombify(), HHChannelBase::zombify(), moose::CompartmentBase::zombify(), Stoich::zombifyModel(), and DataElement::~DataElement().

 {
     return cinfo_;
 }

void Element::clearAllMsgs ( )

Used upon ending of MOOSE session, to rapidly clear out messages.

Used upon ending of MOOSE session, to rapidly clear out messages, secure in the knowledge that the data structures will be destroyed separately.

Definition at line 150 of file Element.cpp.

References m_, markAsDoomed(), msgBinding_, and msgDigest_.

 {
     markAsDoomed();
     m_.clear();
     msgBinding_.clear();
     msgDigest_.clear();
 }

Here is the call graph for this function:

void Element::clearBinding ( BindIndex b )

Clears out all Msgs on specified BindIndex. Used in Shell::set

Definition at line 136 of file Element.cpp.

References Msg::deleteMsg(), markRewired(), and msgBinding_.

 {
     assert( b < msgBinding_.size() );
     vector< MsgFuncBinding > temp = msgBinding_[ b ];
     msgBinding_[ b ].resize( 0 );
     for( vector< MsgFuncBinding >::iterator i = temp.begin();
             i != temp.end(); ++i )
     {
         Msg::deleteMsg( i->mid );
     }
     markRewired();
 }

Here is the call graph for this function:

virtual Element* Element::copyElement	(	Id	newParent,
		Id	newId,
		unsigned int	n,
		bool	toGlobal
	)		const

pure virtual

Copier

Implemented in GlobalDataElement, MsgElement, LocalDataElement, and FieldElement.

Referenced by innerCopyElements().

Here is the caller graph for this function:

virtual char* Element::data	(	unsigned int	rawIndex,
		unsigned int	fieldIndex = `0`
	)		const

pure virtual

Looks up specified field data entry. On regular objects just returns the data entry specified by the rawIndex. On FieldElements like synapses, does a second lookup on the field index. Note that the index is NOT a DataIndex: it is instead the raw index of the data on the current node. Index is also NOT the character offset, but the index to the data array in whatever type the data may be.

The DataIndex has to be filtered through the nodeMap to find a) if the entry is here, and b) what its raw index is.

Returns 0 if either index is out of range.

Implemented in MsgElement, DataElement, and FieldElement.

Referenced by buildFinfoElement(), Eref::data(), FieldElement::data(), DataElement::DataElement(), main(), Cinfo::makeCinfoElements(), FieldElement::numField(), FieldElement::resizeField(), testArith(), testCreateMsg(), testFibonacci(), testGet(), testSendMsg(), testSetGetSynapse(), and testSetGetVec().

Here is the caller graph for this function:

void Element::destroyElementTree ( const vector< Id > & tree )

static

Destroys all Elements in tree, being efficient about not trying to traverse through clearing messages to doomed Elements. Assumes tree includes all child elements. Typically the Neutral::destroy function builds up this tree and then calls this function.

Definition at line 676 of file Element.cpp.

References Id::destroy().

Referenced by Neutral::destroy().

 {
     for( vector< Id >::const_iterator i = tree.begin();
             i != tree.end(); i++ )
         i->element()->markAsDoomed(); // Indicate that Element is doomed
     bool killShell = false;
 
     // Do not destroy the shell till the very end.
     for( vector< Id >::const_iterator i = tree.begin();
             i != tree.end(); i++ )
     {
         if ( *i == Id() )
             killShell = true;
         else
             i->destroy();
     }
     if ( killShell )
         Id().destroy();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::digestMessages ( )

Rebuild digested message array; traverse all messages to do so

Definition at line 569 of file Element.cpp.

References findNumDigest(), msgBinding_, msgDigest_, name_, numData(), Shell::numNodes(), putFuncsInOrder(), putOffNodeTargetsInDigest(), and putTargetsInDigest().

Referenced by msgDigest().

 {
     bool report = 0; // for debugging
     msgDigest_.clear();
     msgDigest_.resize( msgBinding_.size() * numData() );
     vector< bool > temp( Shell::numNodes(), false );
     vector< vector< bool > > targetNodes( numData(), temp );
     // targetNodes[srcDataId][node]. The idea is that if any dataEntry has
     // a target off-node, it should flag the entry here so that it can
     // send the message request to the proxy on that node.
     for ( unsigned int i = 0; i < msgBinding_.size(); ++i )
     {
         // Go through and identify functions with the same ptr.
         vector< FuncOrder > fo = putFuncsInOrder( this, msgBinding_[i] );
         for ( vector< FuncOrder >::const_iterator
                 k = fo.begin(); k != fo.end(); ++k )
         {
             const MsgFuncBinding& mfb = msgBinding_[i][ k->index() ];
             putTargetsInDigest( i, mfb, *k, targetNodes );
         }
         if ( Shell::numNodes() > 1 )
         {
             if ( report )
             {
                 unsigned int numPre = findNumDigest( msgDigest_,
                                                      msgBinding_.size(), numData(), i );
                 putOffNodeTargetsInDigest( i, targetNodes );
                 unsigned int numPost = findNumDigest( msgDigest_,
                                                       msgBinding_.size(), numData(), i );
                 cout << "\nfor Element " << name_;
                 cout << ", Func: " << i << ", numFunc = " << fo.size() <<
                      ", numPre= " << numPre <<
                      ", numPost= " << numPost << endl;
                 for ( unsigned int j = 0; j < numData(); ++j )
                 {
                     cout << endl << j << "  ";
                     for ( unsigned int node = 0; node < Shell::numNodes(); ++node)
                     {
                         cout << (int)targetNodes[j][node];
                     }
                 }
                 cout << endl;
             }
             else
             {
                 putOffNodeTargetsInDigest( i, targetNodes );
             }
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::dropAllMsgsFromSrc ( Id src )

Drop all messages arriving from src onto current Element, regardless of which field they come from.

Definition at line 197 of file Element.cpp.

References Msg::deleteMsg(), Msg::e1(), Msg::e2(), Id::element(), Msg::getMsg(), and m_.

Referenced by setTick().

 {
     static Id clockId( 1 );
     const Element* clock = clockId.element();
     vector< ObjId > msgs;
     for ( vector< ObjId >::const_iterator i = m_.begin();
             i != m_.end(); ++i )
     {
         const Msg* m = Msg::getMsg( *i );
         const Element* src;
         if ( m->e1() == this )
         {
             src = m->e2();
         }
         else
         {
             src = m->e1();
         }
         if ( src == clock )
         {
             msgs.push_back( *i );
         }
     }
     sort( msgs.begin(), msgs.end() );
     // C++ detritus.
     msgs.erase( unique( msgs.begin(), msgs.end() ), msgs.end() );
     for( vector< ObjId >::iterator
             i = msgs.begin(); i != msgs.end(); ++i )
         Msg::deleteMsg( *i );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::dropMsg ( ObjId mid )

Removes the specified msg from the list.

