Id ReadCell::addChannel(
Id compt,
Id proto,
double value,
double dia,
double length )
{
Id copy = shell_->doCopy(
proto,
compt,
"", // newName: same as old name.
1, // n: number of copies
false, // toGlobal
false // copyExtMsgs
);
/////////////////////////////
assert( copy.element()->getName() == proto.element()->getName() );
/////////////////////////////
assert( copy != Id() );
if ( addCanonicalChannel( compt, copy, value, dia, length ) ) return copy;
if ( addSpikeGen( compt, copy, value, dia, length ) ) return copy;
if ( addCaConc( compt, copy, value, dia, length ) ) return copy;
if ( addNernst( compt, copy, value ) ) return copy;
return Id();
}
void ZombiePool::vSetSolver( Id ksolve, Id dsolve )
{
// Nasty unsafe typecast. I would have preferred to pass in a
// safely typed pointer but that would have exposed a low-level
// class for the ZombiePoolInterface.
if ( ksolve.element()->cinfo()->isA( "Ksolve" ) ||
ksolve.element()->cinfo()->isA( "Gsolve" ) ) {
ksolve_= reinterpret_cast< ZombiePoolInterface *>(
ObjId( ksolve, 0 ).data() );
} else if ( ksolve == Id() ) {
ksolve_ = 0;
} else {
cout << "Warning:ZombiePool::vSetSolver: solver class " <<
ksolve.element()->cinfo()->name() <<
" not known.\nShould be Ksolve or Gsolve\n";
ksolve_ = 0;
}
if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_= reinterpret_cast< ZombiePoolInterface *>(
ObjId( dsolve, 0 ).data() );
} else if ( dsolve == Id() ) {
dsolve_ = 0;
} else {
cout << "Warning:ZombiePool::vSetSolver: solver class " <<
dsolve.element()->cinfo()->name() <<
" not known.\nShould be Dsolve\n";
dsolve_ = 0;
}
}
void RefactoringApplier::changeElementInModel(const Id &changeFromId, const Id &changeToId)
{
if (mLogicalModelApi.isLogicalId(changeFromId)) {
return;
}
if (!refactoringElements.contains(changeToId.element())) {
IdList const inLinks = mGraphicalModelApi.mutableGraphicalRepoApi().incomingLinks(changeFromId);
IdList const outLinks = mGraphicalModelApi.mutableGraphicalRepoApi().outgoingLinks(changeFromId);
Id const parentId = mGraphicalModelApi.mutableGraphicalRepoApi().parent(changeFromId);
QVariant const position = mGraphicalModelApi.mutableGraphicalRepoApi().position(changeFromId);
bool const isFromLogicalModel = false;
QString const refactoringsMetamodel = "RefactoringsMetamodel";
QString newEditor = changeToId.editor();
newEditor.chop(refactoringsMetamodel.length());
Id const newId = Id(newEditor, changeToId.diagram(), changeToId.element(), QUuid::createUuid().toString());
Id const newElementId = mGraphicalModelApi.createElement(parentId, newId
, isFromLogicalModel, "ololo", position.toPointF());
for (Id idLink : inLinks) {
mGraphicalModelApi.mutableGraphicalRepoApi().setTo(idLink, newElementId);
}
for (Id idLink : outLinks) {
mGraphicalModelApi.mutableGraphicalRepoApi().setFrom(idLink, newElementId);
}
mGraphicalModelApi.mutableGraphicalRepoApi().removeChild(parentId, changeFromId);
mGraphicalModelApi.mutableGraphicalRepoApi().removeElement(changeFromId);
}
}
void RefactoringApplier::changeElement(Id const &changeFromId, Id const &changeToId)
