/**
Sets up the species and the source compartment. We use the pre-defined
drift-diffusion method gpgmp::DT_ORNSTEIN_UHLENBECK and set the kernel
parameters accordingly.
\see setComputeDriftDiffusivityMethod
\see setParameter
*/
OrnsteinUhlenbeckProblem::OrnsteinUhlenbeckProblem(Real length, int dx, int dy,
Real diffusivityX, Real diffusivityY,
Real gxx, Real gxy, Real gyx, Real gyy,
int numMolecules)
: DiffusionModel(length, dx, dy)
{
// one species
Species *speciesA = addSpecies("A", 1.);
// set boundary mask
const cl_int4 boundaryMask = {{1, 1, 1, 1}};
const cl_int4 sourceMask = {{0, 0, 0, 0}};
setBoundaryMasks(boundaryMask, sourceMask);
// add source compartment
Compartment *compartmentSource = new Compartment("TrueSource", dx/4,dy/4, dx/4, dy/4);
compartmentSource->setInitialAmount(speciesA, numMolecules, gpgmp::HomogeneousDistribution);
addCompartment(compartmentSource);
// add user parameters for kernel
setParameter("diffX", diffusivityX);
setParameter("diffY", diffusivityY);
setParameter("gammaXX", gxx);
setParameter("gammaXY", gxy);
setParameter("gammaYX", gyx);
setParameter("gammaYY", gyy);
// set OU method
setComputeDriftDiffusivityMethod(gpgmp::DT_ORNSTEIN_UHLENBECK);
}
bool CModelExpansion::SetOfModelElements::addObject(const CCopasiObject* x)
{
if (dynamic_cast<const CCompartment*>(x))
{
addCompartment(dynamic_cast<const CCompartment*>(x));
return true;
}
if (dynamic_cast<const CMetab*>(x))
{
addMetab(dynamic_cast<const CMetab*>(x));
return true;
}
if (dynamic_cast<const CReaction*>(x))
{
addReaction(dynamic_cast<const CReaction*>(x));
return true;
}
if (dynamic_cast<const CModelValue*>(x))
{
addGlobalQuantity(dynamic_cast<const CModelValue*>(x));
return true;
}
if (dynamic_cast<const CEvent*>(x))
{
addEvent(dynamic_cast<const CEvent*>(x));
return true;
}
return false;
}
void CModelExpansion::SetOfModelElements::fillComplete(const CModel* pModel)
{
if (!pModel)
return;
size_t i;
for (i = 0; i < pModel->getCompartments().size(); ++i)
addCompartment(pModel->getCompartments()[i]);
for (i = 0; i < pModel->getMetabolites().size(); ++i)
addMetab(pModel->getMetabolites()[i]);
for (i = 0; i < pModel->getReactions().size(); ++i)
addReaction(pModel->getReactions()[i]);
for (i = 0; i < pModel->getModelValues().size(); ++i)
addGlobalQuantity(pModel->getModelValues()[i]);
for (i = 0; i < pModel->getEvents().size(); ++i)
addEvent(pModel->getEvents()[i]);
}
// FIXME: check for memory leaks
JSONcontext* Network::readJSON(const char* file){
JsonParser *parser;
JsonObject *obj;
JsonArray *jnodes;
JsonArray *jedges;
int i,k;
JSONcontext* ctx=new JSONcontext();
GError *error;
g_type_init ();
parser = json_parser_new ();
error = NULL;
json_parser_load_from_file (parser, file, &error);
if (error)
{
g_print ("Unable to parse `%s': %s\n", file, error->message);
g_error_free (error);
g_object_unref (parser);
abort();
}
addCompartment(0,"unknown"); // add dummy compartment, may be overwritten by compartment from json
ctx->root = json_node_copy(json_parser_get_root(parser)); // needs to be copied ??
obj=json_node_get_object (ctx->root);
jnodes=json_object_get_array_member(obj,"nodes");
jedges=json_object_get_array_member(obj,"edges");
g_print ("%i nodes\n",json_array_get_length(jnodes));
for (i=0;i<json_array_get_length(jnodes);i++){
JsonObject *n=json_array_get_object_element(jnodes,i);
JsonObject *data=json_object_get_object_member(n,"data");
const char* type=json_object_get_string_member(n,"type");
const char* id=json_object_get_string_member(n,"id");
if (json_object_has_member(n,"is_abstract") && (json_object_get_boolean_member(n,"is_abstract") || json_object_get_int_member(n,"is_abstract"))){
continue;
}
if (!json_object_has_member(n,"index")){
g_print ("no index defined for %s %s\n",type,id);
abort();
}
int idx=json_object_get_int_member(n,"index");
g_print ("node %d %s id %s\n",idx,type,id);
if(strcmp(type,"Compartment")==0){
addCompartment(idx,id);
} else {
double x=json_object_get_double_member(data,"x");
double y=json_object_get_double_member(data,"y");
double w=json_object_get_double_member(data,"width");
double h=json_object_get_double_member(data,"height");
double d=json_object_get_double_member(data,"dir");
int c=json_object_get_int_member(data,"compartmentidx");
for(k=0;k<7;k++){
if(strcmp(jnodetypes[k],type)==0)break;
}
if (k==7){
g_print ("unknown node type %s\n",type);
abort();
}
addNode(idx,inodetypes[k],id,w,h,x,y,d,c);
if (idx>=ctx->nodeidx->size()) ctx->nodeidx->resize(idx+1);
(*(ctx->nodeidx))[idx]=i;
}
}
g_print ("%i edges\n",json_array_get_length(jedges));
for (i=0;i<json_array_get_length(jedges);i++){
JsonObject *e=json_array_get_object_element(jedges,i);