Called from ~Msg. This requires the usual scan through all msgs, and could get inefficient.

Definition at line 113 of file Element.cpp.

References isDoomed(), m_, markRewired(), and msgBinding_.

Referenced by Msg::~Msg().

 {
     if ( isDoomed() ) // This is a flag that the Element is doomed.
         return;
     // Here we have the spectacularly ugly C++ erase-remove idiot.
     m_.erase( remove( m_.begin(), m_.end(), mid ), m_.end() );
 
     for ( vector< vector< MsgFuncBinding > >::iterator i = msgBinding_.begin(); i != msgBinding_.end(); ++i )
     {
         matchMid match( mid );
         i->erase( remove_if( i->begin(), i->end(), match ), i->end() );
     }
     markRewired();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int Element::findBinding ( MsgFuncBinding b ) const

Returns the binding index of the specified entry. Returns ~0 on failure.

Definition at line 374 of file Element.cpp.

References msgBinding_.

Referenced by findCaller(), getInputMsgs(), and getMsgSourceAndSender().

 {
     for ( unsigned int i = 0; i < msgBinding_.size(); ++i )
     {
         const vector< MsgFuncBinding >& mb = msgBinding_[i];
         vector< MsgFuncBinding>::const_iterator bi =
             find( mb.begin(), mb.end(), b );
         if ( bi != mb.end() )
             return i;
     }
     return ~0;
 }

Here is the caller graph for this function:

ObjId Element::findCaller ( FuncId fid ) const

Returns the first Msg that calls the specified Fid, on current Element. Returns 0 on failure.

Definition at line 350 of file Element.cpp.

References BADINDEX, Msg::e1(), Msg::e2(), findBinding(), Msg::getMsg(), and m_.

Referenced by HSolve::deleteIncomingMessages(), Shell::innerMove(), Neutral::isDescendant(), Neutral::parent(), Neutral::path(), and testAssortedMsg().

 {
     for ( vector< ObjId >::const_iterator i = m_.begin();
             i != m_.end(); ++i )
     {
         const Msg* m = Msg::getMsg( *i );
         const Element* src;
         if ( m->e1() == this )
         {
             src = m->e2();
         }
         else
         {
             src = m->e1();
         }
         unsigned int ret = src->findBinding( MsgFuncBinding( *i, fid ) );
         if ( ret != ~0U )
         {
             return *i;
         }
     }
     return ObjId( 0, BADINDEX );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int Element::getFieldsOfOutgoingMsg	(	ObjId	mid,
		vector< pair< BindIndex, FuncId > > &	ret
	)		const

Fills in vector, each entry of which identifies the src and dest fields respectively. Src field is local and identified by BindIndex Dest field is a FuncId on the remote Element.

Definition at line 1009 of file Element.cpp.

References msgBinding_.

Referenced by Msg::getDestFieldsOnE1(), Msg::getDestFieldsOnE2(), Msg::getSrcFieldsOnE1(), Msg::getSrcFieldsOnE2(), and testMsgSrcDestFields().

 {
     ret.resize( 0 );
     for ( unsigned int i = 0; i < msgBinding_.size(); ++i )
     {
         const vector< MsgFuncBinding >& mb = msgBinding_[i];
         for ( vector< MsgFuncBinding >::const_iterator j = mb.begin();
                 j != mb.end(); ++j )
         {
             if ( j->mid == mid )
             {
                 ret.push_back( pair< BindIndex, FuncId >( i, j->fid ));
             }
         }
     }
     return ret.size();
 }

Here is the caller graph for this function:

unsigned int Element::getInputMsgs	(	vector< ObjId > &	caller,
		FuncId	fid
	)		const

More general function. Fills up vector of ObjIds that call the specified Fid on current Element. Returns # found

Definition at line 984 of file Element.cpp.

References Msg::e1(), Msg::e2(), findBinding(), Msg::getMsg(), and m_.

Referenced by getInputs(), getInputsWithTgtIndex(), and insertSharedMsgs().

 {
     for ( vector< ObjId >::const_iterator i = m_.begin();
             i != m_.end(); ++i )
     {
         const Msg* m = Msg::getMsg( *i );
         const Element* src;
         if ( m->e1() == this )
         {
             src = m->e2();
         }
         else
         {
             src = m->e1();
         }
         unsigned int ret = src->findBinding( MsgFuncBinding( *i, fid ) );
         if ( ret != ~0U )
         {
             caller.push_back( *i );
         }
     }
     return caller.size();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int Element::getInputs	(	vector< Id > &	ret,
		const DestFinfo *	finfo
	)		const

private

Fills in vector of Ids sending messeges to this DestFinfo on this Element. Returns # found

Definition at line 887 of file Element.cpp.

References Msg::e1(), Msg::e2(), DestFinfo::getFid(), getInputMsgs(), Msg::getMsg(), and id().

Referenced by getNeighbors().

 {
     assert( finfo ); // would like to check that finfo is on src.
     unsigned int oldSize = ret.size();
 
     FuncId fid = finfo->getFid();
     vector< ObjId > caller;
     getInputMsgs( caller, fid );
     for ( vector< ObjId >::iterator i = caller.begin();
             i != caller.end(); ++i  )
     {
         const Msg* m = Msg::getMsg( *i );
         assert( m );
 
         Id id = m->e1()->id();
         if ( m->e1() == this )
             id = m->e2()->id();
         ret.push_back( id );
     }
     return ret.size() - oldSize;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int Element::getInputsWithTgtIndex	(	vector< pair< Id, unsigned int > > &	ret,
		const DestFinfo *	finfo
	)		const

Returns vectors of sources of messages to a field or data element. To go with each entry, also return the field or data index of target.

Returns vectors of sources of messages to a field or data element. To go with each entry, also return the field or data index of target. Needed to track which inputs go to with field index of current element. So if A–>x0, B–>x1, and C–>x2, it will return A, B, C, no matter in which order the messages were created. If there are multiple messages to x0, it will return the first.

Definition at line 918 of file Element.cpp.

References Eref::dataIndex(), Msg::e1(), Msg::e2(), Eref::fieldIndex(), Msg::firstTgt(), DestFinfo::getFid(), getInputMsgs(), Msg::getMsg(), hasFields(), and id().