{
Id const beforeId = beforeIdInRule(changeToId);
if (isElementTypesInRuleIdentical(beforeId, changeToId)) {
if (changeToId.element() == "Element") {
if (mRefactoringRepoApi->name(changeToId) == "(Element)") {
return;
}
changeElementName(changeFromId, changeToId);
}
else if (changeToId.element() == "Link") {
if (mRefactoringRepoApi->name(changeToId) != "(Link)") {
changeElementName(changeFromId, changeToId);
}
checkDirection(changeFromId, changeToId, beforeId);
}
else {
changePropertiesInModel(changeFromId, changeToId);
if (!isNodeInRule(beforeId) && !isNodeInRule(changeToId)) {
checkDirection(changeFromId, changeToId, beforeId);
}
}
}
else {
changeElementInModel(changeFromId, changeToId);
}
}
void ZombieFunction::setSolver( Id ksolve, Id dsolve )
{
if ( ksolve.element()->cinfo()->isA( "Ksolve" ) ||
ksolve.element()->cinfo()->isA( "Gsolve" ) ) {
Id sid = Field< Id >::get( ksolve, "stoich" );
_stoich = ObjId( sid, 0 ).data();
if ( _stoich == 0 )
cout << "Warning:ZombieFunction::setSolver: Empty Stoich on Ksolve" << ksolve.path() << endl;
} else if ( ksolve == Id() ) {
_stoich = 0;
} else {
cout << "Warning:ZombieFunction::setSolver: solver class " <<
ksolve.element()->cinfo()->name() <<
" not known.\nShould be Ksolve or Gsolve\n";
_stoich = 0;
}
/*
if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_= ObjId( dsolve, 0 ).data();
} else if ( dsolve == Id() ) {
dsolve_ = 0;
} else {
cout << "Warning:ZombieFunction::vSetSolver: solver class " <<
dsolve.element()->cinfo()->name() <<
" not known.\nShould be Dsolve\n";
dsolve_ = 0;
}
*/
}
void ZombieMMenz::setSolver( Id solver, Id orig )
{
static const DestFinfo* enz = dynamic_cast< const DestFinfo* >(
EnzBase::initCinfo()->findFinfo( "enzDest" ) );
static const SrcFinfo* sub = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toSub" ) );
static const SrcFinfo* prd = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toPrd" ) );
assert( enz );
assert( sub );
assert( prd );
stoich_ = reinterpret_cast< Stoich* >( solver.eref().data() );
/// Now set up the RateTerm
vector< Id > subvec;
vector< Id > prdvec;
unsigned int rateIndex = stoich_->convertIdToReacIndex( orig );
unsigned int num = orig.element()->getNeighbours( subvec, enz );
unsigned int enzIndex = stoich_->convertIdToPoolIndex( subvec[0] );
MMEnzymeBase* meb;
double numKm = 1.0; // Dummy default initial values, later to be reset
double kcat = 1.0;
/*
double numKm = base->zGetNumKm( orig.eref(), 0 );
double kcat = base->zGetKcat( orig.eref(), 0 );
*/
num = orig.element()->getNeighbours( subvec, sub );
if ( num == 1 ) {
unsigned int subIndex = stoich_->convertIdToPoolIndex( subvec[0] );
meb = new MMEnzyme1( numKm, kcat, enzIndex, subIndex );
} else if ( num > 1 ) {
vector< unsigned int > v;
for ( unsigned int i = 0; i < num; ++i )
v.push_back( stoich_->convertIdToPoolIndex( subvec[i] ) );
ZeroOrder* rateTerm = new NOrder( 1.0, v );
meb = new MMEnzyme( numKm, kcat, enzIndex, rateTerm );
} else {
cout << "Error: ZombieMMenz::zombify: No substrates for " <<
orig.path() << endl;
