bool read_record(Driver* driver, string record){
if (record == CONTINUE)
return true;
if (isallspace(record))
return false;
istringstream is(record, ios::in);
string line;
int i = 0;
do{
++i;
line = line.substr(0, line.find(COMMENT));
if (!line.empty() && !isallspace(line)){
char tag = line[0];
string line2 = line.substr(1);
try{
switch(tag){
case OBJTAG:
if (driver->target.empty())
read_objective(driver, line2);
break;
case ARGTAG:
if (driver->arg.empty())
driver->set_args(line2);
break;
//case EXTTAG:
// driver->set_externals(line2, true);//externalise the list provided in line2
// break;
//case INTTAG:
// driver->set_externals(line2, false);//internalise the list provided in line2
// break;
case EXTTAG://w/ simply set externals with '\'
driver->set_externals_gfa(line2);
break;
case VMAXTAG:
driver->lp->setVMax(str2double(line2));
break;
// case TTAG:
// if (driver->thermo) ((ThermoLP*)driver->lp)->setTemperature(T0 + str2double(line2));
// break;
default:
try{
read_constraint(driver, line, tag);
}
catch(exception &e){;}
}
}
catch(exception &e) {
throw runtime_error(string("error in line ") + num2str(i) + ": " + e.what());
}
}
}
while(getline(is, line, NEWLINE));
return true;
}
//w/gni/ read record for Gene nutrient interaction(gni)
bool read_record_gni(Driver* driver, Model* model, string record){
if (record == CONTINUE)
return true;
if (isallspace(record))
return false;
istringstream is(record, ios::in);
string line;
int i = 0;
do{
++i;
line = line.substr(0, line.find(COMMENT));
if (!line.empty() && !isallspace(line)){
char tag = line[0];
string line2 = line.substr(1);
try{
switch(tag){
case OBJTAG:
if (driver->target.empty()) throw runtime_error("please specify a biomass reaction!");
driver->gni->set_nts(line2, driver->externals, driver->model);
// driver->gni->map_nt_reac(model);
break;
case DOLTAG:
driver->gni->set_ntsp(line2);
break;
case ARGTAG:
if (driver->arg.empty())
driver->set_args(line.substr(1));
break;
// case EXTTAG:
// driver->set_externals(line2, true);//externalise the list provided in line2
// break;
// case INTTAG:
// driver->set_externals(line2, false);//internalise the list provided in line2
// break;
case EXTTAG:
driver->set_externals_gfa(line2);
break;
default:
try{
read_constraint_mod(driver, line, tag);
}
catch(exception &e){;}
}
}
catch(exception &e) {
throw runtime_error(string("error in line ") + num2str(i) + ": " + e.what());
}
}
}
while(getline(is, line, NEWLINE));
return true;
}
static list_t *m_search_para(
motion_arg const *a, list_t *l,
int *pn, const void *ctx)
{
/* while in space, find non-space */
for(; l && (!l->line || isallspace(l->line, l->len_line));
l = list_advance_y(l, a->dir, pn, NULL));
/* while in non-space, find space */
for(; l && (l->line && !isallspace(l->line, l->len_line));
l = list_advance_y(l, a->dir, pn, NULL));
return l;
}