 {
     assert( finfo ); // would like to check that finfo is on src.
     ret.clear();
 
     FuncId fid = finfo->getFid();
     vector< ObjId > caller;
     getInputMsgs( caller, fid );
     for ( vector< ObjId >::iterator i = caller.begin();
             i != caller.end(); ++i  )
     {
         const Msg* m = Msg::getMsg( *i );
         assert( m );
 
         if ( m->e1() == this )
         {
             Eref tgt = m->firstTgt( Eref( m->e2(), 0 ) );
             unsigned int idx = this->hasFields() ? tgt.fieldIndex(): tgt.dataIndex();
             ret.push_back( pair< Id, unsigned int >( m->e2()->id(), idx ) );
         }
         else if ( m->e2() == this )
         {
             Eref tgt = m->firstTgt( Eref( m->e1(), 0 ) );
             unsigned int idx = this->hasFields() ? tgt.fieldIndex(): tgt.dataIndex();
             ret.push_back( pair< Id, unsigned int >( m->e1()->id(), idx ) );
         }
     }
     return ret.size();
 }

Here is the call graph for this function:

const vector< MsgFuncBinding > * Element::getMsgAndFunc ( BindIndex b ) const

gets the Msg/Func binding information for specified bindIndex. This is a vector. Returns 0 on failure.

Definition at line 300 of file Element.cpp.

References msgBinding_.

Referenced by Neutral::child(), Neutral::children(), convertConcToNumRateUsingVol(), getMsgTargetAndFunctions(), EnzBase::getNumPrd(), ReacBase::getNumPrd(), EnzBase::getNumSub(), ReacBase::getNumSub(), Neutral::getOutgoingMsgs(), getOutputs(), getReactantVols(), and innerCopyMsgs().

 {
     if ( b < msgBinding_.size() )
         return &( msgBinding_[ b ] );
     return 0;
 }

Here is the caller graph for this function:

unsigned int Element::getMsgSourceAndSender	(	FuncId	fid,
		vector< ObjId > &	src,
		vector< string > &	sender
	)		const

Fills in matching vectors of destination ObjIds and the destination function, for the specified source Finfo and dataId on this Element. Used in Neutral::msgDests and Neutral::msgDestFunctions. Returns number of dests found.

Definition at line 828 of file Element.cpp.

References cinfo(), Msg::e1(), Msg::e2(), findBinding(), Msg::getMsg(), id(), m_, and Cinfo::srcFinfoName().

Referenced by testMsgSrcDestFields().

 {
     for ( vector< ObjId >::const_iterator i = m_.begin();
             i != m_.end(); ++i )
     {
         const Msg* m = Msg::getMsg( *i );
         const Element* src;
         if ( m->e1() == this )
         {
             src = m->e2();
         }
         else
         {
             src = m->e1();
         }
         unsigned int ret = src->findBinding( MsgFuncBinding( *i, fid ) );
         if ( ret != ~0U )
         {
             // problem here, to get dataId
             srcObj.push_back( ObjId( src->id(), 0 ) );
             sender.push_back( src->cinfo()->srcFinfoName( ret ) );
         }
     }
     return srcObj.size();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int Element::getMsgTargetAndFunctions	(	DataId	srcDataId,
		const SrcFinfo *	finfo,
		vector< ObjId > &	tgt,
		vector< string > &	func
	)		const

Fills in matching vectors of destination ObjIds and the destination function, for the specified source Finfo and dataId on this Element. Used in Neutral::msgDests and Neutral::msgDestFunctions. Returns number of dests found.

Definition at line 772 of file Element.cpp.

References cinfo(), Cinfo::destFinfoName(), Msg::e1(), Msg::e2(), SrcFinfo::getBindIndex(), Msg::getMsg(), getMsgAndFunc(), name, numData(), Msg::sources(), and Msg::targets().

Referenced by Stoich::allocateModelObject(), Neutral::getMsgDestFunctions(), Neutral::getMsgDests(), and testMsgSrcDestFields().

 {
     assert( finfo ); // would like to check that finfo is on this.
     assert( srcDataId < this->numData() );
 
     tgt.resize( 0 );
     func.resize( 0 );
 
     const vector< MsgFuncBinding >* msgVec =
         getMsgAndFunc( finfo->getBindIndex() );
     for ( unsigned int i = 0; i < msgVec->size(); ++i )
     {
         const Msg* m = Msg::getMsg( (*msgVec)[i].mid );
         assert( m );
         FuncId fid = (*msgVec)[i].fid;
         if ( m->e1() == this )   // regular direction message.
         {
             string name = m->e2()->cinfo()->destFinfoName( fid );
             vector< vector< Eref > > t;
             m->targets( t );
             assert( t.size() == this->numData() );
             vector< Eref >& row = t[srcDataId];
             for ( vector< Eref >::const_iterator
                     e = row.begin(); e != row.end(); ++e )
             {
                 tgt.push_back( e->objId() );
                 func.push_back( name );
             }
         }
         else if ( m->e2() == this )
         {
             string name = m->e1()->cinfo()->destFinfoName( fid );
             vector< vector< Eref > > t;
             m->sources( t );
             assert( t.size() == this->numData() );
             vector< Eref >& row = t[srcDataId];
             for ( vector< Eref >::const_iterator
                     e = row.begin(); e != row.end(); ++e )
             {
                 tgt.push_back( e->objId() );
                 func.push_back( name );
             }
         }
         else
         {
             assert( 0 );
         }
     }
     return tgt.size();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

vector< ObjId > Element::getMsgTargets	(	DataId	srcDataId,
		const SrcFinfo *	finfo
	)		const

Enumerates msg targets. Will get confused if some are across nodes.

Definition at line 856 of file Element.cpp.

References ALLDATA, SrcFinfo::getBindIndex(), Eref::msgDigest(), and numData().

Referenced by Adaptor::reinit(), and ChemCompt::setEntireVolume().

 {
     assert( finfo ); // would like to check that finfo is on this.
     assert( srcDataId < this->numData() );
 
     vector< ObjId > ret;
     Eref er( const_cast< Element* >( this ), srcDataId );
 
     const vector< MsgDigest >&md = er.msgDigest( finfo->getBindIndex() );
     for ( vector< MsgDigest >::const_iterator
             i = md.begin(); i != md.end(); ++i )
     {
         for ( vector< Eref >::const_iterator
                 j = i->targets.begin(); j != i->targets.end(); ++j )
         {
             if ( j->dataIndex() == ALLDATA )
             {
                 for ( unsigned int k = 0;
                         k < j->element()->numData(); ++k )
                     ret.push_back( ObjId( j->id(), k ) );
             }
             else
             {
                 ret.push_back( j->objId() );
             }
         }
     }
     return ret;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

const string & Element::getName ( ) const

Returns name of Element

Definition at line 56 of file Element.cpp.