cout << "Will ignore and continue, but don't be surprised if "
"simulation fails.\n";
// assert( 0 );
return;
}
num = orig.element()->getNeighbours( prdvec, prd );
stoich_->installMMenz( meb, rateIndex, subvec, prdvec );
}
void Gsolve::setDsolve( Id dsolve )
{
if ( dsolve == Id () ) {
dsolvePtr_ = 0;
dsolve_ = Id();
} else if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_ = dsolve;
dsolvePtr_ = reinterpret_cast< ZombiePoolInterface* >(
dsolve.eref().data() );
} else {
cout << "Warning: Gsolve::setDsolve: Object '" << dsolve.path() <<
"' should be class Dsolve, is: " <<
dsolve.element()->cinfo()->name() << endl;
}
}
bool Shell::isRunning() const
{
static Id clockId( 1 );
assert( clockId.element() != 0 );
return ( reinterpret_cast< const Clock* >( clockId.eref().data() ) )->isRunning();
}
void Shell::doMove( Id orig, ObjId newParent )
{
if ( orig == Id() ) {
cout << "Error: Shell::doMove: Cannot move root Element\n";
return;
}
if ( newParent.element() == 0 ) {
cout << "Error: Shell::doMove: Cannot move object to null parent \n";
return;
}
if ( Neutral::isDescendant( newParent, orig ) ) {
cout << "Error: Shell::doMove: Cannot move object to descendant in tree\n";
return;
}
const string& name = orig.element()->getName();
if ( Neutral::child( newParent.eref(), name ) != Id() ) {
stringstream ss;
ss << "Shell::doMove: Object with same name already present: '"
<< newParent.path() << "/" << name << "'. Move failed.";
warning( ss.str() );
return;
}
SetGet2< Id, ObjId >::set( ObjId(), "move", orig, newParent );
// innerMove( orig, newParent );
}
void Element::dropAllMsgsFromSrc( Id src )
{
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 );
}
void Exploser::refreshPalette(gui::PaletteTreeWidget * const tree, Id const &diagram)
{
QMap<QString, QList<gui::PaletteElement> > groups;
QMap<QString, QString> descriptions;
descriptions[mUserGroupTitle] = mUserGroupDescription;
IdList const childTypes = mApi.editorManagerInterface().elements(diagram);
foreach (Id const &child, childTypes) {
QList<Explosion> const explosions = mApi.editorManagerInterface().explosions(child);
foreach (Explosion const &explosion, explosions) {
if (!explosion.isReusable()) {
continue;
}
Id const target = explosion.target();
IdList const allTargets = mApi.logicalRepoApi().elementsByType(target.element(), true);
foreach (Id const &targetInstance, allTargets) {
if (mApi.isLogicalId(targetInstance) &&
!mApi.logicalRepoApi().incomingExplosions(targetInstance).isEmpty())
{
groups[mUserGroupTitle] << gui::PaletteElement(child
, mApi.logicalRepoApi().name(targetInstance)
, QString(), mApi.editorManagerInterface().icon(child)
, mApi.editorManagerInterface().iconSize(child)
, targetInstance);
}
}
}
}
bool ReadCell::addSpikeGen(
Id compt,
Id chan,
double value,
double dia,
double length )
{
string className = chan.element()->cinfo()->name();
if ( className == "SpikeGen" ) {
shell_->doAddMsg(
"Single",
compt,
"VmSrc",
chan,
"Vm"
);
if ( !graftFlag_ )
++numOthers_;
return Field< double >::set( chan, "threshold", value );
}
return 0;
}
/// Returns the Id of the loaded model.
