void ReadKkit::setupSlaveMsg( const string& src, const string& dest )
{
// Convert the pool to a BufPool, if it isn't one already
Id destId( basePath_ + "/kinetics/" + dest );
assert( destId != Id() );
if( !destId.element()->cinfo()->isA( "BufPool" )) {
destId.element()->zombieSwap( BufPool::initCinfo() );
}
map< string, Id >* nameMap;
// Check if the src is a table or a stim
Id srcId( basePath_ + "/kinetics/" + src );
assert( srcId != Id() );
string output = "output";
if ( srcId.element()->cinfo()->isA( "TableBase" ) ) {
nameMap = &tabIds_;
} else if ( srcId.element()->cinfo()->isA( "PulseGen" ) ) {
nameMap = &stimIds_;
output = "output";
} else {
cout << "Error: Unknown source for SLAVE msg: (" << src <<
", " << dest << ")\n";
return;
}
// NSLAVE is 1, CONCSLAVE is 2.
map< Id, int >::iterator i = poolFlags_.find( destId );
if ( i == poolFlags_.end() || !( i->second & 2 ) ) {
innerAddMsg( src, *nameMap, output, dest, poolIds_,
"setNInit" );
} else {
innerAddMsg( src, *nameMap, output, dest, poolIds_,
"setConcInit" );
double CONCSCALE = 0.001;
// Rescale from uM to millimolar.
if ( nameMap == &tabIds_ ) {
SetGet2< double, double >::set( srcId, "linearTransform",
CONCSCALE, 0 );
} else if ( nameMap == &stimIds_ ) {
double x = Field< double >::get( srcId, "baseLevel" );
Field< double >::set( srcId, "baseLevel", x * CONCSCALE );
x = Field< double >::get( srcId, "firstLevel" );
Field< double >::set( srcId, "firstLevel", x * CONCSCALE );
x = Field< double >::get( srcId, "secondLevel" );
Field< double >::set( srcId, "secondLevel", x * CONCSCALE );
}
}
// cout << "Added slave msg from " << src << " to " << dest << endl;
}
ObjId Shell::doAddMsg( const string& msgType,
ObjId src, const string& srcField,
ObjId dest, const string& destField )
{
#ifdef ENABLE_LOGGER
clock_t t = clock();
#endif
if ( !src.id.element() ) {
cout << myNode_ << ": Error: Shell::doAddMsg: src not found" << endl;
return ObjId();
}
if ( !dest.id.element() ) {
cout << myNode_ << ": Error: Shell::doAddMsg: dest not found" << endl;
return ObjId(0, BADINDEX );
}
const Finfo* f1 = src.id.element()->cinfo()->findFinfo( srcField );
if ( !f1 ) {
cout << myNode_ << ": Shell::doAddMsg: Error: Failed to find field " << srcField <<
" on src: " << src.id.element()->getName() << endl;
return ObjId(0, BADINDEX );
}
const Finfo* f2 = dest.id.element()->cinfo()->findFinfo( destField );
if ( !f2 ) {
cout << myNode_ << ": Shell::doAddMsg: Error: Failed to find field " << destField <<
" on dest: " << dest.id.element()->getName() << endl;
cout << "Available fields are : " << endl
<< mapToString<string, Finfo*>(dest.id.element()->cinfo()->finfoMap());
return ObjId( 0, BADINDEX );
}
if ( ! f1->checkTarget( f2 ) ) {
cout << myNode_ << ": Shell::doAddMsg: Error: Src/Dest Msg type mismatch: " << srcField << "/" << destField << endl;
return ObjId( 0, BADINDEX );
}
const Msg* m = innerAddMsg( msgType, src, srcField, dest, destField, 0 );
SetGet6< string, ObjId, string, ObjId, string, unsigned int >::set(
ObjId(), // Apply command to Shell
"addMsg", // Function to call.
msgType,
src,
srcField,
dest,
destField,
m->mid().dataIndex
);
#ifdef ENABLE_LOGGER
logger.updateGlobalCount("Msgs");
float time = (float(clock() - t)/ CLOCKS_PER_SEC);
logger.creationTime.push_back(time);
#endif
return m->mid();
// const Msg* m = innerAddMsg( msgType, src, srcField, dest, destField );
// return m->mid();
// return Msg::lastMsg()->mid();
}
/**
* Wrapper function, that does the ack. Other functions also use the
* inner function to build message trees, so we don't want it to emit
* multiple acks.