References name_.

Referenced by ReadCell::addChannel(), SharedFinfo::addMsg(), Shell::adopt(), ReadCell::buildChannels(), buildFromProto(), checkChildren(), checkForSpine(), Neutral::child(), FieldElement::copyElement(), Shell::doAddMsg(), doClassSpecificMessaging(), Shell::doMove(), fillSegIndex(), NeuroNode::filterSpines(), NeuroMesh::filterSpines(), findModelParent(), Msg::getDestFieldsOnE1(), Msg::getDestFieldsOnE2(), Neutral::getName(), Msg::getSrcFieldsOnE1(), Msg::getSrcFieldsOnE2(), Shell::innerAddMsg(), Shell::innerMove(), isPartOfDend(), Dsolve::mapXfersBetweenDsolves(), operator<<(), Neutral::path(), FieldElementFinfoBase::postCreationFunc(), ReadCspace::printMol(), Arith::process(), showMsg(), SetGet::strGet(), SetGet::strSet(), testCopy(), testCopyFieldElement(), testMsgField(), testStrSet(), HHChannel2D::vReinit(), HHChannel::vReinit(), wildcardTestFunc(), and FieldElement::zombieSwap().

 {
     return name_;
 }

Here is the caller graph for this function:

unsigned int Element::getNeighbors	(	vector< Id > &	ret,
		const Finfo *	finfo
	)		const

Fills in vector of Ids connected to this Finfo on this Element. Returns # found

Definition at line 949 of file Element.cpp.

References SharedFinfo::dest(), getInputs(), getOutputs(), and SharedFinfo::src().

Referenced by ReadCell::buildCompartment(), findAllConnectedCompartments(), findFuncMsgSrc(), findMeshOfEnz(), findParentComptOfReac(), Neutral::getNeighbors(), isOffSolverReac(), moose::VClamp::reinit(), ZombieReac::setSolver(), ZombieMMenz::setSolver(), ZombieEnz::setSolver(), HSolveUtils::targets(), testShellAddMsg(), and testTwoReacGetNeighbors().

 {
     ret.resize( 0 );
     if ( !finfo )
         return 0;
 
     const SrcFinfo* srcF = dynamic_cast< const SrcFinfo* >( finfo );
     const DestFinfo* destF = dynamic_cast< const DestFinfo* >( finfo );
     const SharedFinfo* sharedF = dynamic_cast< const SharedFinfo* >( finfo );
     assert( srcF || destF || sharedF );
 
 
     if ( srcF )
         return getOutputs( ret, srcF );
     else if ( destF )
         return getInputs( ret, destF );
     else if ( ! sharedF->src().empty() )
         return getOutputs( ret, sharedF->src().front() );
     else if ( ! sharedF->dest().empty() )
     {
         Finfo* subFinfo = sharedF->dest().front();
         const DestFinfo* subDestFinfo =
             dynamic_cast< const DestFinfo* >( subFinfo );
         assert( subDestFinfo );
         return getInputs( ret, subDestFinfo );
     }
     else
     {
         assert( 0 );
     }
     return 0;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

virtual unsigned int Element::getNode ( unsigned int dataIndex ) const

pure virtual

Returns node number of specified dataIndex.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by HopFunc1< A >::dataOpVec(), FieldElement::getNode(), Eref::getNode(), and Eref::isDataHere().

Here is the caller graph for this function:

virtual unsigned int Element::getNumOnNode ( unsigned int node ) const

pure virtual

Returns number of data (or, if relevant, field) entries on specified node.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by HopFunc1< A >::dataOpVec(), and HopFunc2< A1, A2 >::opVec().

Here is the caller graph for this function:

unsigned int Element::getOutputs	(	vector< Id > &	ret,
		const SrcFinfo *	finfo
	)		const

private

Fills in vector of Ids receiving messages from this SrcFinfo. Returns # found

Definition at line 749 of file Element.cpp.

References Msg::e1(), Msg::e2(), SrcFinfo::getBindIndex(), Msg::getMsg(), getMsgAndFunc(), and id().

Referenced by getNeighbors().

 {
     assert( finfo ); // would like to check that finfo is on this.
     unsigned int oldSize = ret.size();
 
     const vector< MsgFuncBinding >* msgVec =
         getMsgAndFunc( finfo->getBindIndex() );
     if ( !msgVec )
         return 0;
     for ( unsigned int i = 0; i < msgVec->size(); ++i )
     {
         const Msg* m = Msg::getMsg( (*msgVec)[i].mid );
         assert( m );
         Id id = m->e2()->id();
         if ( m->e2() == this )
             id = m->e1()->id();
         ret.push_back( id );
     }
 
     return ret.size() - oldSize;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

int Element::getTick ( ) const

Returns Clock tick used by object. -1 means none. -2 means none for now because I am a zombie, but if I should be unzombified please put me back on my default clock tick.

Definition at line 186 of file Element.cpp.

References tick_.

Referenced by Streamer::addTable(), Neutral::getDt(), Neutral::getTick(), Table::reinit(), Streamer::reinit(), and Stoich::unZombifyModel().

 {
     return tick_;
 }

Here is the caller graph for this function:

virtual bool Element::hasFields ( ) const

pure virtual

True if this is a FieldElement having an array of fields on each data entry. Clearly not true for the base Element.

Implemented in MsgElement, DataElement, and FieldElement.

Referenced by Neutral::child(), Shell::doFind(), OneToOneMsg::firstTgt(), getInputsWithTgtIndex(), innerGetVec(), moose_ObjId_getLength(), GetHopFunc< A >::opGetVec(), HopFunc1< A >::opVec(), OpFunc1Base< ProcPtr >::opVecBuffer(), Neutral::path(), OneToOneMsg::sources(), and OneToOneMsg::targets().

Here is the caller graph for this function:

bool Element::hasMsgs ( BindIndex b ) const

Returns true if there are one or more Msgs on the specified BindIndex

Definition at line 307 of file Element.cpp.

References msgBinding_.

Referenced by Clock::buildTicks(), and NeuroMesh::transmitSpineInfo().

 {
     return ( b < msgBinding_.size() && msgBinding_[b].size() > 0 );
 }

Here is the caller graph for this function:

Id Element::id ( ) const

Returns the Id on this Elm

Definition at line 71 of file Element.cpp.

References id_.