Id Shell::doLoadModel( const string& fileName, const string& modelPath, const string& solverClass )
{
ifstream fin( fileName.c_str() );
if ( !fin )
{
LOG( moose::failed, "Shell::doLoadModel: could not open file " << fileName );
return Id();
}
string modelName;
Id parentId;
if ( !( findModelParent ( cwe_, modelPath, parentId, modelName ) ) )
return Id();
string line;
switch ( findModelType( fileName, fin, line ) )
{
case DOTP:
{
ReadCell rc;
return rc.read( fileName, modelName, parentId );
return Id();
}
case SWC:
{
LOG( moose::info, "In doLoadModel for SWC" );
ReadSwc rs( fileName );
Id model = parentId;
if ( !parentId.element()->cinfo()->isA( "Neuron" ) )
{
model = doCreate( "Neuron", parentId, modelName, 1 );
}
rs.build( model, 0.5e-3, 1.0, 1.0, 0.01 );
return model;
}
case KKIT:
{
string sc = solverClass;
ReadKkit rk;
Id ret = rk.read( fileName, modelName, parentId, sc);
return ret;
}
break;
case CSPACE:
{
string sc = solverClass;
ReadCspace rc;
Id ret = rc.readModelString( line, modelName, parentId, sc);
rc.makePlots( 1.0 );
return ret;
}
case UNKNOWN:
default:
cout << "Error: Shell::doLoadModel: File type of '" <<
fileName << "' is unknown\n";
}
return Id();
}
bool isDoingReinit()
{
static Id clockId( 1 );
assert( clockId.element() != 0 );
return ( reinterpret_cast< const Clock* >(
clockId.eref().data() ) )->isDoingReinit();
}
void Exploser::refreshPalette(gui::PaletteTreeWidget * const tree, Id const &diagram)
{
QList<QPair<QString, QList<gui::PaletteElement>>> groups;
QMap<QString, QString> descriptions;
descriptions[mUserGroupTitle] = mUserGroupDescription;
IdList const childTypes = mApi.editorManagerInterface().elements(diagram);
for (Id const &child : childTypes) {
QList<Explosion> const explosions = mApi.editorManagerInterface().explosions(child);
for (Explosion const &explosion : explosions) {
if (!explosion.isReusable()) {
continue;
}
Id const targetNodeOrGroup = explosion.target();
Id target;
if (mApi.editorManagerInterface().isNodeOrEdge(targetNodeOrGroup.editor(), targetNodeOrGroup.element())) {
target = targetNodeOrGroup;
} else {
Pattern const pattern = mApi.editorManagerInterface().getPatternByName(targetNodeOrGroup.element());
target = Id(targetNodeOrGroup.editor(), targetNodeOrGroup.diagram(), pattern.rootType());
}
IdList const allTargets = mApi.logicalRepoApi().elementsByType(target.element(), true);
QList<gui::PaletteElement> groupElements;
for (Id const &targetInstance : allTargets) {
if (mApi.isLogicalId(targetInstance)) {
groupElements << gui::PaletteElement(child
, mApi.logicalRepoApi().name(targetInstance)
, QString(), mApi.editorManagerInterface().icon(child)
, mApi.editorManagerInterface().iconSize(child)
, targetInstance);
}
}
if (!groupElements.isEmpty()) {
groups << qMakePair(mUserGroupTitle, groupElements);
}
}
}
tree->addGroups(groups, descriptions, true, mApi.editorManagerInterface().friendlyName(diagram), true);
}
TEST(IdsTest, gettersTest) {
Id id = Id::loadFromString("qrm:/editor/diagram/element/id");
EXPECT_EQ(id.editor(), "editor");
EXPECT_EQ(id.diagram(), "diagram");
EXPECT_EQ(id.element(), "element");
EXPECT_EQ(id.id(), "id");
EXPECT_EQ(id.type() ,Id("editor", "diagram", "element"));
}
void ZombieCaConc::vSetSolver( const Eref& e, Id hsolve )
{
if ( !hsolve.element()->cinfo()->isA( "HSolve" ) ) {
cout << "Error: ZombieCaConc::vSetSolver: Object: " <<
hsolve.path() << " is not an HSolve. Aborted\n";
hsolve_ = 0;
return;
}
hsolve_ = reinterpret_cast< HSolve* >( hsolve.eref().data() );
}
Id InterpreterEditorManager::element(Id const &id, qrRepo::RepoApi const * const repo, Id const &diagram) const
{
foreach (Id const &element, repo->children(diagram)) {
if (id.element() == repo->name(element) && repo->isLogicalElement(element)) {
return element;
}
}
return Id();
}
int main( int argc, char** argv )
{
bool doUnitTests = 0;
bool doRegressionTests = 0;
unsigned int benchmark = 0;
// This reorders the OpFunc to Fid mapping to ensure it is node and
// compiler independent.
Id shellId = init( argc, argv, doUnitTests, doRegressionTests, benchmark );
// Note that the main loop remains the parser loop, though it may
// spawn a lot of other stuff.