*/
void Shell::handleAddMsg( const Eref& e,
string msgType, ObjId src, string srcField,
ObjId dest, string destField, unsigned int msgIndex )
{
// Node 0 will have already called innerAddMsg to get the msgIndex
if ( myNode() != 0 )
innerAddMsg( msgType, src, srcField, dest, destField, msgIndex );
/*
if ( innerAddMsg( msgType, src, srcField, dest, destField ) )
ack()->send( Eref( shelle_, 0 ), Shell::myNode(), OkStatus );
else
ack()->send( Eref( shelle_, 0), Shell::myNode(), ErrorStatus );
*/
}
// Non-static function. The innerAddMsg needs the shell.
void Shell::addClockMsgs(
const vector< ObjId >& list, const string& field, unsigned int tick,
unsigned int msgIndex )
{
if ( !Id( 1 ).element() )
return;
ObjId clockId( 1 );
dropClockMsgs( list, field ); // Forbid duplicate PROCESS actions.
for ( vector< ObjId >::const_iterator i = list.begin();
i != list.end(); ++i ) {
if ( i->element() ) {
stringstream ss;
ss << "proc" << tick;
const Msg* m = innerAddMsg( "OneToAll",
clockId, ss.str(),
*i, field, msgIndex++ );
if ( m )
i->element()->innerSetTick( tick );
}
}
}
void ReadKkit::addmsg( const vector< string >& args)
{
string src = cleanPath( args[1] ).substr( 10 );
string dest = cleanPath( args[2] ).substr( 10 );
if ( args[3] == "REAC" ) {
if ( args[4] == "A" && args[5] == "B" ) {
// Ignore kchans
if ( chanIds_.find( src ) != chanIds_.end() )
; // found a kchan, do nothing
else
innerAddMsg( src, reacIds_, "sub", dest, poolIds_, "reac");
}
else if ( args[4] == "B" && args[5] == "A" ) {
// Ignore kchans
if ( chanIds_.find( src ) != chanIds_.end() )
; // found a kchan, do nothing
else
// dest pool is product of src reac
innerAddMsg( src, reacIds_, "prd", dest, poolIds_, "reac");
}
else if ( args[4] == "sA" && args[5] == "B" ) {
// Msg from enzyme to substrate.
if ( mmEnzIds_.find( src ) == mmEnzIds_.end() )
innerAddMsg( src, enzIds_, "sub", dest, poolIds_, "reac" );
else
innerAddMsg( src, mmEnzIds_, "sub", dest, poolIds_, "reac" );
}
}
else if ( args[3] == "ENZYME" ) { // Msg from enz pool to enz site
if ( mmEnzIds_.find( dest ) == mmEnzIds_.end() )
innerAddMsg( dest, enzIds_, "enz", src, poolIds_, "reac" );
else
innerAddMsg( src, poolIds_, "nOut", dest, mmEnzIds_, "enzDest", 1);
// innerAddMsg( dest, mmEnzIds_, "enz", src, poolIds_, "nOut", 1);
/*
if ( mmEnzIds_.find( dest ) == mmEnzIds_.end() )
innerAddMsg( src, poolIds_, "reac", dest, enzIds_, "enz" );
else
innerAddMsg( src, poolIds_, "nOut", dest, mmEnzIds_, "enz" );
*/
}
else if ( args[3] == "MM_PRD" ) { // Msg from enz to Prd pool
if ( mmEnzIds_.find( src ) == mmEnzIds_.end() )
innerAddMsg( src, enzIds_, "prd", dest, poolIds_, "reac" );
else
innerAddMsg( src, mmEnzIds_, "prd", dest, poolIds_, "reac" );
}
else if ( args[3] == "PLOT" ) { // Time-course output for pool
string head;
string temp;
dest = pathTail( cleanPath( args[2] ), head );
string graph = pathTail( head, temp );
temp = graph + "/" + dest;
map< string, Id >::const_iterator i = plotIds_.find( temp );
assert( i != plotIds_.end() );
Id plot = i->second;
i = poolIds_.find( src );
Id pool;
if ( i == poolIds_.end() ) {
i = enzIds_.find( src ); // might be plotting an enzCplx.
if ( i == enzIds_.end() ) {
cout << "Error: ReadKkit: Unable to find src for plot: " <<
src << ", " << dest << endl;
assert( 0 );
return;
}
vector< Id > enzcplx;
i->second.element()->getNeighbors( enzcplx,
i->second.element()->cinfo()->findFinfo( "toCplx" ) );
assert( enzcplx.size() == 1 );
pool = enzcplx[0];
} else {
pool = i->second;
}
if ( args[4] == "Co" || args[4] == "CoComplex" ) {
ObjId ret = shell_->doAddMsg( "Single",
plot, "requestOut", pool, "getConc" );
assert( ret != ObjId() );
} else if ( args[4] == "n" || args[4] == "nComplex") {
ObjId ret = shell_->doAddMsg( "Single",
plot, "requestOut", pool, "getN" );
assert( ret != ObjId() );
} else {
cout << "Unknown PLOT msg field '" << args[4] << "'\n";
}
}
else if ( args[3] == "SUMTOTAL" ) { // Summation function.
buildSumTotal( src, dest );
}
else if ( args[3] == "SLAVE" ) { // Summation function.
if ( args[4] == "output" ) {
setupSlaveMsg( src, dest );
}
}
}