Referenced by SharedFinfo::addMsg(), Stoich::allocateModelObject(), Neutral::buildTree(), Neutral::child(), HSolve::deleteIncomingMessages(), OneToOneDataIndexMsg::findOtherEnd(), OneToOneMsg::findOtherEnd(), DiagonalMsg::findOtherEnd(), Msg::getE1(), Msg::getE2(), getInputs(), getInputsWithTgtIndex(), getMsgSourceAndSender(), getOutputs(), Eref::id(), innerCopyElements(), innerCopyMsgs(), Neutral::isDescendant(), Eref::objId(), printGrid(), showFields(), CplxEnzBase::zombify(), ReacBase::zombify(), EnzBase::zombify(), and Stoich::zombifyModel().

 {
     return id_;
 }

Here is the caller graph for this function:

void Element::innerSetTick ( unsigned int tick )

Direct assignment of tick field, without doing any of the message manipulation

Definition at line 191 of file Element.cpp.

References tick_.

 {
     if ( tick < 32 )
         tick_ = tick;
 }

bool Element::isDoomed ( ) const

Definition at line 701 of file Element.cpp.

References isDoomed_.

Referenced by dropMsg(), and Stoich::unZombifyPools().

 {
     return isDoomed_;
 }

Here is the caller graph for this function:

virtual bool Element::isGlobal ( ) const

pure virtual

True if there is a copy of every dataEntry on all nodes.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by HopFunc1< A >::dataOpVec(), PostMaster::dispatchSetBuf(), filterOffNodeTargets(), FieldElement::getNumOnNode(), FieldElement::isGlobal(), GetHopFunc< A >::opGetVec(), HopFunc1< A >::opVec(), HopFunc2< A1, A2 >::opVec(), putTargetsInDigest(), PostMaster::remoteFieldGetVec(), PostMaster::remoteGet(), PostMaster::remoteGetVec(), and testCopyFieldElement().

Here is the caller graph for this function:

virtual unsigned int Element::localDataStart ( ) const

pure virtual

Returns index of first data entry on this node.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by GetHopFunc< A >::getLocalFieldVec(), GetHopFunc< A >::getLocalVec(), innerGetVec(), FieldElement::localDataStart(), HopFunc1< A >::localFieldOpVec(), HopFunc1< A >::localOpVec(), OpFunc1Base< ProcPtr >::opVecBuffer(), OpFunc2Base< A1, A2 >::opVecBuffer(), putTargetsInDigest(), SparseMsg::randomConnect(), SrcFinfo0::send(), SrcFinfo1< T >::send(), SrcFinfo2< T1, T2 >::send(), SrcFinfo3< T1, T2, T3 >::send(), SrcFinfo4< T1, T2, T3, T4 >::send(), SrcFinfo5< T1, T2, T3, T4, T5 >::send(), SrcFinfo6< T1, T2, T3, T4, T5, T6 >::send(), SrcFinfo1< T >::sendTo(), SrcFinfo2< T1, T2 >::sendTo(), SrcFinfo1< T >::sendVec(), OneToOneMsg::sources(), OneToOneMsg::targets(), SparseMsg::updateAfterFill(), ReacBase::zombify(), CplxEnzBase::zombify(), EnzBase::zombify(), CaConcBase::zombify(), PoolBase::zombify(), HHChannelBase::zombify(), and moose::CompartmentBase::zombify().

Here is the caller graph for this function:

void Element::markAsDoomed ( )

Set flag to state that Element is due for destruction. Useful to avoid following messages that will soon be gone.

Definition at line 696 of file Element.cpp.

References isDoomed_.

Referenced by clearAllMsgs(), and ~Element().

 {
     isDoomed_ = true;
 }

Here is the caller graph for this function:

void Element::markRewired ( )

Set flag to state that the messages on this Element have changed, and need to be re-digested.

Definition at line 706 of file Element.cpp.

References isRewired_.

Referenced by addMsg(), addMsgAndFunc(), clearBinding(), dropMsg(), SparseMsg::randomConnect(), OneToAllMsg::setI1(), SingleMsg::setI1(), SingleMsg::setI2(), DiagonalMsg::setStride(), SingleMsg::setTargetField(), SparseMsg::transpose(), and SparseMsg::updateAfterFill().

 {
     isRewired_ = true;
 }

Here is the caller graph for this function:

const vector< MsgDigest > & Element::msgDigest ( unsigned int index )

Raw lookup into MsgDigest vector. One for each MsgSrc X ObjEntry. If the messages have been rewired, this call triggers the re-parsing of all messages before returning the digested msgs.

Definition at line 289 of file Element.cpp.

References digestMessages(), isRewired_, and msgDigest_.

Referenced by Eref::msgDigest(), and testSendMsg().

 {
     if ( isRewired_ )
     {
         digestMessages();
         isRewired_ = false;
     }
     assert( index < msgDigest_.size() );
     return msgDigest_[ index ];
 }

Here is the call graph for this function:

Here is the caller graph for this function:

const vector< ObjId > & Element::msgIn ( ) const

Returns all incoming Msgs.

Definition at line 387 of file Element.cpp.

References m_.

Referenced by Neutral::getIncomingMsgs().

 {
     return m_;
 }

Here is the caller graph for this function:

virtual unsigned int Element::numData ( ) const

pure virtual

Returns number of data entries across all nodes.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by ObjId::bad(), SetGet::checkSet(), DataElement::DataElement(), digestMessages(), Shell::doFind(), fillErefsFromMatrix(), DiagonalMsg::findOtherEnd(), getMsgTargetAndFunctions(), getMsgTargets(), Neutral::getNumData(), innerCopyElements(), FieldElement::numData(), GetHopFunc< A >::opGetVec(), SparseMsg::pairFill(), printGrid(), printMsgDigest(), putOffNodeTargetsInDigest(), SparseMsg::randomConnect(), SrcFinfo0::send(), SrcFinfo2< T1, T2 >::send(), SrcFinfo3< T1, T2, T3 >::send(), SrcFinfo4< T1, T2, T3, T4 >::send(), SrcFinfo5< T1, T2, T3, T4, T5 >::send(), SrcFinfo6< T1, T2, T3, T4, T5, T6 >::send(), SrcFinfo2< T1, T2 >::sendTo(), OneToAllMsg::sources(), SingleMsg::sources(), OneToOneMsg::sources(), OneToOneDataIndexMsg::sources(), DiagonalMsg::sources(), SparseMsg::SparseMsg(), OneToAllMsg::targets(), SingleMsg::targets(), OneToOneDataIndexMsg::targets(), OneToOneMsg::targets(), DiagonalMsg::targets(), testCellDiffn(), testCopyFieldElement(), testCylDiffnWithStoich(), testSetGetSynapse(), testSmallCellDiffn(), and testTaperingCylDiffn().