Element* shelle = shellId.element();
Shell* s = reinterpret_cast< Shell* >( shelle->data( 0 ) );
if ( doUnitTests )
nonMpiTests( s ); // These tests do not need the process loop.
if ( Shell::myNode() == 0 ) {
if ( Shell::numNodes() > 1 ) {
// Use the last clock for the postmaster, so that it is called
// after everything else has been processed and all messages
// are ready to send out.
s->doUseClock( "/postmaster", "process", 9 );
s->doSetClock( 9, 1.0 ); // Use a sensible default.
}
#ifdef DO_UNIT_TESTS
if ( doUnitTests ) {
mpiTests();
processTests( s );
}
// if ( doRegressionTests ) regressionTests();
#endif
// These are outside unit tests because they happen in optimized
// mode, using a command-line argument. As soon as they are done
// the system quits, in order to estimate timing.
if ( benchmark != 0 ) {
mooseBenchmarks( benchmark );
s->doQuit();
} else {
// Here we set off a little event loop to poll user input.
// It deals with the doQuit call too.
if(! quitFlag)
Shell::launchParser();
}
} else {
PostMaster* p = reinterpret_cast< PostMaster* >( ObjId( 3 ).data());
while ( Shell::keepLooping() ) {
p->clearPending();
}
}
Msg::clearAllMsgs();
Id::clearAllElements();
#ifdef USE_MPI
MPI_Finalize();
#endif
return 0;
}
void SbmlReader::getRules() {
unsigned int nr = model_->getNumRules();
//if (nr > 0)
// cout << "\n ##### Need to populate funcpool and sumtotal which is pending due to equations \n";
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
for ( unsigned int r = 0; r < nr; r++ ) {
Rule * rule = model_->getRule(r);
bool assignRule = rule->isAssignment();
if ( assignRule ) {
string rule_variable = rule->getVariable();
map< string,Id >::iterator v_iter;
map< string,Id >::iterator m_iter;
v_iter = molSidMIdMap_.find( rule_variable );
if (v_iter != molSidMIdMap_.end()) {
Id rVariable = molSidMIdMap_.find(rule_variable)->second;
string rstring =molSidMIdMap_.find(rule_variable)->first;
Id sumId = shell->doCreate( "SumFunc", rVariable, "func", 1 );
rVariable.element()->zombieSwap( FuncPool::initCinfo() );
ObjId ret = shell->doAddMsg( "single",
ObjId( sumId, 0 ), "output",
ObjId( rVariable, 0 ), "input" );
assert( ret != ObjId() );
const ASTNode * ast = rule->getMath();
vector< string > ruleMembers;
ruleMembers.clear();
printMembers( ast,ruleMembers );
for ( unsigned int rm = 0; rm < ruleMembers.size(); rm++ ) {
m_iter = molSidMIdMap_.find( ruleMembers[rm] );
if ( m_iter != molSidMIdMap_.end() ) {
Id rMember = molSidMIdMap_.find(ruleMembers[rm])->second;
ObjId ret = shell->doAddMsg( "single",
ObjId( rMember, 0 ), "nOut",
ObjId( sumId, 0 ), "input" );
string test = molSidMIdMap_.find(ruleMembers[rm])->first;
} else {
cerr << "SbmlReader::getRules: Assignment rule member is not a species" << endl;
// In assignment rule there are constants instead of molecule which is yet to deal in moose.
errorFlag_ = true;
}
}
}
}
bool rateRule = rule->isRate();
if ( rateRule ) {
cout << "warning : for now Rate Rule is not handled " << endl;
errorFlag_ = true;
}
bool algebRule = rule->isAlgebraic();
if ( algebRule ) {
cout << "warning: for now Algebraic Rule is not handled" << endl;
errorFlag_ = true;
}
}
}
void HSolve::setSeed( Id seed )
{
if ( !seed.element()->cinfo()->isA( "Compartment" ) )
{
cerr << "Error: HSolve::setSeed(): Seed object '" << seed.path()
<< "' is not derived from type 'Compartment'." << endl;
return;
}
seed_ = seed;
}
void Gsolve::setStoich( Id stoich )
{
// This call is done _before_ setting the path on stoich
assert( stoich.element()->cinfo()->isA( "Stoich" ) );
stoich_ = stoich;
stoichPtr_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
sys_.stoich = stoichPtr_;
sys_.isReady = false;
for ( unsigned int i = 0; i < pools_.size(); ++i )
pools_[i].setStoich( stoichPtr_ );
}
// See what Element::getNeighbors does with 2 sub <----> prd.