const char* type=json_object_get_string_member(e,"type");
if ((!json_object_has_member(e,"sourceidx")) || (!json_object_has_member(e,"targetidx"))){
g_print ("no source/targetindex defined for edge %s %i",type,i);
abort;
}
for(k=0;k<7;k++){
if(strcmp(edgetypes[k],type)==0)break;
}
int from=json_object_get_int_member(e,"sourceidx");
int to=json_object_get_int_member(e,"targetidx");
addEdge(from,to,(Edgetype)k);
g_print ("edge %s %i -> %i\n",edgetypes[k],from,to);
}
g_object_unref(parser);
return ctx;
}
void Network::read(const char* file){
try {
int numc,ci,i,n,m,p,q,k,_index;
int ret;
Nodetype _type;
char s[100],t[100];
float _x,_y, _width, _height,_dir;
FILE* old_stdin=stdin;
printf("importing network\n");
if (file) freopen(file,"r",stdin);
ret=1;
while (ret>0){ret=scanf(" #%[^\n]",s);}; // remove comment lines
if (ret<0) throw "error reading input";
MSCANF(" %d\n",&numc); // num compartments
if (numc>2000){
fprintf(stderr,"too many compartments %d",numc);
abort();
}
printf("number of compartments: %d\n",numc);
for(i=0;i<numc;i++){
MSCANF2(" %d %s\n",&_index,t);
if (_index>numc+1){ // not starting at zero
fprintf(stderr,"compartment index out of bound %d",_index);
abort();
}
addCompartment(_index,t);
}
addCompartment(0,"unknown");
numc++;
MSCANF(" %s\n",s); // "///"
MSCANF(" %d",&n); //number of nodes
printf("number of nodes: %d\n",n);
if (n>10000){
fprintf(stderr,"too many nodes %d",n);
abort();
}
for(i=0;i<n;i++){
MSCANF(" %d\n",&_index);
if (_index>=n){
fprintf(stderr,"node index out of bound %d",_index);
abort();
}
MSCANF(" %s\n",t);
if(strcmp(t,"Compound")==0)_type=compound;
else if(strcmp(t,"Reaction")==0)_type=reaction;
else if(strcmp(t,"Other")==0)_type=other;
else _type=none;
MSCANF("%s\n",s);
MSCANF("%d\n",&ci);
MSCANF2("%f%f",& _x,& _y);
MSCANF3("%f%f%f",& _width,& _height,& _dir);
addNode(_index, _type, s, _width, _height, _x, _y, _dir,ci);
printf("added %s %s %i\n",t,s,_index);
}
MSCANF(" %s\n",s); // "///"
MSCANF(" %d\n",&m); // numer of edges
printf("number of edges: %d\n",m);
if (m>40000){
fprintf(stderr,"too many edges %d",m);
abort();
}
fflush(stdout);
for(i=0;i<m;i++){
MSCANF3("%s %d %d\n",s,&p,&q);
if (p>=n){
fprintf(stderr,"edge node index out of bound %d",p);
abort();
}
if (q>=n){
fprintf(stderr,"edge node index out of bound %d",q);
abort();
}
for(k=0;k<7;k++){
if(strcmp(edgetypes[k],s)==0)break;
}
addEdge(p,q,(Edgetype)k);
}
} catch (char* err){
cout << err <<endl;
abort();
}
}
void CModelExpansion::SetOfModelElements::fillDependencies(const CModel* pModel)
{
if (!pModel) return;
//create a combined set of all elements we know are to be copied
std::set< const CCopasiObject * > combinedSet;
std::set<const CCompartment*>::const_iterator itComp;
for (itComp = mCompartments.begin(); itComp != mCompartments.end(); ++itComp)
{
std::set< const CCopasiObject * > tmp = (*itComp)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CMetab*>::const_iterator itMetab;
for (itMetab = mMetabs.begin(); itMetab != mMetabs.end(); ++itMetab)
{
std::set< const CCopasiObject * > tmp = (*itMetab)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CReaction*>::const_iterator itReac;
for (itReac = mReactions.begin(); itReac != mReactions.end(); ++itReac)
{
std::set< const CCopasiObject * > tmp = (*itReac)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CModelValue*>::const_iterator itQuant;
for (itQuant = mGlobalQuantities.begin(); itQuant != mGlobalQuantities.end(); ++itQuant)
{
std::set< const CCopasiObject * > tmp = (*itQuant)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
/* Events do not contain any relevant objects.
std::set<const CEvent*>::const_iterator itEvent;
for (itEvent = mEvents.begin(); itEvent != mEvents.end(); ++itEvent)
{
std::set< const CCopasiObject * > tmp = (*itEvent)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
*/
//ask the model for the dependencies
std::set< const CCopasiObject * > reacs, metabs, comps, values, events;
pModel->appendDependentModelObjects(combinedSet, reacs, metabs, comps, values, events);
//incorporate the results into the local sets
std::set< const CCopasiObject * >::const_iterator it;
for (it = reacs.begin(); it != reacs.end(); ++it)
addReaction(dynamic_cast<const CReaction*>(*it));
for (it = metabs.begin(); it != metabs.end(); ++it)
addMetab(dynamic_cast<const CMetab*>(*it));
for (it = comps.begin(); it != comps.end(); ++it)
addCompartment(dynamic_cast<const CCompartment*>(*it));
for (it = values.begin(); it != values.end(); ++it)
addGlobalQuantity(dynamic_cast<const CModelValue*>(*it));
for (it = events.begin(); it != events.end(); ++it)
addEvent(dynamic_cast<const CEvent*>(*it));
}