Here is the caller graph for this function:

virtual unsigned int Element::numField ( unsigned int rawIndex ) const

pure virtual

Returns number of field entries for specified data.

Implemented in MsgElement, DataElement, and FieldElement.

Referenced by GetHopFunc< A >::getLocalFieldVec(), Neutral::getNumField(), innerGetVec(), HopFunc1< A >::localFieldOpVec(), HopFunc1< A >::localOpVec(), HopFunc2< A1, A2 >::opVec(), OpFunc1Base< ProcPtr >::opVecBuffer(), OpFunc2Base< A1, A2 >::opVecBuffer(), OneToOneMsg::sources(), OneToOneMsg::targets(), testCopyFieldElement(), and testSyncSynapseSize().

Here is the caller graph for this function:

virtual unsigned int Element::numLocalData ( ) const

pure virtual

Returns number of local data entries on this node.

Implemented in MsgElement, DataElement, and FieldElement.

Referenced by GetHopFunc< A >::getLocalVec(), innerGetVec(), HopFunc1< A >::localOpVec(), FieldElement::numLocalData(), HopFunc2< A1, A2 >::opVec(), OpFunc1Base< ProcPtr >::opVecBuffer(), OpFunc2Base< A1, A2 >::opVecBuffer(), putTargetsInDigest(), SparseMsg::randomConnect(), SrcFinfo1< T >::send(), SrcFinfo1< T >::sendTo(), SrcFinfo1< T >::sendVec(), OneToOneMsg::targets(), SparseMsg::updateAfterFill(), ZombieFunction::zombify(), CplxEnzBase::zombify(), ReacBase::zombify(), EnzBase::zombify(), CaConcBase::zombify(), PoolBase::zombify(), HHChannelBase::zombify(), and moose::CompartmentBase::zombify().

Here is the caller graph for this function:

void Element::printMsgDigest	(	unsigned int	srcIndex,
		unsigned int	dataIndex
	)		const

Utility function for debugging

Definition at line 711 of file Element.cpp.

References msgBinding_, msgDigest_, and numData().

 {
     unsigned int numSrcMsgs = msgBinding_.size();
     unsigned int start = 0;
     unsigned int end = numData();
     if ( dataId < numData() )
     {
         start = dataId;
         end = dataId + 1;
     }
     for (unsigned int i = start; i < end; ++i )
     {
         cout << i << ": ";
         const vector< MsgDigest> & md =
             msgDigest_[numSrcMsgs * i + srcIndex];
         for ( unsigned int j = 0; j < md.size(); ++j )
         {
             cout << j << ": ";
             for ( unsigned int k = 0; k < md[j].targets.size(); ++k )
             {
                 cout << "   " <<
                      md[j].targets[k].dataIndex() << "," <<
                      md[j].targets[k].fieldIndex();
             }
         }
         cout << endl;
     }
 }

Here is the call graph for this function:

void Element::putOffNodeTargetsInDigest	(	unsigned int	srcNum,
		vector< vector< bool > > &	targetNodes
	)

Inner function that adds off-node targets to the MsgDigest

Definition at line 517 of file Element.cpp.

References cinfo(), Msg::e1(), Msg::e2(), MsgFuncBinding::fid, Msg::getMsg(), Cinfo::getOpFunc(), OpFunc::makeHopFunc(), MsgFuncBinding::mid, msgBinding_, msgDigest_, numData(), and Shell::numNodes().

Referenced by digestMessages().

 {
     if ( msgBinding_[ srcNum ].size() == 0 )
         return;
     const MsgFuncBinding& mfb = msgBinding_[ srcNum ][0];
     const Msg* msg = Msg::getMsg( mfb.mid );
     const OpFunc* func;
     if ( msg->e1() == this )
     {
         func = msg->e2()->cinfo()->getOpFunc( mfb.fid );
     }
     else
     {
         func = msg->e1()->cinfo()->getOpFunc( mfb.fid );
     }
     assert( func );
     // How do I eventually destroy these?
     const OpFunc* hop = func->makeHopFunc( srcNum );
     for ( unsigned int i = 0; i < numData(); ++i )
     {
         vector< Eref > tgts;
         for ( unsigned int j = 0; j < Shell::numNodes(); ++j )
         {
             if ( targetNodes[i][j] )
                 tgts.push_back( Eref( this, i, j ) );
             // This is a hack. I encode the target node # in the FieldIndex
             // and the originating Eref in the remainder of the Eref.
             // The HopFunc has to extract both these things to push into
             // the correct SendBuffer.
         }
         if ( tgts.size() > 0 )
         {
             vector< MsgDigest >& md =
                 msgDigest_[ msgBinding_.size() * i + srcNum ];
             md.push_back( MsgDigest( hop, tgts ) );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::putTargetsInDigest	(	unsigned int	srcNum,
		const MsgFuncBinding &	mfb,
		const FuncOrder &	fo,
		vector< vector< bool > > &	targetNodes
	)

Inner function that adds targets to a single function in the MsgDigest

Definition at line 466 of file Element.cpp.

References Msg::e1(), Msg::e2(), filterOffNodeTargets(), FuncOrder::func(), Msg::getMsg(), isGlobal(), localDataStart(), MsgFuncBinding::mid, msgBinding_, msgDigest_, Shell::myNode(), numLocalData(), Shell::numNodes(), Msg::sources(), and Msg::targets().

Referenced by digestMessages().

 {
     const Msg* msg = Msg::getMsg( mfb.mid );
     vector< vector < Eref > > erefs;
     if ( msg->e1() == this )
         msg->targets( erefs );
     else if ( msg->e2() == this )
         msg->sources( erefs );
     else
         assert( 0 );
 
     if ( Shell::numNodes() > 1 )
         filterOffNodeTargets(
             localDataStart(),
             localDataStart() + numLocalData(),
             isGlobal(), Shell::myNode(),
             erefs, targetNodes );
 
     for ( unsigned int j = 0; j < erefs.size(); ++j )
     {
         vector< MsgDigest >& md =
             msgDigest_[ msgBinding_.size() * j + srcNum ];
         // k->func(); erefs[ j ];
         if ( md.size() == 0 || md.back().func != fo.func() )
         {
             md.push_back( MsgDigest( fo.func(), erefs[j] ) );
             /*
             if ( md.back().targets.size() > 0 )
                 cout << "putTargetsInDigest: " << md.back().targets[0] <<
                     ", eref = " << erefs[j][0] << endl;
             else
                 cout << "putTargetsInDigest: empty\n";
             */
         }
         else
         {
             md.back().targets.insert( md.back().targets.end(),
                                       erefs[ j ].begin(),
                                       erefs[ j ].end() );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

virtual unsigned int Element::rawIndex ( unsigned int dataIndex ) const

pure virtual

Converts dataIndex to index on current node. No error check.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by Eref::data(), Neutral::getNumField(), FieldElement::rawIndex(), and Neutral::setNumField().