void testTwoReacGetNeighbors()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id comptId = shell->doCreate( "CubeMesh", Id(), "cube", 1 );
Id meshId( comptId.value() + 1 );
Id subId = shell->doCreate( "Pool", comptId, "sub", 1 );
Id prdId = shell->doCreate( "Pool", comptId, "prd", 1 );
Id reacId = shell->doCreate( "Reac", comptId, "reac", 1 );
ObjId mid = shell->doAddMsg( "OneToOne",
subId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
mid = shell->doAddMsg( "OneToOne",
prdId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
ObjId ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
assert( ret != ObjId() );
vector< Id > pools;
unsigned int num = reacId.element()->getNeighbors( pools,
Reac::initCinfo()->findFinfo( "toSub" ) );
assert( num == 2 );
assert( pools[0] == subId );
assert( pools[1] == subId );
pools.clear();
num = reacId.element()->getNeighbors( pools,
Reac::initCinfo()->findFinfo( "sub" ) );
assert( num == 2 );
assert( pools[0] == subId );
assert( pools[1] == subId );
shell->doDelete( comptId );
cout << "." << flush;
}
void ContextMenuActionTrigger::contextMenuActionTriggered(QString const &name)
{
QString actionName = name.section("###", 0, 0);
QString uuid = name.section("###", 1, 1);
if (actionName == "Add method") {
MethodEditorDialog dialog;
int dialogResult = dialog.exec();
if (dialogResult) {
qDebug() << "ACCEPTED!!!";
Id id = Id::loadFromString(uuid);
if (id.element() == "MethodsContainer") {
Id newMethodId = mApi->createElement(id, Id("Kernel_metamodel", "Kernel",
"Method"));
mApi->setProperty(newMethodId, Qt::DisplayRole, QVariant(dialog.generateMethodString()));
} else if (id.element() == "Class") {
//Id newMethodId = mApi->createElement(id, Id("Kernel_metamodel", "Kernel",
// "Method"));
}
}
} else if (actionName == "Add field") {
FieldEditorDialog dialog;
int dialogResult = dialog.exec();
if (dialogResult) {
qDebug() << "ACCEPTED!!!";
Id id = Id::loadFromString(uuid);
if (id.element() == "FieldsContainer") {
Id newMethodId = mApi->createElement(id, Id("Kernel_metamodel", "Kernel",
"Field"));
mApi->setProperty(newMethodId, Qt::DisplayRole, QVariant(dialog.generateFieldString()));
} else if (id.element() == "Class") {
//Id newMethodId = mApi->createElement(id, Id("Kernel_metamodel", "Kernel",
// "Method"));
}
}
}
}
void checkChildren( Id parent, const string& info )
{
vector< Id > ret;
Neutral::children( parent.eref(), ret );
cout << info << " checkChildren of " <<
parent.element()->getName() << ": " <<
ret.size() << " children\n";
for ( vector< Id >::iterator i = ret.begin(); i != ret.end(); ++i )
{
cout << i->element()->getName() << endl;
}
}
Id ModelsAssistApi::createElement(Id const &parent, Id const &id, Id const &logicalId
, bool isFromLogicalModel, QString const &name, QPointF const &position)
{
Q_ASSERT(parent.idSize() == 4);
Id newId = id;
Id realLogicalId = logicalId;
if (isFromLogicalModel) {
realLogicalId = id;
newId = Id(id.editor(), id.diagram(), id.element(), QUuid::createUuid().toString());
}
mModel.addElementToModel(parent, newId, realLogicalId, name, position);
return newId;
}
/**
* Return the MeshEntry into which the enzyme should be placed.
* This is simple: Just identify the compartment holding the enzyme
* molecule.
*/
Id findMeshOfEnz( Id enz )
{
static const Finfo* enzFinfo =
EnzBase::initCinfo()->findFinfo( "enzOut" );
assert( enzFinfo );
vector< Id > enzVec;
unsigned int numEnz =
enz.element()->getNeighbors( enzVec, enzFinfo );
assert( numEnz == 1 );
vector< Id > meshEntries;
return getCompt( enzVec[0] );
}
void ReadKkit::buildSumTotal( const string& src, const string& dest )
{
map< string, Id >::iterator i = poolIds_.find( dest );
assert( i != poolIds_.end() );
Id destId = i->second;
// Don't bother on buffered pool.
if ( destId.element()->cinfo()->isA( "BufPool" ) )
return;
Id sumId;
// Check if the pool has not yet been converted to handle SumTots.
if ( destId.element()->cinfo()->name() == "Pool" ) {
sumId = shell_->doCreate( "SumFunc", destId, "func", 1 );
// Turn dest into a FuncPool.
destId.element()->zombieSwap( FuncPool::initCinfo() );
ObjId ret = shell_->doAddMsg( "single",
ObjId( sumId, 0 ), "output",
ObjId( destId, 0 ), "input" );
assert( ret != ObjId() );
} else {
sumId = Neutral::child( destId.eref(), "func" );
}
if ( sumId == Id() ) {
cout << "Error: ReadKkit::buildSumTotal: could not make SumFunc on '"
<< dest << "'\n";
return;
}
Id srcId = findSumTotSrc( src );
ObjId ret = shell_->doAddMsg( "single",
ObjId( srcId, 0 ), "nOut",
ObjId( sumId, 0 ), "input" );
assert( ret != ObjId() );
}
Id LogicalModelAssistApi::createElement(const Id &parent, const Id &type)
{
Q_ASSERT(type.idSize() == 3);
Q_ASSERT(parent.idSize() == 4);
const Id newElementId = type.sameTypeId();
const QString elementFriendlyName = mModelsAssistApi.editorManagerInterface().friendlyName(type);
const bool isEdge = mModelsAssistApi.editorManagerInterface().isNodeOrEdge(
newElementId.editor(), newElementId.element()) == -1;
ElementInfo newElement(newElementId, Id(), parent, Id(), {{"name", elementFriendlyName}}, {}, Id(), isEdge);
mLogicalModel.addElementToModel(newElement);
return newElementId;
}
/**
* This function performs a depth-first search (for a compartment) in the tree
* with its root at 'base'. Returns (Id of) a compartment if found, else a
* blank Id.
*/
Id HSolve::deepSearchForCompartment( Id base )
{
/*
* 'cstack' is a stack-of-stacks used to perform the depth-first search.
* The 0th entry in 'cstack' is a stack containing simply the base.
* The i-th entry in 'cstack' contains children of the node at the top
* of the stack at position ( i - 1 ).
* Hence, at any time, the top of the i-th stack is the i-th node on
* the ancestral path from the 'base' node to the 'current' node
* (more below) which is being examined. Also, the remaining nodes in
* the i-th stack are the siblings of this ancestor.
*
* 'current' is the node at the top of the top of 'cstack'. If this node is
* a Compartment, then the search is completed, returning 'current'.
* Otherwise, the children of 'current' are pushed onto 'cstack' for a
* deeper search. If the deeper search yields nothing, then this
* 'current' node is discarded. When an entire stack of siblings is
* exhausted in this way, then this empty stack is discarded, and
* the search moves 1 level up.
*
* 'result' is a blank Id (moose root element) if the search failed.
* Otherwise, it is a compartment that was found under 'base'.
*/
vector< vector< Id > > cstack( 1, vector< Id >( 1, base ) );
Id current;
Id result;
while ( !cstack.empty() )
if ( cstack.back().empty() )
{
cstack.pop_back();
if ( !cstack.empty() )
cstack.back().pop_back();
}
else
{
current = cstack.back().back();
// if ( current()->cinfo() == moose::Compartment::initCinfo() )
// Compartment is base class for SymCompartment.
if ( current.element()->cinfo()->isA( "Compartment" ) )
{
result = current;
break;
}
cstack.push_back( children( current ) );
}
return result;
}