Here is the caller graph for this function:

void Element::replaceCinfo ( const Cinfo * newCinfo )

Support function for zombieSwap, replaces Cinfo.

Definition at line 740 of file Element.cpp.

References cinfo_.

Referenced by Pool::vSetIsBuffered(), FieldElement::zombieSwap(), DataElement::zombieSwap(), and MsgElement::zombieSwap().

 {
     cinfo_ = newCinfo;
     // Stuff to be done for data is handled by derived classes in ZombeSwap.
 }

Here is the caller graph for this function:

virtual void Element::resize ( unsigned int newNumData )

pure virtual

Changes the number of entries in the data. Not permitted for FieldElements since they are just fields on the data.

Implemented in MsgElement, DataElement, FieldElement, and LocalDataElement.

Referenced by LookupField< L, A >::getVec(), Neutral::setNumData(), and Stoich::zombifyModel().

Here is the caller graph for this function:

virtual void Element::resizeField	(	unsigned int	rawIndex,
		unsigned int	newNumField
	)

pure virtual

Changes the number of fields on the specified data entry. Doesn't do anything for the regular Element.

Implemented in MsgElement, DataElement, and FieldElement.

Referenced by SparseMsg::randomConnect(), Neutral::setNumField(), and SparseMsg::updateAfterFill().

Here is the caller graph for this function:

void Element::setName ( const string & val )

Changes name of Element

Definition at line 61 of file Element.cpp.

References name_.

Referenced by Neutral::setName(), testGet(), and testStrGet().

 {
     name_ = val;
 }

Here is the caller graph for this function:

void Element::setTick ( int t )

Assigns clock tick to be used by object. -1 means none. This function does substantial message manipulation to set up the message from the Clock object to the current object to define the Tick. Furthermore, if the object has both init and proc methods, it will set them both up, with the init method on 't-1' and the proc method on 't'

Definition at line 251 of file Element.cpp.

References addClockMsg(), cinfo(), cinfo_, dropAllMsgsFromSrc(), Cinfo::findFinfo(), Cinfo::name(), and tick_.

Referenced by innerCopyElements(), Shell::innerCreate(), Stoich::installAndUnschedFunc(), Stoich::installAndUnschedFuncRate(), Stoich::installAndUnschedFuncReac(), Streamer::reinit(), Neutral::setTick(), Stoich::unZombifyModel(), and zombieSwap().

 {
     Id clockId( 1 );
     if ( t == tick_ )
         return;
     if ( tick_ >= 0 )   // Drop all messages coming here from clock.
     {
         dropAllMsgsFromSrc( clockId );
     }
     tick_ = t;
     if ( t < 0 || t > 31 )    // Only 32 ticks available.
     {
         // Don't need to add new ticks.
         return;
     }
     const Finfo* f2 = cinfo()->findFinfo( "init" );
     if ( f2 && dynamic_cast< const SharedFinfo* >( f2 ) )
     {
         // Must build init msg too. This comes on the previous tick.
         assert( t > 0 );
         addClockMsg( t-1, id(), f2 );
     }
     f2 = cinfo()->findFinfo( "proc" );
     if ( f2 )
     {
         addClockMsg( t, id(), f2 );
     }
     else
     {
         cout << "Element::setTick:Warning: Attempt to assign a tick to a '"
              << cinfo_->name() << "'.\nThis does not support process actions.\n";
         tick_ = -1;
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Element::showFields ( ) const

Utility function for printing out all fields and their values

Definition at line 623 of file Element.cpp.

References cinfo_, Id::eref(), Cinfo::finfoMap(), id(), and name.

 {
     vector< const SrcFinfo* > srcVec;
     vector< const DestFinfo* > destVec;
     vector< const SharedFinfo* > sharedVec;
     vector< const Finfo* > valueVec; // ValueFinfos are what is left.
     for ( map< string, Finfo* >::const_iterator i =
                 cinfo_->finfoMap().begin();
             i != cinfo_->finfoMap().end(); ++i )
     {
         const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( i->second);
         const DestFinfo* df = dynamic_cast< const DestFinfo* >( i->second);
         const SharedFinfo* shf = dynamic_cast< const SharedFinfo* >( i->second);
         if ( sf )
             srcVec.push_back( sf );
         else if ( df )
             destVec.push_back( df );
         else if ( shf )
             sharedVec.push_back( shf );
         else
             valueVec.push_back( i->second );
     }
 
     cout << "Showing SrcFinfos: \n";
     for ( unsigned int i = 0; i < srcVec.size(); ++i )
         cout << i << ": " << srcVec[i]->name() << " Bind=" << srcVec[i]->getBindIndex() << endl;
     cout << "Showing " << destVec.size() << " DestFinfos: \n";
     /*
     for ( unsigned int i = 0; i < destVec.size(); ++i )
         cout << i << ": " << destVec[i]->name() << "    FuncId=" << destVec[i]->getFid() << endl;
         */
     cout << "Showing SharedFinfos: \n";
     for ( unsigned int i = 0; i < sharedVec.size(); ++i )
     {
         cout << i << ": " << sharedVec[i]->name() << "  Src=[ ";
         for ( unsigned int j = 0; j < sharedVec[i]->src().size(); ++j )
             cout << " " << sharedVec[i]->src()[j]->name();
         cout << " ] Dest=[ ";
         for ( unsigned int j = 0; j < sharedVec[i]->dest().size(); ++j )
             cout << " " << sharedVec[i]->dest()[j]->name();
         cout << " ]\n";
     }
     cout << "Listing ValueFinfos: \n";
     Eref er = this->id().eref();
     string val;
     for ( unsigned int i = 0; i < valueVec.size(); ++i )
     {
         valueVec[i]->strGet( er, valueVec[i]->name(), val );
         cout << i << ": " << valueVec[i]->name() << "   " <<
              val << endl;
     }
 }

Here is the call graph for this function:

void Element::showMsg ( ) const

Utility function for traversing and displaying all messages

Definition at line 313 of file Element.cpp.

References cinfo_, Msg::e1(), Msg::e2(), Cinfo::finfoMap(), SrcFinfo::getBindIndex(), Msg::getMsg(), getName(), m_, msgBinding_, Finfo::name(), and name_.

 {
     cout << "Outgoing: \n";
     for ( map< string, Finfo* >::const_iterator i =
                 cinfo_->finfoMap().begin();
             i != cinfo_->finfoMap().end(); ++i )
     {
         const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( i->second );
         if ( sf && msgBinding_.size() > sf->getBindIndex() )
         {
             const vector< MsgFuncBinding >& mb = msgBinding_[ sf->getBindIndex()];
             unsigned int numTgt = mb.size();
             if ( numTgt > 0 )
             {
                 for ( unsigned int j = 0; j < numTgt; ++j )
                 {
                     cout << sf->name() << " bindId=" << sf->getBindIndex() << ": ";
                     cout << j << ": MessageId=" << mb[j].mid <<
                          ", FuncId=" << mb[j].fid <<
                          ", " << Msg::getMsg( mb[j].mid )->e1()->getName() <<
                          " -> " <<
                          Msg::getMsg( mb[j].mid )->e2()->getName() << endl;
                 }
             }
         }
     }
     cout << "Dest and Src: \n";
     for ( unsigned int i = 0; i < m_.size(); ++i )
     {
         const Msg* m = Msg::getMsg( m_[i] );
         cout << i << ": MessageId= " << m_[i] <<
              ", e1= " << m->e1()->name_ <<
              ", e2= " << m->e2()->name_ << endl;
     }
 }

Here is the call graph for this function:

virtual unsigned int Element::startDataIndex ( unsigned int nodeNum ) const

pure virtual

Returns start dataIndex on specified node.

Implemented in MsgElement, GlobalDataElement, LocalDataElement, and FieldElement.

Referenced by HopFunc1< A >::dataOpVec(), and FieldElement::startDataIndex().

Here is the caller graph for this function:

virtual unsigned int Element::totNumLocalField ( ) const

pure virtual

Returns number of field entries on local node. If this is not a FieldElement, returns numLocalData, assuming 1 field per data.

Implemented in MsgElement, DataElement, and FieldElement.

void Element::zombieSwap ( const Cinfo * zCinfo )

virtual

virtual func, this base version must be called by all derived classes

zombieSwap: replaces the Cinfo and data of the zombie. Allocates a new data block using zCinfo, that matches the number of entries of the old data block. Deletes old data. The base version calls the Clock object to assign a suitable default clock.

Reimplemented in MsgElement, DataElement, and FieldElement.

Definition at line 159 of file Element.cpp.

References Clock::lookupDefaultTick(), Cinfo::name(), setTick(), and tick_.

Referenced by ReadKkit::buildSumTotal(), ReadKkit::setupSlaveMsg(), DataElement::zombieSwap(), MsgElement::zombieSwap(), ZombieFunction::zombify(), ReacBase::zombify(), CplxEnzBase::zombify(), EnzBase::zombify(), CaConcBase::zombify(), PoolBase::zombify(), HHChannelBase::zombify(), and moose::CompartmentBase::zombify().

 {
     // cout << name_ << ", cname=" << c->name() << ", t0 = " << this->tick_ << ", t1 = " << Clock::lookupDefaultTick( c->name() ) << endl;
     if ( tick_ == -1 )   // Object is already disabled, let it be.
     {
         return;
     }
     bool zombieInName = ( c->name().substr(0, 6) == "Zombie" );
     if ( tick_ == -2 && !zombieInName )   // Object was a zombie and wants to come home.
     {
         int t = Clock::lookupDefaultTick( c->name() );
         setTick( t );
     }
     else if ( tick_ >= 0 )     // disable clock, with option to return
     {
         if ( zombieInName )
         {
             setTick( -2 );
         }
         else
         {
             int t = Clock::lookupDefaultTick( c->name() );
             setTick( t );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

const Cinfo* Element::cinfo_

private

Stores the unique identifier for Element.

Class information

Definition at line 406 of file Element.h.

Referenced by cinfo(), replaceCinfo(), setTick(), showFields(), and showMsg().

Id Element::id_

private

Name of the Element.

Definition at line 401 of file Element.h.

Referenced by id(), and ~Element().

bool Element::isDoomed_

private

True if the element is marked for destruction.

Definition at line 446 of file Element.h.

Referenced by isDoomed(), and markAsDoomed().

bool Element::isRewired_

private

True if messages have been changed and need to digestMessages.

Definition at line 443 of file Element.h.

Referenced by markRewired(), and msgDigest().

vector< ObjId > Element::m_

private

Message vector. This is the low-level messaging information. Contains info about incoming as well as outgoing Msgs.

Definition at line 412 of file Element.h.

Referenced by addMsg(), clearAllMsgs(), dropAllMsgsFromSrc(), dropMsg(), findCaller(), getInputMsgs(), getMsgSourceAndSender(), msgIn(), showMsg(), and ~Element().

vector< vector < MsgFuncBinding > > Element::msgBinding_

private

Binds an outgoing message to its function. Each index (BindIndex) gives a vector of MsgFuncBindings, which are just pairs of ObjId, FuncId. SrcFinfo keeps track of the BindIndex to look things up. Note that a single BindIndex may refer to multiple Msg/Func pairs. This means that a single MsgSrc may dispatch data through multiple msgs using a single 'send' call.

Definition at line 423 of file Element.h.

Referenced by addMsgAndFunc(), clearAllMsgs(), clearBinding(), digestMessages(), dropMsg(), findBinding(), getFieldsOfOutgoingMsg(), getMsgAndFunc(), hasMsgs(), printMsgDigest(), putOffNodeTargetsInDigest(), putTargetsInDigest(), showMsg(), and ~Element().

vector< vector < MsgDigest > > Element::msgDigest_

private

Digested vector of message traversal sets. Each set has a Func and element to lead off, followed by a list of target indices and fields. The indexing is like this: msgDigest_[ numSrcMsgs * dataIndex + srcMsgIndex ][ func# ] So we look up a vector of MsgDigests, each with a unique func, based on both the dataIndex and the message number. This is designed so that if we expand the number of data entries we don't have to redo the ordering.

Definition at line 437 of file Element.h.

Referenced by clearAllMsgs(), digestMessages(), msgDigest(), printMsgDigest(), putOffNodeTargetsInDigest(), and putTargetsInDigest().

string Element::name_

private

Definition at line 399 of file Element.h.

Referenced by digestMessages(), getName(), setName(), and showMsg().

int Element::tick_

private

Returns tick on which element is scheduled. -1 for disabled.

Definition at line 440 of file Element.h.

Referenced by getTick(), innerSetTick(), setTick(), and zombieSwap().

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

moose-core/basecode/Element.h
moose-core/basecode/Element.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation